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root/OpenMD/trunk/src/io/Globals.cpp
Revision: 1341
Committed: Fri May 8 19:47:05 2009 UTC (15 years, 11 months ago) by skuang
File size: 13081 byte(s)
Log Message: 
Bug fixes and sanity checks for RNEMD (nBins should be even), check to make
sure we aren't selecting inappropriate numbers of integrable Objects

File Contents

# User Rev Content
1 gezelter 404 /*
2 gezelter 246 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3     *
4     * The University of Notre Dame grants you ("Licensee") a
5     * non-exclusive, royalty free, license to use, modify and
6     * redistribute this software in source and binary code form, provided
7     * that the following conditions are met:
8     *
9     * 1. Acknowledgement of the program authors must be made in any
10     * publication of scientific results based in part on use of the
11     * program. An acceptable form of acknowledgement is citation of
12     * the article in which the program was described (Matthew
13     * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14     * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15     * Parallel Simulation Engine for Molecular Dynamics,"
16     * J. Comput. Chem. 26, pp. 252-271 (2005))
17     *
18     * 2. Redistributions of source code must retain the above copyright
19     * notice, this list of conditions and the following disclaimer.
20     *
21     * 3. Redistributions in binary form must reproduce the above copyright
22     * notice, this list of conditions and the following disclaimer in the
23     * documentation and/or other materials provided with the
24     * distribution.
25     *
26     * This software is provided "AS IS," without a warranty of any
27     * kind. All express or implied conditions, representations and
28     * warranties, including any implied warranty of merchantability,
29     * fitness for a particular purpose or non-infringement, are hereby
30     * excluded. The University of Notre Dame and its licensors shall not
31     * be liable for any damages suffered by licensee as a result of
32     * using, modifying or distributing the software or its
33     * derivatives. In no event will the University of Notre Dame or its
34     * licensors be liable for any lost revenue, profit or data, or for
35     * direct, indirect, special, consequential, incidental or punitive
36     * damages, however caused and regardless of the theory of liability,
37     * arising out of the use of or inability to use software, even if the
38     * University of Notre Dame has been advised of the possibility of
39     * such damages.
40     */
41    
42 gezelter 2 #include <stdlib.h>
43     #include <stdio.h>
44     #include <string.h>
45 tim 665 #include <string>
46 gezelter 2
47 tim 3 #include "io/Globals.hpp"
48 tim 816 #include "io/ParamConstraint.hpp"
49     #include "utils/MemoryUtils.hpp"
50 tim 3 #include "utils/simError.h"
51 gezelter 2
52 tim 770 namespace oopse {
53     Globals::Globals() {
54 tim 665 DefineParameter(ForceField, "forceField")
55    
56     DefineOptionalParameter(TargetTemp, "targetTemp");
57     DefineOptionalParameter(Ensemble, "ensemble");
58     DefineOptionalParameter(Dt, "dt");
59     DefineOptionalParameter(RunTime, "runTime");
60     DefineOptionalParameter(FinalConfig, "finalConfig");
61     DefineOptionalParameter(SampleTime, "sampleTime");
62     DefineOptionalParameter(ResetTime, "resetTime");
63     DefineOptionalParameter(StatusTime, "statusTime");
64     DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65     DefineOptionalParameter(SwitchingRadius, "switchingRadius");
66     DefineOptionalParameter(TempSet, "tempSet");
67     DefineOptionalParameter(ThermalTime, "thermalTime");
68 gezelter 1126 DefineOptionalParameter(TargetPressure, "targetPressure");
69 tim 665 DefineOptionalParameter(TauThermostat, "tauThermostat");
70     DefineOptionalParameter(TauBarostat, "tauBarostat");
71     DefineOptionalParameter(ZconsTime, "zconsTime");
72     DefineOptionalParameter(ZconsTol, "zconsTol");
73     DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74     DefineOptionalParameter(Seed, "seed");
75     DefineOptionalParameter(Minimizer, "minimizer");
76     DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77     DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
78     DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79     DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80     DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
81     DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
82     DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
83     DefineOptionalParameter(ZconsGap, "zconsGap");
84     DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
85     DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
86     DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
87     DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88     DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89     DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 gezelter 1078 DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91 tim 665 DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92     DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93     DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
94     DefineOptionalParameter(SurfaceTension, "surfaceTension");
95     DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96 gezelter 1291 DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
97     DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98 tim 665 DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99 chrisfen 726 DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
100 tim 895 DefineOptionalParameter(HydroPropFile, "HydroPropFile");
101 tim 906 DefineOptionalParameter(Viscosity, "viscosity");
102     DefineOptionalParameter(BeadSize, "beadSize");
103 gezelter 945 DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104     DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105 chuckv 1095 DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
106 chuckv 1306 DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
107     DefineOptionalParameter(MTM_Ce, "MTM_Ce");
108     DefineOptionalParameter(MTM_G, "MTM_G");
109     DefineOptionalParameter(MTM_Io, "MTM_Io");
110     DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
111     DefineOptionalParameter(MTM_R, "MTM_R");
112 tim 906
113 gezelter 1327
114 chuckv 1147
115 tim 665 DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
116 gezelter 1126 DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
117 tim 665 DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
118     DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
119     DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
120     DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
121     DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
122 chrisfen 666 DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
123     DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
124     DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
125 gezelter 1078 DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
126     DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
127 chrisfen 1050 DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
128 tim 665 DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
129 chrisfen 726 DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
130 tim 665 DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
131 tim 681 DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
132 gezelter 945 DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
133 chrisfen 998 DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
134 tim 681
135 gezelter 1327 DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
136     DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
137 skuang 1341 DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
138 gezelter 1327 DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139 gezelter 1331 DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
140 gezelter 1327
141    
142 gezelter 1078 deprecatedKeywords_.insert("nComponents");
143     deprecatedKeywords_.insert("nZconstraints");
144     deprecatedKeywords_.insert("initialConfig");
145 gezelter 2
146     }
147    
148 tim 770 Globals::~Globals() {
149 tim 816 MemoryUtils::deletePointers(components_);
150     MemoryUtils::deletePointers(zconstraints_);
151 gezelter 2 }
152    
153 tim 770 void Globals::validate() {
154     DataHolder::validate();
155 gezelter 2
156 tim 672 CheckParameter(ForceField, isNotEmpty());
157     CheckParameter(TargetTemp, isPositive());
158 chuckv 1293 CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("SMIPD"));
159 tim 672 CheckParameter(Dt, isPositive());
160     CheckParameter(RunTime, isPositive());
161     CheckParameter(FinalConfig, isNotEmpty());
162     CheckParameter(SampleTime, isNonNegative());
163     CheckParameter(ResetTime, isNonNegative());
164     CheckParameter(StatusTime, isNonNegative());
165     CheckParameter(CutoffRadius, isPositive());
166     CheckParameter(SwitchingRadius, isNonNegative());
167     CheckParameter(Dielectric, isPositive());
168     CheckParameter(ThermalTime, isNonNegative());
169     CheckParameter(TauThermostat, isPositive());
170     CheckParameter(TauBarostat, isPositive());
171     CheckParameter(ZconsTime, isPositive());
172     CheckParameter(ZconsTol, isPositive());
173     CheckParameter(Seed, isPositive());
174 tim 850 CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
175 tim 672 CheckParameter(MinimizerMaxIter, isPositive());
176     CheckParameter(MinimizerWriteFrq, isPositive());
177     CheckParameter(MinimizerStepSize, isPositive());
178     CheckParameter(MinimizerFTol, isPositive());
179     CheckParameter(MinimizerGTol, isPositive());
180     CheckParameter(MinimizerLSTol, isPositive());
181     CheckParameter(MinimizerLSMaxIter, isPositive());
182     CheckParameter(ZconsGap, isPositive());
183     CheckParameter(ZconsFixtime, isPositive());
184 chrisfen 979 CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
185 tim 672 CheckParameter(ThermodynamicIntegrationK, isPositive());
186     CheckParameter(ForceFieldVariant, isNotEmpty());
187     CheckParameter(ForceFieldFileName, isNotEmpty());
188     CheckParameter(ThermIntDistSpringConst, isPositive());
189     CheckParameter(ThermIntThetaSpringConst, isPositive());
190     CheckParameter(ThermIntOmegaSpringConst, isPositive());
191 tim 850 CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
192     CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
193     CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
194     CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
195 tim 672 //CheckParameter(StatFileFormat,);
196     CheckParameter(OrthoBoxTolerance, isPositive());
197     CheckParameter(ThermIntDistSpringConst, isPositive());
198     CheckParameter(ThermIntThetaSpringConst, isPositive());
199     CheckParameter(ThermIntOmegaSpringConst, isPositive());
200 chrisfen 716 CheckParameter(DampingAlpha,isNonNegative());
201 tim 672 CheckParameter(SkinThickness, isPositive());
202 gezelter 945 CheckParameter(Viscosity, isNonNegative());
203     CheckParameter(BeadSize, isPositive());
204     CheckParameter(FrozenBufferRadius, isPositive());
205     CheckParameter(LangevinBufferRadius, isPositive());
206 chuckv 1095 CheckParameter(NeighborListNeighbors, isPositive());
207 gezelter 1327 CheckParameter(RNEMD_swapTime, isPositive());
208 skuang 1341 CheckParameter(RNEMD_nBins, isPositive() && isEven());
209 gezelter 1327 CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
210 chuckv 1095
211 tim 770 for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
212     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
213 tim 845 std::ostringstream oss;
214     oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
215     throw OOPSEException(oss.str());
216 tim 770 }
217     }
218     }
219    
220     bool Globals::addComponent(Component* comp) {
221     components_.push_back(comp);
222     return true;
223     }
224 gezelter 2
225 tim 770 bool Globals::addZConsStamp(ZConsStamp* zcons) {
226     zconstraints_.push_back(zcons);
227     return true;
228 gezelter 2 }
229    
230 tim 770 bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
231     std::string molStampName = molStamp->getName();
232     std::map<std::string, MoleculeStamp*>::iterator i;
233     bool ret = false;
234     i = moleculeStamps_.find(molStampName);
235     if (i == moleculeStamps_.end()) {
236     moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
237     ret = true;
238     } else {
239 tim 845 std::ostringstream oss;
240     oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
241     throw OOPSEException(oss.str());
242 tim 770 }
243     return ret;
244 gezelter 2 }
245 tim 770
246    
247     }