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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1367 by skuang, Mon Oct 19 13:35:42 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 99 | Line 99 | Globals::Globals() {
99    DefineOptionalParameter(BeadSize, "beadSize");
100    DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102 –  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
103 –  DefineOptionalParameter(ThermalLength, "thermalLength");
102    DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
103    DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
104    DefineOptionalParameter(MTM_Ce, "MTM_Ce");
# Line 108 | 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 136 | Line 134 | Globals::Globals() {
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");
# Line 178 | 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 199 | Line 198 | void Globals::validate() {
198    CheckParameter(DampingAlpha,isNonNegative());
199    CheckParameter(SkinThickness, isPositive());
200    CheckParameter(Viscosity, isNonNegative());
202 –  CheckParameter(ThermalConductivity, isNonNegative());
203 –  CheckParameter(ThermalLength, isNonNegative());
201    CheckParameter(BeadSize, isPositive());
202    CheckParameter(FrozenBufferRadius, isPositive());
203    CheckParameter(LangevinBufferRadius, isPositive());
# Line 209 | Line 206 | void Globals::validate() {
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   }
# Line 245 | 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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