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root/OpenMD/trunk/src/io/Globals.cpp
Revision: 1390
Committed: Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size: 13392 byte(s)
Log Message: 
Almost all of the changes necessary to create OpenMD out of our old
project (OOPSE-4)

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 gezelter 1390 * 1. Redistributions of source code must retain the above copyright
10 gezelter 246 * notice, this list of conditions and the following disclaimer.
11     *
12 gezelter 1390 * 2. Redistributions in binary form must reproduce the above copyright
13 gezelter 246 * 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 gezelter 1390 *
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 gezelter 246 */
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 gezelter 1390 namespace OpenMD {
53 tim 770 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(SurfaceTension, "surfaceTension");
92     DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93 gezelter 1291 DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94     DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95 tim 665 DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96 chrisfen 726 DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97 tim 895 DefineOptionalParameter(HydroPropFile, "HydroPropFile");
98 tim 906 DefineOptionalParameter(Viscosity, "viscosity");
99     DefineOptionalParameter(BeadSize, "beadSize");
100 gezelter 945 DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101     DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102 gezelter 1355 DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
103     DefineOptionalParameter(ThermalLength, "thermalLength");
104 chuckv 1095 DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
105 chuckv 1306 DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
106     DefineOptionalParameter(MTM_Ce, "MTM_Ce");
107     DefineOptionalParameter(MTM_G, "MTM_G");
108     DefineOptionalParameter(MTM_Io, "MTM_Io");
109     DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
110     DefineOptionalParameter(MTM_R, "MTM_R");
111 tim 906
112 gezelter 1327
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 gezelter 1078 DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
120     DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121 chrisfen 1050 DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
122 tim 665 DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
123 chrisfen 726 DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
124 tim 665 DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
125 tim 681 DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
126 gezelter 945 DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
127 chrisfen 998 DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128 tim 681
129 gezelter 1327 DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
130 skuang 1367 DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
131 skuang 1341 DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
132 skuang 1367 DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
133     DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
134     DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
135 gezelter 1331 DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
136 cli2 1360 DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
137 gezelter 1354 DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
138 cli2 1360 DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
139 gezelter 1327
140 cli2 1360
141 gezelter 1078 deprecatedKeywords_.insert("nComponents");
142     deprecatedKeywords_.insert("nZconstraints");
143     deprecatedKeywords_.insert("initialConfig");
144 cli2 1360 deprecatedKeywords_.insert("thermIntDistSpringConst");
145     deprecatedKeywords_.insert("thermIntThetaSpringConst");
146     deprecatedKeywords_.insert("thermIntOmegaSpringConst");
147     deprecatedKeywords_.insert("useSolidThermInt");
148     deprecatedKeywords_.insert("useLiquidThermInt");
149 gezelter 2
150     }
151    
152 tim 770 Globals::~Globals() {
153 tim 816 MemoryUtils::deletePointers(components_);
154     MemoryUtils::deletePointers(zconstraints_);
155 cli2 1360 MemoryUtils::deletePointers(restraints_);
156 gezelter 2 }
157    
158 tim 770 void Globals::validate() {
159     DataHolder::validate();
160 gezelter 2
161 tim 672 CheckParameter(ForceField, isNotEmpty());
162     CheckParameter(TargetTemp, isPositive());
163 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"));
164 tim 672 CheckParameter(Dt, isPositive());
165     CheckParameter(RunTime, isPositive());
166     CheckParameter(FinalConfig, isNotEmpty());
167     CheckParameter(SampleTime, isNonNegative());
168     CheckParameter(ResetTime, isNonNegative());
169     CheckParameter(StatusTime, isNonNegative());
170     CheckParameter(CutoffRadius, isPositive());
171     CheckParameter(SwitchingRadius, isNonNegative());
172     CheckParameter(Dielectric, isPositive());
173     CheckParameter(ThermalTime, isNonNegative());
174     CheckParameter(TauThermostat, isPositive());
175     CheckParameter(TauBarostat, isPositive());
176     CheckParameter(ZconsTime, isPositive());
177     CheckParameter(ZconsTol, isPositive());
178     CheckParameter(Seed, isPositive());
179 tim 850 CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
180 tim 672 CheckParameter(MinimizerMaxIter, isPositive());
181     CheckParameter(MinimizerWriteFrq, isPositive());
182     CheckParameter(MinimizerStepSize, isPositive());
183     CheckParameter(MinimizerFTol, isPositive());
184     CheckParameter(MinimizerGTol, isPositive());
185     CheckParameter(MinimizerLSTol, isPositive());
186     CheckParameter(MinimizerLSMaxIter, isPositive());
187     CheckParameter(ZconsGap, isPositive());
188     CheckParameter(ZconsFixtime, isPositive());
189 chrisfen 979 CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
190 tim 672 CheckParameter(ThermodynamicIntegrationK, isPositive());
191     CheckParameter(ForceFieldVariant, isNotEmpty());
192     CheckParameter(ForceFieldFileName, isNotEmpty());
193 tim 850 CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
194     CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
195     CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
196     CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
197 tim 672 //CheckParameter(StatFileFormat,);
198     CheckParameter(OrthoBoxTolerance, isPositive());
199 chrisfen 716 CheckParameter(DampingAlpha,isNonNegative());
200 tim 672 CheckParameter(SkinThickness, isPositive());
201 gezelter 945 CheckParameter(Viscosity, isNonNegative());
202 gezelter 1355 CheckParameter(ThermalConductivity, isNonNegative());
203     CheckParameter(ThermalLength, isNonNegative());
204 gezelter 945 CheckParameter(BeadSize, isPositive());
205     CheckParameter(FrozenBufferRadius, isPositive());
206     CheckParameter(LangevinBufferRadius, isPositive());
207 chuckv 1095 CheckParameter(NeighborListNeighbors, isPositive());
208 skuang 1367 CheckParameter(RNEMD_exchangeTime, isPositive());
209 skuang 1341 CheckParameter(RNEMD_nBins, isPositive() && isEven());
210 skuang 1367 CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
211     CheckParameter(RNEMD_targetFlux, isNonNegative());
212 chuckv 1095
213 tim 770 for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
214     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
215 tim 845 std::ostringstream oss;
216     oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
217 gezelter 1390 throw OpenMDException(oss.str());
218 tim 770 }
219     }
220     }
221 skuang 1367
222 tim 770 bool Globals::addComponent(Component* comp) {
223     components_.push_back(comp);
224     return true;
225     }
226 gezelter 2
227 tim 770 bool Globals::addZConsStamp(ZConsStamp* zcons) {
228     zconstraints_.push_back(zcons);
229     return true;
230 gezelter 2 }
231    
232 cli2 1360 bool Globals::addRestraintStamp(RestraintStamp* rest) {
233     restraints_.push_back(rest);
234     return true;
235     }
236    
237 tim 770 bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
238     std::string molStampName = molStamp->getName();
239     std::map<std::string, MoleculeStamp*>::iterator i;
240     bool ret = false;
241     i = moleculeStamps_.find(molStampName);
242     if (i == moleculeStamps_.end()) {
243     moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
244     ret = true;
245     } else {
246 tim 845 std::ostringstream oss;
247     oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
248 gezelter 1390 throw OpenMDException(oss.str());
249 tim 770 }
250     return ret;
251 gezelter 2 }
252 tim 770
253    
254     }