| 1 |
|
/* |
| 2 |
< |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 2 |
> |
* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved. |
| 3 |
|
* |
| 4 |
|
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
|
* non-exclusive, royalty free, license to use, modify and |
| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include <stdlib.h> |
| 46 |
|
#include <string> |
| 47 |
|
|
| 48 |
|
#include "io/Globals.hpp" |
| 49 |
+ |
#include "io/ParamConstraint.hpp" |
| 50 |
+ |
#include "utils/MemoryUtils.hpp" |
| 51 |
|
#include "utils/simError.h" |
| 49 |
– |
#ifdef IS_MPI |
| 50 |
– |
#include "io/mpiBASS.h" |
| 51 |
– |
#endif // is_mpi |
| 52 |
|
|
| 53 |
< |
#include "io/ParamConstraint.hpp" |
| 54 |
< |
|
| 55 |
< |
using namespace oopse; |
| 56 |
< |
|
| 57 |
< |
Globals::Globals(){ |
| 58 |
< |
|
| 53 |
> |
namespace OpenMD { |
| 54 |
> |
Globals::Globals() { |
| 55 |
|
DefineParameter(ForceField, "forceField") |
| 60 |
– |
DefineParameter(NComponents, "nComponents") |
| 56 |
|
|
| 57 |
|
DefineOptionalParameter(TargetTemp, "targetTemp"); |
| 58 |
|
DefineOptionalParameter(Ensemble, "ensemble"); |
| 59 |
|
DefineOptionalParameter(Dt, "dt"); |
| 60 |
|
DefineOptionalParameter(RunTime, "runTime"); |
| 66 |
– |
DefineOptionalParameter(InitialConfig, "initialConfig"); |
| 61 |
|
DefineOptionalParameter(FinalConfig, "finalConfig"); |
| 68 |
– |
DefineOptionalParameter(NMol, "nMol"); |
| 69 |
– |
DefineOptionalParameter(Density, "density"); |
| 70 |
– |
DefineOptionalParameter(Box, "box"); |
| 71 |
– |
DefineOptionalParameter(BoxX, "boxX"); |
| 72 |
– |
DefineOptionalParameter(BoxY, "boxY"); |
| 73 |
– |
DefineOptionalParameter(BoxZ, "boxZ"); |
| 62 |
|
DefineOptionalParameter(SampleTime, "sampleTime"); |
| 63 |
|
DefineOptionalParameter(ResetTime, "resetTime"); |
| 64 |
|
DefineOptionalParameter(StatusTime, "statusTime"); |
| 65 |
|
DefineOptionalParameter(CutoffRadius, "cutoffRadius"); |
| 66 |
|
DefineOptionalParameter(SwitchingRadius, "switchingRadius"); |
| 79 |
– |
DefineOptionalParameter(Dielectric, "dielectric"); |
| 67 |
|
DefineOptionalParameter(TempSet, "tempSet"); |
| 68 |
|
DefineOptionalParameter(ThermalTime, "thermalTime"); |
| 69 |
< |
DefineOptionalParameter(TargetPressure, "targetPressure"); |
| 69 |
> |
DefineOptionalParameter(TargetPressure, "targetPressure"); |
| 70 |
|
DefineOptionalParameter(TauThermostat, "tauThermostat"); |
| 71 |
|
DefineOptionalParameter(TauBarostat, "tauBarostat"); |
| 72 |
|
DefineOptionalParameter(ZconsTime, "zconsTime"); |
| 86 |
– |
DefineOptionalParameter(NZconstraints, "nZconstraints"); |
| 73 |
|
DefineOptionalParameter(ZconsTol, "zconsTol"); |
| 74 |
|
DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy"); |
| 75 |
|
DefineOptionalParameter(Seed, "seed"); |
| 76 |
|
DefineOptionalParameter(Minimizer, "minimizer"); |
| 77 |
|
DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter"); |
| 78 |
< |
DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq"); |
| 78 |
> |
DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq"); |
| 79 |
|
DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize"); |
| 80 |
|
DefineOptionalParameter(MinimizerFTol, "minimizerFTol"); |
| 81 |
|
DefineOptionalParameter(MinimizerGTol, "minimizerGTol"); |
| 88 |
|
DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK"); |
| 89 |
|
DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant"); |
| 90 |
|
DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName"); |
| 91 |
< |
DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst"); |
| 106 |
< |
DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst"); |
| 107 |
< |
DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst"); |
| 91 |
> |
DefineOptionalParameter(DampingAlpha, "dampingAlpha"); |
| 92 |
|
DefineOptionalParameter(SurfaceTension, "surfaceTension"); |
| 93 |
|
DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); |
| 94 |
< |
DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod"); |
| 95 |
< |
DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod"); |
| 112 |
< |
DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); |
| 94 |
> |
DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); |
| 95 |
> |
DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); |
| 96 |
|
DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); |
| 97 |
< |
DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard"); |
| 97 |
> |
DefineOptionalParameter(HydroPropFile, "HydroPropFile"); |
| 98 |
> |
DefineOptionalParameter(Viscosity, "viscosity"); |
| 99 |
> |
DefineOptionalParameter(BeadSize, "beadSize"); |
| 100 |
> |
DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius"); |
| 101 |
> |
DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); |
| 102 |
> |
DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors"); |
| 103 |
> |
DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod"); |
| 104 |
> |
DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod"); |
| 105 |
> |
DefineOptionalParameter(MTM_Ce, "MTM_Ce"); |
| 106 |
> |
DefineOptionalParameter(MTM_G, "MTM_G"); |
| 107 |
> |
DefineOptionalParameter(MTM_Io, "MTM_Io"); |
| 108 |
> |
DefineOptionalParameter(MTM_Sigma, "MTM_Sigma"); |
| 109 |
> |
DefineOptionalParameter(MTM_R, "MTM_R"); |
| 110 |
> |
DefineOptionalParameter(Alpha, "alpha"); |
| 111 |
> |
|
| 112 |
> |
|
| 113 |
|
DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); |
| 114 |
+ |
DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true); |
| 115 |
|
DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); |
| 116 |
|
DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false); |
| 117 |
|
DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6); |
| 118 |
< |
DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false); |
| 119 |
< |
DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false); |
| 120 |
< |
DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0); |
| 121 |
< |
DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5); |
| 122 |
< |
DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5); |
| 123 |
< |
DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2); |
| 124 |
< |
DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); |
| 125 |
< |
DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); |
| 118 |
> |
DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE"); |
| 119 |
> |
DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED"); |
| 120 |
> |
DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0); |
| 121 |
> |
DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false); |
| 122 |
> |
DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false); |
| 123 |
> |
DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false); |
| 124 |
> |
DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false); |
| 125 |
> |
DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false); |
| 126 |
|
DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); |
| 127 |
|
DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); |
| 128 |
+ |
DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false); |
| 129 |
+ |
DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false); |
| 130 |
|
|
| 131 |
< |
|
| 132 |
< |
} |
| 133 |
< |
|
| 134 |
< |
Globals::~Globals(){ |
| 135 |
< |
int i; |
| 136 |
< |
if( components != NULL ){ |
| 137 |
< |
for( i=0; i< getNComponents(); i++ ) delete components[i]; |
| 138 |
< |
delete[] components; |
| 139 |
< |
} |
| 140 |
< |
|
| 141 |
< |
if( zConstraints != NULL ){ |
| 142 |
< |
for( i=0; i< getNZconstraints(); i++ ) delete zConstraints[i]; |
| 143 |
< |
delete[] zConstraints; |
| 143 |
< |
} |
| 144 |
< |
|
| 145 |
< |
} |
| 146 |
< |
|
| 147 |
< |
int Globals::globalAssign( event* the_event ){ |
| 148 |
< |
char errorMessage[65535]; |
| 149 |
< |
int key; |
| 150 |
< |
interface_assign_type the_type = the_event->evt.asmt.asmt_type; |
| 151 |
< |
char* lhs = the_event->evt.asmt.lhs; |
| 152 |
< |
std::string keyword(lhs); |
| 153 |
< |
|
| 154 |
< |
bool result = false; |
| 155 |
< |
|
| 156 |
< |
/**@todo fix memory leak */ |
| 157 |
< |
ParamMap::iterator i =parameters_.find(keyword); |
| 158 |
< |
if (i != parameters_.end()) { |
| 159 |
< |
if( the_type == STRING ){ |
| 160 |
< |
result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval)); |
| 161 |
< |
if (!result ) { |
| 162 |
< |
sprintf(errorMessage, "Error in parsing %s: expect %s, but get a string \"%s\".\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.sval); |
| 163 |
< |
the_event->err_msg = strdup(errorMessage); |
| 164 |
< |
} |
| 165 |
< |
} else if( the_type == DOUBLE ){ |
| 166 |
< |
result = i->second->setData(the_event->evt.asmt.rhs.dval); |
| 167 |
< |
if (!result ) |
| 168 |
< |
sprintf(errorMessage, "Error in parsing %s: expect %s, but get a double %f.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.dval ); |
| 169 |
< |
the_event->err_msg = strdup(errorMessage); |
| 170 |
< |
} |
| 171 |
< |
else if (the_type == INT ){ |
| 172 |
< |
result = i->second->setData(the_event->evt.asmt.rhs.ival); |
| 173 |
< |
if (!result ) |
| 174 |
< |
sprintf(errorMessage, "Error in parsing %s: expect %s, but get an int %d.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.ival ); |
| 175 |
< |
the_event->err_msg = strdup(errorMessage); |
| 176 |
< |
|
| 177 |
< |
} else { |
| 178 |
< |
sprintf(errorMessage, "Internal error of parser\n"); |
| 179 |
< |
the_event->err_msg = strdup(errorMessage); |
| 180 |
< |
} |
| 181 |
< |
} else { |
| 182 |
< |
sprintf(errorMessage, "%s is an unrecognized keyword\n", keyword.c_str() ); |
| 183 |
< |
the_event->err_msg = strdup(errorMessage); |
| 184 |
< |
} |
| 185 |
< |
|
| 186 |
< |
if (keyword == "nComponents" && getNComponents() > 0) { |
| 187 |
< |
components = new Component*[getNComponents()]; |
| 188 |
< |
}else if (keyword == "nZconstraints" && getNZconstraints() > 0) { |
| 189 |
< |
zConstraints = new ZconStamp*[getNZconstraints()]; |
| 190 |
< |
} |
| 191 |
< |
|
| 192 |
< |
return result; |
| 193 |
< |
} |
| 194 |
< |
|
| 195 |
< |
int Globals::newComponent( event* the_event ){ |
| 196 |
< |
|
| 197 |
< |
current_component = new Component; |
| 198 |
< |
int index = the_event->evt.blk_index; |
| 199 |
< |
char err[200]; |
| 200 |
< |
|
| 201 |
< |
if( haveNComponents() && index < getNComponents() ) |
| 202 |
< |
components[index] = current_component; |
| 203 |
< |
else{ |
| 204 |
< |
if( haveNComponents() ){ |
| 205 |
< |
sprintf( err, "meta-data parsing error: %d out of nComponents range", |
| 206 |
< |
index ); |
| 207 |
< |
the_event->err_msg = strdup( err ); |
| 208 |
< |
return 0; |
| 209 |
< |
} |
| 210 |
< |
else{ |
| 211 |
< |
the_event->err_msg = strdup("meta-data parsing error: nComponents not given before" |
| 212 |
< |
" first component declaration." ); |
| 213 |
< |
return 0; |
| 214 |
< |
} |
| 215 |
< |
} |
| 216 |
< |
|
| 217 |
< |
return 1; |
| 218 |
< |
} |
| 219 |
< |
|
| 220 |
< |
|
| 221 |
< |
|
| 222 |
< |
int Globals::componentAssign( event* the_event ){ |
| 223 |
< |
|
| 224 |
< |
switch( the_event->evt.asmt.asmt_type ){ |
| 225 |
< |
|
| 226 |
< |
case STRING: |
| 227 |
< |
return current_component->assignString( the_event->evt.asmt.lhs, |
| 228 |
< |
the_event->evt.asmt.rhs.sval, |
| 229 |
< |
&(the_event->err_msg)); |
| 230 |
< |
break; |
| 231 |
< |
|
| 232 |
< |
case DOUBLE: |
| 233 |
< |
return current_component->assignDouble( the_event->evt.asmt.lhs, |
| 234 |
< |
the_event->evt.asmt.rhs.dval, |
| 235 |
< |
&(the_event->err_msg)); |
| 236 |
< |
break; |
| 237 |
< |
|
| 238 |
< |
case INT: |
| 239 |
< |
return current_component->assignInt( the_event->evt.asmt.lhs, |
| 240 |
< |
the_event->evt.asmt.rhs.ival, |
| 241 |
< |
&(the_event->err_msg)); |
| 242 |
< |
break; |
| 243 |
< |
|
| 244 |
< |
default: |
| 245 |
< |
the_event->err_msg = strdup( "Globals error. Invalid component" |
| 246 |
< |
" assignment type" ); |
| 247 |
< |
return 0; |
| 248 |
< |
break; |
| 249 |
< |
} |
| 250 |
< |
return 0; |
| 251 |
< |
} |
| 131 |
> |
DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false); |
| 132 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0); |
| 133 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16); |
| 134 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16); |
| 135 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale"); |
| 136 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0); |
| 137 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all"); |
| 138 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false); |
| 139 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false); |
| 140 |
> |
DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false); |
| 141 |
> |
DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in"); |
| 142 |
> |
DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false); |
| 143 |
> |
DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex"); |
| 144 |
|
|
| 253 |
– |
int Globals::componentEnd( event* the_event ){ |
| 145 |
|
|
| 255 |
– |
the_event->err_msg = current_component->checkMe(); |
| 256 |
– |
if( the_event->err_msg != NULL ) return 0; |
| 146 |
|
|
| 147 |
< |
return 1; |
| 148 |
< |
} |
| 149 |
< |
|
| 150 |
< |
int Globals::newZconstraint( event* the_event ){ |
| 151 |
< |
|
| 152 |
< |
|
| 153 |
< |
int index = the_event->evt.blk_index; |
| 154 |
< |
char err[200]; |
| 266 |
< |
current_zConstraint = new ZconStamp( index ); |
| 267 |
< |
|
| 268 |
< |
if( haveNZconstraints() && index < getNZconstraints() ) |
| 269 |
< |
zConstraints[index] = current_zConstraint; |
| 270 |
< |
else{ |
| 271 |
< |
if( haveNZconstraints() ){ |
| 272 |
< |
sprintf( err, "meta-data parsing error: %d out of nZconstraints range", |
| 273 |
< |
index ); |
| 274 |
< |
the_event->err_msg = strdup( err ); |
| 275 |
< |
return 0; |
| 276 |
< |
} |
| 277 |
< |
else{ |
| 278 |
< |
the_event->err_msg = strdup("meta-data parsing error: nZconstraints" |
| 279 |
< |
" not given before" |
| 280 |
< |
" first zConstraint declaration." ); |
| 281 |
< |
return 0; |
| 282 |
< |
} |
| 283 |
< |
} |
| 284 |
< |
|
| 285 |
< |
return 1; |
| 286 |
< |
} |
| 287 |
< |
|
| 288 |
< |
|
| 289 |
< |
|
| 290 |
< |
int Globals::zConstraintAssign( event* the_event ){ |
| 291 |
< |
|
| 292 |
< |
switch( the_event->evt.asmt.asmt_type ){ |
| 147 |
> |
deprecatedKeywords_.insert("nComponents"); |
| 148 |
> |
deprecatedKeywords_.insert("nZconstraints"); |
| 149 |
> |
deprecatedKeywords_.insert("initialConfig"); |
| 150 |
> |
deprecatedKeywords_.insert("thermIntDistSpringConst"); |
| 151 |
> |
deprecatedKeywords_.insert("thermIntThetaSpringConst"); |
| 152 |
> |
deprecatedKeywords_.insert("thermIntOmegaSpringConst"); |
| 153 |
> |
deprecatedKeywords_.insert("useSolidThermInt"); |
| 154 |
> |
deprecatedKeywords_.insert("useLiquidThermInt"); |
| 155 |
|
|
| 294 |
– |
case STRING: |
| 295 |
– |
return current_zConstraint->assignString( the_event->evt.asmt.lhs, |
| 296 |
– |
the_event->evt.asmt.rhs.sval, |
| 297 |
– |
&(the_event->err_msg)); |
| 298 |
– |
break; |
| 299 |
– |
|
| 300 |
– |
case DOUBLE: |
| 301 |
– |
return current_zConstraint->assignDouble( the_event->evt.asmt.lhs, |
| 302 |
– |
the_event->evt.asmt.rhs.dval, |
| 303 |
– |
&(the_event->err_msg)); |
| 304 |
– |
break; |
| 305 |
– |
|
| 306 |
– |
case INT: |
| 307 |
– |
return current_zConstraint->assignInt( the_event->evt.asmt.lhs, |
| 308 |
– |
the_event->evt.asmt.rhs.ival, |
| 309 |
– |
&(the_event->err_msg)); |
| 310 |
– |
break; |
| 311 |
– |
|
| 312 |
– |
default: |
| 313 |
– |
the_event->err_msg = strdup( "Globals error. Invalid zConstraint" |
| 314 |
– |
" assignment type" ); |
| 315 |
– |
return 0; |
| 316 |
– |
break; |
| 317 |
– |
} |
| 318 |
– |
return 0; |
| 156 |
|
} |
| 157 |
|
|
| 158 |
< |
int Globals::zConstraintEnd( event* the_event ){ |
| 159 |
< |
|
| 160 |
< |
the_event->err_msg = current_zConstraint->checkMe(); |
| 161 |
< |
if( the_event->err_msg != NULL ) return 0; |
| 325 |
< |
|
| 326 |
< |
return 1; |
| 158 |
> |
Globals::~Globals() { |
| 159 |
> |
MemoryUtils::deletePointers(components_); |
| 160 |
> |
MemoryUtils::deletePointers(zconstraints_); |
| 161 |
> |
MemoryUtils::deletePointers(restraints_); |
| 162 |
|
} |
| 163 |
|
|
| 164 |
< |
char* Globals::checkMe( void ){ |
| 164 |
> |
void Globals::validate() { |
| 165 |
> |
DataHolder::validate(); |
| 166 |
|
|
| 331 |
– |
|
| 332 |
– |
std::string err("The following required keywords are missing:\n"); |
| 333 |
– |
short int have_err = 0; |
| 334 |
– |
|
| 335 |
– |
ParamMap::iterator i; |
| 336 |
– |
for (i = parameters_.begin(); i != parameters_.end(); ++i) { |
| 337 |
– |
if (!i->second->isOptional() && i->second->empty()) { |
| 338 |
– |
err += i->second->getKeyword() + "\n"; |
| 339 |
– |
} |
| 340 |
– |
} |
| 341 |
– |
|
| 167 |
|
CheckParameter(ForceField, isNotEmpty()); |
| 343 |
– |
CheckParameter(NComponents,isPositive()); |
| 168 |
|
CheckParameter(TargetTemp, isPositive()); |
| 169 |
< |
CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) ); |
| 169 |
> |
CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("LANGEVINHULL") || isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD")); |
| 170 |
|
CheckParameter(Dt, isPositive()); |
| 171 |
|
CheckParameter(RunTime, isPositive()); |
| 348 |
– |
CheckParameter(InitialConfig, isNotEmpty()); |
| 172 |
|
CheckParameter(FinalConfig, isNotEmpty()); |
| 350 |
– |
CheckParameter(NMol, isPositive()); |
| 351 |
– |
CheckParameter(Density, isPositive()); |
| 352 |
– |
CheckParameter(Box, isPositive()); |
| 353 |
– |
CheckParameter(BoxX, isPositive()); |
| 354 |
– |
CheckParameter(BoxY, isPositive()); |
| 355 |
– |
CheckParameter(BoxZ, isPositive()); |
| 173 |
|
CheckParameter(SampleTime, isNonNegative()); |
| 174 |
|
CheckParameter(ResetTime, isNonNegative()); |
| 175 |
|
CheckParameter(StatusTime, isNonNegative()); |
| 177 |
|
CheckParameter(SwitchingRadius, isNonNegative()); |
| 178 |
|
CheckParameter(Dielectric, isPositive()); |
| 179 |
|
CheckParameter(ThermalTime, isNonNegative()); |
| 363 |
– |
CheckParameter(TargetPressure, isPositive()); |
| 180 |
|
CheckParameter(TauThermostat, isPositive()); |
| 181 |
|
CheckParameter(TauBarostat, isPositive()); |
| 182 |
|
CheckParameter(ZconsTime, isPositive()); |
| 367 |
– |
CheckParameter(NZconstraints, isPositive()); |
| 183 |
|
CheckParameter(ZconsTol, isPositive()); |
| 369 |
– |
//CheckParameter(ZconsForcePolicy,); |
| 184 |
|
CheckParameter(Seed, isPositive()); |
| 185 |
< |
CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG"))); |
| 185 |
> |
CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG")); |
| 186 |
|
CheckParameter(MinimizerMaxIter, isPositive()); |
| 187 |
< |
CheckParameter(MinimizerWriteFrq, isPositive()); |
| 187 |
> |
CheckParameter(MinimizerWriteFreq, isPositive()); |
| 188 |
|
CheckParameter(MinimizerStepSize, isPositive()); |
| 189 |
|
CheckParameter(MinimizerFTol, isPositive()); |
| 190 |
|
CheckParameter(MinimizerGTol, isPositive()); |
| 192 |
|
CheckParameter(MinimizerLSMaxIter, isPositive()); |
| 193 |
|
CheckParameter(ZconsGap, isPositive()); |
| 194 |
|
CheckParameter(ZconsFixtime, isPositive()); |
| 195 |
< |
CheckParameter(ThermodynamicIntegrationLambda, isPositive()); |
| 195 |
> |
CheckParameter(ThermodynamicIntegrationLambda, isNonNegative()); |
| 196 |
|
CheckParameter(ThermodynamicIntegrationK, isPositive()); |
| 197 |
|
CheckParameter(ForceFieldVariant, isNotEmpty()); |
| 198 |
|
CheckParameter(ForceFieldFileName, isNotEmpty()); |
| 199 |
< |
CheckParameter(ThermIntDistSpringConst, isPositive()); |
| 200 |
< |
CheckParameter(ThermIntThetaSpringConst, isPositive()); |
| 201 |
< |
CheckParameter(ThermIntOmegaSpringConst, isPositive()); |
| 202 |
< |
CheckParameter(SurfaceTension, isPositive()); |
| 203 |
< |
CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD"))); |
| 390 |
< |
CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED"))); |
| 391 |
< |
CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL"))); |
| 392 |
< |
CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL"))); |
| 393 |
< |
//CheckParameter(StatFileFormat,); |
| 394 |
< |
//CheckParameter(MixingRule,); |
| 199 |
> |
CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE")); |
| 200 |
> |
CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL")); |
| 201 |
> |
CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD")); |
| 202 |
> |
CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); |
| 203 |
> |
CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL")); |
| 204 |
|
CheckParameter(OrthoBoxTolerance, isPositive()); |
| 396 |
– |
CheckParameter(ThermIntDistSpringConst, isPositive()); |
| 397 |
– |
CheckParameter(ThermIntThetaSpringConst, isPositive()); |
| 398 |
– |
CheckParameter(ThermIntOmegaSpringConst, isPositive()); |
| 205 |
|
CheckParameter(DampingAlpha,isNonNegative()); |
| 206 |
|
CheckParameter(SkinThickness, isPositive()); |
| 207 |
+ |
CheckParameter(Viscosity, isNonNegative()); |
| 208 |
+ |
CheckParameter(BeadSize, isPositive()); |
| 209 |
+ |
CheckParameter(FrozenBufferRadius, isPositive()); |
| 210 |
+ |
CheckParameter(LangevinBufferRadius, isPositive()); |
| 211 |
+ |
CheckParameter(NeighborListNeighbors, isPositive()); |
| 212 |
+ |
CheckParameter(RNEMD_exchangeTime, isPositive()); |
| 213 |
+ |
CheckParameter(RNEMD_nBins, isPositive() && isEven()); |
| 214 |
+ |
CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale")); |
| 215 |
+ |
CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); |
| 216 |
+ |
CheckParameter(Alpha, isPositive()); |
| 217 |
+ |
|
| 218 |
|
|
| 219 |
< |
//@todo memory leak |
| 220 |
< |
if( have_err ) |
| 221 |
< |
return strdup( err.c_str() ); |
| 222 |
< |
|
| 223 |
< |
return NULL; |
| 219 |
> |
for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) { |
| 220 |
> |
if (!(*i)->findMoleculeStamp(moleculeStamps_)) { |
| 221 |
> |
std::ostringstream oss; |
| 222 |
> |
oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl; |
| 223 |
> |
throw OpenMDException(oss.str()); |
| 224 |
> |
} |
| 225 |
> |
} |
| 226 |
> |
} |
| 227 |
|
|
| 228 |
+ |
bool Globals::addComponent(Component* comp) { |
| 229 |
+ |
components_.push_back(comp); |
| 230 |
+ |
return true; |
| 231 |
+ |
} |
| 232 |
|
|
| 233 |
+ |
bool Globals::addZConsStamp(ZConsStamp* zcons) { |
| 234 |
+ |
zconstraints_.push_back(zcons); |
| 235 |
+ |
return true; |
| 236 |
|
} |
| 237 |
|
|
| 238 |
< |
int Globals::globalEnd( event* the_event ){ |
| 239 |
< |
|
| 240 |
< |
the_event->err_msg = checkMe(); |
| 241 |
< |
if( the_event->err_msg != NULL ) return 0; |
| 238 |
> |
bool Globals::addRestraintStamp(RestraintStamp* rest) { |
| 239 |
> |
restraints_.push_back(rest); |
| 240 |
> |
return true; |
| 241 |
> |
} |
| 242 |
|
|
| 243 |
< |
return 1; |
| 243 |
> |
bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) { |
| 244 |
> |
std::string molStampName = molStamp->getName(); |
| 245 |
> |
std::map<std::string, MoleculeStamp*>::iterator i; |
| 246 |
> |
bool ret = false; |
| 247 |
> |
i = moleculeStamps_.find(molStampName); |
| 248 |
> |
if (i == moleculeStamps_.end()) { |
| 249 |
> |
moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp)); |
| 250 |
> |
ret = true; |
| 251 |
> |
} else { |
| 252 |
> |
std::ostringstream oss; |
| 253 |
> |
oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n"; |
| 254 |
> |
throw OpenMDException(oss.str()); |
| 255 |
> |
} |
| 256 |
> |
return ret; |
| 257 |
|
} |
| 258 |
+ |
|
| 259 |
+ |
|
| 260 |
+ |
} |
