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root/group/trunk/OOPSE-4/src/io/Globals.cpp
Revision: 3520
Committed: Mon Sep 7 16:31:51 2009 UTC (15 years, 10 months ago) by cli2
File size: 12964 byte(s)
Log Message: 
Added new restraint infrastructure
Added MolecularRestraints
Added ObjectRestraints
Added RestraintStamp
Updated thermodynamic integration to use ObjectRestraints
Added Quaternion mathematics for twist swing decompositions
Significantly updated RestWriter and RestReader to use dump-like files
Added selections for x, y, and z coordinates of atoms
Removed monolithic Restraints class
Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody
Added some rotational capabilities to prinicpalAxisCalculator

File Contents

# User Rev Content
1 gezelter 2088 /*
2 gezelter 1930 * 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 1490 #include <stdlib.h>
43     #include <stdio.h>
44     #include <string.h>
45 tim 2364 #include <string>
46 gezelter 1490
47 tim 1492 #include "io/Globals.hpp"
48 tim 2515 #include "io/ParamConstraint.hpp"
49     #include "utils/MemoryUtils.hpp"
50 tim 1492 #include "utils/simError.h"
51 gezelter 1490
52 tim 2469 namespace oopse {
53     Globals::Globals() {
54 tim 2364 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 3126 DefineOptionalParameter(TargetPressure, "targetPressure");
69 tim 2364 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 3054 DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91 tim 2364 DefineOptionalParameter(SurfaceTension, "surfaceTension");
92     DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93 gezelter 3448 DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94     DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95 tim 2364 DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96 chrisfen 2425 DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97 tim 2611 DefineOptionalParameter(HydroPropFile, "HydroPropFile");
98 tim 2634 DefineOptionalParameter(Viscosity, "viscosity");
99     DefineOptionalParameter(BeadSize, "beadSize");
100 gezelter 2733 DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101     DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102 gezelter 3515 DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
103     DefineOptionalParameter(ThermalLength, "thermalLength");
104 chuckv 3080 DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
105 chuckv 3463 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 2634
112 gezelter 3486
113 chuckv 3149
114 tim 2364 DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
115 gezelter 3126 DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
116 tim 2364 DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117     DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118     DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
119 gezelter 3054 DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
120     DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121 chrisfen 3020 DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
122 tim 2364 DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
123 chrisfen 2425 DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
124 tim 2364 DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
125 tim 2380 DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
126 gezelter 2733 DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
127 chrisfen 2917 DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128 tim 2380
129 gezelter 3486 DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
130     DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
131 skuang 3501 DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
132 gezelter 3486 DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
133 gezelter 3490 DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
134 cli2 3520 DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135 gezelter 3514 DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136 cli2 3520 DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137 gezelter 3486
138 cli2 3520
139 gezelter 3054 deprecatedKeywords_.insert("nComponents");
140     deprecatedKeywords_.insert("nZconstraints");
141     deprecatedKeywords_.insert("initialConfig");
142 cli2 3520 deprecatedKeywords_.insert("thermIntDistSpringConst");
143     deprecatedKeywords_.insert("thermIntThetaSpringConst");
144     deprecatedKeywords_.insert("thermIntOmegaSpringConst");
145     deprecatedKeywords_.insert("useSolidThermInt");
146     deprecatedKeywords_.insert("useLiquidThermInt");
147 gezelter 1490
148     }
149    
150 tim 2469 Globals::~Globals() {
151 tim 2515 MemoryUtils::deletePointers(components_);
152     MemoryUtils::deletePointers(zconstraints_);
153 cli2 3520 MemoryUtils::deletePointers(restraints_);
154 gezelter 1490 }
155    
156 tim 2469 void Globals::validate() {
157     DataHolder::validate();
158 gezelter 1490
159 tim 2371 CheckParameter(ForceField, isNotEmpty());
160     CheckParameter(TargetTemp, isPositive());
161 chuckv 3450 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 tim 2371 CheckParameter(Dt, isPositive());
163     CheckParameter(RunTime, isPositive());
164     CheckParameter(FinalConfig, isNotEmpty());
165     CheckParameter(SampleTime, isNonNegative());
166     CheckParameter(ResetTime, isNonNegative());
167     CheckParameter(StatusTime, isNonNegative());
168     CheckParameter(CutoffRadius, isPositive());
169     CheckParameter(SwitchingRadius, isNonNegative());
170     CheckParameter(Dielectric, isPositive());
171     CheckParameter(ThermalTime, isNonNegative());
172     CheckParameter(TauThermostat, isPositive());
173     CheckParameter(TauBarostat, isPositive());
174     CheckParameter(ZconsTime, isPositive());
175     CheckParameter(ZconsTol, isPositive());
176     CheckParameter(Seed, isPositive());
177 tim 2549 CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
178 tim 2371 CheckParameter(MinimizerMaxIter, isPositive());
179     CheckParameter(MinimizerWriteFrq, isPositive());
180     CheckParameter(MinimizerStepSize, isPositive());
181     CheckParameter(MinimizerFTol, isPositive());
182     CheckParameter(MinimizerGTol, isPositive());
183     CheckParameter(MinimizerLSTol, isPositive());
184     CheckParameter(MinimizerLSMaxIter, isPositive());
185     CheckParameter(ZconsGap, isPositive());
186     CheckParameter(ZconsFixtime, isPositive());
187 chrisfen 2777 CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
188 tim 2371 CheckParameter(ThermodynamicIntegrationK, isPositive());
189     CheckParameter(ForceFieldVariant, isNotEmpty());
190     CheckParameter(ForceFieldFileName, isNotEmpty());
191 tim 2549 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 2371 //CheckParameter(StatFileFormat,);
196     CheckParameter(OrthoBoxTolerance, isPositive());
197 chrisfen 2415 CheckParameter(DampingAlpha,isNonNegative());
198 tim 2371 CheckParameter(SkinThickness, isPositive());
199 gezelter 2733 CheckParameter(Viscosity, isNonNegative());
200 gezelter 3515 CheckParameter(ThermalConductivity, isNonNegative());
201     CheckParameter(ThermalLength, isNonNegative());
202 gezelter 2733 CheckParameter(BeadSize, isPositive());
203     CheckParameter(FrozenBufferRadius, isPositive());
204     CheckParameter(LangevinBufferRadius, isPositive());
205 chuckv 3080 CheckParameter(NeighborListNeighbors, isPositive());
206 gezelter 3486 CheckParameter(RNEMD_swapTime, isPositive());
207 skuang 3501 CheckParameter(RNEMD_nBins, isPositive() && isEven());
208 gezelter 3486 CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
209 chuckv 3080
210 tim 2469 for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
211     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
212 tim 2544 std::ostringstream oss;
213     oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
214     throw OOPSEException(oss.str());
215 tim 2469 }
216     }
217     }
218    
219     bool Globals::addComponent(Component* comp) {
220     components_.push_back(comp);
221     return true;
222     }
223 gezelter 1490
224 tim 2469 bool Globals::addZConsStamp(ZConsStamp* zcons) {
225     zconstraints_.push_back(zcons);
226     return true;
227 gezelter 1490 }
228    
229 cli2 3520 bool Globals::addRestraintStamp(RestraintStamp* rest) {
230     restraints_.push_back(rest);
231     return true;
232     }
233    
234 tim 2469 bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
235     std::string molStampName = molStamp->getName();
236     std::map<std::string, MoleculeStamp*>::iterator i;
237     bool ret = false;
238     i = moleculeStamps_.find(molStampName);
239     if (i == moleculeStamps_.end()) {
240     moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
241     ret = true;
242     } else {
243 tim 2544 std::ostringstream oss;
244     oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
245     throw OOPSEException(oss.str());
246 tim 2469 }
247     return ret;
248 gezelter 1490 }
249 tim 2469
250    
251     }