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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1354 by gezelter, Mon Jun 15 20:12:09 2009 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
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 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 102 | Line 99 | Globals::Globals() {
99    DefineOptionalParameter(BeadSize, "beadSize");
100    DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102 +  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
103 +  DefineOptionalParameter(ThermalLength, "thermalLength");
104    DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
105    DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
106    DefineOptionalParameter(MTM_Ce, "MTM_Ce");
# Line 117 | Line 116 | Globals::Globals() {
116    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118    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);
119    DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
120    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
# Line 133 | Line 127 | Globals::Globals() {
127    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128  
129    DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
130 <  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
130 >  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
131    DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
132 <  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
132 >  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
133 >  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
134 >  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
135    DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
136 <  DefineOptionalParameterWithDefaultValue(UseRestraints, "UseRestraints", false);
141 <  DefineOptionalParameterWithDefaultValue(Restraint_objectSelection, "Restraint_objectSelection", "select all");
142 <  DefineOptionalParameterWithDefaultValue(Restraint_type, "Restraint_type", "positional");
136 >  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
137    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
138 <  DefineOptionalParameterWithDefaultValue(Restraint_DisplacementSpringConstant, "Restraint_DisplacementSpringConstant", 0.0);
145 <  DefineOptionalParameterWithDefaultValue(Restraint_RollSpringConstant, "Restraint_RollSpringConstant", 0.0);   // phi
146 <  DefineOptionalParameterWithDefaultValue(Restraint_PitchSpringConstant, "Restraint_PitchSpringConstant", 0.0); // theta
147 <  DefineOptionalParameterWithDefaultValue(Restraint_YawSpringConstant, "Restraint_YawSpringConstant", 0.0);     // psi
148 <  
138 >  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
139  
140 +
141    deprecatedKeywords_.insert("nComponents");
142    deprecatedKeywords_.insert("nZconstraints");
143    deprecatedKeywords_.insert("initialConfig");
144 +  deprecatedKeywords_.insert("thermIntDistSpringConst");
145 +  deprecatedKeywords_.insert("thermIntThetaSpringConst");
146 +  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
147 +  deprecatedKeywords_.insert("useSolidThermInt");  
148 +  deprecatedKeywords_.insert("useLiquidThermInt");
149      
150   }
151  
152   Globals::~Globals() {
153      MemoryUtils::deletePointers(components_);
154      MemoryUtils::deletePointers(zconstraints_);
155 +    MemoryUtils::deletePointers(restraints_);
156   }
157  
158   void Globals::validate() {
# Line 193 | Line 190 | void Globals::validate() {
190    CheckParameter(ThermodynamicIntegrationK, isPositive());
191    CheckParameter(ForceFieldVariant, isNotEmpty());
192    CheckParameter(ForceFieldFileName, isNotEmpty());
196 –  CheckParameter(ThermIntDistSpringConst, isPositive());
197 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
198 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
193    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    //CheckParameter(StatFileFormat,);    
198    CheckParameter(OrthoBoxTolerance, isPositive());  
205 –  CheckParameter(ThermIntDistSpringConst, isPositive());
206 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
207 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
199    CheckParameter(DampingAlpha,isNonNegative());
200    CheckParameter(SkinThickness, isPositive());
201    CheckParameter(Viscosity, isNonNegative());
202 +  CheckParameter(ThermalConductivity, isNonNegative());
203 +  CheckParameter(ThermalLength, isNonNegative());
204    CheckParameter(BeadSize, isPositive());
205    CheckParameter(FrozenBufferRadius, isPositive());
206    CheckParameter(LangevinBufferRadius, isPositive());
207    CheckParameter(NeighborListNeighbors, isPositive());
208 <  CheckParameter(RNEMD_swapTime, isPositive());
208 >  CheckParameter(RNEMD_exchangeTime, isPositive());
209    CheckParameter(RNEMD_nBins, isPositive() && isEven());
210 <  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
211 <  CheckParameter(Restraint_DisplacementSpringConstant, isNonNegative());
219 <  CheckParameter(Restraint_RollSpringConstant, isNonNegative());
220 <  CheckParameter(Restraint_PitchSpringConstant, isNonNegative());
221 <  CheckParameter(Restraint_YawSpringConstant, isNonNegative());
222 <  CheckParameter(Restraint_type, isEqualIgnoreCase("P") || isEqualIgnoreCase("O") || isEqualIgnoreCase("P+O") || isEqualIgnoreCase("RMSD_P") || isEqualIgnoreCase("RMSD_O") || isEqualIgnoreCase("RMSD_P+RMSD_O"));
210 >  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  
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 240 | 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 251 | 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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