From 5a65d23f5ec90eb06330d434c8529cab11849ed6 Mon Sep 17 00:00:00 2001 From: Gary Mirams Date: Thu, 30 Apr 2026 16:06:55 +0100 Subject: [PATCH] Modernize: replace boost::shared_ptr with std::shared_ptr in templates and reference models Also add #include to the shared hpp includes template and all reference .hpp files so generated code compiles without boost/shared_ptr.hpp. Co-Authored-By: Claude Sonnet 4.6 --- .../BE/aslanidi_atrial_model_2009.cpp | 6 +- .../aslanidi_atrial_model_2009.cpp_python36 | 6 +- .../BE/aslanidi_atrial_model_2009.hpp | 13 +- ...szigeti_bett_kim_rasmusson_2004_apical.cpp | 6 +- ...ett_kim_rasmusson_2004_apical.cpp_python36 | 6 +- ...szigeti_bett_kim_rasmusson_2004_apical.hpp | 13 +- ...namic_courtemanche_ramirez_nattel_1998.cpp | 12 +- ...rtemanche_ramirez_nattel_1998.cpp_python36 | 12 +- ...namic_courtemanche_ramirez_nattel_1998.hpp | 15 +- ...i_pasqualini_bers_2010_ssBackwardEuler.cpp | 8 +- ...ini_bers_2010_ssBackwardEuler.cpp_python36 | 8 +- ...i_pasqualini_bers_2010_ssBackwardEuler.hpp | 15 +- .../BE/li_mouse_2010.cpp | 6 +- .../BE/li_mouse_2010.cpp_python36 | 6 +- .../BE/li_mouse_2010.hpp | 13 +- .../BE/sachse_moreno_abildskov_2008_b.cpp | 6 +- .../BE/sachse_moreno_abildskov_2008_b.hpp | 13 +- .../BE/test_piecewises_be.cpp | 2 +- .../BE/test_piecewises_be.hpp | 11 +- ...szigeti_bett_kim_rasmusson_2004_apical.cpp | 6 +- ...ett_kim_rasmusson_2004_apical.cpp_python36 | 6 +- ...szigeti_bett_kim_rasmusson_2004_apical.hpp | 13 +- .../BEopt/decker_2009.cpp | 6 +- .../BEopt/decker_2009.cpp_python36 | 6 +- .../BEopt/decker_2009.hpp | 13 +- ...namic_courtemanche_ramirez_nattel_1998.cpp | 12 +- ...rtemanche_ramirez_nattel_1998.cpp_python36 | 12 +- ...namic_courtemanche_ramirez_nattel_1998.hpp | 15 +- .../Shannon2004_with_modifiers.cpp | 8 +- .../Shannon2004_with_modifiers.hpp | 131 +++++++++--------- .../CVODE_DATA_CLAMP/dokos_model_1996.cpp | 2 +- .../CVODE_DATA_CLAMP/dokos_model_1996.hpp | 11 +- .../CVODE_DATA_CLAMP/dynamic_Shannon2004.cpp | 10 +- .../CVODE_DATA_CLAMP/dynamic_Shannon2004.hpp | 13 +- ..._pasqualini_bers_2010_ssCvodeDataClamp.cpp | 8 +- ..._pasqualini_bers_2010_ssCvodeDataClamp.hpp | 15 +- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- ...squalini_bers_2010_ssCvodeDataClampOpt.cpp | 8 +- ...squalini_bers_2010_ssCvodeDataClampOpt.hpp | 15 +- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ...quid_axon_model_1952_modified.cpp_python36 | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- .../Cvode/FaberRudy2000.cpp | 6 +- .../Cvode/difrancesco_noble_model_1985.cpp | 6 +- .../Cvode/difrancesco_noble_model_1985.hpp | 13 +- .../Cvode/dynamic_mahajan_shiferaw_2008.cpp | 10 +- .../Cvode/dynamic_mahajan_shiferaw_2008.hpp | 13 +- .../Cvode/faber_rudy_2000.cpp | 6 +- .../Cvode/faber_rudy_2000.hpp | 13 +- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- ..._aaltosetala_severi_ventricularVersion.cpp | 6 +- ..._aaltosetala_severi_ventricularVersion.hpp | 13 +- .../dynamic_aslanidi_Purkinje_model_2009.cpp | 12 +- .../dynamic_aslanidi_Purkinje_model_2009.hpp | 103 +++++++------- .../Cvode_opt/hilgemann_noble_model_1987.cpp | 6 +- .../Cvode_opt/hilgemann_noble_model_1987.hpp | 13 +- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ...quid_axon_model_1952_modified.cpp_python36 | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- .../aslanidi_atrial_model_2009.cpp | 6 +- .../aslanidi_atrial_model_2009.cpp_python36 | 6 +- .../aslanidi_atrial_model_2009.hpp | 13 +- .../dynamic_Shannon2004.cpp | 12 +- .../dynamic_Shannon2004.cpp_python36 | 12 +- .../dynamic_Shannon2004.hpp | 15 +- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ...quid_axon_model_1952_modified.cpp_python36 | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- .../GRL1/dynamic_demir_model_1994.cpp | 6 +- .../dynamic_demir_model_1994.cpp_python36 | 6 +- .../GRL1/dynamic_demir_model_1994.hpp | 11 +- .../GRL1/dynamic_matsuoka_model_2003.cpp | 10 +- .../GRL1/dynamic_matsuoka_model_2003.hpp | 19 +-- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ...quid_axon_model_1952_modified.cpp_python36 | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- .../GRL1Opt/beeler_reuter_model_1977.cpp | 6 +- .../beeler_reuter_model_1977.cpp_python36 | 6 +- .../GRL1Opt/beeler_reuter_model_1977.hpp | 13 +- .../GRL1Opt/dynamic_matsuoka_model_2003.cpp | 12 +- .../dynamic_matsuoka_model_2003.cpp_python36 | 12 +- .../GRL1Opt/dynamic_matsuoka_model_2003.hpp | 15 +- .../GRL2/dynamic_winslow_model_1999.cpp | 10 +- .../dynamic_winslow_model_1999.cpp_python36 | 10 +- .../GRL2/dynamic_winslow_model_1999.hpp | 13 +- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ...quid_axon_model_1952_modified.cpp_python36 | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- .../dynamic_viswanathan_model_1999_epi.cpp | 12 +- ...ic_viswanathan_model_1999_epi.cpp_python36 | 12 +- .../dynamic_viswanathan_model_1999_epi.hpp | 15 +- .../GRL2Opt/dynamic_winslow_model_1999.cpp | 10 +- .../GRL2Opt/dynamic_winslow_model_1999.hpp | 13 +- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ...quid_axon_model_1952_modified.cpp_python36 | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- .../dynamic_beeler_reuter_model_1977.cpp | 6 +- .../dynamic_beeler_reuter_model_1977.hpp | 13 +- ...fox_mcharg_gilmour_2002_console_script.cpp | 6 +- ...fox_mcharg_gilmour_2002_console_script.hpp | 13 +- .../Normal/luo_rudy_1994.cpp | 6 +- .../Normal/luo_rudy_1994.hpp | 13 +- ...n_dynamic_aslanidi_Purkinje_model_2009.cpp | 6 +- ...n_dynamic_aslanidi_Purkinje_model_2009.hpp | 101 +++++++------- .../Normal/output_class.c | 12 +- .../Normal/output_class.h | 14 +- .../Normal/test_V_not_state_derived_quant.cpp | 2 +- .../Normal/test_V_not_state_derived_quant.hpp | 11 +- .../Normal/test_V_not_state_mparam.cpp | 2 +- .../Normal/test_V_not_state_mparam.hpp | 11 +- .../Normal/zhang_SAN_model_2000_all.cpp | 2 +- .../Normal/zhang_SAN_model_2000_all.hpp | 11 +- ...beeler_reuter_model_1977_lookup_tables.cpp | 6 +- ...uter_model_1977_lookup_tables.cpp_python36 | 6 +- ...beeler_reuter_model_1977_lookup_tables.hpp | 13 +- .../dynamic_aslanidi_Purkinje_model_2009.cpp | 12 +- .../dynamic_aslanidi_Purkinje_model_2009.hpp | 103 +++++++------- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ...quid_axon_model_1952_modified.cpp_python36 | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- ...n_dynamic_aslanidi_Purkinje_model_2009.cpp | 6 +- ...n_dynamic_aslanidi_Purkinje_model_2009.hpp | 101 +++++++------- ...rudy_1991_with_range_cap_dimensionless.cpp | 6 +- ..._with_range_cap_dimensionless.cpp_python36 | 6 +- ...rudy_1991_with_range_cap_dimensionless.hpp | 13 +- .../RL/dynamic_livshitz_rudy_2007.cpp | 10 +- .../RL/dynamic_livshitz_rudy_2007.hpp | 13 +- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- ...szigeti_bett_kim_rasmusson_2004_apical.cpp | 12 +- ...szigeti_bett_kim_rasmusson_2004_apical.hpp | 15 +- ..._huxley_squid_axon_model_1952_modified.cpp | 6 +- ...quid_axon_model_1952_modified.cpp_python36 | 6 +- ..._huxley_squid_axon_model_1952_modified.hpp | 13 +- .../templates/BE/cpp/constructor_declaration | 2 +- .../templates/RL/cpp/constructor_declaration | 2 +- .../templates/Shared/cpp/CHASTE_CLASS_EXPORT | 4 +- .../Shared/cpp/UseCellMLDefaultStimulus | 4 +- .../Shared/cpp/constructor_declaration | 2 +- chaste_codegen/templates/Shared/cpp/includes | 2 +- .../templates/Shared/hpp/CHASTE_CLASS_EXPORT | 8 +- ...Stimulus_IntracellularCalciumConcentration | 2 +- .../templates/Shared/hpp/class_declaration | 4 +- chaste_codegen/templates/Shared/hpp/includes | 1 + .../templates/backward_euler_model.hpp | 2 +- chaste_codegen/templates/cvode_model.hpp | 2 +- .../generalised_rush_larsen_model.hpp | 2 +- chaste_codegen/templates/normal_model.hpp | 2 +- .../templates/rush_larsen_model.hpp | 2 +- 151 files changed, 943 insertions(+), 888 deletions(-) diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.cpp b/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.cpp index 8cb3904a7..29773a0dc 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.cpp @@ -27,7 +27,7 @@ - boost::shared_ptr Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_membrane__Cm_converted = 0.001 * mParameters[4]; // uF @@ -35,7 +35,7 @@ const double var_chaste_interface__membrane__stim_duration_converted = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 500; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -48,7 +48,7 @@ { return mStateVariables[1]; } - Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler::Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler::Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<14>( 29, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.cpp_python36 index f6c5379d5..0a16d4fd9 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.cpp_python36 @@ -26,7 +26,7 @@ - boost::shared_ptr Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_membrane__Cm_converted = 0.001 * mParameters[4]; // uF @@ -34,7 +34,7 @@ const double var_chaste_interface__membrane__stim_duration_converted = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 500; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -47,7 +47,7 @@ { return mStateVariables[1]; } - Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler::Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler::Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<14>( 29, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.hpp b/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.hpp index 2e3fbe1dd..46494a544 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[29] = {false, true, false, false, false, false, fals const bool is_probability[29] = {false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL);void ComputeResidual(double var_chaste_interface__environment__time_converted, const double rCurrentGuess[14], double rResidual[14]); @@ -63,8 +64,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -73,8 +74,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellaslanidi_atrial_model_2009FromCellMLBackwardEuler(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp b/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp index da9a18ac0..8caee0234 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp @@ -27,14 +27,14 @@ - boost::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 71.430000000000007; // millisecond const double var_chaste_interface__membrane__stim_start = 0; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -47,7 +47,7 @@ { return mStateVariables[1]; } - Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler::Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler::Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<32>( 41, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp_python36 index bc65e4046..b5d916c15 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp_python36 @@ -27,14 +27,14 @@ - boost::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 71.430000000000007; // millisecond const double var_chaste_interface__membrane__stim_start = 0; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -47,7 +47,7 @@ { return mStateVariables[1]; } - Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler::Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler::Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<32>( 41, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp b/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp index a83222592..0f1318f71 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[41] = {false, true, true, true, false, false, false, const bool is_probability[41] = {false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL);void ComputeResidual(double var_chaste_interface__environment__time, const double rCurrentGuess[32], double rResidual[32]); @@ -63,8 +64,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -73,8 +74,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEuler(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.cpp b/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.cpp index 169812214..9d5d5b8da 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.cpp @@ -25,7 +25,7 @@ #include "ModelFactory.hpp" -AbstractBackwardEulerCardiacCell<8>* Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractBackwardEulerCardiacCell<8>* Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(p_solver, p_stimulus); } @@ -33,7 +33,7 @@ bool Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::registered - boost::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_membrane__Cm_converted = 9.9999999999999995e-7 * mParameters[9]; // uF @@ -41,7 +41,7 @@ bool Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::registered const double var_chaste_interface__membrane__stim_duration = 2; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -54,7 +54,7 @@ bool Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::registered { return mStateVariables[1]; } - Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<8>( 21, 0, @@ -1021,8 +1021,8 @@ CHASTE_CLASS_EXPORT(Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEul extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.cpp_python36 index c42de6f4c..17bafaa1f 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.cpp_python36 @@ -25,7 +25,7 @@ #include "ModelFactory.hpp" -AbstractBackwardEulerCardiacCell<8>* Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractBackwardEulerCardiacCell<8>* Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(p_solver, p_stimulus); } @@ -33,7 +33,7 @@ bool Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::registered - boost::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_membrane__Cm_converted = 9.9999999999999995e-7 * mParameters[9]; // uF @@ -41,7 +41,7 @@ bool Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::registered const double var_chaste_interface__membrane__stim_duration = 2; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -54,7 +54,7 @@ bool Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::registered { return mStateVariables[1]; } - Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler::Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<8>( 21, 0, @@ -1019,8 +1019,8 @@ CHASTE_CLASS_EXPORT(Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEul extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.hpp b/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.hpp index 40e71e175..a3e76e42e 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -34,16 +35,16 @@ class Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler : public Ab // private: - static AbstractBackwardEulerCardiacCell<8>* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractBackwardEulerCardiacCell<8>* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[21] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true, true, false}; const bool is_probability[21] = {false, false, true, true, true, false, false, false, false, false, false, true, true, true, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL);void ComputeResidual(double var_chaste_interface__environment__time, const double rCurrentGuess[8], double rResidual[8]); @@ -66,8 +67,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -76,8 +77,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEuler(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.cpp b/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.cpp index 8bc5a2974..033efce67 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.cpp @@ -25,7 +25,7 @@ #include "ModelFactory.hpp" -AbstractBackwardEulerCardiacCell<27>* Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractBackwardEulerCardiacCell<27>* Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(p_solver, p_stimulus); } @@ -33,14 +33,14 @@ bool Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::registered = Mod - boost::shared_ptr Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane_potential__stim_amplitude_converted = -9.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane_potential__stim_duration = 5; // msec const double var_chaste_interface__membrane_potential__stim_period = 1000; // msec const double var_chaste_interface__membrane_potential__stim_start = 100; // msec - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane_potential__stim_amplitude_converted), var_chaste_interface__membrane_potential__stim_duration, var_chaste_interface__membrane_potential__stim_period, @@ -53,7 +53,7 @@ bool Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::registered = Mod { return mStateVariables[1]; } - Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<27>( 39, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.cpp_python36 index 9ba8ce0c8..a000d0790 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.cpp_python36 @@ -25,7 +25,7 @@ #include "ModelFactory.hpp" -AbstractBackwardEulerCardiacCell<27>* Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractBackwardEulerCardiacCell<27>* Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(p_solver, p_stimulus); } @@ -33,14 +33,14 @@ bool Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::registered = Mod - boost::shared_ptr Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane_potential__stim_amplitude_converted = -9.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane_potential__stim_duration = 5; // msec const double var_chaste_interface__membrane_potential__stim_period = 1000; // msec const double var_chaste_interface__membrane_potential__stim_start = 100; // msec - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane_potential__stim_amplitude_converted), var_chaste_interface__membrane_potential__stim_duration, var_chaste_interface__membrane_potential__stim_period, @@ -53,7 +53,7 @@ bool Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::registered = Mod { return mStateVariables[1]; } - Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler::Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<27>( 39, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.hpp b/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.hpp index ac5acca84..c64c5cbcd 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -33,16 +34,16 @@ class Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler : public Abstrac // private: - static AbstractBackwardEulerCardiacCell<27>* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractBackwardEulerCardiacCell<27>* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[39] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true, true, true, true, true, true}; const bool is_probability[39] = {false, false, true, true, true, false, false, false, false, false, false, true, true, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL);void ComputeResidual(double var_chaste_interface__environment__time, const double rCurrentGuess[27], double rResidual[27]); @@ -65,8 +66,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -75,8 +76,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellgrandi_pasqualini_bers_2010_ssFromCellMLBackwardEuler(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.cpp b/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.cpp index 6ac6a31a9..eb819406b 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.cpp @@ -27,14 +27,14 @@ - boost::shared_ptr Cellli_mouse_2010FromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Cellli_mouse_2010FromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__cell__stim_amplitude_converted = -15 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__cell__stim_duration = 3; // millisecond const double var_chaste_interface__cell__stim_offset = 0; // millisecond const double var_chaste_interface__cell__stim_period = 333.33300000000003; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__cell__stim_amplitude_converted), var_chaste_interface__cell__stim_duration, var_chaste_interface__cell__stim_period, @@ -47,7 +47,7 @@ { return mStateVariables[1]; } - Cellli_mouse_2010FromCellMLBackwardEuler::Cellli_mouse_2010FromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellli_mouse_2010FromCellMLBackwardEuler::Cellli_mouse_2010FromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<26>( 36, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.cpp_python36 index 98a9e6e44..6af1ca170 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.cpp_python36 @@ -27,14 +27,14 @@ - boost::shared_ptr Cellli_mouse_2010FromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Cellli_mouse_2010FromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__cell__stim_amplitude_converted = -15 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__cell__stim_duration = 3; // millisecond const double var_chaste_interface__cell__stim_offset = 0; // millisecond const double var_chaste_interface__cell__stim_period = 333.33300000000003; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__cell__stim_amplitude_converted), var_chaste_interface__cell__stim_duration, var_chaste_interface__cell__stim_period, @@ -47,7 +47,7 @@ { return mStateVariables[1]; } - Cellli_mouse_2010FromCellMLBackwardEuler::Cellli_mouse_2010FromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellli_mouse_2010FromCellMLBackwardEuler::Cellli_mouse_2010FromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<26>( 36, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.hpp b/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.hpp index 4f517cf73..a61eecb22 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[36] = {false, true, true, true, false, false, false, const bool is_probability[36] = {false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellli_mouse_2010FromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellli_mouse_2010FromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellli_mouse_2010FromCellMLBackwardEuler(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL);void ComputeResidual(double var_chaste_interface__environment__time, const double rCurrentGuess[26], double rResidual[26]); @@ -63,8 +64,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellli_mouse_2010FromCellMLBackwardEuler * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -73,8 +74,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellli_mouse_2010FromCellMLBackwardEuler * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellli_mouse_2010FromCellMLBackwardEuler(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/sachse_moreno_abildskov_2008_b.cpp b/chaste_codegen/data/tests/chaste_reference_models/BE/sachse_moreno_abildskov_2008_b.cpp index c975de3ee..9eac255ef 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/sachse_moreno_abildskov_2008_b.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/sachse_moreno_abildskov_2008_b.cpp @@ -27,14 +27,14 @@ - boost::shared_ptr Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler::UseCellMLDefaultStimulus() + std::shared_ptr Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__I_stim__stim_duration_converted = 1; // millisecond const double var_chaste_interface__I_stim__stim_period_converted = 1000; // millisecond const double var_chaste_interface__I_stim__stim_start_converted = 100; // millisecond const double var_chaste_interface__I_stim__stim_amplitude_converted = 0.0001 * HeartConfig::Instance()->GetCapacitance() / mParameters[2]; // uA_per_cm2 - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__I_stim__stim_amplitude_converted), var_chaste_interface__I_stim__stim_duration_converted, var_chaste_interface__I_stim__stim_period_converted, @@ -44,7 +44,7 @@ return p_cellml_stim; } - Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler::Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler::Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<6>( 7, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/sachse_moreno_abildskov_2008_b.hpp b/chaste_codegen/data/tests/chaste_reference_models/BE/sachse_moreno_abildskov_2008_b.hpp index 6014b3194..70de08237 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/sachse_moreno_abildskov_2008_b.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/sachse_moreno_abildskov_2008_b.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,8 +39,8 @@ const bool is_concentration[7] = {false, false, false, false, false, false, fals const bool is_probability[7] = {false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL);void ComputeResidual(double var_chaste_interface__environment__time_converted, const double rCurrentGuess[6], double rResidual[6]); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellsachse_moreno_abildskov_2008_bFromCellMLBackwardEuler(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/test_piecewises_be.cpp b/chaste_codegen/data/tests/chaste_reference_models/BE/test_piecewises_be.cpp index b1ca1bcb5..33463c820 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/test_piecewises_be.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/test_piecewises_be.cpp @@ -28,7 +28,7 @@ - Celltest_piecewises_beFromCellMLBackwardEuler::Celltest_piecewises_beFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Celltest_piecewises_beFromCellMLBackwardEuler::Celltest_piecewises_beFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<2>( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/test_piecewises_be.hpp b/chaste_codegen/data/tests/chaste_reference_models/BE/test_piecewises_be.hpp index 4a89bba79..d6e6e3f79 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BE/test_piecewises_be.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BE/test_piecewises_be.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,7 +39,7 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - Celltest_piecewises_beFromCellMLBackwardEuler(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Celltest_piecewises_beFromCellMLBackwardEuler(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Celltest_piecewises_beFromCellMLBackwardEuler(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL);void ComputeResidual(double var_chaste_interface__environment__time_converted, const double rCurrentGuess[2], double rResidual[2]); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Celltest_piecewises_beFromCellMLBackwardEuler * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Celltest_piecewises_beFromCellMLBackwardEuler * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Celltest_piecewises_beFromCellMLBackwardEuler(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp b/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp index 2b07a92a8..40601d2a1 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp @@ -691,14 +691,14 @@ class Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEul std::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt_LookupTables::mpInstance; - boost::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 71.430000000000007; // millisecond const double var_chaste_interface__membrane__stim_start = 0; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -711,7 +711,7 @@ std::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt::Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<32>( 41, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp_python36 index 63a7cd0cf..9ff6870f2 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp_python36 @@ -691,14 +691,14 @@ private: std::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt_LookupTables::mpInstance; - boost::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 71.430000000000007; // millisecond const double var_chaste_interface__membrane__stim_start = 0; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -711,7 +711,7 @@ std::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt::Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<32>( 41, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp b/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp index 2ce7f7d61..91278d0ff 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[41] = {false, true, true, true, false, false, false, const bool is_probability[41] = {false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -64,8 +65,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -74,8 +75,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLBackwardEulerOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.cpp b/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.cpp index 15fb93e53..01fcf30d1 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.cpp @@ -768,14 +768,14 @@ class Celldecker_2009FromCellMLBackwardEulerOpt_LookupTables : public AbstractLo std::shared_ptr Celldecker_2009FromCellMLBackwardEulerOpt_LookupTables::mpInstance; - boost::shared_ptr Celldecker_2009FromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() + std::shared_ptr Celldecker_2009FromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // ms const double var_chaste_interface__membrane__stim_offset = 0; // ms const double var_chaste_interface__membrane__stim_period = 1000; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -788,7 +788,7 @@ std::shared_ptr Celldeck { return mStateVariables[1]; } - Celldecker_2009FromCellMLBackwardEulerOpt::Celldecker_2009FromCellMLBackwardEulerOpt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Celldecker_2009FromCellMLBackwardEulerOpt::Celldecker_2009FromCellMLBackwardEulerOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<35>( 46, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.cpp_python36 index 456d57b23..24122a4b5 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.cpp_python36 @@ -768,14 +768,14 @@ private: std::shared_ptr Celldecker_2009FromCellMLBackwardEulerOpt_LookupTables::mpInstance; - boost::shared_ptr Celldecker_2009FromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() + std::shared_ptr Celldecker_2009FromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // ms const double var_chaste_interface__membrane__stim_offset = 0; // ms const double var_chaste_interface__membrane__stim_period = 1000; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -788,7 +788,7 @@ std::shared_ptr Celldeck { return mStateVariables[1]; } - Celldecker_2009FromCellMLBackwardEulerOpt::Celldecker_2009FromCellMLBackwardEulerOpt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Celldecker_2009FromCellMLBackwardEulerOpt::Celldecker_2009FromCellMLBackwardEulerOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<35>( 46, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.hpp b/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.hpp index 7e6a4c755..76922a484 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[46] = {false, true, false, false, false, false, fals const bool is_probability[46] = {false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Celldecker_2009FromCellMLBackwardEulerOpt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Celldecker_2009FromCellMLBackwardEulerOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Celldecker_2009FromCellMLBackwardEulerOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -64,8 +65,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Celldecker_2009FromCellMLBackwardEulerOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -74,8 +75,8 @@ namespace boost inline void load_construct_data( Archive & ar, Celldecker_2009FromCellMLBackwardEulerOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Celldecker_2009FromCellMLBackwardEulerOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.cpp b/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.cpp index 6837116ae..2a06b51bd 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.cpp @@ -25,7 +25,7 @@ #include "ModelFactory.hpp" -AbstractBackwardEulerCardiacCell<8>* Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractBackwardEulerCardiacCell<8>* Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(p_solver, p_stimulus); } @@ -499,14 +499,14 @@ class Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt_LookupTa std::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt_LookupTables::mpInstance; - boost::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -2000 * HeartConfig::Instance()->GetCapacitance() / mParameters[9]; // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 2; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -519,7 +519,7 @@ std::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<8>( 21, 0, @@ -1455,8 +1455,8 @@ CHASTE_CLASS_EXPORT(Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEul extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.cpp_python36 index 677aa3a8e..cd6d614e6 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.cpp_python36 @@ -25,7 +25,7 @@ #include "ModelFactory.hpp" -AbstractBackwardEulerCardiacCell<8>* Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractBackwardEulerCardiacCell<8>* Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(p_solver, p_stimulus); } @@ -499,14 +499,14 @@ private: std::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt_LookupTables::mpInstance; - boost::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -2000 * HeartConfig::Instance()->GetCapacitance() / mParameters[9]; // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 2; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -519,7 +519,7 @@ std::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt::Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractBackwardEulerCardiacCell<8>( 21, 0, @@ -1453,8 +1453,8 @@ CHASTE_CLASS_EXPORT(Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEul extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.hpp b/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.hpp index 53dafd2bf..6ca5d59da 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -34,16 +35,16 @@ class Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt : public // private: - static AbstractBackwardEulerCardiacCell<8>* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractBackwardEulerCardiacCell<8>* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[21] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true, true, false}; const bool is_probability[21] = {false, false, true, true, true, false, false, false, false, false, false, true, true, true, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -67,8 +68,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -77,8 +78,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamiccourtemanche_ramirez_nattel_1998FromCellMLBackwardEulerOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers.cpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers.cpp index 21637c579..2013a5d79 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers.cpp @@ -29,7 +29,7 @@ #include "ModelFactory.hpp" -AbstractCardiacCellWithModifiers* Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractCardiacCellWithModifiers* Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(p_solver, p_stimulus); } @@ -37,14 +37,14 @@ bool Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::registere - boost::shared_ptr Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::UseCellMLDefaultStimulus() + std::shared_ptr Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__cell__stim_amplitude_converted = -9.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__cell__stim_duration = 5; // millisecond const double var_chaste_interface__cell__stim_period = 1000; // millisecond const double var_chaste_interface__cell__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__cell__stim_amplitude_converted), var_chaste_interface__cell__stim_duration, var_chaste_interface__cell__stim_period, @@ -59,7 +59,7 @@ bool Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::registere return NV_Ith_S(mStateVariables, 1); } - Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCellWithModifiers( pOdeSolver, 45, diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers.hpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers.hpp index dea49e784..91ffa3966 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractCardiacCellWithModifiers.hpp" @@ -36,76 +37,76 @@ class Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp : public // // Settable parameters and readable variables // - boost::shared_ptr mp_JSR_calcium_concentration_modifier; - boost::shared_ptr mp_SR_leak_current_max_modifier; - boost::shared_ptr mp_SR_release_current_modifier; - boost::shared_ptr mp_SR_release_current_max_modifier; - boost::shared_ptr mp_SR_uptake_current_max_modifier; - boost::shared_ptr mp_chloride_reversal_potential_modifier; - boost::shared_ptr mp_concentration_clamp_onoff_modifier; - boost::shared_ptr mp_cytosolic_calcium_concentration_modifier; - boost::shared_ptr mp_cytosolic_chloride_concentration_modifier; - boost::shared_ptr mp_cytosolic_potassium_concentration_modifier; - boost::shared_ptr mp_cytosolic_sodium_concentration_modifier; - boost::shared_ptr mp_dyadic_space_calcium_concentration_modifier; - boost::shared_ptr mp_dyadic_space_sodium_concentration_modifier; - boost::shared_ptr mp_extracellular_calcium_concentration_modifier; - boost::shared_ptr mp_extracellular_chloride_concentration_modifier; - boost::shared_ptr mp_extracellular_potassium_concentration_modifier; - boost::shared_ptr mp_extracellular_sodium_concentration_modifier; - boost::shared_ptr mp_faraday_constant_modifier; - boost::shared_ptr mp_gas_constant_modifier; - boost::shared_ptr mp_ICaL__i_CaL_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; - boost::shared_ptr mp_ICab__i_Cab_modifier; - boost::shared_ptr mp_IClb__i_Clb_modifier; - boost::shared_ptr mp_membrane_background_chloride_current_conductance_modifier; - boost::shared_ptr mp_INab__i_Nab_modifier; - boost::shared_ptr mp_ICap__i_Cap_modifier; - boost::shared_ptr mp_membrane_capacitance_modifier; - boost::shared_ptr mp_INa__i_Na_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; - boost::shared_ptr mp_Itof__i_tof_modifier; - boost::shared_ptr mp_membrane_fast_transient_outward_current_conductance_modifier; - boost::shared_ptr mp_IK1__i_K1_modifier; - boost::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_scaling_factor_modifier; - boost::shared_ptr mp_IKr__i_Kr_modifier; - boost::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_IKs__i_Ks_modifier; - boost::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_Itos__i_tos_modifier; - boost::shared_ptr mp_membrane_slow_transient_outward_current_conductance_modifier; - boost::shared_ptr mp_INaCa__i_NaCa_modifier; - boost::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; - boost::shared_ptr mp_membrane_voltage_modifier; - boost::shared_ptr mp_potassium_reversal_potential_modifier; - boost::shared_ptr mp_submembrane_space_calcium_concentration_modifier; - boost::shared_ptr mp_submembrane_space_sodium_concentration_modifier; - boost::shared_ptr mp_temperature_modifier; + std::shared_ptr mp_JSR_calcium_concentration_modifier; + std::shared_ptr mp_SR_leak_current_max_modifier; + std::shared_ptr mp_SR_release_current_modifier; + std::shared_ptr mp_SR_release_current_max_modifier; + std::shared_ptr mp_SR_uptake_current_max_modifier; + std::shared_ptr mp_chloride_reversal_potential_modifier; + std::shared_ptr mp_concentration_clamp_onoff_modifier; + std::shared_ptr mp_cytosolic_calcium_concentration_modifier; + std::shared_ptr mp_cytosolic_chloride_concentration_modifier; + std::shared_ptr mp_cytosolic_potassium_concentration_modifier; + std::shared_ptr mp_cytosolic_sodium_concentration_modifier; + std::shared_ptr mp_dyadic_space_calcium_concentration_modifier; + std::shared_ptr mp_dyadic_space_sodium_concentration_modifier; + std::shared_ptr mp_extracellular_calcium_concentration_modifier; + std::shared_ptr mp_extracellular_chloride_concentration_modifier; + std::shared_ptr mp_extracellular_potassium_concentration_modifier; + std::shared_ptr mp_extracellular_sodium_concentration_modifier; + std::shared_ptr mp_faraday_constant_modifier; + std::shared_ptr mp_gas_constant_modifier; + std::shared_ptr mp_ICaL__i_CaL_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; + std::shared_ptr mp_ICab__i_Cab_modifier; + std::shared_ptr mp_IClb__i_Clb_modifier; + std::shared_ptr mp_membrane_background_chloride_current_conductance_modifier; + std::shared_ptr mp_INab__i_Nab_modifier; + std::shared_ptr mp_ICap__i_Cap_modifier; + std::shared_ptr mp_membrane_capacitance_modifier; + std::shared_ptr mp_INa__i_Na_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; + std::shared_ptr mp_Itof__i_tof_modifier; + std::shared_ptr mp_membrane_fast_transient_outward_current_conductance_modifier; + std::shared_ptr mp_IK1__i_K1_modifier; + std::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_scaling_factor_modifier; + std::shared_ptr mp_IKr__i_Kr_modifier; + std::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_IKs__i_Ks_modifier; + std::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_Itos__i_tos_modifier; + std::shared_ptr mp_membrane_slow_transient_outward_current_conductance_modifier; + std::shared_ptr mp_INaCa__i_NaCa_modifier; + std::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; + std::shared_ptr mp_membrane_voltage_modifier; + std::shared_ptr mp_potassium_reversal_potential_modifier; + std::shared_ptr mp_submembrane_space_calcium_concentration_modifier; + std::shared_ptr mp_submembrane_space_sodium_concentration_modifier; + std::shared_ptr mp_temperature_modifier; private: - static AbstractCardiacCellWithModifiers* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractCardiacCellWithModifiers* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[45] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true, false, false, true, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; const bool is_probability[45] = {false, false, true, true, true, false, false, false, false, false, false, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -125,8 +126,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -135,8 +136,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996.cpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996.cpp index 12f9e6995..429bb9b3d 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996.cpp @@ -37,7 +37,7 @@ return NV_Ith_S(mStateVariables, 1); } - Celldokos_model_1996FromCellMLCvodeDataClamp::Celldokos_model_1996FromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Celldokos_model_1996FromCellMLCvodeDataClamp::Celldokos_model_1996FromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCellWithDataClamp( pOdeSolver, 18, diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996.hpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996.hpp index fd909a60d..a0de0494e 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -40,7 +41,7 @@ const bool is_probability[18] = {false, false, false, false, false, false, false public: double GetIntracellularCalciumConcentration(); - Celldokos_model_1996FromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Celldokos_model_1996FromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Celldokos_model_1996FromCellMLCvodeDataClamp(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -60,8 +61,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Celldokos_model_1996FromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -70,8 +71,8 @@ namespace boost inline void load_construct_data( Archive & ar, Celldokos_model_1996FromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Celldokos_model_1996FromCellMLCvodeDataClamp(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004.cpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004.cpp index 617227af5..8376221ac 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004.cpp @@ -31,14 +31,14 @@ - boost::shared_ptr Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__cell__stim_amplitude_converted = -9.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__cell__stim_duration = 5; // millisecond const double var_chaste_interface__cell__stim_period = 1000; // millisecond const double var_chaste_interface__cell__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__cell__stim_amplitude_converted), var_chaste_interface__cell__stim_duration, var_chaste_interface__cell__stim_period, @@ -53,7 +53,7 @@ return NV_Ith_S(mStateVariables, 1); } - Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp::Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCellWithDataClamp( pOdeSolver, 45, @@ -1438,8 +1438,8 @@ CHASTE_CLASS_EXPORT(Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDa extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004.hpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004.hpp index 4071989a7..e14d8a10e 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -40,9 +41,9 @@ const bool is_concentration[45] = {false, true, false, false, false, false, fals const bool is_probability[45] = {false, false, true, true, true, false, false, false, false, false, false, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvodeDataClamp(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp.cpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp.cpp index 2168088f9..852dbc9c1 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp.cpp @@ -29,7 +29,7 @@ #include "ModelFactory.hpp" -AbstractCvodeCellWithDataClamp* Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractCvodeCellWithDataClamp* Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp(p_solver, p_stimulus); } @@ -37,14 +37,14 @@ bool Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp::registered = Mo - boost::shared_ptr Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp::UseCellMLDefaultStimulus() + std::shared_ptr Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane_potential__stim_amplitude_converted = -9.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane_potential__stim_duration = 5; // msec const double var_chaste_interface__membrane_potential__stim_period = 1000; // msec const double var_chaste_interface__membrane_potential__stim_start = 100; // msec - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane_potential__stim_amplitude_converted), var_chaste_interface__membrane_potential__stim_duration, var_chaste_interface__membrane_potential__stim_period, @@ -59,7 +59,7 @@ bool Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp::registered = Mo return NV_Ith_S(mStateVariables, 1); } - Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp::Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp::Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCellWithDataClamp( pOdeSolver, 39, diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp.hpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp.hpp index fbad54e35..4637e7ac2 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -34,16 +35,16 @@ class Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp : public Abstra // private: - static AbstractCvodeCellWithDataClamp* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractCvodeCellWithDataClamp* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[39] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true, true, true, true, true, true}; const bool is_probability[39] = {false, false, true, true, true, false, false, false, false, false, false, true, true, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -63,8 +64,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -73,8 +74,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClamp(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/hodgkin_huxley_squid_axon_model_1952_modified.cpp index 518f18b55..91687bce1 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -31,14 +31,14 @@ - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -48,7 +48,7 @@ return p_cellml_stim; } - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCellWithDataClamp( pOdeSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 66abfeb04..173e9193b 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,8 +40,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -60,8 +61,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -70,8 +71,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClamp(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt.cpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt.cpp index e42e23fd0..d538aa3dc 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt.cpp @@ -29,7 +29,7 @@ #include "ModelFactory.hpp" -AbstractCvodeCellWithDataClamp* Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractCvodeCellWithDataClamp* Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt(p_solver, p_stimulus); } @@ -382,14 +382,14 @@ class Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt_LookupTables std::shared_ptr Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt_LookupTables::mpInstance; - boost::shared_ptr Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane_potential__stim_amplitude_converted = -9.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane_potential__stim_duration = 5; // msec const double var_chaste_interface__membrane_potential__stim_period = 1000; // msec const double var_chaste_interface__membrane_potential__stim_start = 100; // msec - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane_potential__stim_amplitude_converted), var_chaste_interface__membrane_potential__stim_duration, var_chaste_interface__membrane_potential__stim_period, @@ -404,7 +404,7 @@ std::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt::Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCellWithDataClamp( pOdeSolver, 39, diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt.hpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt.hpp index 288a84e93..19308c232 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -34,16 +35,16 @@ class Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt : public Abs // private: - static AbstractCvodeCellWithDataClamp* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractCvodeCellWithDataClamp* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[39] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true, true, true, true, true, true}; const bool is_probability[39] = {false, false, true, true, true, false, false, false, false, false, false, true, true, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -64,8 +65,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -74,8 +75,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellgrandi_pasqualini_bers_2010_ssFromCellMLCvodeDataClampOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.cpp index c1e38f90a..f68dbbb57 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -255,14 +255,14 @@ class Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampO std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -272,7 +272,7 @@ std::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCellWithDataClamp( pOdeSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 index 12aed2bdd..7ccd81b7f 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 @@ -255,14 +255,14 @@ private: std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -272,7 +272,7 @@ std::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCellWithDataClamp( pOdeSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 98790b69e..73653817e 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,8 +40,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeDataClampOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/FaberRudy2000.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/FaberRudy2000.cpp index eeecb6779..5dcbe5b56 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/FaberRudy2000.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/FaberRudy2000.cpp @@ -27,14 +27,14 @@ #include "CvodeContextManager.hpp" #endif - boost::shared_ptr CellFaberRudy2000FromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr CellFaberRudy2000FromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -25.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration_converted = 2.0; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 1000.0; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 100.0; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -49,7 +49,7 @@ return NV_Ith_S(mStateVariables, 1); } - CellFaberRudy2000FromCellMLCvode::CellFaberRudy2000FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + CellFaberRudy2000FromCellMLCvode::CellFaberRudy2000FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 25, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/difrancesco_noble_model_1985.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/difrancesco_noble_model_1985.cpp index ec8ce516f..868bfc7f8 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/difrancesco_noble_model_1985.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/difrancesco_noble_model_1985.cpp @@ -31,14 +31,14 @@ - boost::shared_ptr Celldifrancesco_noble_model_1985FromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Celldifrancesco_noble_model_1985FromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__stimulus__stim_amplitude_converted = -0.5 * HeartConfig::Instance()->GetCapacitance() / NV_Ith_S(mParameters, 8); // uA_per_cm2 const double var_chaste_interface__stimulus__stim_duration_converted = 5; // millisecond const double var_chaste_interface__stimulus__stim_period_converted = 1000; // millisecond const double var_chaste_interface__stimulus__stim_start_converted = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__stimulus__stim_amplitude_converted), var_chaste_interface__stimulus__stim_duration_converted, var_chaste_interface__stimulus__stim_period_converted, @@ -53,7 +53,7 @@ return NV_Ith_S(mStateVariables, 1); } - Celldifrancesco_noble_model_1985FromCellMLCvode::Celldifrancesco_noble_model_1985FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Celldifrancesco_noble_model_1985FromCellMLCvode::Celldifrancesco_noble_model_1985FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 16, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/difrancesco_noble_model_1985.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/difrancesco_noble_model_1985.hpp index c9a0a09cf..bc8dc095e 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/difrancesco_noble_model_1985.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/difrancesco_noble_model_1985.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,9 +40,9 @@ const bool is_concentration[16] = {false, true, false, false, false, false, fals const bool is_probability[16] = {false, false, false, false, false, true, true, true, true, true, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Celldifrancesco_noble_model_1985FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Celldifrancesco_noble_model_1985FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Celldifrancesco_noble_model_1985FromCellMLCvode(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Celldifrancesco_noble_model_1985FromCellMLCvode * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Celldifrancesco_noble_model_1985FromCellMLCvode * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Celldifrancesco_noble_model_1985FromCellMLCvode(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/dynamic_mahajan_shiferaw_2008.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/dynamic_mahajan_shiferaw_2008.cpp index 1320099a2..05228d82e 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/dynamic_mahajan_shiferaw_2008.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/dynamic_mahajan_shiferaw_2008.cpp @@ -31,14 +31,14 @@ - boost::shared_ptr Dynamicmahajan_shiferaw_2008FromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicmahajan_shiferaw_2008FromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__cell__stim_amplitude_converted = -14.999999999999998 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__cell__stim_duration = 3; // ms const double var_chaste_interface__cell__stim_offset = 100; // ms const double var_chaste_interface__cell__stim_period = 400; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__cell__stim_amplitude_converted), var_chaste_interface__cell__stim_duration, var_chaste_interface__cell__stim_period, @@ -53,7 +53,7 @@ return NV_Ith_S(mStateVariables, 1); } - Dynamicmahajan_shiferaw_2008FromCellMLCvode::Dynamicmahajan_shiferaw_2008FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicmahajan_shiferaw_2008FromCellMLCvode::Dynamicmahajan_shiferaw_2008FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 26, @@ -1040,8 +1040,8 @@ CHASTE_CLASS_EXPORT(Dynamicmahajan_shiferaw_2008FromCellMLCvode) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicmahajan_shiferaw_2008FromCellMLCvode(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/dynamic_mahajan_shiferaw_2008.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/dynamic_mahajan_shiferaw_2008.hpp index 18b61b672..ea3385c21 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/dynamic_mahajan_shiferaw_2008.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/dynamic_mahajan_shiferaw_2008.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -40,9 +41,9 @@ const bool is_concentration[26] = {false, true, false, false, false, false, fals const bool is_probability[26] = {false, false, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamicmahajan_shiferaw_2008FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamicmahajan_shiferaw_2008FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicmahajan_shiferaw_2008FromCellMLCvode(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicmahajan_shiferaw_2008FromCellMLCvode * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicmahajan_shiferaw_2008FromCellMLCvode * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicmahajan_shiferaw_2008FromCellMLCvode(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/faber_rudy_2000.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/faber_rudy_2000.cpp index 6395932d6..cde42c996 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/faber_rudy_2000.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/faber_rudy_2000.cpp @@ -31,14 +31,14 @@ - boost::shared_ptr Cellfaber_rudy_2000FromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Cellfaber_rudy_2000FromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__cell__stim_amplitude_converted = -25.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__cell__stim_duration = 2; // ms const double var_chaste_interface__cell__stim_period = 1000; // ms const double var_chaste_interface__cell__stim_start = 100; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__cell__stim_amplitude_converted), var_chaste_interface__cell__stim_duration, var_chaste_interface__cell__stim_period, @@ -53,7 +53,7 @@ return NV_Ith_S(mStateVariables, 1); } - Cellfaber_rudy_2000FromCellMLCvode::Cellfaber_rudy_2000FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellfaber_rudy_2000FromCellMLCvode::Cellfaber_rudy_2000FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 25, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/faber_rudy_2000.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/faber_rudy_2000.hpp index 7b50be6c8..3cb31a738 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/faber_rudy_2000.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/faber_rudy_2000.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,9 +40,9 @@ const bool is_concentration[25] = {false, true, false, false, false, false, fals const bool is_probability[25] = {false, false, true, true, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellfaber_rudy_2000FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellfaber_rudy_2000FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellfaber_rudy_2000FromCellMLCvode(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellfaber_rudy_2000FromCellMLCvode * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellfaber_rudy_2000FromCellMLCvode * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellfaber_rudy_2000FromCellMLCvode(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/hodgkin_huxley_squid_axon_model_1952_modified.cpp index 28dcdb822..c6afc943b 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -31,14 +31,14 @@ - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -48,7 +48,7 @@ return p_cellml_stim; } - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 38130b5e6..cc9ebfe70 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,8 +40,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -60,8 +61,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -70,8 +71,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/paci_hyttinen_aaltosetala_severi_ventricularVersion.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/paci_hyttinen_aaltosetala_severi_ventricularVersion.cpp index fc4f4a6fe..0d3dab28c 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/paci_hyttinen_aaltosetala_severi_ventricularVersion.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/paci_hyttinen_aaltosetala_severi_ventricularVersion.cpp @@ -31,14 +31,14 @@ - boost::shared_ptr Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__stim_mode__i_stim_Amplitude_converted = 5.5718264182641404 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__stim_mode__i_stim_Period_converted = 1000; // millisecond const double var_chaste_interface__stim_mode__i_stim_PulseDuration_converted = 5; // millisecond const double var_chaste_interface__stim_mode__i_stim_Start_converted = 0; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__stim_mode__i_stim_Amplitude_converted), var_chaste_interface__stim_mode__i_stim_PulseDuration_converted, var_chaste_interface__stim_mode__i_stim_Period_converted, @@ -53,7 +53,7 @@ return NV_Ith_S(mStateVariables, 1); } - Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode::Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode::Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 18, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode/paci_hyttinen_aaltosetala_severi_ventricularVersion.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode/paci_hyttinen_aaltosetala_severi_ventricularVersion.hpp index 81cf22b7c..75b08c162 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode/paci_hyttinen_aaltosetala_severi_ventricularVersion.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode/paci_hyttinen_aaltosetala_severi_ventricularVersion.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,9 +40,9 @@ const bool is_concentration[18] = {false, true, false, false, false, false, fals const bool is_probability[18] = {false, false, true, true, true, true, true, true, true, false, false, false, true, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellpaci_hyttinen_aaltosetala_severi_ventricularVersionFromCellMLCvode(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/dynamic_aslanidi_Purkinje_model_2009.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/dynamic_aslanidi_Purkinje_model_2009.cpp index 1d42f7976..e1cebbf33 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/dynamic_aslanidi_Purkinje_model_2009.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/dynamic_aslanidi_Purkinje_model_2009.cpp @@ -29,7 +29,7 @@ #include "ModelFactory.hpp" -AbstractCardiacCellWithModifiers* Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractCardiacCellWithModifiers* Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt(p_solver, p_stimulus); } @@ -558,14 +558,14 @@ class Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt_LookupTables : publi std::shared_ptr Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt_LookupTables::mpInstance; - boost::shared_ptr Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 1; // millisecond const double var_chaste_interface__membrane__stim_period = 800; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -580,7 +580,7 @@ std::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt::Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCellWithModifiers( pOdeSolver, 30, @@ -1458,8 +1458,8 @@ CHASTE_CLASS_EXPORT(Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/dynamic_aslanidi_Purkinje_model_2009.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/dynamic_aslanidi_Purkinje_model_2009.hpp index 7ce5481bc..d6ed4c39b 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/dynamic_aslanidi_Purkinje_model_2009.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/dynamic_aslanidi_Purkinje_model_2009.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractCardiacCellWithModifiers.hpp" @@ -37,62 +38,62 @@ class Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt : public AbstractCar // // Settable parameters and readable variables // - boost::shared_ptr mp_JSR_calcium_concentration_modifier; - boost::shared_ptr mp_SR_leak_current_max_modifier; - boost::shared_ptr mp_SR_release_current_modifier; - boost::shared_ptr mp_SR_release_current_max_modifier; - boost::shared_ptr mp_SR_uptake_current_max_modifier; - boost::shared_ptr mp_concentration_clamp_onoff_modifier; - boost::shared_ptr mp_cytosolic_calcium_concentration_modifier; - boost::shared_ptr mp_cytosolic_potassium_concentration_modifier; - boost::shared_ptr mp_cytosolic_sodium_concentration_modifier; - boost::shared_ptr mp_dyadic_space_calcium_concentration_modifier; - boost::shared_ptr mp_extracellular_calcium_concentration_modifier; - boost::shared_ptr mp_extracellular_potassium_concentration_modifier; - boost::shared_ptr mp_extracellular_sodium_concentration_modifier; - boost::shared_ptr mp_i_Ca_L__i_Ca_L_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; - boost::shared_ptr mp_i_Na__i_Na_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; - boost::shared_ptr mp_i_K1__i_K1_modifier; - boost::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_Kr__i_Kr_modifier; - boost::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_Ks__i_Ks_modifier; - boost::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_NaCa__i_NaCa_modifier; - boost::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; - boost::shared_ptr mp_i_to_1__i_to_1_modifier; - boost::shared_ptr mp_membrane_transient_outward_current_conductance_modifier; - boost::shared_ptr mp_membrane_voltage_modifier; + std::shared_ptr mp_JSR_calcium_concentration_modifier; + std::shared_ptr mp_SR_leak_current_max_modifier; + std::shared_ptr mp_SR_release_current_modifier; + std::shared_ptr mp_SR_release_current_max_modifier; + std::shared_ptr mp_SR_uptake_current_max_modifier; + std::shared_ptr mp_concentration_clamp_onoff_modifier; + std::shared_ptr mp_cytosolic_calcium_concentration_modifier; + std::shared_ptr mp_cytosolic_potassium_concentration_modifier; + std::shared_ptr mp_cytosolic_sodium_concentration_modifier; + std::shared_ptr mp_dyadic_space_calcium_concentration_modifier; + std::shared_ptr mp_extracellular_calcium_concentration_modifier; + std::shared_ptr mp_extracellular_potassium_concentration_modifier; + std::shared_ptr mp_extracellular_sodium_concentration_modifier; + std::shared_ptr mp_i_Ca_L__i_Ca_L_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; + std::shared_ptr mp_i_Na__i_Na_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; + std::shared_ptr mp_i_K1__i_K1_modifier; + std::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_Kr__i_Kr_modifier; + std::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_Ks__i_Ks_modifier; + std::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_NaCa__i_NaCa_modifier; + std::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; + std::shared_ptr mp_i_to_1__i_to_1_modifier; + std::shared_ptr mp_membrane_transient_outward_current_conductance_modifier; + std::shared_ptr mp_membrane_voltage_modifier; private: - static AbstractCardiacCellWithModifiers* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractCardiacCellWithModifiers* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[30] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, false, true, false, false, true, true, false, false}; const bool is_probability[30] = {false, false, true, true, true, false, false, true, true, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -113,8 +114,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -123,8 +124,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicaslanidi_Purkinje_model_2009FromCellMLCvodeOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/hilgemann_noble_model_1987.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/hilgemann_noble_model_1987.cpp index aed12e9d4..78b9ceb10 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/hilgemann_noble_model_1987.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/hilgemann_noble_model_1987.cpp @@ -321,14 +321,14 @@ class Cellhilgemann_noble_model_1987FromCellMLCvodeOpt_LookupTables : public Abs std::shared_ptr Cellhilgemann_noble_model_1987FromCellMLCvodeOpt_LookupTables::mpInstance; - boost::shared_ptr Cellhilgemann_noble_model_1987FromCellMLCvodeOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhilgemann_noble_model_1987FromCellMLCvodeOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -0.20000000000000001 * HeartConfig::Instance()->GetCapacitance() / NV_Ith_S(mParameters, 8); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration_converted = 2; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 1000; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -343,7 +343,7 @@ std::shared_ptr C return NV_Ith_S(mStateVariables, 1); } - Cellhilgemann_noble_model_1987FromCellMLCvodeOpt::Cellhilgemann_noble_model_1987FromCellMLCvodeOpt(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhilgemann_noble_model_1987FromCellMLCvodeOpt::Cellhilgemann_noble_model_1987FromCellMLCvodeOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 15, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/hilgemann_noble_model_1987.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/hilgemann_noble_model_1987.hpp index 14dfa1f0d..4f36495b9 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/hilgemann_noble_model_1987.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt/hilgemann_noble_model_1987.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,9 +40,9 @@ const bool is_concentration[15] = {false, true, false, false, false, false, fals const bool is_probability[15] = {false, false, true, true, true, true, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellhilgemann_noble_model_1987FromCellMLCvodeOpt(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellhilgemann_noble_model_1987FromCellMLCvodeOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhilgemann_noble_model_1987FromCellMLCvodeOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhilgemann_noble_model_1987FromCellMLCvodeOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhilgemann_noble_model_1987FromCellMLCvodeOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhilgemann_noble_model_1987FromCellMLCvodeOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp index 35dfc9ffa..0f60f811c 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -255,14 +255,14 @@ class Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt_Lookup std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -272,7 +272,7 @@ std::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 index ccddd802b..111904f87 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 @@ -255,14 +255,14 @@ private: std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -272,7 +272,7 @@ std::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 04271dcd0..f83553c0f 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,8 +40,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvodeOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.cpp index 5e8763461..efbee72aa 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.cpp @@ -31,7 +31,7 @@ - boost::shared_ptr Cellaslanidi_atrial_model_2009FromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Cellaslanidi_atrial_model_2009FromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_membrane__Cm_converted = 0.001 * NV_Ith_S(mParameters, 4); // uF @@ -39,7 +39,7 @@ const double var_chaste_interface__membrane__stim_duration_converted = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 500; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -54,7 +54,7 @@ return NV_Ith_S(mStateVariables, 1); } - Cellaslanidi_atrial_model_2009FromCellMLCvode::Cellaslanidi_atrial_model_2009FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellaslanidi_atrial_model_2009FromCellMLCvode::Cellaslanidi_atrial_model_2009FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 29, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.cpp_python36 index 31f3dfb3d..08834e150 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.cpp_python36 @@ -29,7 +29,7 @@ - boost::shared_ptr Cellaslanidi_atrial_model_2009FromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Cellaslanidi_atrial_model_2009FromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_membrane__Cm_converted = 0.001 * NV_Ith_S(mParameters, 4); // uF @@ -37,7 +37,7 @@ const double var_chaste_interface__membrane__stim_duration_converted = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 500; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -52,7 +52,7 @@ return NV_Ith_S(mStateVariables, 1); } - Cellaslanidi_atrial_model_2009FromCellMLCvode::Cellaslanidi_atrial_model_2009FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellaslanidi_atrial_model_2009FromCellMLCvode::Cellaslanidi_atrial_model_2009FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 29, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.hpp index 7031a18f8..e348d51c4 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/aslanidi_atrial_model_2009.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,9 +40,9 @@ const bool is_concentration[29] = {false, true, false, false, false, false, fals const bool is_probability[29] = {false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellaslanidi_atrial_model_2009FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellaslanidi_atrial_model_2009FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellaslanidi_atrial_model_2009FromCellMLCvode(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellaslanidi_atrial_model_2009FromCellMLCvode * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellaslanidi_atrial_model_2009FromCellMLCvode * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellaslanidi_atrial_model_2009FromCellMLCvode(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.cpp index e5733f956..7346798c6 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.cpp @@ -29,7 +29,7 @@ #include "ModelFactory.hpp" -AbstractCvodeCell* Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractCvodeCell* Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(p_solver, p_stimulus); } @@ -37,14 +37,14 @@ bool Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::registered = Mo - boost::shared_ptr Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__cell__stim_amplitude_converted = -9.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__cell__stim_duration = 5; // millisecond const double var_chaste_interface__cell__stim_period = 1000; // millisecond const double var_chaste_interface__cell__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__cell__stim_amplitude_converted), var_chaste_interface__cell__stim_duration, var_chaste_interface__cell__stim_period, @@ -59,7 +59,7 @@ bool Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::registered = Mo return NV_Ith_S(mStateVariables, 1); } - Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 45, @@ -2140,8 +2140,8 @@ CHASTE_CLASS_EXPORT(Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.cpp_python36 index d443c5efd..22ba69808 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.cpp_python36 @@ -29,7 +29,7 @@ #include "ModelFactory.hpp" -AbstractCvodeCell* Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractCvodeCell* Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(p_solver, p_stimulus); } @@ -37,14 +37,14 @@ bool Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::registered = Mo - boost::shared_ptr Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__cell__stim_amplitude_converted = -9.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__cell__stim_duration = 5; // millisecond const double var_chaste_interface__cell__stim_period = 1000; // millisecond const double var_chaste_interface__cell__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__cell__stim_amplitude_converted), var_chaste_interface__cell__stim_duration, var_chaste_interface__cell__stim_period, @@ -59,7 +59,7 @@ bool Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::registered = Mo return NV_Ith_S(mStateVariables, 1); } - Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode::Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 45, @@ -2163,8 +2163,8 @@ CHASTE_CLASS_EXPORT(Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.hpp index 739ac6c6a..4785cd735 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/dynamic_Shannon2004.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -35,16 +36,16 @@ class Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode : public Abstra // private: - static AbstractCvodeCell* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractCvodeCell* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[45] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true, false, false, true, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; const bool is_probability[45] = {false, false, true, true, true, false, false, false, false, false, false, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -65,8 +66,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -75,8 +76,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicshannon_wang_puglisi_weber_bers_2004FromCellMLCvode(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp index f37e178d1..083a401bc 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -31,14 +31,14 @@ - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -48,7 +48,7 @@ return p_cellml_stim; } - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 index cfaf824ba..9163c67f1 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 @@ -31,14 +31,14 @@ - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -48,7 +48,7 @@ return p_cellml_stim; } - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractCvodeCell( pOdeSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 828995ce9..14398817a 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -14,6 +14,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -39,8 +40,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLCvode(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.cpp index 4be991895..c63da0433 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.cpp @@ -30,7 +30,7 @@ { return mStateVariables[1]; } - Dynamicdemir_model_1994FromCellMLGRL1::Dynamicdemir_model_1994FromCellMLGRL1(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicdemir_model_1994FromCellMLGRL1::Dynamicdemir_model_1994FromCellMLGRL1(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 27, 0, @@ -2821,8 +2821,8 @@ CHASTE_CLASS_EXPORT(Dynamicdemir_model_1994FromCellMLGRL1) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicdemir_model_1994FromCellMLGRL1(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.cpp_python36 index edbd808c8..f6dfcf10b 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.cpp_python36 @@ -29,7 +29,7 @@ { return mStateVariables[1]; } - Dynamicdemir_model_1994FromCellMLGRL1::Dynamicdemir_model_1994FromCellMLGRL1(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicdemir_model_1994FromCellMLGRL1::Dynamicdemir_model_1994FromCellMLGRL1(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 27, 0, @@ -2819,8 +2819,8 @@ CHASTE_CLASS_EXPORT(Dynamicdemir_model_1994FromCellMLGRL1) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicdemir_model_1994FromCellMLGRL1(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.hpp index 0e9c0c7a2..0990e010b 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_demir_model_1994.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -40,7 +41,7 @@ const bool is_probability[27] = {false, false, false, false, false, false, false public: double GetIntracellularCalciumConcentration(); - Dynamicdemir_model_1994FromCellMLGRL1(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamicdemir_model_1994FromCellMLGRL1(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicdemir_model_1994FromCellMLGRL1(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -117,8 +118,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicdemir_model_1994FromCellMLGRL1 * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -127,8 +128,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicdemir_model_1994FromCellMLGRL1 * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicdemir_model_1994FromCellMLGRL1(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_matsuoka_model_2003.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_matsuoka_model_2003.cpp index 1adaa9650..733d0f9ff 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_matsuoka_model_2003.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_matsuoka_model_2003.cpp @@ -21,7 +21,7 @@ #include "IsNan.hpp" #include "MathsCustomFunctions.hpp" - boost::shared_ptr Dynamicmatsuoka_model_2003FromCellMLGRL1::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicmatsuoka_model_2003FromCellMLGRL1::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_membrane__Cm_converted = 9.9999999999999995e-7 * mParameters[0]; // uF @@ -29,7 +29,7 @@ const double var_chaste_interface__membrane__stim_duration = 2.0; // millisecond const double var_chaste_interface__membrane__stim_period = 400.0; // millisecond const double var_chaste_interface__membrane__stim_start = 50.0; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -39,7 +39,7 @@ return p_cellml_stim; } - Dynamicmatsuoka_model_2003FromCellMLGRL1::Dynamicmatsuoka_model_2003FromCellMLGRL1(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicmatsuoka_model_2003FromCellMLGRL1::Dynamicmatsuoka_model_2003FromCellMLGRL1(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 37, 0, @@ -3752,8 +3752,8 @@ CHASTE_CLASS_EXPORT(Dynamicmatsuoka_model_2003FromCellMLGRL1) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicmatsuoka_model_2003FromCellMLGRL1(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_matsuoka_model_2003.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_matsuoka_model_2003.hpp index 0d4797657..5cc2ed0c4 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_matsuoka_model_2003.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1/dynamic_matsuoka_model_2003.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractCardiacCellWithModifiers.hpp" @@ -36,14 +37,14 @@ class Dynamicmatsuoka_model_2003FromCellMLGRL1 : public AbstractCardiacCellWithM // // Settable parameters and readable variables // - boost::shared_ptr mp_cytosolic_calcium_concentration_modifier; - boost::shared_ptr mp_membrane_capacitance_modifier; - boost::shared_ptr mp_membrane_voltage_modifier; + std::shared_ptr mp_cytosolic_calcium_concentration_modifier; + std::shared_ptr mp_membrane_capacitance_modifier; + std::shared_ptr mp_membrane_voltage_modifier; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Dynamicmatsuoka_model_2003FromCellMLGRL1(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Dynamicmatsuoka_model_2003FromCellMLGRL1(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicmatsuoka_model_2003FromCellMLGRL1(); double GetIIonic(const std::vector* pStateVariables=NULL); void UpdateTransmembranePotential(double var_chaste_interface__environment__time); @@ -139,8 +140,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicmatsuoka_model_2003FromCellMLGRL1 * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -149,8 +150,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicmatsuoka_model_2003FromCellMLGRL1 * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicmatsuoka_model_2003FromCellMLGRL1(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.cpp index 93d90713f..e5d4ee803 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -26,14 +26,14 @@ - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -43,7 +43,7 @@ return p_cellml_stim; } - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 index aaa4c9313..87201c517 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 @@ -26,14 +26,14 @@ - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -43,7 +43,7 @@ return p_cellml_stim; } - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 8616dfcf7..da9178063 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,8 +39,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -70,8 +71,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1 * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -80,8 +81,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1 * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL1(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.cpp index 164285d9f..cb710f289 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.cpp @@ -360,14 +360,14 @@ class Cellbeeler_reuter_model_1977FromCellMLGRL1Opt_LookupTables : public Abstra std::shared_ptr Cellbeeler_reuter_model_1977FromCellMLGRL1Opt_LookupTables::mpInstance; - boost::shared_ptr Cellbeeler_reuter_model_1977FromCellMLGRL1Opt::UseCellMLDefaultStimulus() + std::shared_ptr Cellbeeler_reuter_model_1977FromCellMLGRL1Opt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__stimulus_protocol__IstimAmplitude_converted = 50.000000000000007; // uA_per_cm2 const double var_chaste_interface__stimulus_protocol__IstimPeriod = 1000; // ms const double var_chaste_interface__stimulus_protocol__IstimPulseDuration = 1; // ms const double var_chaste_interface__stimulus_protocol__IstimStart = 10; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__stimulus_protocol__IstimAmplitude_converted), var_chaste_interface__stimulus_protocol__IstimPulseDuration, var_chaste_interface__stimulus_protocol__IstimPeriod, @@ -380,7 +380,7 @@ std::shared_ptr Cell { return mStateVariables[1]; } - Cellbeeler_reuter_model_1977FromCellMLGRL1Opt::Cellbeeler_reuter_model_1977FromCellMLGRL1Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellbeeler_reuter_model_1977FromCellMLGRL1Opt::Cellbeeler_reuter_model_1977FromCellMLGRL1Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 8, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.cpp_python36 index 33860204f..c221121d5 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.cpp_python36 @@ -360,14 +360,14 @@ private: std::shared_ptr Cellbeeler_reuter_model_1977FromCellMLGRL1Opt_LookupTables::mpInstance; - boost::shared_ptr Cellbeeler_reuter_model_1977FromCellMLGRL1Opt::UseCellMLDefaultStimulus() + std::shared_ptr Cellbeeler_reuter_model_1977FromCellMLGRL1Opt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__stimulus_protocol__IstimAmplitude_converted = 50.000000000000007; // uA_per_cm2 const double var_chaste_interface__stimulus_protocol__IstimPeriod = 1000; // ms const double var_chaste_interface__stimulus_protocol__IstimPulseDuration = 1; // ms const double var_chaste_interface__stimulus_protocol__IstimStart = 10; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__stimulus_protocol__IstimAmplitude_converted), var_chaste_interface__stimulus_protocol__IstimPulseDuration, var_chaste_interface__stimulus_protocol__IstimPeriod, @@ -380,7 +380,7 @@ std::shared_ptr Cell { return mStateVariables[1]; } - Cellbeeler_reuter_model_1977FromCellMLGRL1Opt::Cellbeeler_reuter_model_1977FromCellMLGRL1Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellbeeler_reuter_model_1977FromCellMLGRL1Opt::Cellbeeler_reuter_model_1977FromCellMLGRL1Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 8, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.hpp index a8897e424..777e981fb 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[8] = {false, true, false, false, false, false, false const bool is_probability[8] = {false, false, true, true, true, true, true, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellbeeler_reuter_model_1977FromCellMLGRL1Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Cellbeeler_reuter_model_1977FromCellMLGRL1Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellbeeler_reuter_model_1977FromCellMLGRL1Opt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -80,8 +81,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellbeeler_reuter_model_1977FromCellMLGRL1Opt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -90,8 +91,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellbeeler_reuter_model_1977FromCellMLGRL1Opt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellbeeler_reuter_model_1977FromCellMLGRL1Opt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.cpp index 357d7df8f..9439b11c2 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.cpp @@ -24,7 +24,7 @@ #include "ModelFactory.hpp" -AbstractGeneralizedRushLarsenCardiacCell* Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractGeneralizedRushLarsenCardiacCell* Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(p_solver, p_stimulus); } @@ -674,14 +674,14 @@ class Dynamicmatsuoka_model_2003FromCellMLGRL1Opt_LookupTables : public Abstract std::shared_ptr Dynamicmatsuoka_model_2003FromCellMLGRL1Opt_LookupTables::mpInstance; - boost::shared_ptr Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -4000 * HeartConfig::Instance()->GetCapacitance() / mParameters[9]; // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 2; // millisecond const double var_chaste_interface__membrane__stim_period = 400; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -691,7 +691,7 @@ std::shared_ptr Dynami return p_cellml_stim; } - Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 37, 0, @@ -5071,8 +5071,8 @@ CHASTE_CLASS_EXPORT(Dynamicmatsuoka_model_2003FromCellMLGRL1Opt) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.cpp_python36 index bbd10221c..3a3b39942 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.cpp_python36 @@ -24,7 +24,7 @@ #include "ModelFactory.hpp" -AbstractGeneralizedRushLarsenCardiacCell* Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractGeneralizedRushLarsenCardiacCell* Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(p_solver, p_stimulus); } @@ -674,14 +674,14 @@ private: std::shared_ptr Dynamicmatsuoka_model_2003FromCellMLGRL1Opt_LookupTables::mpInstance; - boost::shared_ptr Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -4000 * HeartConfig::Instance()->GetCapacitance() / mParameters[9]; // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 2; // millisecond const double var_chaste_interface__membrane__stim_period = 400; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -691,7 +691,7 @@ std::shared_ptr Dynami return p_cellml_stim; } - Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicmatsuoka_model_2003FromCellMLGRL1Opt::Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 37, 0, @@ -5076,8 +5076,8 @@ CHASTE_CLASS_EXPORT(Dynamicmatsuoka_model_2003FromCellMLGRL1Opt) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.hpp index ea268feec..82e0e4929 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/dynamic_matsuoka_model_2003.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -34,15 +35,15 @@ class Dynamicmatsuoka_model_2003FromCellMLGRL1Opt : public AbstractGeneralizedRu // private: - static AbstractGeneralizedRushLarsenCardiacCell* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractGeneralizedRushLarsenCardiacCell* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[37] = {false, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; const bool is_probability[37] = {false, false, false, false, false, true, false, false, true, true, false, false, true, true, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -140,8 +141,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicmatsuoka_model_2003FromCellMLGRL1Opt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -150,8 +151,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicmatsuoka_model_2003FromCellMLGRL1Opt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicmatsuoka_model_2003FromCellMLGRL1Opt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.cpp index b341b1892..583c5a4a1 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.cpp @@ -26,14 +26,14 @@ - boost::shared_ptr Dynamicwinslow_model_1999FromCellMLGRL2::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicwinslow_model_1999FromCellMLGRL2::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -21.126799999999999 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration_converted = 2; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 1000; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -46,7 +46,7 @@ { return mStateVariables[1]; } - Dynamicwinslow_model_1999FromCellMLGRL2::Dynamicwinslow_model_1999FromCellMLGRL2(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicwinslow_model_1999FromCellMLGRL2::Dynamicwinslow_model_1999FromCellMLGRL2(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 33, 0, @@ -3442,8 +3442,8 @@ CHASTE_CLASS_EXPORT(Dynamicwinslow_model_1999FromCellMLGRL2) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicwinslow_model_1999FromCellMLGRL2(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.cpp_python36 index 115381eb9..3ea66acc4 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.cpp_python36 @@ -26,14 +26,14 @@ - boost::shared_ptr Dynamicwinslow_model_1999FromCellMLGRL2::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicwinslow_model_1999FromCellMLGRL2::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -21.126799999999999 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration_converted = 2; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 1000; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -46,7 +46,7 @@ { return mStateVariables[1]; } - Dynamicwinslow_model_1999FromCellMLGRL2::Dynamicwinslow_model_1999FromCellMLGRL2(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicwinslow_model_1999FromCellMLGRL2::Dynamicwinslow_model_1999FromCellMLGRL2(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 33, 0, @@ -3432,8 +3432,8 @@ CHASTE_CLASS_EXPORT(Dynamicwinslow_model_1999FromCellMLGRL2) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicwinslow_model_1999FromCellMLGRL2(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.hpp index 1aa2841bf..a75a7a095 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2/dynamic_winslow_model_1999.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -39,9 +40,9 @@ const bool is_concentration[33] = {false, true, false, false, false, false, fals const bool is_probability[33] = {false, false, true, true, true, false, false, false, false, true, true, false, false, false, false, false, false, false, false, false, false, true, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamicwinslow_model_1999FromCellMLGRL2(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamicwinslow_model_1999FromCellMLGRL2(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicwinslow_model_1999FromCellMLGRL2(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -130,8 +131,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicwinslow_model_1999FromCellMLGRL2 * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -140,8 +141,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicwinslow_model_1999FromCellMLGRL2 * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicwinslow_model_1999FromCellMLGRL2(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.cpp index 8be4b35b7..db0fe0e5c 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -26,14 +26,14 @@ - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -43,7 +43,7 @@ return p_cellml_stim; } - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 index 2662b80e9..75051bcd5 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 @@ -26,14 +26,14 @@ - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -43,7 +43,7 @@ return p_cellml_stim; } - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.hpp index e9ed236cc..95d684cf4 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,8 +39,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -70,8 +71,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2 * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -80,8 +81,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2 * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.cpp index 55b7c46e4..f75ad9f1c 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.cpp @@ -24,7 +24,7 @@ #include "ModelFactory.hpp" -AbstractGeneralizedRushLarsenCardiacCell* Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractGeneralizedRushLarsenCardiacCell* Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(p_solver, p_stimulus); } @@ -553,14 +553,14 @@ class Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt_LookupTables : public A std::shared_ptr Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt_LookupTables::mpInstance; - boost::shared_ptr Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -25.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration_converted = 2; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 1000; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -573,7 +573,7 @@ std::shared_ptr { return mStateVariables[1]; } - Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 25, 0, @@ -3446,8 +3446,8 @@ CHASTE_CLASS_EXPORT(Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.cpp_python36 index 0b70a4625..c2d51da33 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.cpp_python36 @@ -24,7 +24,7 @@ #include "ModelFactory.hpp" -AbstractGeneralizedRushLarsenCardiacCell* Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractGeneralizedRushLarsenCardiacCell* Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(p_solver, p_stimulus); } @@ -553,14 +553,14 @@ private: std::shared_ptr Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt_LookupTables::mpInstance; - boost::shared_ptr Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -25.5 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration_converted = 2; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 1000; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -573,7 +573,7 @@ std::shared_ptr { return mStateVariables[1]; } - Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt::Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 25, 0, @@ -3463,8 +3463,8 @@ CHASTE_CLASS_EXPORT(Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.hpp index bd776ac22..f74c95d12 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_viswanathan_model_1999_epi.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -34,16 +35,16 @@ class Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt : public AbstractGenera // private: - static AbstractGeneralizedRushLarsenCardiacCell* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractGeneralizedRushLarsenCardiacCell* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[25] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true}; const bool is_probability[25] = {false, false, false, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -117,8 +118,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -127,8 +128,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicviswanathan_model_1999_epiFromCellMLGRL2Opt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_winslow_model_1999.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_winslow_model_1999.cpp index 77a50e74f..90b11d899 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_winslow_model_1999.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_winslow_model_1999.cpp @@ -21,14 +21,14 @@ #include "IsNan.hpp" #include "MathsCustomFunctions.hpp" - boost::shared_ptr Dynamicwinslow_model_1999FromCellMLGRL2Opt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicwinslow_model_1999FromCellMLGRL2Opt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -21.126799999999999 * HeartConfig::Instance()->GetCapacitance(); // microA_per_microF const double var_chaste_interface__membrane__stim_duration = 2.0; // millisecond const double var_chaste_interface__membrane__stim_period = 1000.0; // millisecond const double var_chaste_interface__membrane__stim_start = 100.0; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -38,7 +38,7 @@ return p_cellml_stim; } - Dynamicwinslow_model_1999FromCellMLGRL2Opt::Dynamicwinslow_model_1999FromCellMLGRL2Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicwinslow_model_1999FromCellMLGRL2Opt::Dynamicwinslow_model_1999FromCellMLGRL2Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 33, 0, @@ -2995,8 +2995,8 @@ CHASTE_CLASS_EXPORT(Dynamicwinslow_model_1999FromCellMLGRL2Opt) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicwinslow_model_1999FromCellMLGRL2Opt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_winslow_model_1999.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_winslow_model_1999.hpp index 224f28d13..513c3f1ad 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_winslow_model_1999.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/dynamic_winslow_model_1999.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -35,8 +36,8 @@ class Dynamicwinslow_model_1999FromCellMLGRL2Opt : public AbstractGeneralizedRus public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Dynamicwinslow_model_1999FromCellMLGRL2Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Dynamicwinslow_model_1999FromCellMLGRL2Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicwinslow_model_1999FromCellMLGRL2Opt(); double GetIIonic(const std::vector* pStateVariables=NULL); void UpdateTransmembranePotential(double var_chaste_interface__environment__time_converted); @@ -124,8 +125,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicwinslow_model_1999FromCellMLGRL2Opt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -134,8 +135,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicwinslow_model_1999FromCellMLGRL2Opt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicwinslow_model_1999FromCellMLGRL2Opt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp index b5ce43475..8cbb0a8ab 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -250,14 +250,14 @@ class Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt_LookupT std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -267,7 +267,7 @@ std::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 index 762a39ecd..10351e072 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 @@ -250,14 +250,14 @@ private: std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -267,7 +267,7 @@ std::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractGeneralizedRushLarsenCardiacCell( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 119bf02a5..eeb1ed22d 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,8 +39,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -71,8 +72,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -81,8 +82,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLGRL2Opt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/dynamic_beeler_reuter_model_1977.cpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/dynamic_beeler_reuter_model_1977.cpp index 1434905bd..fad4d6b9e 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/dynamic_beeler_reuter_model_1977.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/dynamic_beeler_reuter_model_1977.cpp @@ -21,14 +21,14 @@ #include "IsNan.hpp" #include "MathsCustomFunctions.hpp" - boost::shared_ptr Cellbeeler_reuter_model_1977FromCellML::UseCellMLDefaultStimulus() + std::shared_ptr Cellbeeler_reuter_model_1977FromCellML::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__stimulus_protocol__IstimAmplitude = 5000000000000007; // uA_per_cm2 const double var_chaste_interface__stimulus_protocol__IstimPeriod = 1000; // millisecond const double var_chaste_interface__stimulus_protocol__IstimPulseDuration = 1.0; // millisecond const double var_chaste_interface__stimulus_protocol__IstimStart = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__stimulus_protocol__IstimAmplitude), var_chaste_interface__stimulus_protocol__IstimPulseDuration, var_chaste_interface__stimulus_protocol__IstimPeriod, @@ -41,7 +41,7 @@ { return mStateVariables[1]; } - Cellbeeler_reuter_model_1977FromCellML::Cellbeeler_reuter_model_1977FromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellbeeler_reuter_model_1977FromCellML::Cellbeeler_reuter_model_1977FromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 8, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/dynamic_beeler_reuter_model_1977.hpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/dynamic_beeler_reuter_model_1977.hpp index 9162074c4..018132590 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/dynamic_beeler_reuter_model_1977.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/dynamic_beeler_reuter_model_1977.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -34,9 +35,9 @@ class Cellbeeler_reuter_model_1977FromCellML : public AbstractCardiacCell public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellbeeler_reuter_model_1977FromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Cellbeeler_reuter_model_1977FromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Cellbeeler_reuter_model_1977FromCellML(); double GetIIonic(const std::vector* pStateVariables=NULL); void EvaluateYDerivatives(double var_chaste_interface__environment__time, const std::vector& rY, std::vector& rDY); @@ -56,8 +57,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellbeeler_reuter_model_1977FromCellML * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -66,8 +67,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellbeeler_reuter_model_1977FromCellML * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellbeeler_reuter_model_1977FromCellML(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/fox_mcharg_gilmour_2002_console_script.cpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/fox_mcharg_gilmour_2002_console_script.cpp index 0bfa64612..62d3a6b05 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/fox_mcharg_gilmour_2002_console_script.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/fox_mcharg_gilmour_2002_console_script.cpp @@ -26,14 +26,14 @@ - boost::shared_ptr Cellfox_mcharg_gilmour_2002FromCellML::UseCellMLDefaultStimulus() + std::shared_ptr Cellfox_mcharg_gilmour_2002FromCellML::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 1; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -46,7 +46,7 @@ { return mStateVariables[1]; } - Cellfox_mcharg_gilmour_2002FromCellML::Cellfox_mcharg_gilmour_2002FromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellfox_mcharg_gilmour_2002FromCellML::Cellfox_mcharg_gilmour_2002FromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 13, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/fox_mcharg_gilmour_2002_console_script.hpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/fox_mcharg_gilmour_2002_console_script.hpp index 2bacd16da..de676611c 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/fox_mcharg_gilmour_2002_console_script.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/fox_mcharg_gilmour_2002_console_script.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[13] = {false, true, false, false, false, false, fals const bool is_probability[13] = {false, false, true, true, true, false, false, false, false, true, true, true, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellfox_mcharg_gilmour_2002FromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Cellfox_mcharg_gilmour_2002FromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Cellfox_mcharg_gilmour_2002FromCellML(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellfox_mcharg_gilmour_2002FromCellML * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellfox_mcharg_gilmour_2002FromCellML * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellfox_mcharg_gilmour_2002FromCellML(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/luo_rudy_1994.cpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/luo_rudy_1994.cpp index 447bcdcb9..f13156ee1 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/luo_rudy_1994.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/luo_rudy_1994.cpp @@ -26,13 +26,13 @@ - boost::shared_ptr Cellluo_rudy_1994FromCellML::UseCellMLDefaultStimulus() + std::shared_ptr Cellluo_rudy_1994FromCellML::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stimCurrent_converted = 50.000000000000007; // uA_per_cm2 const double var_chaste_interface__membrane__stimDuration = 0.5; // ms const double var_chaste_interface__membrane__stimPeriod = 1000; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stimCurrent_converted), var_chaste_interface__membrane__stimDuration, var_chaste_interface__membrane__stimPeriod, @@ -45,7 +45,7 @@ { return mStateVariables[1]; } - Cellluo_rudy_1994FromCellML::Cellluo_rudy_1994FromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellluo_rudy_1994FromCellML::Cellluo_rudy_1994FromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 12, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/luo_rudy_1994.hpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/luo_rudy_1994.hpp index c32f251f2..c449960da 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/luo_rudy_1994.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/luo_rudy_1994.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[12] = {false, true, false, false, false, false, fals const bool is_probability[12] = {false, false, false, false, true, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellluo_rudy_1994FromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Cellluo_rudy_1994FromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Cellluo_rudy_1994FromCellML(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellluo_rudy_1994FromCellML * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellluo_rudy_1994FromCellML * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellluo_rudy_1994FromCellML(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/non_dynamic_aslanidi_Purkinje_model_2009.cpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/non_dynamic_aslanidi_Purkinje_model_2009.cpp index 82dadca51..7e6d0f834 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/non_dynamic_aslanidi_Purkinje_model_2009.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/non_dynamic_aslanidi_Purkinje_model_2009.cpp @@ -26,14 +26,14 @@ - boost::shared_ptr Cellaslanidi_Purkinje_model_2009FromCellML::UseCellMLDefaultStimulus() + std::shared_ptr Cellaslanidi_Purkinje_model_2009FromCellML::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 1; // millisecond const double var_chaste_interface__membrane__stim_period = 800; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -46,7 +46,7 @@ { return mStateVariables[1]; } - Cellaslanidi_Purkinje_model_2009FromCellML::Cellaslanidi_Purkinje_model_2009FromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellaslanidi_Purkinje_model_2009FromCellML::Cellaslanidi_Purkinje_model_2009FromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCellWithModifiers( pSolver, 30, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/non_dynamic_aslanidi_Purkinje_model_2009.hpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/non_dynamic_aslanidi_Purkinje_model_2009.hpp index e1ee4ad73..61f259ecb 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/non_dynamic_aslanidi_Purkinje_model_2009.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/non_dynamic_aslanidi_Purkinje_model_2009.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractCardiacCellWithModifiers.hpp" @@ -35,50 +36,50 @@ class Cellaslanidi_Purkinje_model_2009FromCellML : public AbstractCardiacCellWit // // Settable parameters and readable variables // - boost::shared_ptr mp_JSR_calcium_concentration_modifier; - boost::shared_ptr mp_SR_leak_current_max_modifier; - boost::shared_ptr mp_SR_release_current_modifier; - boost::shared_ptr mp_SR_release_current_max_modifier; - boost::shared_ptr mp_SR_uptake_current_max_modifier; - boost::shared_ptr mp_concentration_clamp_onoff_modifier; - boost::shared_ptr mp_cytosolic_calcium_concentration_modifier; - boost::shared_ptr mp_cytosolic_potassium_concentration_modifier; - boost::shared_ptr mp_cytosolic_sodium_concentration_modifier; - boost::shared_ptr mp_dyadic_space_calcium_concentration_modifier; - boost::shared_ptr mp_extracellular_calcium_concentration_modifier; - boost::shared_ptr mp_extracellular_potassium_concentration_modifier; - boost::shared_ptr mp_extracellular_sodium_concentration_modifier; - boost::shared_ptr mp_i_Ca_L__i_Ca_L_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; - boost::shared_ptr mp_i_Na__i_Na_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; - boost::shared_ptr mp_i_K1__i_K1_modifier; - boost::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_Kr__i_Kr_modifier; - boost::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_Ks__i_Ks_modifier; - boost::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_NaCa__i_NaCa_modifier; - boost::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; - boost::shared_ptr mp_i_to_1__i_to_1_modifier; - boost::shared_ptr mp_membrane_transient_outward_current_conductance_modifier; - boost::shared_ptr mp_membrane_voltage_modifier; + std::shared_ptr mp_JSR_calcium_concentration_modifier; + std::shared_ptr mp_SR_leak_current_max_modifier; + std::shared_ptr mp_SR_release_current_modifier; + std::shared_ptr mp_SR_release_current_max_modifier; + std::shared_ptr mp_SR_uptake_current_max_modifier; + std::shared_ptr mp_concentration_clamp_onoff_modifier; + std::shared_ptr mp_cytosolic_calcium_concentration_modifier; + std::shared_ptr mp_cytosolic_potassium_concentration_modifier; + std::shared_ptr mp_cytosolic_sodium_concentration_modifier; + std::shared_ptr mp_dyadic_space_calcium_concentration_modifier; + std::shared_ptr mp_extracellular_calcium_concentration_modifier; + std::shared_ptr mp_extracellular_potassium_concentration_modifier; + std::shared_ptr mp_extracellular_sodium_concentration_modifier; + std::shared_ptr mp_i_Ca_L__i_Ca_L_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; + std::shared_ptr mp_i_Na__i_Na_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; + std::shared_ptr mp_i_K1__i_K1_modifier; + std::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_Kr__i_Kr_modifier; + std::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_Ks__i_Ks_modifier; + std::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_NaCa__i_NaCa_modifier; + std::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; + std::shared_ptr mp_i_to_1__i_to_1_modifier; + std::shared_ptr mp_membrane_transient_outward_current_conductance_modifier; + std::shared_ptr mp_membrane_voltage_modifier; private: @@ -86,9 +87,9 @@ const bool is_concentration[30] = {false, true, false, false, false, false, fals const bool is_probability[30] = {false, false, true, true, true, false, false, true, true, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellaslanidi_Purkinje_model_2009FromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Cellaslanidi_Purkinje_model_2009FromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Cellaslanidi_Purkinje_model_2009FromCellML(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -109,8 +110,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellaslanidi_Purkinje_model_2009FromCellML * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -119,8 +120,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellaslanidi_Purkinje_model_2009FromCellML * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellaslanidi_Purkinje_model_2009FromCellML(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/output_class.c b/chaste_codegen/data/tests/chaste_reference_models/Normal/output_class.c index 18c293165..db941a381 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/output_class.c +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/output_class.c @@ -24,7 +24,7 @@ #include "ModelFactory.hpp" -AbstractCardiacCell* Chaste_CG::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractCardiacCell* Chaste_CG::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Chaste_CG(p_solver, p_stimulus); } @@ -32,14 +32,14 @@ bool Chaste_CG::registered = ModelFactory::Register("output_class", "Normal", (M - boost::shared_ptr Chaste_CG::UseCellMLDefaultStimulus() + std::shared_ptr Chaste_CG::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -0.0030000000000000001 * HeartConfig::Instance()->GetCapacitance() / mParameters[10]; // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration_converted = 3; // millisecond const double var_chaste_interface__membrane__stim_period_converted = 1000; // millisecond const double var_chaste_interface__membrane__stim_start_converted = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration_converted, var_chaste_interface__membrane__stim_period_converted, @@ -52,7 +52,7 @@ bool Chaste_CG::registered = ModelFactory::Register("output_class", "Normal", (M { return mStateVariables[1]; } - Chaste_CG::Chaste_CG(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Chaste_CG::Chaste_CG(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 22, @@ -819,8 +819,8 @@ CHASTE_CLASS_EXPORT(Chaste_CG) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Chaste_CG(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/output_class.h b/chaste_codegen/data/tests/chaste_reference_models/Normal/output_class.h index ddfabca97..59da3206a 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/output_class.h +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/output_class.h @@ -34,16 +34,16 @@ class Chaste_CG : public AbstractCardiacCell, public AbstractDynamicallyLoadable // private: - static AbstractCardiacCell* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractCardiacCell* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[22] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, true, true, true, false, true, false, false}; const bool is_probability[22] = {false, false, false, false, false, true, true, true, true, true, true, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Chaste_CG(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Chaste_CG(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Chaste_CG(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -64,8 +64,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Chaste_CG * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -74,8 +74,8 @@ namespace boost inline void load_construct_data( Archive & ar, Chaste_CG * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Chaste_CG(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_derived_quant.cpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_derived_quant.cpp index bef3b7f29..65b8241c2 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_derived_quant.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_derived_quant.cpp @@ -27,7 +27,7 @@ - Celltest_V_not_state_derived_quantFromCellML::Celltest_V_not_state_derived_quantFromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Celltest_V_not_state_derived_quantFromCellML::Celltest_V_not_state_derived_quantFromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 1, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_derived_quant.hpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_derived_quant.hpp index 02b23f2f9..a41d7572c 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_derived_quant.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_derived_quant.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,7 +39,7 @@ const bool is_concentration[1] = {false}; const bool is_probability[1] = {false}; public: - Celltest_V_not_state_derived_quantFromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Celltest_V_not_state_derived_quantFromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Celltest_V_not_state_derived_quantFromCellML(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -59,8 +60,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Celltest_V_not_state_derived_quantFromCellML * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -69,8 +70,8 @@ namespace boost inline void load_construct_data( Archive & ar, Celltest_V_not_state_derived_quantFromCellML * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Celltest_V_not_state_derived_quantFromCellML(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_mparam.cpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_mparam.cpp index 53e8c534f..9fbdca77e 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_mparam.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_mparam.cpp @@ -27,7 +27,7 @@ - Celltest_V_not_state_mparamFromCellML::Celltest_V_not_state_mparamFromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Celltest_V_not_state_mparamFromCellML::Celltest_V_not_state_mparamFromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 1, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_mparam.hpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_mparam.hpp index cf084a0d9..9a6706fb7 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_mparam.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/test_V_not_state_mparam.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,7 +39,7 @@ const bool is_concentration[1] = {false}; const bool is_probability[1] = {false}; public: - Celltest_V_not_state_mparamFromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Celltest_V_not_state_mparamFromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Celltest_V_not_state_mparamFromCellML(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -59,8 +60,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Celltest_V_not_state_mparamFromCellML * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -69,8 +70,8 @@ namespace boost inline void load_construct_data( Archive & ar, Celltest_V_not_state_mparamFromCellML * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Celltest_V_not_state_mparamFromCellML(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/zhang_SAN_model_2000_all.cpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/zhang_SAN_model_2000_all.cpp index b10d434c9..0ea16f5f8 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/zhang_SAN_model_2000_all.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/zhang_SAN_model_2000_all.cpp @@ -24,7 +24,7 @@ - Cellzhang_SAN_model_2000_allFromCellML::Cellzhang_SAN_model_2000_allFromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellzhang_SAN_model_2000_allFromCellML::Cellzhang_SAN_model_2000_allFromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 15, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Normal/zhang_SAN_model_2000_all.hpp b/chaste_codegen/data/tests/chaste_reference_models/Normal/zhang_SAN_model_2000_all.hpp index ee049c7fe..a37e52cdb 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Normal/zhang_SAN_model_2000_all.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Normal/zhang_SAN_model_2000_all.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -34,7 +35,7 @@ class Cellzhang_SAN_model_2000_allFromCellML : public AbstractCardiacCell public: - Cellzhang_SAN_model_2000_allFromCellML(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Cellzhang_SAN_model_2000_allFromCellML(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Cellzhang_SAN_model_2000_allFromCellML(); double GetIIonic(const std::vector* pStateVariables=NULL); void EvaluateYDerivatives(double var_chaste_interface__environment__time_converted, const std::vector& rY, std::vector& rDY); @@ -54,8 +55,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellzhang_SAN_model_2000_allFromCellML * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -64,8 +65,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellzhang_SAN_model_2000_allFromCellML * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellzhang_SAN_model_2000_allFromCellML(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.cpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.cpp index f3598e116..2c3fba02b 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.cpp @@ -448,14 +448,14 @@ class Cellbeeler_reuter_model_1977FromCellMLOpt_LookupTables : public AbstractLo std::shared_ptr Cellbeeler_reuter_model_1977FromCellMLOpt_LookupTables::mpInstance; - boost::shared_ptr Cellbeeler_reuter_model_1977FromCellMLOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellbeeler_reuter_model_1977FromCellMLOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__stimulus_protocol__IstimAmplitude_converted = 50.000000000000007; // uA_per_cm2 const double var_chaste_interface__stimulus_protocol__IstimPeriod = 1000; // ms const double var_chaste_interface__stimulus_protocol__IstimPulseDuration = 1; // ms const double var_chaste_interface__stimulus_protocol__IstimStart = 10; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__stimulus_protocol__IstimAmplitude_converted), var_chaste_interface__stimulus_protocol__IstimPulseDuration, var_chaste_interface__stimulus_protocol__IstimPeriod, @@ -468,7 +468,7 @@ std::shared_ptr Cellbeel { return mStateVariables[1]; } - Cellbeeler_reuter_model_1977FromCellMLOpt::Cellbeeler_reuter_model_1977FromCellMLOpt(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellbeeler_reuter_model_1977FromCellMLOpt::Cellbeeler_reuter_model_1977FromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 8, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.cpp_python36 index 6aa6d38cf..89684c6da 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.cpp_python36 @@ -448,14 +448,14 @@ private: std::shared_ptr Cellbeeler_reuter_model_1977FromCellMLOpt_LookupTables::mpInstance; - boost::shared_ptr Cellbeeler_reuter_model_1977FromCellMLOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellbeeler_reuter_model_1977FromCellMLOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__stimulus_protocol__IstimAmplitude_converted = 50.000000000000007; // uA_per_cm2 const double var_chaste_interface__stimulus_protocol__IstimPeriod = 1000; // ms const double var_chaste_interface__stimulus_protocol__IstimPulseDuration = 1; // ms const double var_chaste_interface__stimulus_protocol__IstimStart = 10; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__stimulus_protocol__IstimAmplitude_converted), var_chaste_interface__stimulus_protocol__IstimPulseDuration, var_chaste_interface__stimulus_protocol__IstimPeriod, @@ -468,7 +468,7 @@ std::shared_ptr Cellbeel { return mStateVariables[1]; } - Cellbeeler_reuter_model_1977FromCellMLOpt::Cellbeeler_reuter_model_1977FromCellMLOpt(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellbeeler_reuter_model_1977FromCellMLOpt::Cellbeeler_reuter_model_1977FromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 8, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.hpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.hpp index 0dd28675c..bb27e6e16 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[8] = {false, true, false, false, false, false, false const bool is_probability[8] = {false, false, true, true, true, true, true, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellbeeler_reuter_model_1977FromCellMLOpt(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Cellbeeler_reuter_model_1977FromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Cellbeeler_reuter_model_1977FromCellMLOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellbeeler_reuter_model_1977FromCellMLOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellbeeler_reuter_model_1977FromCellMLOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellbeeler_reuter_model_1977FromCellMLOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/dynamic_aslanidi_Purkinje_model_2009.cpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/dynamic_aslanidi_Purkinje_model_2009.cpp index 5c3fceb92..4039215cc 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/dynamic_aslanidi_Purkinje_model_2009.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/dynamic_aslanidi_Purkinje_model_2009.cpp @@ -24,7 +24,7 @@ #include "ModelFactory.hpp" -AbstractCardiacCellWithModifiers* Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractCardiacCellWithModifiers* Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt(p_solver, p_stimulus); } @@ -553,14 +553,14 @@ class Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt_LookupTables : public Abs std::shared_ptr Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt_LookupTables::mpInstance; - boost::shared_ptr Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 1; // millisecond const double var_chaste_interface__membrane__stim_period = 800; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -573,7 +573,7 @@ std::shared_ptr D { return mStateVariables[1]; } - Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt::Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt::Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCellWithModifiers( pSolver, 30, @@ -1434,8 +1434,8 @@ CHASTE_CLASS_EXPORT(Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/dynamic_aslanidi_Purkinje_model_2009.hpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/dynamic_aslanidi_Purkinje_model_2009.hpp index 4bfdf1ff9..454eee3cc 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/dynamic_aslanidi_Purkinje_model_2009.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/dynamic_aslanidi_Purkinje_model_2009.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractCardiacCellWithModifiers.hpp" @@ -36,62 +37,62 @@ class Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt : public AbstractCardiacC // // Settable parameters and readable variables // - boost::shared_ptr mp_JSR_calcium_concentration_modifier; - boost::shared_ptr mp_SR_leak_current_max_modifier; - boost::shared_ptr mp_SR_release_current_modifier; - boost::shared_ptr mp_SR_release_current_max_modifier; - boost::shared_ptr mp_SR_uptake_current_max_modifier; - boost::shared_ptr mp_concentration_clamp_onoff_modifier; - boost::shared_ptr mp_cytosolic_calcium_concentration_modifier; - boost::shared_ptr mp_cytosolic_potassium_concentration_modifier; - boost::shared_ptr mp_cytosolic_sodium_concentration_modifier; - boost::shared_ptr mp_dyadic_space_calcium_concentration_modifier; - boost::shared_ptr mp_extracellular_calcium_concentration_modifier; - boost::shared_ptr mp_extracellular_potassium_concentration_modifier; - boost::shared_ptr mp_extracellular_sodium_concentration_modifier; - boost::shared_ptr mp_i_Ca_L__i_Ca_L_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; - boost::shared_ptr mp_i_Na__i_Na_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; - boost::shared_ptr mp_i_K1__i_K1_modifier; - boost::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_Kr__i_Kr_modifier; - boost::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_Ks__i_Ks_modifier; - boost::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_NaCa__i_NaCa_modifier; - boost::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; - boost::shared_ptr mp_i_to_1__i_to_1_modifier; - boost::shared_ptr mp_membrane_transient_outward_current_conductance_modifier; - boost::shared_ptr mp_membrane_voltage_modifier; + std::shared_ptr mp_JSR_calcium_concentration_modifier; + std::shared_ptr mp_SR_leak_current_max_modifier; + std::shared_ptr mp_SR_release_current_modifier; + std::shared_ptr mp_SR_release_current_max_modifier; + std::shared_ptr mp_SR_uptake_current_max_modifier; + std::shared_ptr mp_concentration_clamp_onoff_modifier; + std::shared_ptr mp_cytosolic_calcium_concentration_modifier; + std::shared_ptr mp_cytosolic_potassium_concentration_modifier; + std::shared_ptr mp_cytosolic_sodium_concentration_modifier; + std::shared_ptr mp_dyadic_space_calcium_concentration_modifier; + std::shared_ptr mp_extracellular_calcium_concentration_modifier; + std::shared_ptr mp_extracellular_potassium_concentration_modifier; + std::shared_ptr mp_extracellular_sodium_concentration_modifier; + std::shared_ptr mp_i_Ca_L__i_Ca_L_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; + std::shared_ptr mp_i_Na__i_Na_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; + std::shared_ptr mp_i_K1__i_K1_modifier; + std::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_Kr__i_Kr_modifier; + std::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_Ks__i_Ks_modifier; + std::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_NaCa__i_NaCa_modifier; + std::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; + std::shared_ptr mp_i_to_1__i_to_1_modifier; + std::shared_ptr mp_membrane_transient_outward_current_conductance_modifier; + std::shared_ptr mp_membrane_voltage_modifier; private: - static AbstractCardiacCellWithModifiers* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractCardiacCellWithModifiers* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[30] = {false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, false, true, false, false, true, true, false, false}; const bool is_probability[30] = {false, false, true, true, true, false, false, true, true, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -113,8 +114,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -123,8 +124,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicaslanidi_Purkinje_model_2009FromCellMLOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp index dfc0e14ce..55418a16e 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -250,14 +250,14 @@ class Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt_LookupTable std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -267,7 +267,7 @@ std::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 index 235fda79f..b56057f06 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 @@ -250,14 +250,14 @@ private: std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -267,7 +267,7 @@ std::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 4, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 8f9a681f0..333033b3f 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,8 +39,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/non_dynamic_aslanidi_Purkinje_model_2009.cpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/non_dynamic_aslanidi_Purkinje_model_2009.cpp index 697a88b18..7bf397c46 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/non_dynamic_aslanidi_Purkinje_model_2009.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/non_dynamic_aslanidi_Purkinje_model_2009.cpp @@ -547,14 +547,14 @@ class Cellaslanidi_Purkinje_model_2009FromCellMLOpt_LookupTables : public Abstra std::shared_ptr Cellaslanidi_Purkinje_model_2009FromCellMLOpt_LookupTables::mpInstance; - boost::shared_ptr Cellaslanidi_Purkinje_model_2009FromCellMLOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellaslanidi_Purkinje_model_2009FromCellMLOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 1; // millisecond const double var_chaste_interface__membrane__stim_period = 800; // millisecond const double var_chaste_interface__membrane__stim_start = 100; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -567,7 +567,7 @@ std::shared_ptr Cell { return mStateVariables[1]; } - Cellaslanidi_Purkinje_model_2009FromCellMLOpt::Cellaslanidi_Purkinje_model_2009FromCellMLOpt(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Cellaslanidi_Purkinje_model_2009FromCellMLOpt::Cellaslanidi_Purkinje_model_2009FromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCellWithModifiers( pSolver, 30, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/non_dynamic_aslanidi_Purkinje_model_2009.hpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/non_dynamic_aslanidi_Purkinje_model_2009.hpp index 7c38bf4df..2435c8968 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/non_dynamic_aslanidi_Purkinje_model_2009.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/non_dynamic_aslanidi_Purkinje_model_2009.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractCardiacCellWithModifiers.hpp" @@ -35,50 +36,50 @@ class Cellaslanidi_Purkinje_model_2009FromCellMLOpt : public AbstractCardiacCell // // Settable parameters and readable variables // - boost::shared_ptr mp_JSR_calcium_concentration_modifier; - boost::shared_ptr mp_SR_leak_current_max_modifier; - boost::shared_ptr mp_SR_release_current_modifier; - boost::shared_ptr mp_SR_release_current_max_modifier; - boost::shared_ptr mp_SR_uptake_current_max_modifier; - boost::shared_ptr mp_concentration_clamp_onoff_modifier; - boost::shared_ptr mp_cytosolic_calcium_concentration_modifier; - boost::shared_ptr mp_cytosolic_potassium_concentration_modifier; - boost::shared_ptr mp_cytosolic_sodium_concentration_modifier; - boost::shared_ptr mp_dyadic_space_calcium_concentration_modifier; - boost::shared_ptr mp_extracellular_calcium_concentration_modifier; - boost::shared_ptr mp_extracellular_potassium_concentration_modifier; - boost::shared_ptr mp_extracellular_sodium_concentration_modifier; - boost::shared_ptr mp_i_Ca_L__i_Ca_L_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_tau_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; - boost::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; - boost::shared_ptr mp_i_Na__i_Na_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; - boost::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; - boost::shared_ptr mp_i_K1__i_K1_modifier; - boost::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_Kr__i_Kr_modifier; - boost::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_Ks__i_Ks_modifier; - boost::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; - boost::shared_ptr mp_i_NaCa__i_NaCa_modifier; - boost::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; - boost::shared_ptr mp_i_to_1__i_to_1_modifier; - boost::shared_ptr mp_membrane_transient_outward_current_conductance_modifier; - boost::shared_ptr mp_membrane_voltage_modifier; + std::shared_ptr mp_JSR_calcium_concentration_modifier; + std::shared_ptr mp_SR_leak_current_max_modifier; + std::shared_ptr mp_SR_release_current_modifier; + std::shared_ptr mp_SR_release_current_max_modifier; + std::shared_ptr mp_SR_uptake_current_max_modifier; + std::shared_ptr mp_concentration_clamp_onoff_modifier; + std::shared_ptr mp_cytosolic_calcium_concentration_modifier; + std::shared_ptr mp_cytosolic_potassium_concentration_modifier; + std::shared_ptr mp_cytosolic_sodium_concentration_modifier; + std::shared_ptr mp_dyadic_space_calcium_concentration_modifier; + std::shared_ptr mp_extracellular_calcium_concentration_modifier; + std::shared_ptr mp_extracellular_potassium_concentration_modifier; + std::shared_ptr mp_extracellular_sodium_concentration_modifier; + std::shared_ptr mp_i_Ca_L__i_Ca_L_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_conductance_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_d_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f2_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa2_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_fCa_gate_tau_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_modifier; + std::shared_ptr mp_membrane_L_type_calcium_current_f_gate_tau_modifier; + std::shared_ptr mp_i_Na__i_Na_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_conductance_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_h_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_j_gate_tau_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_m_gate_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_reduced_inactivation_modifier; + std::shared_ptr mp_membrane_fast_sodium_current_shift_inactivation_modifier; + std::shared_ptr mp_i_K1__i_K1_modifier; + std::shared_ptr mp_membrane_inward_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_Kr__i_Kr_modifier; + std::shared_ptr mp_membrane_rapid_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_Ks__i_Ks_modifier; + std::shared_ptr mp_membrane_slow_delayed_rectifier_potassium_current_conductance_modifier; + std::shared_ptr mp_i_NaCa__i_NaCa_modifier; + std::shared_ptr mp_membrane_sodium_calcium_exchanger_current_conductance_modifier; + std::shared_ptr mp_i_to_1__i_to_1_modifier; + std::shared_ptr mp_membrane_transient_outward_current_conductance_modifier; + std::shared_ptr mp_membrane_voltage_modifier; private: @@ -86,9 +87,9 @@ const bool is_concentration[30] = {false, true, false, false, false, false, fals const bool is_probability[30] = {false, false, true, true, true, false, false, true, true, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Cellaslanidi_Purkinje_model_2009FromCellMLOpt(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Cellaslanidi_Purkinje_model_2009FromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Cellaslanidi_Purkinje_model_2009FromCellMLOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -110,8 +111,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellaslanidi_Purkinje_model_2009FromCellMLOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -120,8 +121,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellaslanidi_Purkinje_model_2009FromCellMLOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellaslanidi_Purkinje_model_2009FromCellMLOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.cpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.cpp index b4bf7b0ce..415e873d5 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.cpp @@ -360,7 +360,7 @@ class Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt_LookupTab std::shared_ptr Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt_LookupTables::mpInstance; - boost::shared_ptr Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt::UseCellMLDefaultStimulus() + std::shared_ptr Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -25.5; // microA_per_cm2 @@ -368,7 +368,7 @@ std::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -381,7 +381,7 @@ std::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt::Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 8, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.cpp_python36 index 47b1b1e5e..e73870bec 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.cpp_python36 @@ -360,7 +360,7 @@ private: std::shared_ptr Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt_LookupTables::mpInstance; - boost::shared_ptr Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt::UseCellMLDefaultStimulus() + std::shared_ptr Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -25.5; // microA_per_cm2 @@ -368,7 +368,7 @@ std::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -381,7 +381,7 @@ std::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus) + Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt::Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus) : AbstractCardiacCell( pSolver, 8, diff --git a/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.hpp b/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.hpp index fd71687b4..b06ce4691 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,9 +39,9 @@ const bool is_concentration[8] = {false, false, false, false, false, false, fals const bool is_probability[8] = {false, true, true, true, true, true, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); ~Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Celltest_luo_rudy_1991_with_range_cap_dimensionlessFromCellMLOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/RL/dynamic_livshitz_rudy_2007.cpp b/chaste_codegen/data/tests/chaste_reference_models/RL/dynamic_livshitz_rudy_2007.cpp index e2f8136fa..9ef5e87b0 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/RL/dynamic_livshitz_rudy_2007.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/RL/dynamic_livshitz_rudy_2007.cpp @@ -26,14 +26,14 @@ - boost::shared_ptr Dynamiclivshitz_rudy_2007FromCellMLRushLarsen::UseCellMLDefaultStimulus() + std::shared_ptr Dynamiclivshitz_rudy_2007FromCellMLRushLarsen::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__cell__stim_amplitude_converted = -15 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__cell__stim_duration = 3; // ms const double var_chaste_interface__cell__stim_offset = 100; // ms const double var_chaste_interface__cell__stim_period = 400; // ms - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__cell__stim_amplitude_converted), var_chaste_interface__cell__stim_duration, var_chaste_interface__cell__stim_period, @@ -43,7 +43,7 @@ return p_cellml_stim; } - Dynamiclivshitz_rudy_2007FromCellMLRushLarsen::Dynamiclivshitz_rudy_2007FromCellMLRushLarsen(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamiclivshitz_rudy_2007FromCellMLRushLarsen::Dynamiclivshitz_rudy_2007FromCellMLRushLarsen(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractRushLarsenCardiacCell( 18, 0, @@ -787,8 +787,8 @@ CHASTE_CLASS_EXPORT(Dynamiclivshitz_rudy_2007FromCellMLRushLarsen) extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamiclivshitz_rudy_2007FromCellMLRushLarsen(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/RL/dynamic_livshitz_rudy_2007.hpp b/chaste_codegen/data/tests/chaste_reference_models/RL/dynamic_livshitz_rudy_2007.hpp index 9b9971f27..506a65675 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/RL/dynamic_livshitz_rudy_2007.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/RL/dynamic_livshitz_rudy_2007.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -39,8 +40,8 @@ const bool is_concentration[18] = {false, false, false, false, false, false, fal const bool is_probability[18] = {false, true, true, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Dynamiclivshitz_rudy_2007FromCellMLRushLarsen(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Dynamiclivshitz_rudy_2007FromCellMLRushLarsen(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamiclivshitz_rudy_2007FromCellMLRushLarsen(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamiclivshitz_rudy_2007FromCellMLRushLarsen * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamiclivshitz_rudy_2007FromCellMLRushLarsen * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamiclivshitz_rudy_2007FromCellMLRushLarsen(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/RL/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/RL/hodgkin_huxley_squid_axon_model_1952_modified.cpp index 063bcd9eb..35188def5 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/RL/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/RL/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -26,14 +26,14 @@ - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -43,7 +43,7 @@ return p_cellml_stim; } - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractRushLarsenCardiacCell( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/RL/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/RL/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 93d2b4a7d..56da299fb 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/RL/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/RL/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,8 +39,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen(); void VerifyStateVariables(); double GetIIonic(const std::vector* pStateVariables=NULL); @@ -61,8 +62,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -71,8 +72,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsen(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/RLopt/dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp b/chaste_codegen/data/tests/chaste_reference_models/RLopt/dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp index 2f0b9d76f..49c2ad062 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/RLopt/dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/RLopt/dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp @@ -24,7 +24,7 @@ #include "ModelFactory.hpp" -AbstractRushLarsenCardiacCell* Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +AbstractRushLarsenCardiacCell* Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt(p_solver, p_stimulus); } @@ -575,14 +575,14 @@ class Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLars std::shared_ptr Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt_LookupTables::mpInstance; - boost::shared_ptr Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt::UseCellMLDefaultStimulus() + std::shared_ptr Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude_converted = -80 * HeartConfig::Instance()->GetCapacitance(); // uA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 71.430000000000007; // millisecond const double var_chaste_interface__membrane__stim_start = 0; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude_converted), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -595,7 +595,7 @@ std::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt::Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractRushLarsenCardiacCell( 41, 0, @@ -1536,8 +1536,8 @@ CHASTE_CLASS_EXPORT(Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFrom extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt(pSolver, pStimulus); } diff --git a/chaste_codegen/data/tests/chaste_reference_models/RLopt/dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp b/chaste_codegen/data/tests/chaste_reference_models/RLopt/dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp index 07d17da55..7a651d769 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/RLopt/dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/RLopt/dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractDynamicallyLoadableEntity.hpp" @@ -34,16 +35,16 @@ class Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLars // private: - static AbstractRushLarsenCardiacCell* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static AbstractRushLarsenCardiacCell* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered; private: const bool is_concentration[41] = {false, true, true, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, false, false, false, false, false, false, false, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false}; const bool is_probability[41] = {false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); double GetIntracellularCalciumConcentration(); - Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -66,8 +67,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -76,8 +77,8 @@ namespace boost inline void load_construct_data( Archive & ar, Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Dynamicbondarenko_szigeti_bett_kim_rasmusson_2004_apicalFromCellMLRushLarsenOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.cpp b/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.cpp index c1662264f..50c15e4b1 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.cpp +++ b/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.cpp @@ -250,14 +250,14 @@ class Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt_L std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -267,7 +267,7 @@ std::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractRushLarsenCardiacCell( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 b/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 index 69982b8c8..dc4659588 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 +++ b/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.cpp_python36 @@ -250,14 +250,14 @@ private: std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt_LookupTables::mpInstance; - boost::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt::UseCellMLDefaultStimulus() + std::shared_ptr Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata const double var_chaste_interface__membrane__stim_amplitude = -20; // microA_per_cm2 const double var_chaste_interface__membrane__stim_duration = 0.5; // millisecond const double var_chaste_interface__membrane__stim_period = 1000; // millisecond const double var_chaste_interface__membrane__stim_start = 10; // millisecond - boost::shared_ptr p_cellml_stim(new RegularStimulus( + std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs(var_chaste_interface__membrane__stim_amplitude), var_chaste_interface__membrane__stim_duration, var_chaste_interface__membrane__stim_period, @@ -267,7 +267,7 @@ std::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt::Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : AbstractRushLarsenCardiacCell( 4, 0, diff --git a/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.hpp b/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.hpp index 106cc8a20..17c1ab6fd 100644 --- a/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.hpp +++ b/chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified.hpp @@ -13,6 +13,7 @@ //! //! +#include #include "ChasteSerialization.hpp" #include #include "AbstractStimulusFunction.hpp" @@ -38,8 +39,8 @@ const bool is_concentration[4] = {false, false, false, false}; const bool is_probability[4] = {false, false, false, false}; public: - boost::shared_ptr UseCellMLDefaultStimulus(); - Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + std::shared_ptr UseCellMLDefaultStimulus(); + Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); ~Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt(); void VerifyStateVariables(); AbstractLookupTableCollection* GetLookupTableCollection(); @@ -62,8 +63,8 @@ namespace boost inline void save_construct_data( Archive & ar, const Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -72,8 +73,8 @@ namespace boost inline void load_construct_data( Archive & ar, Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t)Cellhodgkin_huxley_squid_axon_model_1952_modifiedFromCellMLRushLarsenOpt(p_solver, p_stimulus); diff --git a/chaste_codegen/templates/BE/cpp/constructor_declaration b/chaste_codegen/templates/BE/cpp/constructor_declaration index 858b21db2..799575427 100644 --- a/chaste_codegen/templates/BE/cpp/constructor_declaration +++ b/chaste_codegen/templates/BE/cpp/constructor_declaration @@ -1,4 +1,4 @@ - {{class_name}}::{{class_name}}(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + {{class_name}}::{{class_name}}(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : {{base_class}}<{{nonlinear_state_vars|length}}>( {{state_vars|length}}, {{membrane_voltage_index}}, diff --git a/chaste_codegen/templates/RL/cpp/constructor_declaration b/chaste_codegen/templates/RL/cpp/constructor_declaration index 8f2074f4f..3aba2c284 100644 --- a/chaste_codegen/templates/RL/cpp/constructor_declaration +++ b/chaste_codegen/templates/RL/cpp/constructor_declaration @@ -1,4 +1,4 @@ - {{class_name}}::{{class_name}}(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus) + {{class_name}}::{{class_name}}(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus) : {% if modifiers|length > 0 %}AbstractCardiacCellWithModifiers<{% endif%}{{base_class}}{%- if modifiers|length > 0 %} >{% endif%}( {{state_vars|length}}, {{membrane_voltage_index}}, diff --git a/chaste_codegen/templates/Shared/cpp/CHASTE_CLASS_EXPORT b/chaste_codegen/templates/Shared/cpp/CHASTE_CLASS_EXPORT index 1473f4fef..7fe212791 100644 --- a/chaste_codegen/templates/Shared/cpp/CHASTE_CLASS_EXPORT +++ b/chaste_codegen/templates/Shared/cpp/CHASTE_CLASS_EXPORT @@ -5,8 +5,8 @@ CHASTE_CLASS_EXPORT({{class_name}}) {% if dynamically_loadable %}extern "C" { AbstractCardiacCellInterface* MakeCardiacCell( - boost::shared_ptr pSolver, - boost::shared_ptr pStimulus) + std::shared_ptr pSolver, + std::shared_ptr pStimulus) { return new {{class_name}}(pSolver, pStimulus); } diff --git a/chaste_codegen/templates/Shared/cpp/UseCellMLDefaultStimulus b/chaste_codegen/templates/Shared/cpp/UseCellMLDefaultStimulus index f845dc4d6..e1e546710 100644 --- a/chaste_codegen/templates/Shared/cpp/UseCellMLDefaultStimulus +++ b/chaste_codegen/templates/Shared/cpp/UseCellMLDefaultStimulus @@ -1,9 +1,9 @@ {%- if default_stimulus_equations["equations"]|length > 0 %} - boost::shared_ptr {{class_name}}::UseCellMLDefaultStimulus() + std::shared_ptr {{class_name}}::UseCellMLDefaultStimulus() { // Use the default stimulus specified by CellML metadata {% for eq in default_stimulus_equations["equations"] %}{%- if not eq.lhs_modifiable %}const double {{ eq.lhs }} = {{ eq.rhs }}; // {{eq.units}} - {% endif %}{% endfor %}boost::shared_ptr p_cellml_stim(new RegularStimulus( + {% endif %}{% endfor %}std::shared_ptr p_cellml_stim(new RegularStimulus( -fabs({{default_stimulus_equations["membrane_stimulus_current_amplitude"]}}), {{default_stimulus_equations["membrane_stimulus_current_duration"]}}, {{default_stimulus_equations["membrane_stimulus_current_period"]}}, diff --git a/chaste_codegen/templates/Shared/cpp/constructor_declaration b/chaste_codegen/templates/Shared/cpp/constructor_declaration index dd896325b..25e5fffea 100644 --- a/chaste_codegen/templates/Shared/cpp/constructor_declaration +++ b/chaste_codegen/templates/Shared/cpp/constructor_declaration @@ -1,5 +1,5 @@ {% if is_cvode is defined and is_cvode %}{% set solver = "pOdeSolver"%}{% else %}{% set solver = "pSolver"%}{% endif %} - {{class_name}}::{{class_name}}(boost::shared_ptr {{solver}}{%- if is_cvode is defined and is_cvode %} /* unused; should be empty */{% endif %}, boost::shared_ptr pIntracellularStimulus) + {{class_name}}::{{class_name}}(std::shared_ptr {{solver}}{%- if is_cvode is defined and is_cvode %} /* unused; should be empty */{% endif %}, std::shared_ptr pIntracellularStimulus) : {% if modifiers|length > 0 %}AbstractCardiacCellWithModifiers<{% endif%}{{base_class}}{%- if modifiers|length > 0 %} >{% endif%}( {{solver}}, {{state_vars|length}}, diff --git a/chaste_codegen/templates/Shared/cpp/includes b/chaste_codegen/templates/Shared/cpp/includes index 2e4048eb7..6a11ad680 100644 --- a/chaste_codegen/templates/Shared/cpp/includes +++ b/chaste_codegen/templates/Shared/cpp/includes @@ -16,7 +16,7 @@ {% endif%} {% if use_model_factory %}#include "ModelFactory.hpp" -{% if modifiers|length > 0 %}AbstractCardiacCellWithModifiers<{% endif%}{{base_class}}{%- if modifiers|length > 0 %} >{% endif%}* {{class_name}}::CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus) { +{% if modifiers|length > 0 %}AbstractCardiacCellWithModifiers<{% endif%}{{base_class}}{%- if modifiers|length > 0 %} >{% endif%}* {{class_name}}::CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus) { return new {{class_name}}(p_solver, p_stimulus); } diff --git a/chaste_codegen/templates/Shared/hpp/CHASTE_CLASS_EXPORT b/chaste_codegen/templates/Shared/hpp/CHASTE_CLASS_EXPORT index a69f897af..ee8d9061e 100644 --- a/chaste_codegen/templates/Shared/hpp/CHASTE_CLASS_EXPORT +++ b/chaste_codegen/templates/Shared/hpp/CHASTE_CLASS_EXPORT @@ -12,8 +12,8 @@ namespace boost inline void save_construct_data( Archive & ar, const {{class_name}} * t, const unsigned int fileVersion) { - const boost::shared_ptr p_solver = t->GetSolver(); - const boost::shared_ptr p_stimulus = t->GetStimulusFunction(); + const std::shared_ptr p_solver = t->GetSolver(); + const std::shared_ptr p_stimulus = t->GetStimulusFunction(); ar << p_solver; ar << p_stimulus; } @@ -22,8 +22,8 @@ namespace boost inline void load_construct_data( Archive & ar, {{class_name}} * t, const unsigned int fileVersion) { - boost::shared_ptr p_solver; - boost::shared_ptr p_stimulus; + std::shared_ptr p_solver; + std::shared_ptr p_stimulus; ar >> p_solver; ar >> p_stimulus; ::new(t){{class_name}}(p_solver, p_stimulus); diff --git a/chaste_codegen/templates/Shared/hpp/DefaultStimulus_IntracellularCalciumConcentration b/chaste_codegen/templates/Shared/hpp/DefaultStimulus_IntracellularCalciumConcentration index 0b4f77242..99f87df0b 100644 --- a/chaste_codegen/templates/Shared/hpp/DefaultStimulus_IntracellularCalciumConcentration +++ b/chaste_codegen/templates/Shared/hpp/DefaultStimulus_IntracellularCalciumConcentration @@ -1,5 +1,5 @@ {%- if default_stimulus_equations["equations"]|length > 0 %} - boost::shared_ptr UseCellMLDefaultStimulus(); + std::shared_ptr UseCellMLDefaultStimulus(); {%- endif %} {%- if use_get_intracellular_calcium_concentration %} double GetIntracellularCalciumConcentration(); diff --git a/chaste_codegen/templates/Shared/hpp/class_declaration b/chaste_codegen/templates/Shared/hpp/class_declaration index 4d05172e0..62f0dd9a2 100644 --- a/chaste_codegen/templates/Shared/hpp/class_declaration +++ b/chaste_codegen/templates/Shared/hpp/class_declaration @@ -15,11 +15,11 @@ class {{class_name}} : public {% if modifiers|length > 0 %}AbstractCardiacCellWi // // Settable parameters and readable variables //{% for mod in modifiers %} - boost::shared_ptr {{mod.modifier}}; + std::shared_ptr {{mod.modifier}}; {%- endfor %} {% if use_model_factory %}private: - static {% if modifiers|length > 0 %}AbstractCardiacCellWithModifiers<{% endif%}{{base_class}}{%- if modifiers|length > 0 %} >{% endif%}* CreateMethod(boost::shared_ptr p_solver, boost::shared_ptr p_stimulus); + static {% if modifiers|length > 0 %}AbstractCardiacCellWithModifiers<{% endif%}{{base_class}}{%- if modifiers|length > 0 %} >{% endif%}* CreateMethod(std::shared_ptr p_solver, std::shared_ptr p_stimulus); static bool registered;{% endif%} private: const bool is_concentration[{{state_vars|length}}] = {%raw%}{{%endraw%}{%for state_var in state_vars %}{%if not loop.first %}, {%endif%}{%if state_var.is_concentration%}true{%else%}false{%endif%}{%endfor%}}; diff --git a/chaste_codegen/templates/Shared/hpp/includes b/chaste_codegen/templates/Shared/hpp/includes index a725d1a9f..451fe371f 100644 --- a/chaste_codegen/templates/Shared/hpp/includes +++ b/chaste_codegen/templates/Shared/hpp/includes @@ -1,3 +1,4 @@ +#include #include "ChasteSerialization.hpp" #include {%- if modifiers|length > 0 %} diff --git a/chaste_codegen/templates/backward_euler_model.hpp b/chaste_codegen/templates/backward_euler_model.hpp index ea7cc7982..df93d13e1 100644 --- a/chaste_codegen/templates/backward_euler_model.hpp +++ b/chaste_codegen/templates/backward_euler_model.hpp @@ -3,7 +3,7 @@ #include "{{base_class}}.hpp" {% with %}{% set base_class = base_class ~ "<"~nonlinear_state_vars|length~">" %}{% include "Shared/hpp/class_declaration" %}{% endwith %} {% include "Shared/hpp/DefaultStimulus_IntracellularCalciumConcentration" %} - {{class_name}}(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + {{class_name}}(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); {% include "Shared/hpp/destructor_verify_state_variables_GetIIonic" %} {%- if nonlinear_state_vars|length > 0 %}void ComputeResidual(double {{free_variable.var_name}}, const double rCurrentGuess[{{nonlinear_state_vars|length}}], double rResidual[{{nonlinear_state_vars|length}}]); void ComputeJacobian(double {{free_variable.var_name}}, const double rCurrentGuess[{{nonlinear_state_vars|length}}], double rJacobian[{{nonlinear_state_vars|length}}][{{nonlinear_state_vars|length}}]);{% endif -%} diff --git a/chaste_codegen/templates/cvode_model.hpp b/chaste_codegen/templates/cvode_model.hpp index 28b362557..9436da657 100644 --- a/chaste_codegen/templates/cvode_model.hpp +++ b/chaste_codegen/templates/cvode_model.hpp @@ -4,7 +4,7 @@ #include "{{base_class}}.hpp" {% include "Shared/hpp/class_declaration" %} {% include "Shared/hpp/DefaultStimulus_IntracellularCalciumConcentration" %} - {{class_name}}(boost::shared_ptr pOdeSolver /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + {{class_name}}(std::shared_ptr pOdeSolver /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); {% include "Shared/hpp/destructor_verify_state_variables_GetIIonic" %} void EvaluateYDerivatives(double {{free_variable.var_name}}, const {{vector_decl}} rY, {{vector_decl}} rDY); {%- if derived_quantities|length > 0 %} diff --git a/chaste_codegen/templates/generalised_rush_larsen_model.hpp b/chaste_codegen/templates/generalised_rush_larsen_model.hpp index 54da7740b..ecc343a70 100644 --- a/chaste_codegen/templates/generalised_rush_larsen_model.hpp +++ b/chaste_codegen/templates/generalised_rush_larsen_model.hpp @@ -3,7 +3,7 @@ #include "{{base_class}}.hpp" {% include "Shared/hpp/class_declaration" %} {% include "Shared/hpp/DefaultStimulus_IntracellularCalciumConcentration" %} - {{class_name}}(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + {{class_name}}(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); {% include "Shared/hpp/destructor_verify_state_variables_GetIIonic" %} void UpdateTransmembranePotential(double {{free_variable.var_name}}); void ComputeOneStepExceptVoltage(double {{free_variable.var_name}}); diff --git a/chaste_codegen/templates/normal_model.hpp b/chaste_codegen/templates/normal_model.hpp index 1b0c1b463..b19c4affe 100644 --- a/chaste_codegen/templates/normal_model.hpp +++ b/chaste_codegen/templates/normal_model.hpp @@ -3,7 +3,7 @@ #include "{{base_class}}.hpp" {% include "Shared/hpp/class_declaration" %} {% include "Shared/hpp/DefaultStimulus_IntracellularCalciumConcentration" %} - {{class_name}}(boost::shared_ptr pSolver, boost::shared_ptr pIntracellularStimulus); + {{class_name}}(std::shared_ptr pSolver, std::shared_ptr pIntracellularStimulus); {% include "Shared/hpp/destructor_verify_state_variables_GetIIonic" %} void EvaluateYDerivatives(double {{free_variable.var_name}}, const {{vector_decl}} rY, {{vector_decl}} rDY); {% include "Shared/hpp/ComputeDerivedQuantities" %} diff --git a/chaste_codegen/templates/rush_larsen_model.hpp b/chaste_codegen/templates/rush_larsen_model.hpp index c5ba899b2..bc189a9e2 100644 --- a/chaste_codegen/templates/rush_larsen_model.hpp +++ b/chaste_codegen/templates/rush_larsen_model.hpp @@ -3,7 +3,7 @@ #include "{{base_class}}.hpp" {% include "Shared/hpp/class_declaration" %} {% include "Shared/hpp/DefaultStimulus_IntracellularCalciumConcentration" %} - {{class_name}}(boost::shared_ptr /* unused; should be empty */, boost::shared_ptr pIntracellularStimulus); + {{class_name}}(std::shared_ptr /* unused; should be empty */, std::shared_ptr pIntracellularStimulus); {% include "Shared/hpp/destructor_verify_state_variables_GetIIonic" %} void EvaluateEquations(double {{free_variable.var_name}}, std::vector &rDY, std::vector &rAlphaOrTau, std::vector &rBetaOrInf); void ComputeOneStepExceptVoltage(const std::vector &rDY, const std::vector &rAlphaOrTau, const std::vector &rBetaOrInf);