src/io/Globals.cpp

/*
 * Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#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 oopse {
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(MinimizerWriteFrq, "minimizerWriteFrq");
  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(ThermIntDistSpringConst, "thermIntDistSpringConst");
  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
  DefineOptionalParameter(SurfaceTension, "surfaceTension");
  DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
  DefineOptionalParameter(Viscosity, "viscosity");
  DefineOptionalParameter(BeadSize, "beadSize");
  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
  
  
  DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
  DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
  DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
  DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 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);

  deprecatedKeywords_.insert("nComponents");
  deprecatedKeywords_.insert("nZconstraints");
  deprecatedKeywords_.insert("initialConfig");
    
}

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

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

  CheckParameter(ForceField, isNotEmpty());
  CheckParameter(TargetTemp, isPositive());
  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT"));
  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(MinimizerWriteFrq, 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(ThermIntDistSpringConst, isPositive());
  CheckParameter(ThermIntThetaSpringConst, isPositive());
  CheckParameter(ThermIntOmegaSpringConst, isPositive());
  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); 
  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
  //CheckParameter(StatFileFormat,);     
  CheckParameter(OrthoBoxTolerance, isPositive());  
  CheckParameter(ThermIntDistSpringConst, isPositive());
  CheckParameter(ThermIntThetaSpringConst, isPositive());
  CheckParameter(ThermIntOmegaSpringConst, isPositive());
  CheckParameter(DampingAlpha,isNonNegative());
  CheckParameter(SkinThickness, isPositive());
  CheckParameter(Viscosity, isNonNegative());
  CheckParameter(BeadSize, isPositive());
  CheckParameter(FrozenBufferRadius, isPositive());
  CheckParameter(LangevinBufferRadius, isPositive());
  CheckParameter(NeighborListNeighbors, 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 OOPSEException(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::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 OOPSEException(oss.str());  
    }
    return ret;
}
 

}
Revision:	1291
Committed:	Thu Sep 11 19:40:59 2008 UTC (16 years, 7 months ago) by gezelter
File size:	12056 byte(s)
Log Message:	Added some logic to print out a special pair distance as a column in the stat file. To use this feature, use taggedAtomPair = "0, 10" and printTaggedPairDistance = "true" in the md file. Then, the distance between integrableObjects 0 and 10 will be computed and printed in the stat file on each statWrite.
#	User	Rev	Content
1	gezelter	404	/*
2	gezelter	246	* Copyright (c) 2005 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	gezelter	2	#include <stdlib.h>
43			#include <stdio.h>
44			#include <string.h>
45	tim	665	#include <string>
46	gezelter	2
47	tim	3	#include "io/Globals.hpp"
48	tim	816	#include "io/ParamConstraint.hpp"
49			#include "utils/MemoryUtils.hpp"
50	tim	3	#include "utils/simError.h"
51	gezelter	2
52	tim	770	namespace oopse {
53			Globals::Globals() {
54	tim	665	DefineParameter(ForceField, "forceField")
55
56			DefineOptionalParameter(TargetTemp, "targetTemp");
57			DefineOptionalParameter(Ensemble, "ensemble");
58			DefineOptionalParameter(Dt, "dt");
59			DefineOptionalParameter(RunTime, "runTime");
60			DefineOptionalParameter(FinalConfig, "finalConfig");
61			DefineOptionalParameter(SampleTime, "sampleTime");
62			DefineOptionalParameter(ResetTime, "resetTime");
63			DefineOptionalParameter(StatusTime, "statusTime");
64			DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65			DefineOptionalParameter(SwitchingRadius, "switchingRadius");
66			DefineOptionalParameter(TempSet, "tempSet");
67			DefineOptionalParameter(ThermalTime, "thermalTime");
68	gezelter	1126	DefineOptionalParameter(TargetPressure, "targetPressure");
69	tim	665	DefineOptionalParameter(TauThermostat, "tauThermostat");
70			DefineOptionalParameter(TauBarostat, "tauBarostat");
71			DefineOptionalParameter(ZconsTime, "zconsTime");
72			DefineOptionalParameter(ZconsTol, "zconsTol");
73			DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74			DefineOptionalParameter(Seed, "seed");
75			DefineOptionalParameter(Minimizer, "minimizer");
76			DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77			DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
78			DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79			DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80			DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
81			DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
82			DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
83			DefineOptionalParameter(ZconsGap, "zconsGap");
84			DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
85			DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
86			DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
87			DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88			DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89			DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90	gezelter	1078	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91	tim	665	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92			DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93			DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
94			DefineOptionalParameter(SurfaceTension, "surfaceTension");
95			DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96	gezelter	1291	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
97			DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98	tim	665	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99	chrisfen	726	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
100	tim	895	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
101	tim	906	DefineOptionalParameter(Viscosity, "viscosity");
102			DefineOptionalParameter(BeadSize, "beadSize");
103	gezelter	945	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104			DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105	chuckv	1095	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
106	tim	906
107	chuckv	1147
108	tim	665	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
109	gezelter	1126	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
110	tim	665	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
111			DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
112			DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
113			DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
114			DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
115	chrisfen	666	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
116			DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
117			DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
118	gezelter	1078	DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
119			DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
120	chrisfen	1050	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
121	tim	665	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
122	chrisfen	726	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
123	tim	665	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
124	tim	681	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME\|TOTAL_ENERGY\|POTENTIAL_ENERGY\|KINETIC_ENERGY\|TEMPERATURE\|PRESSURE\|VOLUME\|CONSERVED_QUANTITY");
125	gezelter	945	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
126	chrisfen	998	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
127	tim	681
128	gezelter	1078	deprecatedKeywords_.insert("nComponents");
129			deprecatedKeywords_.insert("nZconstraints");
130			deprecatedKeywords_.insert("initialConfig");
131	gezelter	2
132			}
133
134	tim	770	Globals::~Globals() {
135	tim	816	MemoryUtils::deletePointers(components_);
136			MemoryUtils::deletePointers(zconstraints_);
137	gezelter	2	}
138
139	tim	770	void Globals::validate() {
140			DataHolder::validate();
141	gezelter	2
142	tim	672	CheckParameter(ForceField, isNotEmpty());
143			CheckParameter(TargetTemp, isPositive());
144	gezelter	1032	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") \|\| isEqualIgnoreCase("NVT") \|\| isEqualIgnoreCase("NPTi") \|\| isEqualIgnoreCase("NPTf") \|\| isEqualIgnoreCase("NPTxyz") \|\| isEqualIgnoreCase("NPAT") \|\| isEqualIgnoreCase("LANGEVINDYNAMICS") \|\| isEqualIgnoreCase("LD") \|\| isEqualIgnoreCase("NPRT") \|\| isEqualIgnoreCase("NPGT") \|\| isEqualIgnoreCase("NGammaT") \|\| isEqualIgnoreCase("NGT"));
145	tim	672	CheckParameter(Dt, isPositive());
146			CheckParameter(RunTime, isPositive());
147			CheckParameter(FinalConfig, isNotEmpty());
148			CheckParameter(SampleTime, isNonNegative());
149			CheckParameter(ResetTime, isNonNegative());
150			CheckParameter(StatusTime, isNonNegative());
151			CheckParameter(CutoffRadius, isPositive());
152			CheckParameter(SwitchingRadius, isNonNegative());
153			CheckParameter(Dielectric, isPositive());
154			CheckParameter(ThermalTime, isNonNegative());
155			CheckParameter(TauThermostat, isPositive());
156			CheckParameter(TauBarostat, isPositive());
157			CheckParameter(ZconsTime, isPositive());
158			CheckParameter(ZconsTol, isPositive());
159			CheckParameter(Seed, isPositive());
160	tim	850	CheckParameter(Minimizer, isEqualIgnoreCase("SD") \|\| isEqualIgnoreCase("CG"));
161	tim	672	CheckParameter(MinimizerMaxIter, isPositive());
162			CheckParameter(MinimizerWriteFrq, isPositive());
163			CheckParameter(MinimizerStepSize, isPositive());
164			CheckParameter(MinimizerFTol, isPositive());
165			CheckParameter(MinimizerGTol, isPositive());
166			CheckParameter(MinimizerLSTol, isPositive());
167			CheckParameter(MinimizerLSMaxIter, isPositive());
168			CheckParameter(ZconsGap, isPositive());
169			CheckParameter(ZconsFixtime, isPositive());
170	chrisfen	979	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
171	tim	672	CheckParameter(ThermodynamicIntegrationK, isPositive());
172			CheckParameter(ForceFieldVariant, isNotEmpty());
173			CheckParameter(ForceFieldFileName, isNotEmpty());
174			CheckParameter(ThermIntDistSpringConst, isPositive());
175			CheckParameter(ThermIntThetaSpringConst, isPositive());
176			CheckParameter(ThermIntOmegaSpringConst, isPositive());
177	tim	850	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") \|\| isEqualIgnoreCase("SHIFTED_POTENTIAL") \|\| isEqualIgnoreCase("SHIFTED_FORCE") \|\| isEqualIgnoreCase("REACTION_FIELD"));
178			CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") \|\| isEqualIgnoreCase("DAMPED"));
179			CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") \|\| isEqualIgnoreCase("MAX") \|\| isEqualIgnoreCase("TRADITIONAL"));
180			CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") \|\| isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
181	tim	672	//CheckParameter(StatFileFormat,);
182			CheckParameter(OrthoBoxTolerance, isPositive());
183			CheckParameter(ThermIntDistSpringConst, isPositive());
184			CheckParameter(ThermIntThetaSpringConst, isPositive());
185			CheckParameter(ThermIntOmegaSpringConst, isPositive());
186	chrisfen	716	CheckParameter(DampingAlpha,isNonNegative());
187	tim	672	CheckParameter(SkinThickness, isPositive());
188	gezelter	945	CheckParameter(Viscosity, isNonNegative());
189			CheckParameter(BeadSize, isPositive());
190			CheckParameter(FrozenBufferRadius, isPositive());
191			CheckParameter(LangevinBufferRadius, isPositive());
192	chuckv	1095	CheckParameter(NeighborListNeighbors, isPositive());
193
194	tim	770	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
195			if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
196	tim	845	std::ostringstream oss;
197			oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
198			throw OOPSEException(oss.str());
199	tim	770	}
200			}
201			}
202
203			bool Globals::addComponent(Component* comp) {
204			components_.push_back(comp);
205			return true;
206			}
207	gezelter	2
208	tim	770	bool Globals::addZConsStamp(ZConsStamp* zcons) {
209			zconstraints_.push_back(zcons);
210			return true;
211	gezelter	2	}
212
213	tim	770	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
214			std::string molStampName = molStamp->getName();
215			std::map<std::string, MoleculeStamp*>::iterator i;
216			bool ret = false;
217			i = moleculeStamps_.find(molStampName);
218			if (i == moleculeStamps_.end()) {
219			moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
220			ret = true;
221			} else {
222	tim	845	std::ostringstream oss;
223			oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
224			throw OOPSEException(oss.str());
225	tim	770	}
226			return ret;
227	gezelter	2	}
228	tim	770
229
230			}