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 |
setOutputName(getPrefix(filename) + ".gxyz"); |
52 |
|
53 |
} |
54 |
|
55 |
|
56 |
void GofXyz::preProcess() { |
57 |
/* |
58 |
for (int i = 0; i < avgGofr_.size(); ++i) { |
59 |
std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
60 |
} |
61 |
*/ |
62 |
} |
63 |
|
64 |
void GofXyz::initalizeHistogram() { |
65 |
/* |
66 |
npairs_ = 0; |
67 |
for (int i = 0; i < histogram_.size(); ++i) |
68 |
std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
69 |
*/ |
70 |
} |
71 |
|
72 |
|
73 |
void GofXyz::processHistogram() { |
74 |
|
75 |
/* |
76 |
double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
77 |
double pairDensity = npairs_ /volume; |
78 |
double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
79 |
|
80 |
for(int i = 0 ; i < histogram_.size(); ++i){ |
81 |
|
82 |
double rLower = i * deltaR_; |
83 |
double rUpper = rLower + deltaR_; |
84 |
double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
85 |
double nIdeal = volSlice * pairConstant; |
86 |
|
87 |
for (int j = 0; j < histogram_[i].size(); ++j){ |
88 |
avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
89 |
} |
90 |
} |
91 |
*/ |
92 |
} |
93 |
|
94 |
void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
95 |
|
96 |
/* |
97 |
if (sd1 == sd2) { |
98 |
return; |
99 |
} |
100 |
|
101 |
Vector3d pos1 = sd1->getPos(); |
102 |
Vector3d pos2 = sd2->getPos(); |
103 |
Vector3d r12 = pos1 - pos2; |
104 |
currentSnapshot_->wrapVector(r12); |
105 |
|
106 |
double distance = r12.length(); |
107 |
int whichRBin = distance / deltaR_; |
108 |
|
109 |
|
110 |
double cosAngle = evaluateAngle(sd1, sd2); |
111 |
double halfBin = (nAngleBins_ - 1) * 0.5; |
112 |
int whichThetaBin = halfBin * (cosAngle + 1.0) |
113 |
++histogram_[whichRBin][whichThetaBin]; |
114 |
|
115 |
++npairs_; |
116 |
*/ |
117 |
} |
118 |
|
119 |
void GofXyz::writeRdf() { |
120 |
std::ofstream rdfStream(outputFilename_.c_str()); |
121 |
if (rdfStream.is_open()) { |
122 |
rdfStream << "#radial distribution function\n"; |
123 |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
124 |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
125 |
rdfStream << "#r\tcorrValue\n"; |
126 |
for (int i = 0; i < histogram_.size(); ++i) { |
127 |
double x = deltaR_ * (i + 0.5); |
128 |
|
129 |
for(int j = 0; j < histogram_[i].size(); ++j) { |
130 |
double y = deltaR_ * (j+ 0.5); |
131 |
|
132 |
for(int k = 0;k < histogram_[i].size(); ++k) { |
133 |
double z = deltaR_ * (k + 0.5); |
134 |
rdfStream << x << "\t" << y << "\t" << z << "\t" << histogram_[i][j][k]/nProcessed_ << "\n"; |
135 |
} |
136 |
} |
137 |
} |
138 |
|
139 |
} else { |
140 |
|
141 |
|
142 |
} |
143 |
|
144 |
rdfStream.close(); |
145 |
} |
146 |
|
147 |
} |
148 |
|
149 |
|
150 |
|