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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1331 by gezelter, Thu Apr 2 16:04:52 2009 UTC vs.
Revision 1423 by gezelter, Tue Mar 30 15:05:13 2010 UTC

# Line 1 | Line 1
1   /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2 > * Copyright (c) 2005, 2010 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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
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 + *
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   */
41  
42   #include <stdlib.h>
# Line 49 | Line 49
49   #include "utils/MemoryUtils.hpp"
50   #include "utils/simError.h"
51  
52 < namespace oopse {
52 > namespace OpenMD {
53   Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
55  
# Line 74 | Line 74 | Globals::Globals() {
74    DefineOptionalParameter(Seed, "seed");
75    DefineOptionalParameter(Minimizer, "minimizer");
76    DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77 <  DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
77 >  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
78    DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79    DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80    DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
# Line 88 | Line 88 | Globals::Globals() {
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90    DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91 –  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92 –  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93 –  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
91    DefineOptionalParameter(SurfaceTension, "surfaceTension");
92    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
# Line 109 | Line 106 | Globals::Globals() {
106    DefineOptionalParameter(MTM_Io, "MTM_Io");
107    DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
108    DefineOptionalParameter(MTM_R, "MTM_R");
109 <  
109 >  DefineOptionalParameter(Alpha, "alpha");
110  
111    
112    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
# Line 117 | Line 114 | Globals::Globals() {
114    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
115    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
116    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
120 –  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
121 –  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
122 –  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
123 –  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
124 –  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
117    DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
118    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
# Line 133 | Line 125 | Globals::Globals() {
125    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
126  
127    DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
128 <  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
129 <  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 15);
130 <  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
128 >  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
129 >  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
130 >  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
131 >  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
132 >  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
133    DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
134 <  
134 >  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135 >  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136 >  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137 >  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
138  
139 +
140    deprecatedKeywords_.insert("nComponents");
141    deprecatedKeywords_.insert("nZconstraints");
142    deprecatedKeywords_.insert("initialConfig");
143 +  deprecatedKeywords_.insert("thermIntDistSpringConst");
144 +  deprecatedKeywords_.insert("thermIntThetaSpringConst");
145 +  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
146 +  deprecatedKeywords_.insert("useSolidThermInt");  
147 +  deprecatedKeywords_.insert("useLiquidThermInt");
148      
149   }
150  
151   Globals::~Globals() {
152      MemoryUtils::deletePointers(components_);
153      MemoryUtils::deletePointers(zconstraints_);
154 +    MemoryUtils::deletePointers(restraints_);
155   }
156  
157   void Globals::validate() {
# Line 173 | Line 177 | void Globals::validate() {
177    CheckParameter(Seed, isPositive());
178    CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
179    CheckParameter(MinimizerMaxIter, isPositive());
180 <  CheckParameter(MinimizerWriteFrq, isPositive());
180 >  CheckParameter(MinimizerWriteFreq, isPositive());
181    CheckParameter(MinimizerStepSize, isPositive());
182    CheckParameter(MinimizerFTol, isPositive());
183    CheckParameter(MinimizerGTol, isPositive());
# Line 185 | Line 189 | void Globals::validate() {
189    CheckParameter(ThermodynamicIntegrationK, isPositive());
190    CheckParameter(ForceFieldVariant, isNotEmpty());
191    CheckParameter(ForceFieldFileName, isNotEmpty());
188 –  CheckParameter(ThermIntDistSpringConst, isPositive());
189 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
190 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
192    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
193    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
194    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
195    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
196    //CheckParameter(StatFileFormat,);    
197    CheckParameter(OrthoBoxTolerance, isPositive());  
197 –  CheckParameter(ThermIntDistSpringConst, isPositive());
198 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
199 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
198    CheckParameter(DampingAlpha,isNonNegative());
199    CheckParameter(SkinThickness, isPositive());
200    CheckParameter(Viscosity, isNonNegative());
# Line 204 | Line 202 | void Globals::validate() {
202    CheckParameter(FrozenBufferRadius, isPositive());
203    CheckParameter(LangevinBufferRadius, isPositive());
204    CheckParameter(NeighborListNeighbors, isPositive());
205 <  CheckParameter(RNEMD_swapTime, isPositive());
206 <  CheckParameter(RNEMD_nBins, isPositive());
207 <  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
205 >  CheckParameter(RNEMD_exchangeTime, isPositive());
206 >  CheckParameter(RNEMD_nBins, isPositive() && isEven());
207 >  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
208 >  CheckParameter(RNEMD_targetFlux, isNonNegative());
209 >  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
210 >  CheckParameter(Alpha, isPositive());
211  
212 +  
213    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
214      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
215          std::ostringstream oss;
216          oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
217 <        throw OOPSEException(oss.str());          
217 >        throw OpenMDException(oss.str());          
218      }
219    }
220   }
221 <    
221 >  
222   bool Globals::addComponent(Component* comp) {
223      components_.push_back(comp);
224      return true;
# Line 227 | Line 229 | bool Globals::addZConsStamp(ZConsStamp* zcons) {
229      return true;
230   }
231  
232 + bool Globals::addRestraintStamp(RestraintStamp* rest) {
233 +    restraints_.push_back(rest);
234 +    return true;
235 + }
236 +
237   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
238      std::string molStampName = molStamp->getName();
239      std::map<std::string, MoleculeStamp*>::iterator i;
# Line 238 | Line 245 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
245      } else {
246          std::ostringstream oss;
247          oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
248 <        throw OOPSEException(oss.str());  
248 >        throw OpenMDException(oss.str());  
249      }
250      return ret;
251   }

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