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(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(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:	2020
Committed:	Mon Sep 22 19:18:35 2014 UTC (10 years, 7 months ago) by gezelter
File size:	16196 byte(s)
Log Message:	Fixes for restraints, renaming of UniformField
#	Content
1	/*
2	* Copyright (c) 2005, 2010 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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include <stdlib.h>
44	#include <stdio.h>
45	#include <string.h>
46	#include <string>
47
48	#include "io/Globals.hpp"
49	#include "io/ParamConstraint.hpp"
50	#include "utils/MemoryUtils.hpp"
51	#include "utils/simError.h"
52
53	namespace OpenMD {
54	Globals::Globals() {
55
56	flucQpars_ = new FluctuatingChargeParameters();
57	rnemdPars_ = new RNEMDParameters();
58	minimizerPars_ = new MinimizerParameters();
59
60	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	DefineOptionalParameter(UniformField, "uniformField");
95	//DefineOptionalParameter(PeriodicField, "periodicField");
96	//DefineOptionalParameter(PeriodicFieldStrength, "periodicFieldStrength");
97
98
99	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
100	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
101	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
102	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
103	DefineOptionalParameter(Viscosity, "viscosity");
104	DefineOptionalParameter(BeadSize, "beadSize");
105	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
106	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
107	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
108	DefineOptionalParameter(UseMultipleTemperatureMethod,
109	"useMultipleTemperatureMethod");
110	DefineOptionalParameter(ElectrostaticSummationMethod,
111	"electrostaticSummationMethod");
112	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
113	DefineOptionalParameter(MTM_G, "MTM_G");
114	DefineOptionalParameter(MTM_Io, "MTM_Io");
115	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
116	DefineOptionalParameter(MTM_R, "MTM_R");
117	DefineOptionalParameter(Alpha, "alpha");
118	DefineOptionalParameter(ConstraintTime, "constraintTime");
119
120
121	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
122	"usePeriodicBoundaryConditions",
123	true);
124	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
125	true);
126	DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
127	"useLongRangeCorrections", true);
128	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
129	false);
130	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
131	"useInitialExtendedSystemState",
132	false);
133	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
134	"orthoBoxTolerance", 1E-6);
135	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
136	"SHIFTED_FORCE");
137	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
138	"electrostaticScreeningMethod",
139	"DAMPED");
140	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
141	DefineOptionalParameterWithDefaultValue(CompressDumpFile,
142	"compressDumpFile", false);
143	DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
144	false);
145	DefineOptionalParameterWithDefaultValue(OutputForceVector,
146	"outputForceVector", false);
147	DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
148	"outputParticlePotential", false);
149	DefineOptionalParameterWithDefaultValue(OutputElectricField,
150	"outputElectricField", false);
151	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
152	"outputFluctuatingCharges", false);
153	DefineOptionalParameterWithDefaultValue(OutputSitePotential,
154	"outputSitePotential", false);
155	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
156	1.0);
157	DefineOptionalParameterWithDefaultValue(StatFileFormat,
158	"statFileFormat",
159	"TIME\|TOTAL_ENERGY\|POTENTIAL_ENERGY\|KINETIC_ENERGY\|TEMPERATURE\|PRESSURE\|VOLUME\|CONSERVED_QUANTITY");
160	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
161	"useSphericalBoundaryConditions",
162	false);
163	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
164	"accumulateBoxDipole", false);
165	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
166	false);
167	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
168	"idealCrystal.in");
169	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
170	"useThermodynamicIntegration",
171	false);
172	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
173
174	deprecatedKeywords_.insert("nComponents");
175	deprecatedKeywords_.insert("nZconstraints");
176	deprecatedKeywords_.insert("initialConfig");
177	deprecatedKeywords_.insert("thermIntDistSpringConst");
178	deprecatedKeywords_.insert("thermIntThetaSpringConst");
179	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
180	deprecatedKeywords_.insert("useSolidThermInt");
181	deprecatedKeywords_.insert("useLiquidThermInt");
182	deprecatedKeywords_.insert("minimizerMaxIter");
183	deprecatedKeywords_.insert("minimizerWriteFreq");
184	deprecatedKeywords_.insert("minimizerStepSize");
185	deprecatedKeywords_.insert("minimizerFTol");
186	deprecatedKeywords_.insert("minimizerGTol");
187	deprecatedKeywords_.insert("minimizerLSTol");
188	deprecatedKeywords_.insert("minimizerLSMaxIter");
189	deprecatedKeywords_.insert("electricField");
190
191
192	}
193
194	Globals::~Globals() {
195	MemoryUtils::deletePointers(components_);
196	MemoryUtils::deletePointers(zconstraints_);
197	MemoryUtils::deletePointers(restraints_);
198	delete flucQpars_;
199	delete rnemdPars_;
200	delete minimizerPars_;
201	}
202
203	void Globals::validate() {
204	DataHolder::validate();
205
206	CheckParameter(ForceField, isNotEmpty());
207	CheckParameter(TargetTemp, isPositive());
208	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") \|\|
209	isEqualIgnoreCase("NVT") \|\| isEqualIgnoreCase("NPTi") \|\|
210	isEqualIgnoreCase("NPTf") \|\| isEqualIgnoreCase("NPTxyz") \|\|
211	isEqualIgnoreCase("NPTsz") \|\| isEqualIgnoreCase("NPAT") \|\|
212	isEqualIgnoreCase("NPA") \|\|
213	isEqualIgnoreCase("LANGEVINDYNAMICS") \|\|
214	isEqualIgnoreCase("LD") \|\| isEqualIgnoreCase("NPRT") \|\|
215	isEqualIgnoreCase("NPGT") \|\| isEqualIgnoreCase("NGammaT") \|\|
216	isEqualIgnoreCase("NGT") \|\|
217	isEqualIgnoreCase("LANGEVINHULL") \|\|
218	isEqualIgnoreCase("LHULL") \|\| isEqualIgnoreCase("SMIPD"));
219	CheckParameter(Dt, isPositive());
220	CheckParameter(RunTime, isPositive());
221	CheckParameter(FinalConfig, isNotEmpty());
222	CheckParameter(SampleTime, isNonNegative());
223	CheckParameter(ResetTime, isNonNegative());
224	CheckParameter(StatusTime, isNonNegative());
225	CheckParameter(CutoffRadius, isPositive());
226	CheckParameter(SwitchingRadius, isNonNegative());
227	CheckParameter(Dielectric, isPositive());
228	CheckParameter(ThermalTime, isNonNegative());
229	CheckParameter(TauThermostat, isPositive());
230	CheckParameter(TauBarostat, isPositive());
231	CheckParameter(ZconsTime, isPositive());
232	CheckParameter(ZconsTol, isPositive());
233	CheckParameter(Seed, isPositive());
234	CheckParameter(ZconsGap, isPositive());
235	CheckParameter(ZconsFixtime, isPositive());
236	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
237	CheckParameter(ThermodynamicIntegrationK, isPositive());
238	CheckParameter(ForceFieldVariant, isNotEmpty());
239	CheckParameter(ForceFieldFileName, isNotEmpty());
240	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") \|\|
241	isEqualIgnoreCase("SWITCHED") \|\|
242	isEqualIgnoreCase("SHIFTED_POTENTIAL") \|\|
243	isEqualIgnoreCase("SHIFTED_FORCE") \|\|
244	isEqualIgnoreCase("TAYLOR_SHIFTED") \|\|
245	isEqualIgnoreCase("EWALD_FULL"));
246	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") \|\|
247	isEqualIgnoreCase("MAX") \|\|
248	isEqualIgnoreCase("TRADITIONAL"));
249	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") \|\|
250	isEqualIgnoreCase("HARD") \|\| isEqualIgnoreCase("SWITCHED") \|\|
251	isEqualIgnoreCase("SHIFTED_POTENTIAL") \|\|
252	isEqualIgnoreCase("SHIFTED_FORCE") \|\|
253	isEqualIgnoreCase("REACTION_FIELD") \|\|
254	isEqualIgnoreCase("TAYLOR_SHIFTED"));
255	CheckParameter(ElectrostaticScreeningMethod,
256	isEqualIgnoreCase("UNDAMPED") \|\| isEqualIgnoreCase("DAMPED"));
257	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") \|\|
258	isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
259	CheckParameter(OrthoBoxTolerance, isPositive());
260	CheckParameter(DampingAlpha,isNonNegative());
261	CheckParameter(SkinThickness, isPositive());
262	CheckParameter(Viscosity, isNonNegative());
263	CheckParameter(BeadSize, isPositive());
264	CheckParameter(FrozenBufferRadius, isPositive());
265	CheckParameter(LangevinBufferRadius, isPositive());
266	CheckParameter(NeighborListNeighbors, isPositive());
267	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") \|\|
268	isEqualIgnoreCase("AlphaShape"));
269	CheckParameter(Alpha, isPositive());
270
271	for(std::vector<Component*>::iterator i = components_.begin();
272	i != components_.end(); ++i) {
273	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
274	std::ostringstream oss;
275	oss << "Globals Error: can not find molecule stamp for component "
276	<< (*i)->getType() << std::endl;
277	throw OpenMDException(oss.str());
278	}
279	}
280	}
281
282	bool Globals::addComponent(Component* comp) {
283	components_.push_back(comp);
284	return true;
285	}
286
287	bool Globals::addZConsStamp(ZConsStamp* zcons) {
288	zconstraints_.push_back(zcons);
289	return true;
290	}
291
292	bool Globals::addRestraintStamp(RestraintStamp* rest) {
293	restraints_.push_back(rest);
294	return true;
295	}
296
297	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
298	if (flucQpars_ != NULL)
299	delete flucQpars_;
300
301	flucQpars_ = fqp;
302	return true;
303	}
304
305	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
306	if (rnemdPars_ != NULL)
307	delete rnemdPars_;
308
309	rnemdPars_ = rnemdPars;
310	return true;
311	}
312
313	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
314	if (minimizerPars_ != NULL)
315	delete minimizerPars_;
316
317	minimizerPars_ = miniPars;
318	return true;
319	}
320
321	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
322	std::string molStampName = molStamp->getName();
323	std::map<std::string, MoleculeStamp*>::iterator i;
324	bool ret = false;
325	i = moleculeStamps_.find(molStampName);
326	if (i == moleculeStamps_.end()) {
327	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
328	ret = true;
329	} else {
330	std::ostringstream oss;
331	oss << "Globals Error: Molecule Stamp " << molStamp->getName()
332	<< "appears multiple times\n";
333	throw OpenMDException(oss.str());
334	}
335	return ret;
336	}
337	}