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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC vs.
Revision 1402 by chuckv, Fri Jan 8 17:15:27 2010 UTC

# Line 1 | Line 1
1   /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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. 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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 37 | Line 28
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, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <stdlib.h>
# Line 49 | Line 49
49   #include "utils/MemoryUtils.hpp"
50   #include "utils/simError.h"
51  
52 < namespace oopse {
52 > namespace OpenMD {
53   Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
55  
# Line 57 | Line 57 | Globals::Globals() {
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
60 –  //DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
# Line 66 | Line 65 | Globals::Globals() {
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
66    DefineOptionalParameter(TempSet, "tempSet");
67    DefineOptionalParameter(ThermalTime, "thermalTime");
68 <  DefineOptionalParameter(TargetPressure, "targetPressure");
68 >  DefineOptionalParameter(TargetPressure, "targetPressure");  
69    DefineOptionalParameter(TauThermostat, "tauThermostat");
70    DefineOptionalParameter(TauBarostat, "tauBarostat");
71    DefineOptionalParameter(ZconsTime, "zconsTime");
# Line 88 | Line 87 | Globals::Globals() {
87    DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 <  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92 <  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93 <  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
90 >  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91    DefineOptionalParameter(SurfaceTension, "surfaceTension");
92    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
94 <  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
93 >  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94 >  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
# Line 102 | Line 99 | Globals::Globals() {
99    DefineOptionalParameter(BeadSize, "beadSize");
100    DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102 +  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
103 +  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
104 +  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
105 +  DefineOptionalParameter(MTM_G, "MTM_G");
106 +  DefineOptionalParameter(MTM_Io, "MTM_Io");
107 +  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
108 +  DefineOptionalParameter(MTM_R, "MTM_R");
109 +  DefineOptionalParameter(Alpha, "alpha");
110 +
111    
112    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
113 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
114    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
115    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
116    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
117 <  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
118 <  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
112 <  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
113 <  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
114 <  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
115 <  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
117 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
118 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
120    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
121    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
# Line 121 | Line 124 | Globals::Globals() {
124    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
125    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
126  
127 +  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
128 +  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
129 +  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
130 +  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
131 +  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
132 +  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
133 +  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
134 +  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135 +  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136 +  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137 +  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
138  
139 <    deprecatedKeywords_.insert("nComponents");
140 <    deprecatedKeywords_.insert("nZconstraints");
141 <    deprecatedKeywords_.insert("initialConfig");
139 >
140 >  deprecatedKeywords_.insert("nComponents");
141 >  deprecatedKeywords_.insert("nZconstraints");
142 >  deprecatedKeywords_.insert("initialConfig");
143 >  deprecatedKeywords_.insert("thermIntDistSpringConst");
144 >  deprecatedKeywords_.insert("thermIntThetaSpringConst");
145 >  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
146 >  deprecatedKeywords_.insert("useSolidThermInt");  
147 >  deprecatedKeywords_.insert("useLiquidThermInt");
148      
149   }
150  
151   Globals::~Globals() {
152      MemoryUtils::deletePointers(components_);
153      MemoryUtils::deletePointers(zconstraints_);
154 +    MemoryUtils::deletePointers(restraints_);
155   }
156  
157   void Globals::validate() {
# Line 138 | Line 159 | void Globals::validate() {
159  
160    CheckParameter(ForceField, isNotEmpty());
161    CheckParameter(TargetTemp, isPositive());
162 <  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"));
162 >  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"));
163    CheckParameter(Dt, isPositive());
164    CheckParameter(RunTime, isPositive());
144 –  //CheckParameter(InitialConfig, isNotEmpty());
165    CheckParameter(FinalConfig, isNotEmpty());
166    CheckParameter(SampleTime, isNonNegative());
167    CheckParameter(ResetTime, isNonNegative());
# Line 150 | Line 170 | void Globals::validate() {
170    CheckParameter(SwitchingRadius, isNonNegative());
171    CheckParameter(Dielectric, isPositive());
172    CheckParameter(ThermalTime,  isNonNegative());
153 –  //  CheckParameter(TargetPressure,  isPositive());
173    CheckParameter(TauThermostat, isPositive());
174    CheckParameter(TauBarostat, isPositive());
175    CheckParameter(ZconsTime, isPositive());
# Line 170 | Line 189 | void Globals::validate() {
189    CheckParameter(ThermodynamicIntegrationK, isPositive());
190    CheckParameter(ForceFieldVariant, isNotEmpty());
191    CheckParameter(ForceFieldFileName, isNotEmpty());
173 –  CheckParameter(ThermIntDistSpringConst, isPositive());
174 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
175 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
176 –  //  CheckParameter(SurfaceTension, isNonNegative());
192    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
193    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
194    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
195    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
196    //CheckParameter(StatFileFormat,);    
197    CheckParameter(OrthoBoxTolerance, isPositive());  
183 –  CheckParameter(ThermIntDistSpringConst, isPositive());
184 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
185 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
198    CheckParameter(DampingAlpha,isNonNegative());
199    CheckParameter(SkinThickness, isPositive());
200    CheckParameter(Viscosity, isNonNegative());
201    CheckParameter(BeadSize, isPositive());
202    CheckParameter(FrozenBufferRadius, isPositive());
203    CheckParameter(LangevinBufferRadius, isPositive());
204 +  CheckParameter(NeighborListNeighbors, isPositive());
205 +  CheckParameter(RNEMD_exchangeTime, isPositive());
206 +  CheckParameter(RNEMD_nBins, isPositive() && isEven());
207 +  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
208 +  CheckParameter(RNEMD_targetFlux, isNonNegative());
209 +  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
210 +  CheckParameter(Alpha, isPositive());
211 +
212 +  
213    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
214      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
215          std::ostringstream oss;
216          oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
217 <        throw OOPSEException(oss.str());          
217 >        throw OpenMDException(oss.str());          
218      }
219    }
220   }
221 <    
221 >  
222   bool Globals::addComponent(Component* comp) {
223      components_.push_back(comp);
224      return true;
# Line 208 | Line 229 | bool Globals::addZConsStamp(ZConsStamp* zcons) {
229      return true;
230   }
231  
232 + bool Globals::addRestraintStamp(RestraintStamp* rest) {
233 +    restraints_.push_back(rest);
234 +    return true;
235 + }
236 +
237   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
238      std::string molStampName = molStamp->getName();
239      std::map<std::string, MoleculeStamp*>::iterator i;
# Line 219 | Line 245 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
245      } else {
246          std::ostringstream oss;
247          oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
248 <        throw OOPSEException(oss.str());  
248 >        throw OpenMDException(oss.str());  
249      }
250      return ret;
251   }

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