| 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. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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> |
| 44 |
#include <fstream> |
| 45 |
#include "applications/staticProps/GofAngle2.hpp" |
| 46 |
#include "utils/simError.h" |
| 47 |
|
| 48 |
namespace OpenMD { |
| 49 |
|
| 50 |
GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, |
| 51 |
const std::string& sele2, int nangleBins) |
| 52 |
: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) { |
| 53 |
|
| 54 |
setOutputName(getPrefix(filename) + ".gto"); |
| 55 |
|
| 56 |
deltaCosAngle_ = 2.0 / nAngleBins_; |
| 57 |
|
| 58 |
histogram_.resize(nAngleBins_); |
| 59 |
avgGofr_.resize(nAngleBins_); |
| 60 |
for (int i = 0 ; i < nAngleBins_; ++i) { |
| 61 |
histogram_[i].resize(nAngleBins_); |
| 62 |
avgGofr_[i].resize(nAngleBins_); |
| 63 |
} |
| 64 |
|
| 65 |
} |
| 66 |
|
| 67 |
|
| 68 |
void GofAngle2::preProcess() { |
| 69 |
|
| 70 |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 71 |
std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
| 72 |
} |
| 73 |
} |
| 74 |
|
| 75 |
void GofAngle2::initalizeHistogram() { |
| 76 |
npairs_ = 0; |
| 77 |
for (int i = 0; i < histogram_.size(); ++i) |
| 78 |
std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
| 79 |
} |
| 80 |
|
| 81 |
|
| 82 |
void GofAngle2::processHistogram() { |
| 83 |
|
| 84 |
//std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>) |
| 85 |
|
| 86 |
} |
| 87 |
|
| 88 |
void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 89 |
|
| 90 |
if (sd1 == sd2) { |
| 91 |
return; |
| 92 |
} |
| 93 |
|
| 94 |
Vector3d pos1 = sd1->getPos(); |
| 95 |
Vector3d pos2 = sd2->getPos(); |
| 96 |
Vector3d r12 = pos1 - pos2; |
| 97 |
if (usePeriodicBoundaryConditions_) |
| 98 |
currentSnapshot_->wrapVector(r12); |
| 99 |
Vector3d dipole1 = sd1->getElectroFrame().getColumn(2); |
| 100 |
Vector3d dipole2 = sd2->getElectroFrame().getColumn(2); |
| 101 |
|
| 102 |
r12.normalize(); |
| 103 |
dipole1.normalize(); |
| 104 |
dipole2.normalize(); |
| 105 |
|
| 106 |
|
| 107 |
RealType cosAngle1 = dot(r12, dipole1); |
| 108 |
RealType cosAngle2 = dot(dipole1, dipole2); |
| 109 |
|
| 110 |
RealType halfBin = (nAngleBins_ - 1) * 0.5; |
| 111 |
int angleBin1 = halfBin * (cosAngle1 + 1.0); |
| 112 |
int angleBin2 = halfBin * (cosAngle2 + 1.0); |
| 113 |
|
| 114 |
++histogram_[angleBin1][angleBin2]; |
| 115 |
++npairs_; |
| 116 |
} |
| 117 |
|
| 118 |
void GofAngle2::writeRdf() { |
| 119 |
std::ofstream rdfStream(outputFilename_.c_str()); |
| 120 |
if (rdfStream.is_open()) { |
| 121 |
rdfStream << "#radial distribution function\n"; |
| 122 |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 123 |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 124 |
rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; |
| 125 |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 126 |
RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; |
| 127 |
|
| 128 |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
| 129 |
RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 130 |
rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t"; |
| 131 |
} |
| 132 |
|
| 133 |
rdfStream << "\n"; |
| 134 |
} |
| 135 |
|
| 136 |
} else { |
| 137 |
|
| 138 |
sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str()); |
| 139 |
painCave.isFatal = 1; |
| 140 |
simError(); |
| 141 |
} |
| 142 |
|
| 143 |
rdfStream.close(); |
| 144 |
} |
| 145 |
|
| 146 |
} |
