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root/OpenMD/trunk/src/io/Globals.cpp
Revision: 1306
Committed: Thu Oct 16 18:25:36 2008 UTC (16 years, 6 months ago) by chuckv
File size: 12402 byte(s)
Log Message: 
Returned old LD forces to SMIPDForceManager.

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 chuckv 1147
114 tim 665 DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
115 gezelter 1126 DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
116 tim 665 DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117     DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118     DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
119     DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
120     DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
121 chrisfen 666 DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
122     DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
123     DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
124 gezelter 1078 DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
125     DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
126 chrisfen 1050 DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
127 tim 665 DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
128 chrisfen 726 DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
129 tim 665 DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
130 tim 681 DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
131 gezelter 945 DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
132 chrisfen 998 DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
133 tim 681
134 gezelter 1078 deprecatedKeywords_.insert("nComponents");
135     deprecatedKeywords_.insert("nZconstraints");
136     deprecatedKeywords_.insert("initialConfig");
137 gezelter 2
138     }
139    
140 tim 770 Globals::~Globals() {
141 tim 816 MemoryUtils::deletePointers(components_);
142     MemoryUtils::deletePointers(zconstraints_);
143 gezelter 2 }
144    
145 tim 770 void Globals::validate() {
146     DataHolder::validate();
147 gezelter 2
148 tim 672 CheckParameter(ForceField, isNotEmpty());
149     CheckParameter(TargetTemp, isPositive());
150 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"));
151 tim 672 CheckParameter(Dt, isPositive());
152     CheckParameter(RunTime, isPositive());
153     CheckParameter(FinalConfig, isNotEmpty());
154     CheckParameter(SampleTime, isNonNegative());
155     CheckParameter(ResetTime, isNonNegative());
156     CheckParameter(StatusTime, isNonNegative());
157     CheckParameter(CutoffRadius, isPositive());
158     CheckParameter(SwitchingRadius, isNonNegative());
159     CheckParameter(Dielectric, isPositive());
160     CheckParameter(ThermalTime, isNonNegative());
161     CheckParameter(TauThermostat, isPositive());
162     CheckParameter(TauBarostat, isPositive());
163     CheckParameter(ZconsTime, isPositive());
164     CheckParameter(ZconsTol, isPositive());
165     CheckParameter(Seed, isPositive());
166 tim 850 CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
167 tim 672 CheckParameter(MinimizerMaxIter, isPositive());
168     CheckParameter(MinimizerWriteFrq, isPositive());
169     CheckParameter(MinimizerStepSize, isPositive());
170     CheckParameter(MinimizerFTol, isPositive());
171     CheckParameter(MinimizerGTol, isPositive());
172     CheckParameter(MinimizerLSTol, isPositive());
173     CheckParameter(MinimizerLSMaxIter, isPositive());
174     CheckParameter(ZconsGap, isPositive());
175     CheckParameter(ZconsFixtime, isPositive());
176 chrisfen 979 CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
177 tim 672 CheckParameter(ThermodynamicIntegrationK, isPositive());
178     CheckParameter(ForceFieldVariant, isNotEmpty());
179     CheckParameter(ForceFieldFileName, isNotEmpty());
180     CheckParameter(ThermIntDistSpringConst, isPositive());
181     CheckParameter(ThermIntThetaSpringConst, isPositive());
182     CheckParameter(ThermIntOmegaSpringConst, isPositive());
183 tim 850 CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
184     CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
185     CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
186     CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
187 tim 672 //CheckParameter(StatFileFormat,);
188     CheckParameter(OrthoBoxTolerance, isPositive());
189     CheckParameter(ThermIntDistSpringConst, isPositive());
190     CheckParameter(ThermIntThetaSpringConst, isPositive());
191     CheckParameter(ThermIntOmegaSpringConst, isPositive());
192 chrisfen 716 CheckParameter(DampingAlpha,isNonNegative());
193 tim 672 CheckParameter(SkinThickness, isPositive());
194 gezelter 945 CheckParameter(Viscosity, isNonNegative());
195     CheckParameter(BeadSize, isPositive());
196     CheckParameter(FrozenBufferRadius, isPositive());
197     CheckParameter(LangevinBufferRadius, isPositive());
198 chuckv 1095 CheckParameter(NeighborListNeighbors, isPositive());
199    
200 tim 770 for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
201     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
202 tim 845 std::ostringstream oss;
203     oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
204     throw OOPSEException(oss.str());
205 tim 770 }
206     }
207     }
208    
209     bool Globals::addComponent(Component* comp) {
210     components_.push_back(comp);
211     return true;
212     }
213 gezelter 2
214 tim 770 bool Globals::addZConsStamp(ZConsStamp* zcons) {
215     zconstraints_.push_back(zcons);
216     return true;
217 gezelter 2 }
218    
219 tim 770 bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
220     std::string molStampName = molStamp->getName();
221     std::map<std::string, MoleculeStamp*>::iterator i;
222     bool ret = false;
223     i = moleculeStamps_.find(molStampName);
224     if (i == moleculeStamps_.end()) {
225     moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
226     ret = true;
227     } else {
228 tim 845 std::ostringstream oss;
229     oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
230     throw OOPSEException(oss.str());
231 tim 770 }
232     return ret;
233 gezelter 2 }
234 tim 770
235    
236     }