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(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(ThermalConductivity, "thermalConductivity");
  DefineOptionalParameter(ThermalLength, "thermalLength");
  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
  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");
  

  DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
  DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
  DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
  DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
  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);

  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);


  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("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || 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(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(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(DampingAlpha,isNonNegative());
  CheckParameter(SkinThickness, isPositive());
  CheckParameter(Viscosity, isNonNegative());
  CheckParameter(ThermalConductivity, isNonNegative());
  CheckParameter(ThermalLength, isNonNegative());
  CheckParameter(BeadSize, isPositive());
  CheckParameter(FrozenBufferRadius, isPositive());
  CheckParameter(LangevinBufferRadius, isPositive());
  CheckParameter(NeighborListNeighbors, isPositive());
  CheckParameter(RNEMD_swapTime, isPositive());
  CheckParameter(RNEMD_nBins, isPositive() && isEven());
  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));

  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::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 OOPSEException(oss.str());  
    }
    return ret;
}
 

}
Revision:	1360
Committed:	Mon Sep 7 16:31:51 2009 UTC (15 years, 7 months ago) by cli2
File size:	12964 byte(s)
Log Message:	Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
#	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(SurfaceTension, "surfaceTension");
92			DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93	gezelter	1291	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94			DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95	tim	665	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
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	gezelter	1355	DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
103			DefineOptionalParameter(ThermalLength, "thermalLength");
104	chuckv	1095	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
105	chuckv	1306	DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
106			DefineOptionalParameter(MTM_Ce, "MTM_Ce");
107			DefineOptionalParameter(MTM_G, "MTM_G");
108			DefineOptionalParameter(MTM_Io, "MTM_Io");
109			DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
110			DefineOptionalParameter(MTM_R, "MTM_R");
111	tim	906
112	gezelter	1327
113	chuckv	1147
114	tim	665	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
115	gezelter	1126	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
116	tim	665	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117			DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118			DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
119	gezelter	1078	DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
120			DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121	chrisfen	1050	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
122	tim	665	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
123	chrisfen	726	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 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			DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
131	skuang	1341	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
132	gezelter	1327	DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
133	gezelter	1331	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
134	cli2	1360	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135	gezelter	1354	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136	cli2	1360	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137	gezelter	1327
138	cli2	1360
139	gezelter	1078	deprecatedKeywords_.insert("nComponents");
140			deprecatedKeywords_.insert("nZconstraints");
141			deprecatedKeywords_.insert("initialConfig");
142	cli2	1360	deprecatedKeywords_.insert("thermIntDistSpringConst");
143			deprecatedKeywords_.insert("thermIntThetaSpringConst");
144			deprecatedKeywords_.insert("thermIntOmegaSpringConst");
145			deprecatedKeywords_.insert("useSolidThermInt");
146			deprecatedKeywords_.insert("useLiquidThermInt");
147	gezelter	2
148			}
149
150	tim	770	Globals::~Globals() {
151	tim	816	MemoryUtils::deletePointers(components_);
152			MemoryUtils::deletePointers(zconstraints_);
153	cli2	1360	MemoryUtils::deletePointers(restraints_);
154	gezelter	2	}
155
156	tim	770	void Globals::validate() {
157			DataHolder::validate();
158	gezelter	2
159	tim	672	CheckParameter(ForceField, isNotEmpty());
160			CheckParameter(TargetTemp, isPositive());
161	chuckv	1293	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") \|\| isEqualIgnoreCase("SMIPD"));
162	tim	672	CheckParameter(Dt, isPositive());
163			CheckParameter(RunTime, isPositive());
164			CheckParameter(FinalConfig, isNotEmpty());
165			CheckParameter(SampleTime, isNonNegative());
166			CheckParameter(ResetTime, isNonNegative());
167			CheckParameter(StatusTime, isNonNegative());
168			CheckParameter(CutoffRadius, isPositive());
169			CheckParameter(SwitchingRadius, isNonNegative());
170			CheckParameter(Dielectric, isPositive());
171			CheckParameter(ThermalTime, isNonNegative());
172			CheckParameter(TauThermostat, isPositive());
173			CheckParameter(TauBarostat, isPositive());
174			CheckParameter(ZconsTime, isPositive());
175			CheckParameter(ZconsTol, isPositive());
176			CheckParameter(Seed, isPositive());
177	tim	850	CheckParameter(Minimizer, isEqualIgnoreCase("SD") \|\| isEqualIgnoreCase("CG"));
178	tim	672	CheckParameter(MinimizerMaxIter, isPositive());
179			CheckParameter(MinimizerWriteFrq, isPositive());
180			CheckParameter(MinimizerStepSize, isPositive());
181			CheckParameter(MinimizerFTol, isPositive());
182			CheckParameter(MinimizerGTol, isPositive());
183			CheckParameter(MinimizerLSTol, isPositive());
184			CheckParameter(MinimizerLSMaxIter, isPositive());
185			CheckParameter(ZconsGap, isPositive());
186			CheckParameter(ZconsFixtime, isPositive());
187	chrisfen	979	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
188	tim	672	CheckParameter(ThermodynamicIntegrationK, isPositive());
189			CheckParameter(ForceFieldVariant, isNotEmpty());
190			CheckParameter(ForceFieldFileName, isNotEmpty());
191	tim	850	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") \|\| isEqualIgnoreCase("SHIFTED_POTENTIAL") \|\| isEqualIgnoreCase("SHIFTED_FORCE") \|\| isEqualIgnoreCase("REACTION_FIELD"));
192			CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") \|\| isEqualIgnoreCase("DAMPED"));
193			CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") \|\| isEqualIgnoreCase("MAX") \|\| isEqualIgnoreCase("TRADITIONAL"));
194			CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") \|\| isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
195	tim	672	//CheckParameter(StatFileFormat,);
196			CheckParameter(OrthoBoxTolerance, isPositive());
197	chrisfen	716	CheckParameter(DampingAlpha,isNonNegative());
198	tim	672	CheckParameter(SkinThickness, isPositive());
199	gezelter	945	CheckParameter(Viscosity, isNonNegative());
200	gezelter	1355	CheckParameter(ThermalConductivity, isNonNegative());
201			CheckParameter(ThermalLength, isNonNegative());
202	gezelter	945	CheckParameter(BeadSize, isPositive());
203			CheckParameter(FrozenBufferRadius, isPositive());
204			CheckParameter(LangevinBufferRadius, isPositive());
205	chuckv	1095	CheckParameter(NeighborListNeighbors, isPositive());
206	gezelter	1327	CheckParameter(RNEMD_swapTime, isPositive());
207	skuang	1341	CheckParameter(RNEMD_nBins, isPositive() && isEven());
208	gezelter	1327	CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") \|\| isEqualIgnoreCase("Px") \|\| isEqualIgnoreCase("Py") \|\| isEqualIgnoreCase("Pz"));
209	chuckv	1095
210	tim	770	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
211			if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
212	tim	845	std::ostringstream oss;
213			oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
214			throw OOPSEException(oss.str());
215	tim	770	}
216			}
217			}
218
219			bool Globals::addComponent(Component* comp) {
220			components_.push_back(comp);
221			return true;
222			}
223	gezelter	2
224	tim	770	bool Globals::addZConsStamp(ZConsStamp* zcons) {
225			zconstraints_.push_back(zcons);
226			return true;
227	gezelter	2	}
228
229	cli2	1360	bool Globals::addRestraintStamp(RestraintStamp* rest) {
230			restraints_.push_back(rest);
231			return true;
232			}
233
234	tim	770	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
235			std::string molStampName = molStamp->getName();
236			std::map<std::string, MoleculeStamp*>::iterator i;
237			bool ret = false;
238			i = moleculeStamps_.find(molStampName);
239			if (i == moleculeStamps_.end()) {
240			moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
241			ret = true;
242			} else {
243	tim	845	std::ostringstream oss;
244			oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
245			throw OOPSEException(oss.str());
246	tim	770	}
247			return ret;
248	gezelter	2	}
249	tim	770
250
251			}