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gezelter |
2088 |
/* |
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gezelter |
1930 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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gezelter |
1490 |
#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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tim |
2364 |
#include <string> |
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gezelter |
1490 |
|
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tim |
1492 |
#include "io/Globals.hpp" |
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#include "utils/simError.h" |
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gezelter |
1490 |
#ifdef IS_MPI |
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tim |
1492 |
#include "io/mpiBASS.h" |
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gezelter |
1490 |
#endif // is_mpi |
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tim |
2371 |
#include "io/ParamConstraint.hpp" |
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gezelter |
1490 |
|
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Globals::Globals(){ |
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tim |
2364 |
|
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DefineParameter(ForceField, "forceField") |
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DefineParameter(NComponents, "nComponents") |
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DefineOptionalParameter(TargetTemp, "targetTemp"); |
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DefineOptionalParameter(Ensemble, "ensemble"); |
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DefineOptionalParameter(Dt, "dt"); |
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DefineOptionalParameter(RunTime, "runTime"); |
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DefineOptionalParameter(InitialConfig, "initialConfig"); |
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DefineOptionalParameter(FinalConfig, "finalConfig"); |
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DefineOptionalParameter(NMol, "nMol"); |
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DefineOptionalParameter(Density, "density"); |
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DefineOptionalParameter(Box, "box"); |
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DefineOptionalParameter(BoxX, "boxX"); |
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DefineOptionalParameter(BoxY, "boxY"); |
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DefineOptionalParameter(BoxZ, "boxZ"); |
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DefineOptionalParameter(SampleTime, "sampleTime"); |
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DefineOptionalParameter(ResetTime, "resetTime"); |
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DefineOptionalParameter(StatusTime, "statusTime"); |
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DefineOptionalParameter(CutoffRadius, "cutoffRadius"); |
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DefineOptionalParameter(SwitchingRadius, "switchingRadius"); |
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DefineOptionalParameter(Dielectric, "dielectric"); |
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DefineOptionalParameter(TempSet, "tempSet"); |
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DefineOptionalParameter(ThermalTime, "thermalTime"); |
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DefineOptionalParameter(TargetPressure, "targetPressure"); |
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DefineOptionalParameter(TauThermostat, "tauThermostat"); |
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DefineOptionalParameter(TauBarostat, "tauBarostat"); |
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DefineOptionalParameter(ZconsTime, "zconsTime"); |
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DefineOptionalParameter(NZconstraints, "nZconstraints"); |
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DefineOptionalParameter(ZconsTol, "zconsTol"); |
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DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy"); |
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DefineOptionalParameter(Seed, "seed"); |
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DefineOptionalParameter(Minimizer, "minimizer"); |
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DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter"); |
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DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq"); |
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DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize"); |
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DefineOptionalParameter(MinimizerFTol, "minimizerFTol"); |
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DefineOptionalParameter(MinimizerGTol, "minimizerGTol"); |
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DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol"); |
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DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter"); |
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DefineOptionalParameter(ZconsGap, "zconsGap"); |
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DefineOptionalParameter(ZconsFixtime, "zconsFixtime"); |
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DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD"); |
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DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda"); |
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DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK"); |
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DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant"); |
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DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName"); |
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DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst"); |
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DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst"); |
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DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst"); |
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DefineOptionalParameter(SurfaceTension, "surfaceTension"); |
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DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); |
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DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod"); |
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chrisfen |
2415 |
DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod"); |
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tim |
2364 |
DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); |
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chrisfen |
2425 |
DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); |
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tim |
2364 |
DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard"); |
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DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); |
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DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); |
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DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false); |
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DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6); |
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DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false); |
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DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false); |
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chrisfen |
2365 |
DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0); |
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DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5); |
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DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5); |
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chrisfen |
2415 |
DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2); |
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tim |
2364 |
DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); |
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chrisfen |
2425 |
DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); |
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tim |
2364 |
DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); |
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tim |
2380 |
DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); |
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tim |
2364 |
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gezelter |
1490 |
} |
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tim |
2364 |
int Globals::globalAssign( event* the_event ){ |
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tim |
2373 |
char errorMessage[65535]; |
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tim |
2364 |
int key; |
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interface_assign_type the_type = the_event->evt.asmt.asmt_type; |
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char* lhs = the_event->evt.asmt.lhs; |
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std::string keyword(lhs); |
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chrisfen |
2101 |
|
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tim |
2372 |
bool result = false; |
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gezelter |
1490 |
|
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tim |
2373 |
/**@todo fix memory leak */ |
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tim |
2364 |
ParamMap::iterator i =parameters_.find(keyword); |
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if (i != parameters_.end()) { |
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if( the_type == STRING ){ |
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result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval)); |
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if (!result ) { |
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tim |
2373 |
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); |
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the_event->err_msg = strdup(errorMessage); |
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tim |
2364 |
} |
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} else if( the_type == DOUBLE ){ |
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result = i->second->setData(the_event->evt.asmt.rhs.dval); |
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if (!result ) |
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tim |
2373 |
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 ); |
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the_event->err_msg = strdup(errorMessage); |
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tim |
2364 |
} |
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else if (the_type == INT ){ |
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result = i->second->setData(the_event->evt.asmt.rhs.ival); |
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if (!result ) |
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tim |
2373 |
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 ); |
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the_event->err_msg = strdup(errorMessage); |
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tim |
2364 |
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} else { |
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tim |
2373 |
sprintf(errorMessage, "Internal error of parser\n"); |
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the_event->err_msg = strdup(errorMessage); |
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tim |
2364 |
} |
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tim |
2373 |
} else { |
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sprintf(errorMessage, "%s is an unrecognized keyword\n", keyword.c_str() ); |
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the_event->err_msg = strdup(errorMessage); |
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tim |
2364 |
} |
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if (keyword == "nComponents" && getNComponents() > 0) { |
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components = new Component*[getNComponents()]; |
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}else if (keyword == "nZconstraints" && getNZconstraints() > 0) { |
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zConstraints = new ZconStamp*[getNZconstraints()]; |
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} |
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gezelter |
1490 |
|
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tim |
2364 |
return result; |
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gezelter |
1490 |
} |
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int Globals::newComponent( event* the_event ){ |
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current_component = new Component; |
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int index = the_event->evt.blk_index; |
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char err[200]; |
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tim |
2364 |
if( haveNComponents() && index < getNComponents() ) |
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gezelter |
1490 |
components[index] = current_component; |
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else{ |
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tim |
2364 |
if( haveNComponents() ){ |
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gezelter |
1490 |
sprintf( err, "meta-data parsing error: %d out of nComponents range", |
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index ); |
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the_event->err_msg = strdup( err ); |
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return 0; |
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} |
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else{ |
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the_event->err_msg = strdup("meta-data parsing error: nComponents not given before" |
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" first component declaration." ); |
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return 0; |
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} |
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} |
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return 1; |
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} |
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int Globals::componentAssign( event* the_event ){ |
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switch( the_event->evt.asmt.asmt_type ){ |
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case STRING: |
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return current_component->assignString( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.sval, |
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&(the_event->err_msg)); |
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break; |
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case DOUBLE: |
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return current_component->assignDouble( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.dval, |
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&(the_event->err_msg)); |
| 221 |
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break; |
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case INT: |
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return current_component->assignInt( the_event->evt.asmt.lhs, |
| 225 |
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the_event->evt.asmt.rhs.ival, |
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&(the_event->err_msg)); |
| 227 |
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break; |
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default: |
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the_event->err_msg = strdup( "Globals error. Invalid component" |
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" assignment type" ); |
| 232 |
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return 0; |
| 233 |
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break; |
| 234 |
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} |
| 235 |
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return 0; |
| 236 |
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} |
| 237 |
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| 238 |
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int Globals::componentEnd( event* the_event ){ |
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| 240 |
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the_event->err_msg = current_component->checkMe(); |
| 241 |
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if( the_event->err_msg != NULL ) return 0; |
| 242 |
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| 243 |
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return 1; |
| 244 |
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} |
| 245 |
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| 246 |
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int Globals::newZconstraint( event* the_event ){ |
| 247 |
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| 248 |
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| 249 |
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int index = the_event->evt.blk_index; |
| 250 |
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char err[200]; |
| 251 |
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current_zConstraint = new ZconStamp( index ); |
| 252 |
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| 253 |
tim |
2364 |
if( haveNZconstraints() && index < getNZconstraints() ) |
| 254 |
gezelter |
1490 |
zConstraints[index] = current_zConstraint; |
| 255 |
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else{ |
| 256 |
tim |
2364 |
if( haveNZconstraints() ){ |
| 257 |
gezelter |
1490 |
sprintf( err, "meta-data parsing error: %d out of nZconstraints range", |
| 258 |
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index ); |
| 259 |
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the_event->err_msg = strdup( err ); |
| 260 |
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return 0; |
| 261 |
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} |
| 262 |
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else{ |
| 263 |
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the_event->err_msg = strdup("meta-data parsing error: nZconstraints" |
| 264 |
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" not given before" |
| 265 |
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" first zConstraint declaration." ); |
| 266 |
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return 0; |
| 267 |
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} |
| 268 |
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} |
| 269 |
tim |
2364 |
|
| 270 |
gezelter |
1490 |
return 1; |
| 271 |
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} |
| 272 |
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| 273 |
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| 274 |
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| 275 |
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int Globals::zConstraintAssign( event* the_event ){ |
| 276 |
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| 277 |
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switch( the_event->evt.asmt.asmt_type ){ |
| 278 |
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| 279 |
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case STRING: |
| 280 |
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return current_zConstraint->assignString( the_event->evt.asmt.lhs, |
| 281 |
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the_event->evt.asmt.rhs.sval, |
| 282 |
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&(the_event->err_msg)); |
| 283 |
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break; |
| 284 |
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| 285 |
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case DOUBLE: |
| 286 |
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return current_zConstraint->assignDouble( the_event->evt.asmt.lhs, |
| 287 |
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the_event->evt.asmt.rhs.dval, |
| 288 |
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&(the_event->err_msg)); |
| 289 |
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break; |
| 290 |
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| 291 |
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case INT: |
| 292 |
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return current_zConstraint->assignInt( the_event->evt.asmt.lhs, |
| 293 |
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the_event->evt.asmt.rhs.ival, |
| 294 |
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&(the_event->err_msg)); |
| 295 |
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break; |
| 296 |
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| 297 |
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default: |
| 298 |
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the_event->err_msg = strdup( "Globals error. Invalid zConstraint" |
| 299 |
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" assignment type" ); |
| 300 |
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return 0; |
| 301 |
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break; |
| 302 |
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} |
| 303 |
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return 0; |
| 304 |
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} |
| 305 |
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| 306 |
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int Globals::zConstraintEnd( event* the_event ){ |
| 307 |
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| 308 |
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the_event->err_msg = current_zConstraint->checkMe(); |
| 309 |
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if( the_event->err_msg != NULL ) return 0; |
| 310 |
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| 311 |
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return 1; |
| 312 |
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} |
| 313 |
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|
| 314 |
tim |
2364 |
char* Globals::checkMe( void ){ |
| 315 |
tim |
2109 |
|
| 316 |
gezelter |
1490 |
|
| 317 |
tim |
2364 |
std::string err("The following required keywords are missing:\n"); |
| 318 |
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short int have_err = 0; |
| 319 |
gezelter |
1490 |
|
| 320 |
tim |
2364 |
ParamMap::iterator i; |
| 321 |
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for (i = parameters_.begin(); i != parameters_.end(); ++i) { |
| 322 |
|
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if (!i->second->isOptional() && i->second->empty()) { |
| 323 |
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err += i->second->getKeyword() + "\n"; |
| 324 |
gezelter |
1490 |
} |
| 325 |
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} |
| 326 |
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| 327 |
tim |
2371 |
CheckParameter(ForceField, isNotEmpty()); |
| 328 |
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CheckParameter(NComponents,isPositive()); |
| 329 |
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CheckParameter(TargetTemp, isPositive()); |
| 330 |
chrisfen |
2425 |
CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || |
| 331 |
|
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isEqualIgnoreCase(std::string("NVT")) || |
| 332 |
|
|
isEqualIgnoreCase(std::string("NPTi")) || |
| 333 |
|
|
isEqualIgnoreCase(std::string("NPTf")) || |
| 334 |
|
|
isEqualIgnoreCase(std::string("NPTxyz")) ); |
| 335 |
tim |
2371 |
CheckParameter(Dt, isPositive()); |
| 336 |
|
|
CheckParameter(RunTime, isPositive()); |
| 337 |
|
|
CheckParameter(InitialConfig, isNotEmpty()); |
| 338 |
|
|
CheckParameter(FinalConfig, isNotEmpty()); |
| 339 |
|
|
CheckParameter(NMol, isPositive()); |
| 340 |
|
|
CheckParameter(Density, isPositive()); |
| 341 |
|
|
CheckParameter(Box, isPositive()); |
| 342 |
|
|
CheckParameter(BoxX, isPositive()); |
| 343 |
|
|
CheckParameter(BoxY, isPositive()); |
| 344 |
|
|
CheckParameter(BoxZ, isPositive()); |
| 345 |
|
|
CheckParameter(SampleTime, isNonNegative()); |
| 346 |
|
|
CheckParameter(ResetTime, isNonNegative()); |
| 347 |
|
|
CheckParameter(StatusTime, isNonNegative()); |
| 348 |
|
|
CheckParameter(CutoffRadius, isPositive()); |
| 349 |
|
|
CheckParameter(SwitchingRadius, isNonNegative()); |
| 350 |
|
|
CheckParameter(Dielectric, isPositive()); |
| 351 |
|
|
CheckParameter(ThermalTime, isNonNegative()); |
| 352 |
|
|
CheckParameter(TargetPressure, isPositive()); |
| 353 |
|
|
CheckParameter(TauThermostat, isPositive()); |
| 354 |
|
|
CheckParameter(TauBarostat, isPositive()); |
| 355 |
|
|
CheckParameter(ZconsTime, isPositive()); |
| 356 |
|
|
CheckParameter(NZconstraints, isPositive()); |
| 357 |
|
|
CheckParameter(ZconsTol, isPositive()); |
| 358 |
|
|
//CheckParameter(ZconsForcePolicy,); |
| 359 |
|
|
CheckParameter(Seed, isPositive()); |
| 360 |
chrisfen |
2425 |
CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || |
| 361 |
|
|
isEqualIgnoreCase(std::string("CG"))); |
| 362 |
tim |
2371 |
CheckParameter(MinimizerMaxIter, isPositive()); |
| 363 |
|
|
CheckParameter(MinimizerWriteFrq, isPositive()); |
| 364 |
|
|
CheckParameter(MinimizerStepSize, isPositive()); |
| 365 |
|
|
CheckParameter(MinimizerFTol, isPositive()); |
| 366 |
|
|
CheckParameter(MinimizerGTol, isPositive()); |
| 367 |
|
|
CheckParameter(MinimizerLSTol, isPositive()); |
| 368 |
|
|
CheckParameter(MinimizerLSMaxIter, isPositive()); |
| 369 |
|
|
CheckParameter(ZconsGap, isPositive()); |
| 370 |
|
|
CheckParameter(ZconsFixtime, isPositive()); |
| 371 |
|
|
CheckParameter(ThermodynamicIntegrationLambda, isPositive()); |
| 372 |
|
|
CheckParameter(ThermodynamicIntegrationK, isPositive()); |
| 373 |
|
|
CheckParameter(ForceFieldVariant, isNotEmpty()); |
| 374 |
|
|
CheckParameter(ForceFieldFileName, isNotEmpty()); |
| 375 |
|
|
CheckParameter(ThermIntDistSpringConst, isPositive()); |
| 376 |
|
|
CheckParameter(ThermIntThetaSpringConst, isPositive()); |
| 377 |
|
|
CheckParameter(ThermIntOmegaSpringConst, isPositive()); |
| 378 |
|
|
CheckParameter(SurfaceTension, isPositive()); |
| 379 |
chrisfen |
2425 |
CheckParameter(ElectrostaticSummationMethod, |
| 380 |
|
|
isEqualIgnoreCase(std::string("NONE")) || |
| 381 |
|
|
isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || |
| 382 |
|
|
isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || |
| 383 |
|
|
isEqualIgnoreCase(std::string("REACTION_FIELD"))); |
| 384 |
|
|
CheckParameter(ElectrostaticScreeningMethod, |
| 385 |
|
|
isEqualIgnoreCase(std::string("UNDAMPED")) || |
| 386 |
|
|
isEqualIgnoreCase(std::string("DAMPED"))); |
| 387 |
|
|
CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || |
| 388 |
|
|
isEqualIgnoreCase(std::string("MAX")) || |
| 389 |
|
|
isEqualIgnoreCase(std::string("TRADITIONAL"))); |
| 390 |
|
|
CheckParameter(SwitchingFunctionType, |
| 391 |
|
|
isEqualIgnoreCase(std::string("CUBIC")) || |
| 392 |
|
|
isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL"))); |
| 393 |
tim |
2371 |
//CheckParameter(StatFileFormat,); |
| 394 |
|
|
//CheckParameter(MixingRule,); |
| 395 |
|
|
CheckParameter(OrthoBoxTolerance, isPositive()); |
| 396 |
|
|
CheckParameter(ThermIntDistSpringConst, isPositive()); |
| 397 |
|
|
CheckParameter(ThermIntThetaSpringConst, isPositive()); |
| 398 |
|
|
CheckParameter(ThermIntOmegaSpringConst, isPositive()); |
| 399 |
chrisfen |
2415 |
CheckParameter(DampingAlpha,isNonNegative()); |
| 400 |
tim |
2371 |
CheckParameter(SkinThickness, isPositive()); |
| 401 |
|
|
|
| 402 |
tim |
2364 |
//@todo memory leak |
| 403 |
|
|
if( have_err ) |
| 404 |
|
|
return strdup( err.c_str() ); |
| 405 |
gezelter |
1490 |
|
| 406 |
tim |
2364 |
return NULL; |
| 407 |
gezelter |
1490 |
|
| 408 |
|
|
|
| 409 |
|
|
} |
| 410 |
|
|
|
| 411 |
|
|
int Globals::globalEnd( event* the_event ){ |
| 412 |
|
|
|
| 413 |
|
|
the_event->err_msg = checkMe(); |
| 414 |
|
|
if( the_event->err_msg != NULL ) return 0; |
| 415 |
|
|
|
| 416 |
|
|
return 1; |
| 417 |
|
|
} |
