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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
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* 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include <algorithm> |
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#include "applications/staticProps/GofZ.hpp" |
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#include "utils/simError.h" |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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GofZ::GofZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins) |
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: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){ |
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std::fill(avgGofz_.begin(), avgGofz_.end(), 0.0); |
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} |
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|
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< |
void GofZ::initalizeHistogram() { |
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> |
void GofZ::initializeHistogram() { |
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std::fill(histogram_.begin(), histogram_.end(), 0); |
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} |
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|
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RealType pairDensity = nPairs /volume * 2.0; |
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RealType pairConstant = ( 2.0 * NumericConstant::PI * pairDensity ); |
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|
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< |
for(int i = 0 ; i < histogram_.size(); ++i){ |
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> |
for(unsigned int i = 0 ; i < histogram_.size(); ++i){ |
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|
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|
RealType zLower = i * deltaZ_; |
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|
RealType zUpper = zLower + deltaZ_; |
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rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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rdfStream << "#r\tcorrValue\n"; |
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< |
for (int i = 0; i < avgGofz_.size(); ++i) { |
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> |
for (unsigned int i = 0; i < avgGofz_.size(); ++i) { |
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RealType z = deltaZ_ * (i + 0.5); |
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rdfStream << z << "\t" << avgGofz_[i]/nProcessed_ << "\n"; |
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} |
