| 6 |
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* 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. |
| 28 |
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* 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 |
|
*/ |
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|
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#include <cmath> |
| 45 |
|
#include "io/StatWriter.hpp" |
| 46 |
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#include "minimizers/Minimizer.hpp" |
| 47 |
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#include "primitives/Molecule.hpp" |
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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RealType dotProduct(const std::vector<RealType>& v1, const std::vector<RealType>& v2) { |
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if (v1.size() != v2.size()) { |
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|
| 64 |
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info(rhs), usingShake(false) { |
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|
|
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|
forceMan = new ForceManager(info); |
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< |
paramSet= new MinimizerParameterSet(info), |
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< |
calcDim(); |
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> |
paramSet= new MinimizerParameterSet(info), calcDim(); |
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curX = getCoor(); |
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curG.resize(ndim); |
| 70 |
|
|
| 829 |
|
int convgStatus; |
| 830 |
|
int stepStatus; |
| 831 |
|
int maxIter; |
| 832 |
< |
int writeFrq; |
| 832 |
> |
int writeFreq; |
| 833 |
|
int nextWriteIter; |
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|
Snapshot* curSnapshot =info->getSnapshotManager()->getCurrentSnapshot(); |
| 835 |
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DumpWriter dumpWriter(info); |
| 840 |
|
|
| 841 |
|
init(); |
| 842 |
|
|
| 843 |
< |
writeFrq = paramSet->getWriteFrq(); |
| 843 |
> |
writeFreq = paramSet->getWriteFreq(); |
| 844 |
|
|
| 845 |
< |
nextWriteIter = writeFrq; |
| 845 |
> |
nextWriteIter = writeFreq; |
| 846 |
|
|
| 847 |
|
maxIter = paramSet->getMaxIteration(); |
| 848 |
|
|
| 870 |
|
curSnapshot->increaseTime(1); |
| 871 |
|
|
| 872 |
|
if (curIter == nextWriteIter) { |
| 873 |
< |
nextWriteIter += writeFrq; |
| 873 |
> |
nextWriteIter += writeFreq; |
| 874 |
|
calcF(); |
| 875 |
< |
dumpWriter.writeDump(); |
| 875 |
> |
dumpWriter.writeDumpAndEor(); |
| 876 |
|
statWriter.writeStat(curSnapshot->statData); |
| 877 |
|
} |
| 878 |
|
|
| 902 |
|
|
| 903 |
|
|
| 904 |
|
RealType Minimizer::calcPotential() { |
| 905 |
< |
forceMan->calcForces(true, false); |
| 905 |
> |
forceMan->calcForces(); |
| 906 |
|
|
| 907 |
|
Snapshot* curSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 908 |
|
RealType potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
