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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 1398 by gezelter, Tue Dec 8 22:17:02 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 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 127 | Line 125 | Globals::Globals() {
125    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
126  
127    DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
128 <  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
128 >  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
129    DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
130 <  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
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    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
# Line 197 | Line 197 | void Globals::validate() {
197    CheckParameter(DampingAlpha,isNonNegative());
198    CheckParameter(SkinThickness, isPositive());
199    CheckParameter(Viscosity, isNonNegative());
200 –  CheckParameter(ThermalConductivity, isNonNegative());
201 –  CheckParameter(ThermalLength, isNonNegative());
200    CheckParameter(BeadSize, isPositive());
201    CheckParameter(FrozenBufferRadius, isPositive());
202    CheckParameter(LangevinBufferRadius, isPositive());
203    CheckParameter(NeighborListNeighbors, isPositive());
204 <  CheckParameter(RNEMD_swapTime, isPositive());
204 >  CheckParameter(RNEMD_exchangeTime, isPositive());
205    CheckParameter(RNEMD_nBins, isPositive() && isEven());
206 <  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
206 >  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
207 >  CheckParameter(RNEMD_targetFlux, isNonNegative());
208  
209    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
210      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
211          std::ostringstream oss;
212          oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
213 <        throw OOPSEException(oss.str());          
213 >        throw OpenMDException(oss.str());          
214      }
215    }
216   }
217 <    
217 >  
218   bool Globals::addComponent(Component* comp) {
219      components_.push_back(comp);
220      return true;
# Line 242 | Line 241 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
241      } else {
242          std::ostringstream oss;
243          oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
244 <        throw OOPSEException(oss.str());  
244 >        throw OpenMDException(oss.str());  
245      }
246      return ret;
247   }

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