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, 234107 (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() {
  
    flucQpars_ = new FluctuatingChargeParameters();
    rnemdPars_ = new RNEMDParameters();
    minimizerPars_ = new MinimizerParameters();

    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(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(ElectricField, "electricField");
    DefineOptionalParameter(UniformField, "uniformField");
    DefineOptionalParameter(UniformGradientStrength, "uniformGradientStrength");
    DefineOptionalParameter(UniformGradientDirection1, "uniformGradientDirection1");
    DefineOptionalParameter(UniformGradientDirection2, "uniformGradientDirection2");
    //DefineOptionalParameter(PeriodicField, "periodicField");
    //DefineOptionalParameter(PeriodicFieldStrength, "periodicFieldStrength");
    

    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");
    DefineOptionalParameter(ConstraintTime, "constraintTime");

  
    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, 
                                            "usePeriodicBoundaryConditions", 
                                            true);
    DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", 
                                            true);
    DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections, 
                                            "useLongRangeCorrections", 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", false);
    DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux", 
                                            false);
    DefineOptionalParameterWithDefaultValue(OutputForceVector, 
                                            "outputForceVector", false);
    DefineOptionalParameterWithDefaultValue(OutputParticlePotential, 
                                            "outputParticlePotential", false);
    DefineOptionalParameterWithDefaultValue(OutputElectricField, 
                                            "outputElectricField", false);
    DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, 
                                            "outputFluctuatingCharges", false);
    DefineOptionalParameterWithDefaultValue(OutputSitePotential, 
                                            "outputSitePotential", false);
    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(AccumulateBoxQuadrupole, 
                                            "accumulateBoxQuadrupole", 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");
    deprecatedKeywords_.insert("minimizerMaxIter");
    deprecatedKeywords_.insert("minimizerWriteFreq");
    deprecatedKeywords_.insert("minimizerStepSize");
    deprecatedKeywords_.insert("minimizerFTol");
    deprecatedKeywords_.insert("minimizerGTol");
    deprecatedKeywords_.insert("minimizerLSTol");
    deprecatedKeywords_.insert("minimizerLSMaxIter");
    deprecatedKeywords_.insert("electricField");

    
  }

  Globals::~Globals() {
    MemoryUtils::deletePointers(components_);
    MemoryUtils::deletePointers(zconstraints_);
    MemoryUtils::deletePointers(restraints_);
    delete flucQpars_;
    delete rnemdPars_;
    delete minimizerPars_;
  }

  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("NPA") || 
                   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(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") || 
                   isEqualIgnoreCase("TAYLOR_SHIFTED") ||
                   isEqualIgnoreCase("EWALD_FULL"));
    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") || 
                   isEqualIgnoreCase("TAYLOR_SHIFTED"));
    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(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::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
    if (flucQpars_ != NULL)
      delete flucQpars_;
    
    flucQpars_ = fqp;
    return true;
  }

  bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
    if (rnemdPars_ != NULL)
      delete rnemdPars_;
    
    rnemdPars_ = rnemdPars;
    return true;
  }

  bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
    if (minimizerPars_ != NULL)
      delete minimizerPars_;
    
    minimizerPars_ = miniPars;
    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:	2034
Committed:	Mon Nov 3 16:49:03 2014 UTC (10 years, 6 months ago) by gezelter
File size:	16596 byte(s)
Log Message:	Updating UniformGradient to the new parameter structure (two unit vectors and a gradient strength).
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	gezelter	1879	Globals::Globals() {
55	gezelter	1782
56	gezelter	1879	flucQpars_ = new FluctuatingChargeParameters();
57			rnemdPars_ = new RNEMDParameters();
58			minimizerPars_ = new MinimizerParameters();
59	gezelter	1782
60	gezelter	1879	DefineParameter(ForceField, "forceField");
61
62			DefineOptionalParameter(TargetTemp, "targetTemp");
63			DefineOptionalParameter(Ensemble, "ensemble");
64			DefineOptionalParameter(Dt, "dt");
65			DefineOptionalParameter(RunTime, "runTime");
66			DefineOptionalParameter(FinalConfig, "finalConfig");
67			DefineOptionalParameter(SampleTime, "sampleTime");
68			DefineOptionalParameter(ResetTime, "resetTime");
69			DefineOptionalParameter(StatusTime, "statusTime");
70			DefineOptionalParameter(CutoffRadius, "cutoffRadius");
71			DefineOptionalParameter(SwitchingRadius, "switchingRadius");
72			DefineOptionalParameter(TempSet, "tempSet");
73			DefineOptionalParameter(ThermalTime, "thermalTime");
74			DefineOptionalParameter(TargetPressure, "targetPressure");
75			DefineOptionalParameter(TauThermostat, "tauThermostat");
76			DefineOptionalParameter(TauBarostat, "tauBarostat");
77			DefineOptionalParameter(ZconsTime, "zconsTime");
78			DefineOptionalParameter(ZconsTol, "zconsTol");
79			DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80			DefineOptionalParameter(Seed, "seed");
81			DefineOptionalParameter(ZconsGap, "zconsGap");
82			DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83			DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
84			DefineOptionalParameter(ThermodynamicIntegrationLambda,
85			"thermodynamicIntegrationLambda");
86			DefineOptionalParameter(ThermodynamicIntegrationK,
87			"thermodynamicIntegrationK");
88			DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89			DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90			DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91			DefineOptionalParameter(SurfaceTension, "surfaceTension");
92			DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93			DefineOptionalParameter(ElectricField, "electricField");
94	gezelter	2020	DefineOptionalParameter(UniformField, "uniformField");
95	gezelter	2034	DefineOptionalParameter(UniformGradientStrength, "uniformGradientStrength");
96			DefineOptionalParameter(UniformGradientDirection1, "uniformGradientDirection1");
97			DefineOptionalParameter(UniformGradientDirection2, "uniformGradientDirection2");
98	gezelter	2020	//DefineOptionalParameter(PeriodicField, "periodicField");
99			//DefineOptionalParameter(PeriodicFieldStrength, "periodicFieldStrength");
100
101	gezelter	1782
102	gezelter	1879	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
103			DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
104			DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
105			DefineOptionalParameter(HydroPropFile, "HydroPropFile");
106			DefineOptionalParameter(Viscosity, "viscosity");
107			DefineOptionalParameter(BeadSize, "beadSize");
108			DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
109			DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
110			DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
111			DefineOptionalParameter(UseMultipleTemperatureMethod,
112			"useMultipleTemperatureMethod");
113			DefineOptionalParameter(ElectrostaticSummationMethod,
114			"electrostaticSummationMethod");
115			DefineOptionalParameter(MTM_Ce, "MTM_Ce");
116			DefineOptionalParameter(MTM_G, "MTM_G");
117			DefineOptionalParameter(MTM_Io, "MTM_Io");
118			DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
119			DefineOptionalParameter(MTM_R, "MTM_R");
120			DefineOptionalParameter(Alpha, "alpha");
121	gezelter	1981	DefineOptionalParameter(ConstraintTime, "constraintTime");
122	gezelter	1327
123	chuckv	1147
124	gezelter	1879	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
125			"usePeriodicBoundaryConditions",
126			true);
127			DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
128			true);
129			DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
130			"useLongRangeCorrections", true);
131			DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
132			false);
133			DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
134			"useInitialExtendedSystemState",
135			false);
136			DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
137			"orthoBoxTolerance", 1E-6);
138			DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
139			"SHIFTED_FORCE");
140			DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
141			"electrostaticScreeningMethod",
142			"DAMPED");
143			DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
144			DefineOptionalParameterWithDefaultValue(CompressDumpFile,
145			"compressDumpFile", false);
146			DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
147			false);
148			DefineOptionalParameterWithDefaultValue(OutputForceVector,
149			"outputForceVector", false);
150			DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
151			"outputParticlePotential", false);
152			DefineOptionalParameterWithDefaultValue(OutputElectricField,
153			"outputElectricField", false);
154			DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
155			"outputFluctuatingCharges", false);
156	gezelter	1993	DefineOptionalParameterWithDefaultValue(OutputSitePotential,
157			"outputSitePotential", false);
158	gezelter	1879	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
159			1.0);
160			DefineOptionalParameterWithDefaultValue(StatFileFormat,
161			"statFileFormat",
162			"TIME\|TOTAL_ENERGY\|POTENTIAL_ENERGY\|KINETIC_ENERGY\|TEMPERATURE\|PRESSURE\|VOLUME\|CONSERVED_QUANTITY");
163			DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
164			"useSphericalBoundaryConditions",
165			false);
166			DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
167			"accumulateBoxDipole", false);
168	gezelter	2022	DefineOptionalParameterWithDefaultValue(AccumulateBoxQuadrupole,
169			"accumulateBoxQuadrupole", false);
170	gezelter	1879	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
171			false);
172			DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
173			"idealCrystal.in");
174			DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
175			"useThermodynamicIntegration",
176			false);
177			DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
178	tim	681
179	gezelter	1879	deprecatedKeywords_.insert("nComponents");
180			deprecatedKeywords_.insert("nZconstraints");
181			deprecatedKeywords_.insert("initialConfig");
182			deprecatedKeywords_.insert("thermIntDistSpringConst");
183			deprecatedKeywords_.insert("thermIntThetaSpringConst");
184			deprecatedKeywords_.insert("thermIntOmegaSpringConst");
185			deprecatedKeywords_.insert("useSolidThermInt");
186			deprecatedKeywords_.insert("useLiquidThermInt");
187			deprecatedKeywords_.insert("minimizerMaxIter");
188			deprecatedKeywords_.insert("minimizerWriteFreq");
189			deprecatedKeywords_.insert("minimizerStepSize");
190			deprecatedKeywords_.insert("minimizerFTol");
191			deprecatedKeywords_.insert("minimizerGTol");
192			deprecatedKeywords_.insert("minimizerLSTol");
193			deprecatedKeywords_.insert("minimizerLSMaxIter");
194	gezelter	2020	deprecatedKeywords_.insert("electricField");
195	gezelter	1327
196	gezelter	2
197	gezelter	1879	}
198	gezelter	2
199	gezelter	1879	Globals::~Globals() {
200	tim	816	MemoryUtils::deletePointers(components_);
201			MemoryUtils::deletePointers(zconstraints_);
202	cli2	1360	MemoryUtils::deletePointers(restraints_);
203	gezelter	1964	delete flucQpars_;
204			delete rnemdPars_;
205			delete minimizerPars_;
206	gezelter	1879	}
207	gezelter	2
208	gezelter	1879	void Globals::validate() {
209			DataHolder::validate();
210	gezelter	2
211	gezelter	1879	CheckParameter(ForceField, isNotEmpty());
212			CheckParameter(TargetTemp, isPositive());
213			CheckParameter(Ensemble, isEqualIgnoreCase("NVE") \|\|
214			isEqualIgnoreCase("NVT") \|\| isEqualIgnoreCase("NPTi") \|\|
215			isEqualIgnoreCase("NPTf") \|\| isEqualIgnoreCase("NPTxyz") \|\|
216			isEqualIgnoreCase("NPTsz") \|\| isEqualIgnoreCase("NPAT") \|\|
217	gezelter	2011	isEqualIgnoreCase("NPA") \|\|
218	gezelter	1879	isEqualIgnoreCase("LANGEVINDYNAMICS") \|\|
219			isEqualIgnoreCase("LD") \|\| isEqualIgnoreCase("NPRT") \|\|
220			isEqualIgnoreCase("NPGT") \|\| isEqualIgnoreCase("NGammaT") \|\|
221			isEqualIgnoreCase("NGT") \|\|
222			isEqualIgnoreCase("LANGEVINHULL") \|\|
223			isEqualIgnoreCase("LHULL") \|\| isEqualIgnoreCase("SMIPD"));
224			CheckParameter(Dt, isPositive());
225			CheckParameter(RunTime, isPositive());
226			CheckParameter(FinalConfig, isNotEmpty());
227			CheckParameter(SampleTime, isNonNegative());
228			CheckParameter(ResetTime, isNonNegative());
229			CheckParameter(StatusTime, isNonNegative());
230			CheckParameter(CutoffRadius, isPositive());
231			CheckParameter(SwitchingRadius, isNonNegative());
232			CheckParameter(Dielectric, isPositive());
233			CheckParameter(ThermalTime, isNonNegative());
234			CheckParameter(TauThermostat, isPositive());
235			CheckParameter(TauBarostat, isPositive());
236			CheckParameter(ZconsTime, isPositive());
237			CheckParameter(ZconsTol, isPositive());
238			CheckParameter(Seed, isPositive());
239			CheckParameter(ZconsGap, isPositive());
240			CheckParameter(ZconsFixtime, isPositive());
241			CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
242			CheckParameter(ThermodynamicIntegrationK, isPositive());
243			CheckParameter(ForceFieldVariant, isNotEmpty());
244			CheckParameter(ForceFieldFileName, isNotEmpty());
245			CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") \|\|
246			isEqualIgnoreCase("SWITCHED") \|\|
247			isEqualIgnoreCase("SHIFTED_POTENTIAL") \|\|
248			isEqualIgnoreCase("SHIFTED_FORCE") \|\|
249	gezelter	1915	isEqualIgnoreCase("TAYLOR_SHIFTED") \|\|
250			isEqualIgnoreCase("EWALD_FULL"));
251	gezelter	1879	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") \|\|
252			isEqualIgnoreCase("MAX") \|\|
253			isEqualIgnoreCase("TRADITIONAL"));
254			CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") \|\|
255			isEqualIgnoreCase("HARD") \|\| isEqualIgnoreCase("SWITCHED") \|\|
256			isEqualIgnoreCase("SHIFTED_POTENTIAL") \|\|
257			isEqualIgnoreCase("SHIFTED_FORCE") \|\|
258			isEqualIgnoreCase("REACTION_FIELD") \|\|
259			isEqualIgnoreCase("TAYLOR_SHIFTED"));
260			CheckParameter(ElectrostaticScreeningMethod,
261			isEqualIgnoreCase("UNDAMPED") \|\| isEqualIgnoreCase("DAMPED"));
262			CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") \|\|
263			isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
264			CheckParameter(OrthoBoxTolerance, isPositive());
265			CheckParameter(DampingAlpha,isNonNegative());
266			CheckParameter(SkinThickness, isPositive());
267			CheckParameter(Viscosity, isNonNegative());
268			CheckParameter(BeadSize, isPositive());
269			CheckParameter(FrozenBufferRadius, isPositive());
270			CheckParameter(LangevinBufferRadius, isPositive());
271			CheckParameter(NeighborListNeighbors, isPositive());
272			CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") \|\|
273			isEqualIgnoreCase("AlphaShape"));
274			CheckParameter(Alpha, isPositive());
275	chuckv	1402
276	gezelter	1879	for(std::vector<Component*>::iterator i = components_.begin();
277			i != components_.end(); ++i) {
278			if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
279	tim	845	std::ostringstream oss;
280	gezelter	1879	oss << "Globals Error: can not find molecule stamp for component "
281			<< (*i)->getType() << std::endl;
282	gezelter	1390	throw OpenMDException(oss.str());
283	gezelter	1879	}
284	tim	770	}
285			}
286	gezelter	1879
287			bool Globals::addComponent(Component* comp) {
288	tim	770	components_.push_back(comp);
289			return true;
290	gezelter	1879	}
291	gezelter	2
292	gezelter	1879	bool Globals::addZConsStamp(ZConsStamp* zcons) {
293	tim	770	zconstraints_.push_back(zcons);
294			return true;
295	gezelter	1879	}
296	gezelter	2
297	gezelter	1879	bool Globals::addRestraintStamp(RestraintStamp* rest) {
298	cli2	1360	restraints_.push_back(rest);
299			return true;
300	gezelter	1879	}
301	cli2	1360
302	gezelter	1879	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
303			if (flucQpars_ != NULL)
304			delete flucQpars_;
305	gezelter	1782
306	gezelter	1879	flucQpars_ = fqp;
307			return true;
308			}
309	gezelter	1782
310	gezelter	1879	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
311			if (rnemdPars_ != NULL)
312			delete rnemdPars_;
313	gezelter	1782
314	gezelter	1879	rnemdPars_ = rnemdPars;
315			return true;
316			}
317	gezelter	1782
318	gezelter	1879	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
319			if (minimizerPars_ != NULL)
320			delete minimizerPars_;
321	gezelter	1782
322	gezelter	1879	minimizerPars_ = miniPars;
323			return true;
324			}
325	gezelter	1782
326	gezelter	1879	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
327	tim	770	std::string molStampName = molStamp->getName();
328			std::map<std::string, MoleculeStamp*>::iterator i;
329			bool ret = false;
330			i = moleculeStamps_.find(molStampName);
331			if (i == moleculeStamps_.end()) {
332	gezelter	1879	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
333			ret = true;
334	tim	770	} else {
335	gezelter	1879	std::ostringstream oss;
336			oss << "Globals Error: Molecule Stamp " << molStamp->getName()
337			<< "appears multiple times\n";
338			throw OpenMDException(oss.str());
339	tim	770	}
340			return ret;
341	gezelter	1879	}
342	gezelter	2	}