| 1 |
tim |
1990 |
/* |
| 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/GofR.hpp" |
| 45 |
|
|
|
| 46 |
|
|
namespace oopse { |
| 47 |
|
|
|
| 48 |
|
|
GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len) |
| 49 |
|
|
: RadialDistrFunc(info, filename, sele1, sele2, len){ |
| 50 |
|
|
|
| 51 |
|
|
histogram_.resize(nbins_); |
| 52 |
|
|
avgGofr_.resize(nbins_); |
| 53 |
|
|
} |
| 54 |
|
|
|
| 55 |
|
|
|
| 56 |
|
|
void GofR::preProcess() { |
| 57 |
|
|
avgGofr_.resize(nbins_); |
| 58 |
|
|
std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0); |
| 59 |
|
|
} |
| 60 |
|
|
|
| 61 |
|
|
void GofR::initalizeHistogram() { |
| 62 |
|
|
npairs_ = 0; |
| 63 |
|
|
std::fill(histogram_.begin(), histogram_.end(), 0); |
| 64 |
|
|
} |
| 65 |
|
|
|
| 66 |
|
|
|
| 67 |
|
|
void GofR::processHistogram() { |
| 68 |
|
|
|
| 69 |
|
|
double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 70 |
|
|
double pairDensity = npairs_ /volume; |
| 71 |
|
|
double pairConstant = ( 4.0 * PI * pairDensity ) / 3.0; |
| 72 |
|
|
|
| 73 |
|
|
for(int i = 0 ; i < histogram_.size(); ++i){ |
| 74 |
|
|
|
| 75 |
|
|
double rLower = i * delta_; |
| 76 |
|
|
double rUpper = rLower + delta_; |
| 77 |
|
|
double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
| 78 |
|
|
double nIdeal = volSlice * pairConstant; |
| 79 |
|
|
|
| 80 |
|
|
avgGofr_[i] += histogram_[i] / nIdeal; |
| 81 |
|
|
} |
| 82 |
|
|
|
| 83 |
|
|
} |
| 84 |
|
|
|
| 85 |
|
|
void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 86 |
|
|
|
| 87 |
|
|
if (sd1 == sd2) { |
| 88 |
|
|
return; |
| 89 |
|
|
} |
| 90 |
|
|
|
| 91 |
|
|
Vector3d pos1 = sd1->getPos(); |
| 92 |
|
|
Vector3d pos2 = sd2->getPos(); |
| 93 |
|
|
Vector3d r12 = pos1 - pos2; |
| 94 |
|
|
|
| 95 |
|
|
double distance = (pos1 - pos2).length(); |
| 96 |
|
|
|
| 97 |
|
|
int whichBin = distance / delta_; |
| 98 |
|
|
histogram_[whichBin] ++; |
| 99 |
|
|
npairs_++; |
| 100 |
|
|
} |
| 101 |
|
|
|
| 102 |
|
|
|
| 103 |
|
|
void GofR::writeRdf() { |
| 104 |
|
|
std::ofstream rdfStream(outputFilename_.c_str()); |
| 105 |
|
|
if (rdfStream.is_open()) { |
| 106 |
|
|
rdfStream << "#radial distribution function\n"; |
| 107 |
|
|
rdfStream << "#selection1: " << selectionScript1_; |
| 108 |
|
|
rdfStream << "#selection2: " << selectionScript2_; |
| 109 |
|
|
|
| 110 |
|
|
} else { |
| 111 |
|
|
|
| 112 |
|
|
|
| 113 |
|
|
} |
| 114 |
|
|
} |
| 115 |
|
|
|
| 116 |
|
|
} |
| 117 |
|
|
|
