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root/group/trunk/OOPSE-4/src/io/Globals.cpp
Revision: 3013
Committed: Thu Sep 21 18:25:17 2006 UTC (19 years, 1 month ago) by chrisfen
File size: 11840 byte(s)
Log Message: 
fixed the half self term for wolf electrostatics and OOPSE now chooses a cutoff radius dependent alpha for damped electrostatics

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 tim 2982 //DefineOptionalParameter(InitialConfig, "initialConfig");
61 tim 2364 DefineOptionalParameter(FinalConfig, "finalConfig");
62     DefineOptionalParameter(SampleTime, "sampleTime");
63     DefineOptionalParameter(ResetTime, "resetTime");
64     DefineOptionalParameter(StatusTime, "statusTime");
65     DefineOptionalParameter(CutoffRadius, "cutoffRadius");
66     DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67     DefineOptionalParameter(Dielectric, "dielectric");
68     DefineOptionalParameter(TempSet, "tempSet");
69     DefineOptionalParameter(ThermalTime, "thermalTime");
70     DefineOptionalParameter(TargetPressure, "targetPressure");
71     DefineOptionalParameter(TauThermostat, "tauThermostat");
72     DefineOptionalParameter(TauBarostat, "tauBarostat");
73     DefineOptionalParameter(ZconsTime, "zconsTime");
74     DefineOptionalParameter(ZconsTol, "zconsTol");
75     DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
76     DefineOptionalParameter(Seed, "seed");
77     DefineOptionalParameter(Minimizer, "minimizer");
78     DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
79     DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
80     DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
81     DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
82     DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
83     DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
84     DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
85     DefineOptionalParameter(ZconsGap, "zconsGap");
86     DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
87     DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
88     DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
89     DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
90     DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
91     DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
92     DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
93     DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
94     DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
95     DefineOptionalParameter(SurfaceTension, "surfaceTension");
96     DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
97     DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
98 chrisfen 2415 DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99 tim 2364 DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
100 chrisfen 2425 DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
101 tim 2611 DefineOptionalParameter(HydroPropFile, "HydroPropFile");
102 tim 2634 DefineOptionalParameter(Viscosity, "viscosity");
103     DefineOptionalParameter(BeadSize, "beadSize");
104 gezelter 2733 DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
105     DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
106 tim 2634
107 tim 2364 DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
108     DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
109     DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
110     DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
111     DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
112     DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
113 chrisfen 2365 DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
114     DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
115     DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
116 chrisfen 3013 DefineOptionalParameter(DampingAlpha, "dampingAlpha");
117 tim 2364 DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
118 chrisfen 2425 DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
119 tim 2364 DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
120 tim 2380 DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
121 gezelter 2733 DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
122 chrisfen 2917 DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
123 tim 2380
124 gezelter 1490
125 tim 2469 deprecatedKeywords_.insert("nComponents");
126     deprecatedKeywords_.insert("nZconstraints");
127 tim 2982 deprecatedKeywords_.insert("initialConfig");
128 gezelter 1490
129     }
130    
131 tim 2469 Globals::~Globals() {
132 tim 2515 MemoryUtils::deletePointers(components_);
133     MemoryUtils::deletePointers(zconstraints_);
134 gezelter 1490 }
135    
136 tim 2469 void Globals::validate() {
137     DataHolder::validate();
138 gezelter 1490
139 tim 2371 CheckParameter(ForceField, isNotEmpty());
140     CheckParameter(TargetTemp, isPositive());
141 gezelter 2994 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"));
142 tim 2371 CheckParameter(Dt, isPositive());
143     CheckParameter(RunTime, isPositive());
144 tim 2982 //CheckParameter(InitialConfig, isNotEmpty());
145 tim 2371 CheckParameter(FinalConfig, isNotEmpty());
146     CheckParameter(SampleTime, isNonNegative());
147     CheckParameter(ResetTime, isNonNegative());
148     CheckParameter(StatusTime, isNonNegative());
149     CheckParameter(CutoffRadius, isPositive());
150     CheckParameter(SwitchingRadius, isNonNegative());
151     CheckParameter(Dielectric, isPositive());
152     CheckParameter(ThermalTime, isNonNegative());
153 xsun 2976 // CheckParameter(TargetPressure, isPositive());
154 tim 2371 CheckParameter(TauThermostat, isPositive());
155     CheckParameter(TauBarostat, isPositive());
156     CheckParameter(ZconsTime, isPositive());
157     CheckParameter(ZconsTol, isPositive());
158     CheckParameter(Seed, isPositive());
159 tim 2549 CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
160 tim 2371 CheckParameter(MinimizerMaxIter, isPositive());
161     CheckParameter(MinimizerWriteFrq, isPositive());
162     CheckParameter(MinimizerStepSize, isPositive());
163     CheckParameter(MinimizerFTol, isPositive());
164     CheckParameter(MinimizerGTol, isPositive());
165     CheckParameter(MinimizerLSTol, isPositive());
166     CheckParameter(MinimizerLSMaxIter, isPositive());
167     CheckParameter(ZconsGap, isPositive());
168     CheckParameter(ZconsFixtime, isPositive());
169 chrisfen 2777 CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
170 tim 2371 CheckParameter(ThermodynamicIntegrationK, isPositive());
171     CheckParameter(ForceFieldVariant, isNotEmpty());
172     CheckParameter(ForceFieldFileName, isNotEmpty());
173     CheckParameter(ThermIntDistSpringConst, isPositive());
174     CheckParameter(ThermIntThetaSpringConst, isPositive());
175     CheckParameter(ThermIntOmegaSpringConst, isPositive());
176 xsun 2976 // CheckParameter(SurfaceTension, isNonNegative());
177 tim 2549 CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
178     CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
179     CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
180     CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
181 tim 2371 //CheckParameter(StatFileFormat,);
182     CheckParameter(OrthoBoxTolerance, isPositive());
183     CheckParameter(ThermIntDistSpringConst, isPositive());
184     CheckParameter(ThermIntThetaSpringConst, isPositive());
185     CheckParameter(ThermIntOmegaSpringConst, isPositive());
186 chrisfen 2415 CheckParameter(DampingAlpha,isNonNegative());
187 tim 2371 CheckParameter(SkinThickness, isPositive());
188 gezelter 2733 CheckParameter(Viscosity, isNonNegative());
189     CheckParameter(BeadSize, isPositive());
190     CheckParameter(FrozenBufferRadius, isPositive());
191     CheckParameter(LangevinBufferRadius, isPositive());
192 tim 2469 for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
193     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
194 tim 2544 std::ostringstream oss;
195     oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
196     throw OOPSEException(oss.str());
197 tim 2469 }
198     }
199     }
200    
201     bool Globals::addComponent(Component* comp) {
202     components_.push_back(comp);
203     return true;
204     }
205 gezelter 1490
206 tim 2469 bool Globals::addZConsStamp(ZConsStamp* zcons) {
207     zconstraints_.push_back(zcons);
208     return true;
209 gezelter 1490 }
210    
211 tim 2469 bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
212     std::string molStampName = molStamp->getName();
213     std::map<std::string, MoleculeStamp*>::iterator i;
214     bool ret = false;
215     i = moleculeStamps_.find(molStampName);
216     if (i == moleculeStamps_.end()) {
217     moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
218     ret = true;
219     } else {
220 tim 2544 std::ostringstream oss;
221     oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
222     throw OOPSEException(oss.str());
223 tim 2469 }
224     return ret;
225 gezelter 1490 }
226 tim 2469
227    
228     }