| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 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 |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
#include <algorithm> |
| 43 |
#include <fstream> |
| 44 |
#include "applications/staticProps/GofXyz.hpp" |
| 45 |
#include "utils/simError.h" |
| 46 |
|
| 47 |
namespace oopse { |
| 48 |
|
| 49 |
GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
| 50 |
: RadialDistrFunc(info, filename, sele1, sele2){ |
| 51 |
|
| 52 |
} |
| 53 |
|
| 54 |
|
| 55 |
void GofXyz::preProcess() { |
| 56 |
|
| 57 |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 58 |
std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
| 59 |
} |
| 60 |
} |
| 61 |
|
| 62 |
void GofXyz::initalizeHistogram() { |
| 63 |
npairs_ = 0; |
| 64 |
for (int i = 0; i < histogram_.size(); ++i) |
| 65 |
std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
| 66 |
} |
| 67 |
|
| 68 |
|
| 69 |
void GofXyz::processHistogram() { |
| 70 |
|
| 71 |
double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 72 |
double pairDensity = npairs_ /volume; |
| 73 |
double pairConstant = ( 4.0 * PI * pairDensity ) / 3.0; |
| 74 |
|
| 75 |
for(int i = 0 ; i < histogram_.size(); ++i){ |
| 76 |
|
| 77 |
double rLower = i * deltaR_; |
| 78 |
double rUpper = rLower + deltaR_; |
| 79 |
double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
| 80 |
double nIdeal = volSlice * pairConstant; |
| 81 |
|
| 82 |
for (int j = 0; j < histogram_[i].size(); ++j){ |
| 83 |
avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
| 84 |
} |
| 85 |
} |
| 86 |
|
| 87 |
} |
| 88 |
|
| 89 |
void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 90 |
|
| 91 |
if (sd1 == sd2) { |
| 92 |
return; |
| 93 |
} |
| 94 |
|
| 95 |
Vector3d pos1 = sd1->getPos(); |
| 96 |
Vector3d pos2 = sd2->getPos(); |
| 97 |
Vector3d r12 = pos1 - pos2; |
| 98 |
currentSnapshot_->wrapVector(r12); |
| 99 |
|
| 100 |
double distance = r12.length(); |
| 101 |
int whichRBin = distance / deltaR_; |
| 102 |
|
| 103 |
|
| 104 |
double cosAngle = evaluateAngle(sd1, sd2); |
| 105 |
double halfBin = (nAngleBins_ - 1) * 0.5; |
| 106 |
int whichThetaBin = halfBin * (cosAngle + 1.0) |
| 107 |
++histogram_[whichRBin][whichThetaBin]; |
| 108 |
|
| 109 |
++npairs_; |
| 110 |
} |
| 111 |
|
| 112 |
void GofXyz::writeRdf() { |
| 113 |
std::ofstream rdfStream(outputFilename_.c_str()); |
| 114 |
if (rdfStream.is_open()) { |
| 115 |
rdfStream << "#radial distribution function\n"; |
| 116 |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 117 |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 118 |
rdfStream << "#r\tcorrValue\n"; |
| 119 |
for (int i = 0; i < histogram_.size(); ++i) { |
| 120 |
double x = deltaR_ * (i + 0.5); |
| 121 |
|
| 122 |
for(int j = 0; j < histogram_[i].size(); ++j) { |
| 123 |
double y = deltaR_ * (j+ 0.5); |
| 124 |
|
| 125 |
for(int k = 0;k < histogram_[i].size(); ++k) { |
| 126 |
double z = deltaR_ * (k + 0.5); |
| 127 |
rdfStream << x << "\t" << y << "\t" << z << "\t" << histogram_[i][j][k]/nProcessed_ << "\n"; |
| 128 |
} |
| 129 |
} |
| 130 |
|
| 131 |
} else { |
| 132 |
|
| 133 |
|
| 134 |
} |
| 135 |
|
| 136 |
rdfStream.close(); |
| 137 |
} |
| 138 |
|
| 139 |
} |
| 140 |
|
| 141 |
|
| 142 |
|
