| 49 |
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#include <string> |
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#include <map> |
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| 52 |
– |
#include "io/BASS_interface.h" |
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#include "types/Component.hpp" |
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< |
#include "types/MakeStamps.hpp" |
| 54 |
< |
#include "types/ZconStamp.hpp" |
| 53 |
> |
#include "types/ZconsStamp.hpp" |
| 54 |
> |
#include "types/MoleculeStamp.hpp" |
| 55 |
> |
#include "utils/ParameterManager.hpp" |
| 56 |
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| 57 |
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| 58 |
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|
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/** |
| 60 |
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* @class Globals Globals.hpp "io/Globals.hpp" |
| 61 |
< |
* @brief parsing and storing global parameters for simulation |
| 62 |
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* @todo need refactorying |
| 63 |
< |
*/ |
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class Globals{ |
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> |
namespace oopse { |
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> |
class Globals : public DataHolder { |
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> |
public: |
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> |
Globals(); |
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> |
virtual ~Globals(); |
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> |
|
| 63 |
> |
DeclareParameter(ForceField, std::string); |
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> |
DeclareParameter(TargetTemp, RealType); |
| 65 |
> |
DeclareParameter(Ensemble, std::string); |
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> |
DeclareParameter(Dt, RealType); |
| 67 |
> |
DeclareParameter(RunTime, RealType); |
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> |
DeclareParameter(InitialConfig, std::string); |
| 69 |
> |
DeclareParameter(FinalConfig, std::string); |
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> |
DeclareParameter(SampleTime, RealType); |
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> |
DeclareParameter(ResetTime, RealType); |
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> |
DeclareParameter(StatusTime, RealType); |
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> |
DeclareParameter(CutoffRadius, RealType); |
| 74 |
> |
DeclareParameter(SwitchingRadius, RealType); |
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> |
DeclareParameter(Dielectric, RealType); |
| 76 |
> |
DeclareParameter(TempSet, bool); |
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> |
DeclareParameter(ThermalTime, RealType); |
| 78 |
> |
DeclareParameter(UsePeriodicBoundaryConditions, bool); |
| 79 |
> |
DeclareParameter(TargetPressure, RealType); |
| 80 |
> |
DeclareParameter(TauThermostat, RealType); |
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> |
DeclareParameter(TauBarostat, RealType); |
| 82 |
> |
DeclareParameter(ZconsTime, RealType); |
| 83 |
> |
DeclareParameter(ZconsTol, RealType); |
| 84 |
> |
DeclareParameter(ZconsForcePolicy, std::string); |
| 85 |
> |
DeclareParameter(Seed, int); |
| 86 |
> |
DeclareParameter(UseInitalTime, bool); |
| 87 |
> |
DeclareParameter(UseIntialExtendedSystemState, bool); |
| 88 |
> |
DeclareParameter(OrthoBoxTolerance, RealType); |
| 89 |
> |
DeclareParameter(Minimizer, std::string); |
| 90 |
> |
DeclareParameter(MinimizerMaxIter, RealType); |
| 91 |
> |
DeclareParameter(MinimizerWriteFrq, int); |
| 92 |
> |
DeclareParameter(MinimizerStepSize, RealType); |
| 93 |
> |
DeclareParameter(MinimizerFTol, RealType); |
| 94 |
> |
DeclareParameter(MinimizerGTol, RealType); |
| 95 |
> |
DeclareParameter(MinimizerLSTol, RealType); |
| 96 |
> |
DeclareParameter(MinimizerLSMaxIter, int); |
| 97 |
> |
DeclareParameter(ZconsGap, RealType); |
| 98 |
> |
DeclareParameter(ZconsFixtime, RealType); |
| 99 |
> |
DeclareParameter(ZconsUsingSMD, bool); |
| 100 |
> |
DeclareParameter(UseSolidThermInt, bool); |
| 101 |
> |
DeclareParameter(UseLiquidThermInt, bool); |
| 102 |
> |
DeclareParameter(ThermodynamicIntegrationLambda, RealType); |
| 103 |
> |
DeclareParameter(ThermodynamicIntegrationK, RealType); |
| 104 |
> |
DeclareParameter(ForceFieldVariant, std::string); |
| 105 |
> |
DeclareParameter(ForceFieldFileName, std::string); |
| 106 |
> |
DeclareParameter(ThermIntDistSpringConst, RealType); |
| 107 |
> |
DeclareParameter(ThermIntThetaSpringConst, RealType); |
| 108 |
> |
DeclareParameter(ThermIntOmegaSpringConst, RealType); |
| 109 |
> |
DeclareParameter(SurfaceTension, RealType); |
| 110 |
> |
DeclareParameter(PrintPressureTensor, bool); |
| 111 |
> |
DeclareParameter(ElectrostaticSummationMethod, std::string); |
| 112 |
> |
DeclareParameter(ElectrostaticScreeningMethod, std::string); |
| 113 |
> |
DeclareParameter(DampingAlpha, RealType); |
| 114 |
> |
DeclareParameter(CutoffPolicy, std::string); |
| 115 |
> |
DeclareParameter(SwitchingFunctionType, std::string); |
| 116 |
> |
DeclareParameter(CompressDumpFile, bool); |
| 117 |
> |
DeclareParameter(OutputForceVector, bool); |
| 118 |
> |
DeclareParameter(SkinThickness, RealType); |
| 119 |
> |
DeclareParameter(StatFileFormat, std::string); |
| 120 |
> |
DeclareParameter(HydroPropFile, std::string); |
| 121 |
> |
DeclareParameter(Viscosity, RealType); |
| 122 |
> |
DeclareParameter(BeadSize, RealType); |
| 123 |
> |
DeclareParameter(UseSphericalBoundaryConditions, bool); |
| 124 |
> |
DeclareParameter(FrozenBufferRadius, RealType); |
| 125 |
> |
DeclareParameter(LangevinBufferRadius, RealType); |
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public: |
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|
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Globals(); |
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~Globals(); |
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> |
public: |
| 128 |
> |
bool addComponent(Component* comp); |
| 129 |
> |
bool addZConsStamp(ZConsStamp* zcons); |
| 130 |
> |
bool addMoleculeStamp(MoleculeStamp* molStamp); |
| 131 |
> |
int getNComponents() {return components_.size();} |
| 132 |
> |
std::vector<Component*> getComponents() {return components_;} |
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Component* getComponentAt(int index) {return components_.at(index);} |
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void initalize(); |
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int newComponent( event* the_event ); |
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int componentAssign( event* the_event ); |
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< |
int componentEnd( event* the_event ); |
| 135 |
> |
int getNZconsStamps() {return zconstraints_.size();} |
| 136 |
> |
std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;} |
| 137 |
> |
ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);} |
| 138 |
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| 139 |
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int newZconstraint( event* the_event ); |
| 140 |
< |
int zConstraintAssign( event* the_event ); |
| 141 |
< |
int zConstraintEnd( event* the_event ); |
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< |
|
| 143 |
< |
int globalAssign( event* the_event ); |
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int globalEnd( event* the_event ); |
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< |
|
| 84 |
< |
char* getForceField( void ) { return force_field; } |
| 85 |
< |
int getNComponents( void ) { return n_components; } |
| 86 |
< |
double getTargetTemp( void ) { return target_temp; } |
| 87 |
< |
double getTargetPressure( void ) { return target_pressure; } |
| 88 |
< |
double getQmass( void ) { return q_mass; } |
| 89 |
< |
double getTauThermostat( void ) { return tau_thermostat; } |
| 90 |
< |
double getTauBarostat( void ) { return tau_barostat; } |
| 91 |
< |
char* getEnsemble( void ) { return ensemble; } |
| 92 |
< |
double getDt( void ) { return dt; } |
| 93 |
< |
double getRunTime( void ) { return run_time; } |
| 94 |
< |
|
| 95 |
< |
int getNzConstraints( void ) { return n_zConstraints; } |
| 96 |
< |
char* getInitialConfig( void ) { return initial_config; } |
| 97 |
< |
char* getFinalConfig( void ) { return final_config; } |
| 98 |
< |
int getNMol( void ) { return n_mol; } |
| 99 |
< |
double getDensity( void ) { return density; } |
| 100 |
< |
double getBox( void ) { return box; } |
| 101 |
< |
double getBoxX( void ) { return box_x; } |
| 102 |
< |
double getBoxY( void ) { return box_y; } |
| 103 |
< |
double getBoxZ( void ) { return box_z; } |
| 104 |
< |
double getSampleTime( void ) { return sample_time; } |
| 105 |
< |
double getStatusTime( void ) { return status_time; } |
| 106 |
< |
double getResetTime( void ) { return resetTime; } |
| 107 |
< |
double getThermalTime( void ) { return thermal_time; } |
| 108 |
< |
double getDielectric( void ) { return dielectric; } |
| 109 |
< |
double getRcut( void ) { return rcut; } |
| 110 |
< |
double getRsw( void ) { return rsw; } |
| 111 |
< |
int getTempSet( void ) { return tempSet; } |
| 112 |
< |
int getUseInitTime( void ) { return useInitTime; } |
| 113 |
< |
int getUseInitXSstate( void ) { return useInitXSstate; } |
| 114 |
< |
double getOrthoBoxTolerance(void) { return orthoBoxTolerance; } |
| 115 |
< |
int getPBC( void ) { return usePBC; } |
| 116 |
< |
int getUseRF( void ) { return useRF; } |
| 117 |
< |
char* getMixingRule( void) { return mixingRule; } |
| 118 |
< |
double getZconsTime(void) { return zcons_time; } |
| 119 |
< |
double getZconsTol(void) { return zcons_tol; } |
| 120 |
< |
char* getZconsForcePolicy(void) { return zconsForcePolicy; } |
| 121 |
< |
double getZconsGap(void) { return zcons_gap; } |
| 122 |
< |
double getZconsFixtime(void) { return zcons_fixtime; } |
| 123 |
< |
int getZconsUsingSMD(void) { return zcons_using_smd; } |
| 124 |
< |
int getSeed(void) { return seed; } |
| 125 |
< |
char* getMinimizer(void) { return minimizer_name; } |
| 126 |
< |
int getMinMaxIter(void) { return minimizer_maxiteration; } |
| 127 |
< |
int getMinWriteFrq(void) { return minimizer_writefrq; } |
| 128 |
< |
double getMinStepSize(void) { return minimizer_stepsize; } |
| 129 |
< |
double getMinFTol(void) { return minimizer_ftol; } |
| 130 |
< |
double getMinGTol(void) { return minimizer_gtol; } |
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< |
double getMinLSTol(void) { return minimizer_ls_tol; } |
| 132 |
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int getMinLSMaxIter(void) { return minimizer_ls_maxiteration; } |
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int getUseSolidThermInt(void) { return useSolidThermInt; } |
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int getUseLiquidThermInt(void) { return useLiquidThermInt; } |
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double getThermIntLambda(void) { return thermodynamic_integration_lambda; } |
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double getThermIntK(void) { return thermodynamic_integration_k; } |
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char* getForceFieldVariant( void ) { return forcefield_variant; } |
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< |
char* getForceFieldFileName() { return forcefield_filename; } |
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double getDistSpringConst(void) { return therm_int_dist_spring; } |
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< |
double getThetaSpringConst(void) { return therm_int_theta_spring; } |
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< |
double getOmegaSpringConst(void) { return therm_int_omega_spring; } |
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< |
double getSurfaceTension(void) { return surface_tension; } |
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< |
bool getPrintPressureTensor(void) { return print_pressure_tensor;} |
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char* getCoulombicCorrection(void) { return coulombicCorrection; } |
| 145 |
< |
double getDampingAlpha(void) { return dampingAlpha; } |
| 146 |
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char* getCutoffPolicy(void) { return cutoffPolicy; } |
| 147 |
< |
|
| 148 |
< |
short int haveDt( void ) { return have_dt; } |
| 149 |
< |
short int haveRunTime( void ) { return have_run_time; } |
| 150 |
< |
short int haveEnsemble( void ) { return have_ensemble; } |
| 151 |
< |
short int haveTargetTemp( void ) { return have_target_temp; } |
| 152 |
< |
short int haveInitialConfig( void ) { return have_initial_config; } |
| 153 |
< |
short int haveFinalConfig( void ) { return have_final_config; } |
| 154 |
< |
short int haveNMol( void ) { return have_n_mol; } |
| 155 |
< |
short int haveDensity( void ) { return have_density; } |
| 156 |
< |
short int haveBox( void ) { return have_box; } |
| 157 |
< |
short int haveBoxX( void ) { return have_box_x; } |
| 158 |
< |
short int haveBoxY( void ) { return have_box_y; } |
| 159 |
< |
short int haveBoxZ( void ) { return have_box_z; } |
| 160 |
< |
short int haveSampleTime( void ) { return have_sample_time; } |
| 161 |
< |
short int haveResetTime( void ) { return have_reset_time; } |
| 162 |
< |
short int haveStatusTime( void ) { return have_status_time; } |
| 163 |
< |
short int haveThermalTime( void ) { return have_thermal_time; } |
| 164 |
< |
short int haveRcut( void ) { return have_rcut; } |
| 165 |
< |
short int haveRsw( void ) { return have_rsw; } |
| 166 |
< |
short int haveDielectric( void ) { return have_dielectric; } |
| 167 |
< |
short int haveTempSet( void ) { return have_tempSet; } |
| 168 |
< |
short int haveTargetPressure( void ){ return have_target_pressure; } |
| 169 |
< |
short int haveQmass( void ) { return have_q_mass; } |
| 170 |
< |
short int haveTauThermostat( void ) { return have_tau_thermostat; } |
| 171 |
< |
short int haveTauBarostat( void ) { return have_tau_barostat; } |
| 172 |
< |
short int haveZconstraintTime(void) { return have_zcons_time; } |
| 173 |
< |
short int haveZconstraints( void ) { return have_zConstraints; } |
| 174 |
< |
short int haveZconsTol(void) { return have_zcons_tol; } |
| 175 |
< |
short int haveZconsForcePolicy(void){ return have_zcons_force_policy; } |
| 176 |
< |
short int haveZConsGap(void) { return have_zcons_gap; } |
| 177 |
< |
short int haveZConsFixTime(void) { return have_zcons_fixtime; } |
| 178 |
< |
short int haveZConsUsingSMD(void) { return have_zcons_using_smd; } |
| 179 |
< |
short int haveSeed(void) { return have_seed; } |
| 180 |
< |
short int haveMinimizer(void) { return have_minimizer; } |
| 181 |
< |
short int haveMinMaxIter(void) { return have_minimizer_maxiteration; } |
| 182 |
< |
short int haveMinWriteFrq(void) { return have_minimizer_writefrq; } |
| 183 |
< |
short int haveMinStepSize(void) { return have_minimizer_stepsize; } |
| 184 |
< |
short int haveMinFTol(void) { return have_minimizer_ftol; } |
| 185 |
< |
short int haveMinGTol(void) { return have_minimizer_gtol; } |
| 186 |
< |
short int haveMinLSTol(void) { return have_minimizer_ls_tol; } |
| 187 |
< |
short int haveMinLSMaxIter(void) { return have_minimizer_ls_maxiteration;} |
| 188 |
< |
short int haveThermIntLambda(void) { return have_thermodynamic_integration_lambda; } |
| 189 |
< |
short int haveThermIntK(void) { return have_thermodynamic_integration_k; } |
| 190 |
< |
short int haveForceFieldVariant(void) { return have_forcefield_variant; } |
| 191 |
< |
short int haveForceFieldFileName(void) { return have_forcefield_filename; } |
| 192 |
< |
short int haveDistSpringConst(void) { return have_dist_spring_constant; } |
| 193 |
< |
short int haveThetaSpringConst(void) { return have_theta_spring_constant; } |
| 194 |
< |
short int haveOmegaSpringConst(void) { return have_omega_spring_constant; } |
| 195 |
< |
short int haveSurfaceTension(void) { return have_surface_tension; } |
| 196 |
< |
short int havePrintPressureTensor(void) {return have_print_pressure_tensor;} |
| 197 |
< |
short int haveCoulombicCorrection(void) {return have_coulombic_correction;} |
| 198 |
< |
short int haveDampingAlpha(void) { return have_damping_alpha; } |
| 199 |
< |
short int haveCutoffPolicy(void) { return have_cutoff_policy; } |
| 139 |
> |
virtual void validate(); |
| 140 |
> |
private: |
| 141 |
> |
|
| 142 |
> |
std::vector<Component*> components_; |
| 143 |
> |
std::vector<ZConsStamp*> zconstraints_; |
| 144 |
> |
std::map<std::string, MoleculeStamp*> moleculeStamps_; |
| 145 |
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|
| 201 |
– |
/* other accessors */ |
| 202 |
– |
Component** getComponents( void ) { return components; } |
| 203 |
– |
ZconStamp** getZconStamp( void ) { return zConstraints; } |
| 204 |
– |
|
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private: |
| 206 |
– |
|
| 207 |
– |
|
| 208 |
– |
typedef std::map<std::string, int> CommandMapType; |
| 209 |
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CommandMapType command_table; |
| 210 |
– |
|
| 211 |
– |
|
| 212 |
– |
char* checkMe( void ); |
| 213 |
– |
|
| 214 |
– |
Component* current_component; |
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Component** components; // the array of components |
| 216 |
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|
| 217 |
– |
ZconStamp* current_zConstraint; |
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– |
ZconStamp** zConstraints; // the array of zConstraints |
| 219 |
– |
|
| 220 |
– |
char force_field[100]; |
| 221 |
– |
int n_components; |
| 222 |
– |
int n_zConstraints; |
| 223 |
– |
double target_temp; |
| 224 |
– |
double target_pressure; |
| 225 |
– |
char ensemble[100]; |
| 226 |
– |
char mixingRule[100]; |
| 227 |
– |
double dt; |
| 228 |
– |
double run_time; |
| 229 |
– |
char initial_config[120]; |
| 230 |
– |
char final_config[120]; |
| 231 |
– |
int n_mol; |
| 232 |
– |
double density; |
| 233 |
– |
double box; |
| 234 |
– |
double box_x, box_y, box_z; |
| 235 |
– |
double sample_time; |
| 236 |
– |
double status_time; |
| 237 |
– |
double resetTime; |
| 238 |
– |
double orthoBoxTolerance; |
| 239 |
– |
double thermal_time; |
| 240 |
– |
double rcut; |
| 241 |
– |
double rsw; |
| 242 |
– |
double dielectric; |
| 243 |
– |
int tempSet; |
| 244 |
– |
int useInitTime; |
| 245 |
– |
int useInitXSstate; |
| 246 |
– |
int usePBC; |
| 247 |
– |
int useRF; |
| 248 |
– |
double q_mass; |
| 249 |
– |
double tau_thermostat; |
| 250 |
– |
double tau_barostat; |
| 251 |
– |
double zcons_time; |
| 252 |
– |
double zcons_tol; |
| 253 |
– |
char zconsForcePolicy[100]; |
| 254 |
– |
double zcons_gap; |
| 255 |
– |
double zcons_fixtime; |
| 256 |
– |
int zcons_using_smd; |
| 257 |
– |
|
| 258 |
– |
int seed; |
| 259 |
– |
char minimizer_name[100]; |
| 260 |
– |
int minimizer_maxiteration; |
| 261 |
– |
int minimizer_writefrq; |
| 262 |
– |
double minimizer_stepsize; |
| 263 |
– |
double minimizer_ftol; |
| 264 |
– |
double minimizer_gtol; |
| 265 |
– |
double minimizer_ls_tol; |
| 266 |
– |
int minimizer_ls_maxiteration; |
| 267 |
– |
int useSolidThermInt; |
| 268 |
– |
int useLiquidThermInt; |
| 269 |
– |
double thermodynamic_integration_lambda; |
| 270 |
– |
double thermodynamic_integration_k; |
| 271 |
– |
char forcefield_variant[100]; |
| 272 |
– |
char forcefield_filename[100]; |
| 273 |
– |
double therm_int_dist_spring; |
| 274 |
– |
double therm_int_theta_spring; |
| 275 |
– |
double therm_int_omega_spring; |
| 276 |
– |
double surface_tension; |
| 277 |
– |
bool print_pressure_tensor; |
| 278 |
– |
char coulombicCorrection[100]; |
| 279 |
– |
double dampingAlpha; |
| 280 |
– |
char cutoffPolicy[100]; |
| 281 |
– |
|
| 282 |
– |
//required arguments |
| 283 |
– |
short int have_force_field, have_n_components, have_target_temp; |
| 284 |
– |
short int have_target_pressure, have_ensemble, have_dt, have_run_time; |
| 285 |
– |
|
| 286 |
– |
// optional arguments |
| 287 |
– |
short int have_initial_config, have_final_config, have_n_mol; |
| 288 |
– |
short int have_density, have_box, have_box_x, have_box_y, have_box_z; |
| 289 |
– |
short int have_sample_time, have_status_time, have_rcut, have_dielectric; |
| 290 |
– |
short int have_tempSet, have_thermal_time, have_rsw, have_q_mass; |
| 291 |
– |
short int have_tau_thermostat, have_tau_barostat; |
| 292 |
– |
short int have_zcons_time, have_zConstraints, have_n_zConstraints; |
| 293 |
– |
short int have_zcons_tol, have_seed; |
| 294 |
– |
short int have_zcons_force_policy, have_reset_time; |
| 295 |
– |
short int have_zcons_gap, have_zcons_fixtime; |
| 296 |
– |
short int have_zcons_using_smd; |
| 297 |
– |
short int have_minimizer, have_minimizer_maxiteration; |
| 298 |
– |
short int have_minimizer_writefrq, have_minimizer_stepsize; |
| 299 |
– |
short int have_minimizer_ftol, have_minimizer_gtol; |
| 300 |
– |
short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration; |
| 301 |
– |
short int have_thermodynamic_integration_lambda; |
| 302 |
– |
short int have_thermodynamic_integration_k; |
| 303 |
– |
short int have_forcefield_variant; |
| 304 |
– |
short int have_forcefield_filename; |
| 305 |
– |
short int have_dist_spring_constant; |
| 306 |
– |
short int have_theta_spring_constant; |
| 307 |
– |
short int have_omega_spring_constant; |
| 308 |
– |
short int have_surface_tension; |
| 309 |
– |
short int have_print_pressure_tensor; |
| 310 |
– |
short int have_coulombic_correction; |
| 311 |
– |
short int have_damping_alpha; |
| 312 |
– |
short int have_cutoff_policy; |
| 146 |
|
}; |
| 147 |
< |
|
| 147 |
> |
} |
| 148 |
|
#endif |
| 149 |
+ |
|
