src/io/Globals.cpp

/*
 * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <string>

#include "io/Globals.hpp"
#include "io/ParamConstraint.hpp"
#include "utils/MemoryUtils.hpp"
#include "utils/simError.h"

namespace OpenMD {
Globals::Globals() {
  DefineParameter(ForceField, "forceField")
 
  DefineOptionalParameter(TargetTemp, "targetTemp");
  DefineOptionalParameter(Ensemble, "ensemble");
  DefineOptionalParameter(Dt, "dt");
  DefineOptionalParameter(RunTime, "runTime");
  DefineOptionalParameter(FinalConfig, "finalConfig");
  DefineOptionalParameter(SampleTime, "sampleTime");
  DefineOptionalParameter(ResetTime, "resetTime");
  DefineOptionalParameter(StatusTime, "statusTime");
  DefineOptionalParameter(CutoffRadius, "cutoffRadius");
  DefineOptionalParameter(SwitchingRadius, "switchingRadius");
  DefineOptionalParameter(TempSet, "tempSet");
  DefineOptionalParameter(ThermalTime, "thermalTime");
  DefineOptionalParameter(TargetPressure, "targetPressure");  
  DefineOptionalParameter(TauThermostat, "tauThermostat");
  DefineOptionalParameter(TauBarostat, "tauBarostat");
  DefineOptionalParameter(ZconsTime, "zconsTime");
  DefineOptionalParameter(ZconsTol, "zconsTol");
  DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
  DefineOptionalParameter(Seed, "seed");
  DefineOptionalParameter(Minimizer, "minimizer");
  DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
  DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
  DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
  DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
  DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
  DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
  DefineOptionalParameter(ZconsGap, "zconsGap");
  DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
  DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
  DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
  DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
  DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
  DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
  DefineOptionalParameter(SurfaceTension, "surfaceTension");
  DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
  DefineOptionalParameter(Viscosity, "viscosity");
  DefineOptionalParameter(BeadSize, "beadSize");
  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
  DefineOptionalParameter(MTM_G, "MTM_G");
  DefineOptionalParameter(MTM_Io, "MTM_Io");
  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
  DefineOptionalParameter(MTM_R, "MTM_R");
  DefineOptionalParameter(Alpha, "alpha");

  
  DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
  DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
  DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
  DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
  DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 0);
  DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);

  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
  DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
  DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");


  deprecatedKeywords_.insert("nComponents");
  deprecatedKeywords_.insert("nZconstraints");
  deprecatedKeywords_.insert("initialConfig");
  deprecatedKeywords_.insert("thermIntDistSpringConst");
  deprecatedKeywords_.insert("thermIntThetaSpringConst");
  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
  deprecatedKeywords_.insert("useSolidThermInt");  
  deprecatedKeywords_.insert("useLiquidThermInt");
    
}

Globals::~Globals() {
    MemoryUtils::deletePointers(components_);
    MemoryUtils::deletePointers(zconstraints_);
    MemoryUtils::deletePointers(restraints_);
}

void Globals::validate() {
  DataHolder::validate();

  CheckParameter(ForceField, isNotEmpty());
  CheckParameter(TargetTemp, isPositive());
  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"));
  CheckParameter(Dt, isPositive());
  CheckParameter(RunTime, isPositive());
  CheckParameter(FinalConfig, isNotEmpty());
  CheckParameter(SampleTime, isNonNegative());
  CheckParameter(ResetTime, isNonNegative());
  CheckParameter(StatusTime, isNonNegative());
  CheckParameter(CutoffRadius, isPositive());
  CheckParameter(SwitchingRadius, isNonNegative());
  CheckParameter(Dielectric, isPositive());
  CheckParameter(ThermalTime,  isNonNegative());
  CheckParameter(TauThermostat, isPositive());
  CheckParameter(TauBarostat, isPositive());
  CheckParameter(ZconsTime, isPositive());
  CheckParameter(ZconsTol, isPositive());
  CheckParameter(Seed, isPositive());
  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
  CheckParameter(MinimizerMaxIter, isPositive());
  CheckParameter(MinimizerWriteFreq, isPositive());
  CheckParameter(MinimizerStepSize, isPositive());
  CheckParameter(MinimizerFTol, isPositive());
  CheckParameter(MinimizerGTol, isPositive());
  CheckParameter(MinimizerLSTol, isPositive());
  CheckParameter(MinimizerLSMaxIter, isPositive());
  CheckParameter(ZconsGap, isPositive());
  CheckParameter(ZconsFixtime, isPositive());
  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
  CheckParameter(ThermodynamicIntegrationK, isPositive());
  CheckParameter(ForceFieldVariant, isNotEmpty());
  CheckParameter(ForceFieldFileName, isNotEmpty());
  CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); 
  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
  CheckParameter(OrthoBoxTolerance, isPositive());  
  CheckParameter(DampingAlpha,isNonNegative());
  CheckParameter(SkinThickness, isPositive());
  CheckParameter(Viscosity, isNonNegative());
  CheckParameter(BeadSize, isPositive());
  CheckParameter(FrozenBufferRadius, isPositive());
  CheckParameter(LangevinBufferRadius, isPositive());
  CheckParameter(NeighborListNeighbors, isPositive());
  CheckParameter(RNEMD_exchangeTime, isPositive());
  CheckParameter(RNEMD_nBins, isPositive() && isEven());
  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); 
  CheckParameter(Alpha, isPositive()); 

  
  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
        std::ostringstream oss;
        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
        throw OpenMDException(oss.str());           
    }
  }
}

bool Globals::addComponent(Component* comp) {
    components_.push_back(comp);
    return true;
}

bool Globals::addZConsStamp(ZConsStamp* zcons) {
    zconstraints_.push_back(zcons);
    return true;
}

bool Globals::addRestraintStamp(RestraintStamp* rest) {
    restraints_.push_back(rest);
    return true;
}

bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
    std::string molStampName = molStamp->getName();
    std::map<std::string, MoleculeStamp*>::iterator i;
    bool ret = false;
    i = moleculeStamps_.find(molStampName);
    if (i == moleculeStamps_.end()) {
        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
        ret = true;
    } else {
        std::ostringstream oss;
        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
        throw OpenMDException(oss.str());  
    }
    return ret;
}
 

}
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	14030 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	404	/*
2	chuckv	1402	* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3	gezelter	246	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	2	#include <stdlib.h>
44			#include <stdio.h>
45			#include <string.h>
46	tim	665	#include <string>
47	gezelter	2
48	tim	3	#include "io/Globals.hpp"
49	tim	816	#include "io/ParamConstraint.hpp"
50			#include "utils/MemoryUtils.hpp"
51	tim	3	#include "utils/simError.h"
52	gezelter	2
53	gezelter	1390	namespace OpenMD {
54	tim	770	Globals::Globals() {
55	tim	665	DefineParameter(ForceField, "forceField")
56
57			DefineOptionalParameter(TargetTemp, "targetTemp");
58			DefineOptionalParameter(Ensemble, "ensemble");
59			DefineOptionalParameter(Dt, "dt");
60			DefineOptionalParameter(RunTime, "runTime");
61			DefineOptionalParameter(FinalConfig, "finalConfig");
62			DefineOptionalParameter(SampleTime, "sampleTime");
63			DefineOptionalParameter(ResetTime, "resetTime");
64			DefineOptionalParameter(StatusTime, "statusTime");
65			DefineOptionalParameter(CutoffRadius, "cutoffRadius");
66			DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67			DefineOptionalParameter(TempSet, "tempSet");
68			DefineOptionalParameter(ThermalTime, "thermalTime");
69	gezelter	1126	DefineOptionalParameter(TargetPressure, "targetPressure");
70	tim	665	DefineOptionalParameter(TauThermostat, "tauThermostat");
71			DefineOptionalParameter(TauBarostat, "tauBarostat");
72			DefineOptionalParameter(ZconsTime, "zconsTime");
73			DefineOptionalParameter(ZconsTol, "zconsTol");
74			DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
75			DefineOptionalParameter(Seed, "seed");
76			DefineOptionalParameter(Minimizer, "minimizer");
77			DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
78	gezelter	1423	DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
79	tim	665	DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
80			DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
81			DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
82			DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
83			DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
84			DefineOptionalParameter(ZconsGap, "zconsGap");
85			DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
86			DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
87			DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
88			DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
89			DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
90			DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
91	gezelter	1078	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
92	tim	665	DefineOptionalParameter(SurfaceTension, "surfaceTension");
93			DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
94	gezelter	1291	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
95			DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
96	chrisfen	726	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97	tim	895	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
98	tim	906	DefineOptionalParameter(Viscosity, "viscosity");
99			DefineOptionalParameter(BeadSize, "beadSize");
100	gezelter	945	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101			DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102	chuckv	1095	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
103	chuckv	1306	DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
104	gezelter	1528	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
105	chuckv	1306	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	chuckv	1402	DefineOptionalParameter(Alpha, "alpha");
111	gezelter	1327
112	chuckv	1147
113	tim	665	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
114	gezelter	1126	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
115	tim	665	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
116			DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
117			DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
118	gezelter	1528	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
119	gezelter	1078	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
120	gezelter	1528	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
121	tim	665	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
122	chrisfen	726	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
123	gezelter	1629	DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 0);
124	tim	665	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
125	tim	681	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME\|TOTAL_ENERGY\|POTENTIAL_ENERGY\|KINETIC_ENERGY\|TEMPERATURE\|PRESSURE\|VOLUME\|CONSERVED_QUANTITY");
126	gezelter	945	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
127	chrisfen	998	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128	tim	681
129	gezelter	1327	DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
130	skuang	1367	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
131	skuang	1341	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
132	skuang	1367	DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
133			DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
134			DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
135	gezelter	1331	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
136	gezelter	1629	DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
137			DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
138	cli2	1360	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
139	gezelter	1354	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
140	cli2	1360	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
141	chuckv	1402	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
142	gezelter	1327
143	cli2	1360
144	gezelter	1528
145	gezelter	1078	deprecatedKeywords_.insert("nComponents");
146			deprecatedKeywords_.insert("nZconstraints");
147			deprecatedKeywords_.insert("initialConfig");
148	cli2	1360	deprecatedKeywords_.insert("thermIntDistSpringConst");
149			deprecatedKeywords_.insert("thermIntThetaSpringConst");
150			deprecatedKeywords_.insert("thermIntOmegaSpringConst");
151			deprecatedKeywords_.insert("useSolidThermInt");
152			deprecatedKeywords_.insert("useLiquidThermInt");
153	gezelter	2
154			}
155
156	tim	770	Globals::~Globals() {
157	tim	816	MemoryUtils::deletePointers(components_);
158			MemoryUtils::deletePointers(zconstraints_);
159	cli2	1360	MemoryUtils::deletePointers(restraints_);
160	gezelter	2	}
161
162	tim	770	void Globals::validate() {
163			DataHolder::validate();
164	gezelter	2
165	tim	672	CheckParameter(ForceField, isNotEmpty());
166			CheckParameter(TargetTemp, isPositive());
167	gezelter	1629	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"));
168	tim	672	CheckParameter(Dt, isPositive());
169			CheckParameter(RunTime, isPositive());
170			CheckParameter(FinalConfig, isNotEmpty());
171			CheckParameter(SampleTime, isNonNegative());
172			CheckParameter(ResetTime, isNonNegative());
173			CheckParameter(StatusTime, isNonNegative());
174			CheckParameter(CutoffRadius, isPositive());
175			CheckParameter(SwitchingRadius, isNonNegative());
176			CheckParameter(Dielectric, isPositive());
177			CheckParameter(ThermalTime, isNonNegative());
178			CheckParameter(TauThermostat, isPositive());
179			CheckParameter(TauBarostat, isPositive());
180			CheckParameter(ZconsTime, isPositive());
181			CheckParameter(ZconsTol, isPositive());
182			CheckParameter(Seed, isPositive());
183	tim	850	CheckParameter(Minimizer, isEqualIgnoreCase("SD") \|\| isEqualIgnoreCase("CG"));
184	tim	672	CheckParameter(MinimizerMaxIter, isPositive());
185	gezelter	1423	CheckParameter(MinimizerWriteFreq, isPositive());
186	tim	672	CheckParameter(MinimizerStepSize, isPositive());
187			CheckParameter(MinimizerFTol, isPositive());
188			CheckParameter(MinimizerGTol, isPositive());
189			CheckParameter(MinimizerLSTol, isPositive());
190			CheckParameter(MinimizerLSMaxIter, isPositive());
191			CheckParameter(ZconsGap, isPositive());
192			CheckParameter(ZconsFixtime, isPositive());
193	chrisfen	979	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
194	tim	672	CheckParameter(ThermodynamicIntegrationK, isPositive());
195			CheckParameter(ForceFieldVariant, isNotEmpty());
196			CheckParameter(ForceFieldFileName, isNotEmpty());
197	gezelter	1528	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") \|\| isEqualIgnoreCase("SWITCHED") \|\| isEqualIgnoreCase("SHIFTED_POTENTIAL") \|\| isEqualIgnoreCase("SHIFTED_FORCE"));
198	gezelter	1576	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") \|\| isEqualIgnoreCase("MAX") \|\| isEqualIgnoreCase("TRADITIONAL"));
199	gezelter	1616	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") \|\| isEqualIgnoreCase("HARD") \|\| isEqualIgnoreCase("SWITCHED") \|\| isEqualIgnoreCase("SHIFTED_POTENTIAL") \|\| isEqualIgnoreCase("SHIFTED_FORCE") \|\| isEqualIgnoreCase("REACTION_FIELD"));
200	tim	850	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") \|\| isEqualIgnoreCase("DAMPED"));
201			CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") \|\| isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
202	tim	672	CheckParameter(OrthoBoxTolerance, isPositive());
203	chrisfen	716	CheckParameter(DampingAlpha,isNonNegative());
204	tim	672	CheckParameter(SkinThickness, isPositive());
205	gezelter	945	CheckParameter(Viscosity, isNonNegative());
206			CheckParameter(BeadSize, isPositive());
207			CheckParameter(FrozenBufferRadius, isPositive());
208			CheckParameter(LangevinBufferRadius, isPositive());
209	chuckv	1095	CheckParameter(NeighborListNeighbors, isPositive());
210	skuang	1367	CheckParameter(RNEMD_exchangeTime, isPositive());
211	skuang	1341	CheckParameter(RNEMD_nBins, isPositive() && isEven());
212	skuang	1367	CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") \|\| isEqualIgnoreCase("KineticScale") \|\| isEqualIgnoreCase("Px") \|\| isEqualIgnoreCase("Py") \|\| isEqualIgnoreCase("Pz") \|\| isEqualIgnoreCase("PxScale") \|\| isEqualIgnoreCase("PyScale") \|\| isEqualIgnoreCase("PzScale"));
213	chuckv	1402	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") \|\| isEqualIgnoreCase("AlphaShape"));
214			CheckParameter(Alpha, isPositive());
215	chuckv	1095
216	chuckv	1402
217	tim	770	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
218			if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
219	tim	845	std::ostringstream oss;
220			oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
221	gezelter	1390	throw OpenMDException(oss.str());
222	tim	770	}
223			}
224			}
225	gezelter	1613
226	tim	770	bool Globals::addComponent(Component* comp) {
227			components_.push_back(comp);
228			return true;
229			}
230	gezelter	2
231	tim	770	bool Globals::addZConsStamp(ZConsStamp* zcons) {
232			zconstraints_.push_back(zcons);
233			return true;
234	gezelter	2	}
235
236	cli2	1360	bool Globals::addRestraintStamp(RestraintStamp* rest) {
237			restraints_.push_back(rest);
238			return true;
239			}
240
241	tim	770	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
242			std::string molStampName = molStamp->getName();
243			std::map<std::string, MoleculeStamp*>::iterator i;
244			bool ret = false;
245			i = moleculeStamps_.find(molStampName);
246			if (i == moleculeStamps_.end()) {
247			moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
248			ret = true;
249			} else {
250	tim	845	std::ostringstream oss;
251			oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
252	gezelter	1390	throw OpenMDException(oss.str());
253	tim	770	}
254			return ret;
255	gezelter	2	}
256	tim	770
257
258			}