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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1398 by gezelter, Tue Dec 8 22:17:02 2009 UTC

# Line 6 | Line 6
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 45 | Line 45
45   #include <string>
46  
47   #include "io/Globals.hpp"
48 + #include "io/ParamConstraint.hpp"
49 + #include "utils/MemoryUtils.hpp"
50   #include "utils/simError.h"
51  
52 < #include "io/ParamConstraint.hpp"
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");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67 –  DefineOptionalParameter(Dielectric, "dielectric");
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 89 | Line 87 | Globals::Globals() {
87    DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 <  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
93 <  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
94 <  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 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
97 >  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
98 >  DefineOptionalParameter(Viscosity, "viscosity");
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 >  
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);
119 <  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
109 <  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
110 <  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
111 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
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);
122    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
123    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
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  
138 <    deprecatedKeywords_.insert("nComponents");
139 <    deprecatedKeywords_.insert("nZconstraints");
138 >
139 >  deprecatedKeywords_.insert("nComponents");
140 >  deprecatedKeywords_.insert("nZconstraints");
141 >  deprecatedKeywords_.insert("initialConfig");
142 >  deprecatedKeywords_.insert("thermIntDistSpringConst");
143 >  deprecatedKeywords_.insert("thermIntThetaSpringConst");
144 >  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
145 >  deprecatedKeywords_.insert("useSolidThermInt");  
146 >  deprecatedKeywords_.insert("useLiquidThermInt");
147      
148   }
149  
150   Globals::~Globals() {
151 <
152 <
151 >    MemoryUtils::deletePointers(components_);
152 >    MemoryUtils::deletePointers(zconstraints_);
153 >    MemoryUtils::deletePointers(restraints_);
154   }
155  
156   void Globals::validate() {
# Line 130 | Line 158 | void Globals::validate() {
158  
159    CheckParameter(ForceField, isNotEmpty());
160    CheckParameter(TargetTemp, isPositive());
161 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
161 >  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    CheckParameter(Dt, isPositive());
163    CheckParameter(RunTime, isPositive());
136 –  CheckParameter(InitialConfig, isNotEmpty());
164    CheckParameter(FinalConfig, isNotEmpty());
165    CheckParameter(SampleTime, isNonNegative());
166    CheckParameter(ResetTime, isNonNegative());
# Line 142 | Line 169 | void Globals::validate() {
169    CheckParameter(SwitchingRadius, isNonNegative());
170    CheckParameter(Dielectric, isPositive());
171    CheckParameter(ThermalTime,  isNonNegative());
145 –  CheckParameter(TargetPressure,  isPositive());
172    CheckParameter(TauThermostat, isPositive());
173    CheckParameter(TauBarostat, isPositive());
174    CheckParameter(ZconsTime, isPositive());
175    CheckParameter(ZconsTol, isPositive());
176    CheckParameter(Seed, isPositive());
177 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
177 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
178    CheckParameter(MinimizerMaxIter, isPositive());
179    CheckParameter(MinimizerWriteFrq, isPositive());
180    CheckParameter(MinimizerStepSize, isPositive());
# Line 158 | Line 184 | void Globals::validate() {
184    CheckParameter(MinimizerLSMaxIter, isPositive());
185    CheckParameter(ZconsGap, isPositive());
186    CheckParameter(ZconsFixtime, isPositive());
187 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
187 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
188    CheckParameter(ThermodynamicIntegrationK, isPositive());
189    CheckParameter(ForceFieldVariant, isNotEmpty());
190    CheckParameter(ForceFieldFileName, isNotEmpty());
191 <  CheckParameter(ThermIntDistSpringConst, isPositive());
192 <  CheckParameter(ThermIntThetaSpringConst, isPositive());
193 <  CheckParameter(ThermIntOmegaSpringConst, isPositive());
194 <  CheckParameter(SurfaceTension, isPositive());
169 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
170 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
171 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
172 <  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
191 >  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    //CheckParameter(StatFileFormat,);    
174 –  //CheckParameter(MixingRule,);
196    CheckParameter(OrthoBoxTolerance, isPositive());  
176 –  CheckParameter(ThermIntDistSpringConst, isPositive());
177 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
178 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
197    CheckParameter(DampingAlpha,isNonNegative());
198    CheckParameter(SkinThickness, isPositive());
199 +  CheckParameter(Viscosity, isNonNegative());
200 +  CheckParameter(BeadSize, isPositive());
201 +  CheckParameter(FrozenBufferRadius, isPositive());
202 +  CheckParameter(LangevinBufferRadius, isPositive());
203 +  CheckParameter(NeighborListNeighbors, isPositive());
204 +  CheckParameter(RNEMD_exchangeTime, isPositive());
205 +  CheckParameter(RNEMD_nBins, isPositive() && isEven());
206 +  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
207 +  CheckParameter(RNEMD_targetFlux, isNonNegative());
208  
209    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
210      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
211 <        std::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
211 >        std::ostringstream oss;
212 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
213 >        throw OpenMDException(oss.str());          
214      }
215    }
216   }
217 <    
217 >  
218   bool Globals::addComponent(Component* comp) {
219      components_.push_back(comp);
220      return true;
# Line 196 | Line 225 | bool Globals::addZConsStamp(ZConsStamp* zcons) {
225      return true;
226   }
227  
228 + bool Globals::addRestraintStamp(RestraintStamp* rest) {
229 +    restraints_.push_back(rest);
230 +    return true;
231 + }
232 +
233   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
234      std::string molStampName = molStamp->getName();
235      std::map<std::string, MoleculeStamp*>::iterator i;
# Line 205 | Line 239 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
239          moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
240          ret = true;
241      } else {
242 <
242 >        std::ostringstream oss;
243 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
244 >        throw OpenMDException(oss.str());  
245      }
246      return ret;
247   }

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