| 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, double len, int nrbins) |
| 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){ |
| 52 |
|
|
| 53 |
< |
deltaR_ = len_ /nRBins_; |
| 53 |
> |
deltaR_ = len_ /nRBins_; |
| 54 |
|
|
| 55 |
< |
histogram_.resize(nRBins_); |
| 56 |
< |
avgGofr_.resize(nRBins_); |
| 55 |
> |
histogram_.resize(nRBins_); |
| 56 |
> |
avgGofr_.resize(nRBins_); |
| 57 |
|
|
| 58 |
< |
setOutputName(getPrefix(filename) + ".gofr"); |
| 59 |
< |
} |
| 58 |
> |
setOutputName(getPrefix(filename) + ".gofr"); |
| 59 |
> |
} |
| 60 |
|
|
| 61 |
|
|
| 62 |
< |
void GofR::preProcess() { |
| 62 |
> |
void GofR::preProcess() { |
| 63 |
|
std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0); |
| 64 |
< |
} |
| 64 |
> |
} |
| 65 |
|
|
| 66 |
< |
void GofR::initalizeHistogram() { |
| 66 |
> |
void GofR::initializeHistogram() { |
| 67 |
|
std::fill(histogram_.begin(), histogram_.end(), 0); |
| 68 |
< |
} |
| 68 |
> |
} |
| 69 |
|
|
| 70 |
|
|
| 71 |
< |
void GofR::processHistogram() { |
| 71 |
> |
void GofR::processHistogram() { |
| 72 |
|
|
| 73 |
|
int nPairs = getNPairs(); |
| 74 |
< |
double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 75 |
< |
double pairDensity = nPairs /volume * 2.0; |
| 76 |
< |
double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
| 74 |
> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 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 |
< |
double rLower = i * deltaR_; |
| 81 |
< |
double rUpper = rLower + deltaR_; |
| 82 |
< |
double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
| 83 |
< |
double nIdeal = volSlice * pairConstant; |
| 80 |
> |
RealType rLower = i * deltaR_; |
| 81 |
> |
RealType rUpper = rLower + deltaR_; |
| 82 |
> |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
| 83 |
> |
RealType nIdeal = volSlice * pairConstant; |
| 84 |
|
|
| 85 |
< |
avgGofr_[i] += histogram_[i] / nIdeal; |
| 85 |
> |
avgGofr_[i] += histogram_[i] / nIdeal; |
| 86 |
|
} |
| 87 |
|
|
| 88 |
< |
} |
| 88 |
> |
} |
| 89 |
|
|
| 90 |
< |
void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 90 |
> |
void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 91 |
|
|
| 92 |
|
if (sd1 == sd2) { |
| 93 |
< |
return; |
| 93 |
> |
return; |
| 94 |
|
} |
| 95 |
|
|
| 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 |
< |
double distance = r12.length(); |
| 102 |
> |
RealType distance = r12.length(); |
| 103 |
|
|
| 104 |
|
if (distance < len_) { |
| 105 |
< |
int whichBin = distance / deltaR_; |
| 106 |
< |
histogram_[whichBin] += 2; |
| 105 |
> |
int whichBin = distance / deltaR_; |
| 106 |
> |
histogram_[whichBin] += 2; |
| 107 |
|
} |
| 108 |
< |
} |
| 108 |
> |
} |
| 109 |
|
|
| 110 |
|
|
| 111 |
< |
void GofR::writeRdf() { |
| 111 |
> |
void GofR::writeRdf() { |
| 112 |
|
std::ofstream rdfStream(outputFilename_.c_str()); |
| 113 |
|
if (rdfStream.is_open()) { |
| 114 |
< |
rdfStream << "#radial distribution function\n"; |
| 115 |
< |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 116 |
< |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 117 |
< |
rdfStream << "#r\tcorrValue\n"; |
| 118 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 119 |
< |
double r = deltaR_ * (i + 0.5); |
| 120 |
< |
rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n"; |
| 121 |
< |
} |
| 120 |
< |
|
| 114 |
> |
rdfStream << "#radial distribution function\n"; |
| 115 |
> |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 116 |
> |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 117 |
> |
rdfStream << "#r\tcorrValue\n"; |
| 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 |
> |
} |
| 122 |
|
} else { |
| 123 |
|
|
| 124 |
< |
sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str()); |
| 125 |
< |
painCave.isFatal = 1; |
| 126 |
< |
simError(); |
| 124 |
> |
sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str()); |
| 125 |
> |
painCave.isFatal = 1; |
| 126 |
> |
simError(); |
| 127 |
|
} |
| 128 |
|
|
| 129 |
|
rdfStream.close(); |
| 130 |
< |
} |
| 130 |
> |
} |
| 131 |
|
|
| 132 |
|
} |
| 133 |
|
|
