| 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. |
| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include <algorithm> |
| 45 |
|
#include "applications/staticProps/GofR.hpp" |
| 46 |
|
#include "utils/simError.h" |
| 47 |
|
|
| 48 |
< |
namespace oopse { |
| 48 |
> |
namespace OpenMD { |
| 49 |
|
|
| 50 |
|
GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins) |
| 51 |
|
: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){ |
| 63 |
|
std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0); |
| 64 |
|
} |
| 65 |
|
|
| 66 |
< |
void GofR::initalizeHistogram() { |
| 66 |
> |
void GofR::initializeHistogram() { |
| 67 |
|
std::fill(histogram_.begin(), histogram_.end(), 0); |
| 68 |
|
} |
| 69 |
|
|
| 75 |
|
RealType pairDensity = nPairs /volume * 2.0; |
| 76 |
|
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
| 77 |
|
|
| 78 |
< |
for(int i = 0 ; i < histogram_.size(); ++i){ |
| 78 |
> |
for(unsigned int i = 0 ; i < histogram_.size(); ++i){ |
| 79 |
|
|
| 80 |
|
RealType rLower = i * deltaR_; |
| 81 |
|
RealType rUpper = rLower + deltaR_; |
| 96 |
|
Vector3d pos1 = sd1->getPos(); |
| 97 |
|
Vector3d pos2 = sd2->getPos(); |
| 98 |
|
Vector3d r12 = pos2 - pos1; |
| 99 |
< |
currentSnapshot_->wrapVector(r12); |
| 99 |
> |
if (usePeriodicBoundaryConditions_) |
| 100 |
> |
currentSnapshot_->wrapVector(r12); |
| 101 |
|
|
| 102 |
|
RealType distance = r12.length(); |
| 103 |
|
|
| 115 |
|
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 116 |
|
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 117 |
|
rdfStream << "#r\tcorrValue\n"; |
| 118 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 118 |
> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
| 119 |
|
RealType r = deltaR_ * (i + 0.5); |
| 120 |
|
rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n"; |
| 121 |
|
} |
| 120 |
– |
|
| 122 |
|
} else { |
| 123 |
|
|
| 124 |
|
sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str()); |
