| 1 |
/* |
| 2 |
* Copyright (c) 2007 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
* |
| 41 |
* Created by J. Daniel Gezelter on 07/27/07. |
| 42 |
* @author J. Daniel Gezelter |
| 43 |
* @version $Id: BondAngleDistribution.cpp,v 1.2 2009-11-25 20:01:59 gezelter Exp $ |
| 44 |
* |
| 45 |
*/ |
| 46 |
|
| 47 |
#include "applications/staticProps/BondAngleDistribution.hpp" |
| 48 |
#include "utils/simError.h" |
| 49 |
#include "io/DumpReader.hpp" |
| 50 |
#include "primitives/Molecule.hpp" |
| 51 |
#include "utils/NumericConstant.hpp" |
| 52 |
|
| 53 |
namespace OpenMD { |
| 54 |
|
| 55 |
BondAngleDistribution::BondAngleDistribution(SimInfo* info, |
| 56 |
const std::string& filename, |
| 57 |
const std::string& sele, |
| 58 |
double rCut, int nbins) : StaticAnalyser(info, filename), |
| 59 |
selectionScript_(sele), |
| 60 |
evaluator_(info), seleMan_(info){ |
| 61 |
|
| 62 |
setOutputName(getPrefix(filename) + ".bad"); |
| 63 |
|
| 64 |
evaluator_.loadScriptString(sele); |
| 65 |
if (!evaluator_.isDynamic()) { |
| 66 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 67 |
} |
| 68 |
|
| 69 |
// Set up cutoff radius and order of the Legendre Polynomial: |
| 70 |
|
| 71 |
rCut_ = rCut; |
| 72 |
nBins_ = nbins; |
| 73 |
|
| 74 |
|
| 75 |
// Theta can take values from 0 to 180 |
| 76 |
deltaTheta_ = (180.0) / nBins_; |
| 77 |
histogram_.resize(nBins_); |
| 78 |
} |
| 79 |
|
| 80 |
BondAngleDistribution::~BondAngleDistribution() { |
| 81 |
histogram_.clear(); |
| 82 |
} |
| 83 |
|
| 84 |
void BondAngleDistribution::initalizeHistogram() { |
| 85 |
for (int bin = 0; bin < nBins_; bin++) { |
| 86 |
histogram_[bin] = 0; |
| 87 |
} |
| 88 |
} |
| 89 |
|
| 90 |
void BondAngleDistribution::process() { |
| 91 |
Molecule* mol; |
| 92 |
Atom* atom; |
| 93 |
RigidBody* rb; |
| 94 |
int myIndex; |
| 95 |
SimInfo::MoleculeIterator mi; |
| 96 |
Molecule::RigidBodyIterator rbIter; |
| 97 |
Molecule::AtomIterator ai; |
| 98 |
StuntDouble* sd; |
| 99 |
Vector3d vec; |
| 100 |
std::vector<Vector3d> bondvec; |
| 101 |
std::vector<RealType> bonddist; |
| 102 |
RealType costheta; |
| 103 |
RealType r; |
| 104 |
RealType dist; |
| 105 |
|
| 106 |
int nBonds; |
| 107 |
|
| 108 |
int i, j; |
| 109 |
|
| 110 |
DumpReader reader(info_, dumpFilename_); |
| 111 |
int nFrames = reader.getNFrames(); |
| 112 |
frameCounter_ = 0; |
| 113 |
|
| 114 |
nTotBonds_ = 0; |
| 115 |
|
| 116 |
for (int istep = 0; istep < nFrames; istep += step_) { |
| 117 |
reader.readFrame(istep); |
| 118 |
frameCounter_++; |
| 119 |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 120 |
|
| 121 |
if (evaluator_.isDynamic()) { |
| 122 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 123 |
} |
| 124 |
|
| 125 |
// update the positions of atoms which belong to the rigidbodies |
| 126 |
|
| 127 |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 128 |
mol = info_->nextMolecule(mi)) { |
| 129 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 130 |
rb = mol->nextRigidBody(rbIter)) { |
| 131 |
rb->updateAtoms(); |
| 132 |
} |
| 133 |
} |
| 134 |
|
| 135 |
// outer loop is over the selected StuntDoubles: |
| 136 |
|
| 137 |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 138 |
sd = seleMan_.nextSelected(i)) { |
| 139 |
|
| 140 |
myIndex = sd->getGlobalIndex(); |
| 141 |
nBonds = 0; |
| 142 |
bondvec.clear(); |
| 143 |
|
| 144 |
// inner loop is over all other atoms in the system: |
| 145 |
|
| 146 |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 147 |
mol = info_->nextMolecule(mi)) { |
| 148 |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 149 |
atom = mol->nextAtom(ai)) { |
| 150 |
|
| 151 |
if (atom->getGlobalIndex() != myIndex) { |
| 152 |
|
| 153 |
vec = sd->getPos() - atom->getPos(); |
| 154 |
|
| 155 |
if (usePeriodicBoundaryConditions_) |
| 156 |
currentSnapshot_->wrapVector(vec); |
| 157 |
|
| 158 |
// Calculate "bonds" and make a pair list |
| 159 |
|
| 160 |
r = vec.length(); |
| 161 |
|
| 162 |
// Check to see if neighbor is in bond cutoff |
| 163 |
|
| 164 |
if (r < rCut_) { |
| 165 |
// Add neighbor to bond list's |
| 166 |
bondvec.push_back(vec); |
| 167 |
nBonds++; |
| 168 |
nTotBonds_++; |
| 169 |
} |
| 170 |
} |
| 171 |
} |
| 172 |
|
| 173 |
|
| 174 |
for (int i = 0; i < nBonds-1; i++ ){ |
| 175 |
Vector3d vec1 = bondvec[i]; |
| 176 |
vec1.normalize(); |
| 177 |
for(int j = i+1; j < nBonds; j++){ |
| 178 |
Vector3d vec2 = bondvec[j]; |
| 179 |
|
| 180 |
vec2.normalize(); |
| 181 |
|
| 182 |
RealType theta = acos(dot(vec1,vec2))*180.0/NumericConstant::PI; |
| 183 |
|
| 184 |
|
| 185 |
if (theta > 180.0){ |
| 186 |
theta = 360.0 - theta; |
| 187 |
} |
| 188 |
int whichBin = theta/deltaTheta_; |
| 189 |
|
| 190 |
histogram_[whichBin] += 2; |
| 191 |
} |
| 192 |
} |
| 193 |
} |
| 194 |
} |
| 195 |
} |
| 196 |
|
| 197 |
|
| 198 |
writeBondAngleDistribution(); |
| 199 |
} |
| 200 |
|
| 201 |
|
| 202 |
void BondAngleDistribution::writeBondAngleDistribution() { |
| 203 |
|
| 204 |
std::ofstream osbad(getOutputFileName().c_str()); |
| 205 |
|
| 206 |
|
| 207 |
RealType norm = (RealType)nTotBonds_*((RealType)nTotBonds_-1.0)/2.0; |
| 208 |
if (osbad.is_open()) { |
| 209 |
|
| 210 |
// Normalize by number of frames and write it out: |
| 211 |
for (int i = 0; i < nBins_; ++i) { |
| 212 |
RealType Thetaval = i * deltaTheta_; |
| 213 |
osbad << Thetaval; |
| 214 |
osbad << "\t" << (RealType)histogram_[i]/norm/frameCounter_; |
| 215 |
|
| 216 |
osbad << "\n"; |
| 217 |
} |
| 218 |
|
| 219 |
osbad.close(); |
| 220 |
|
| 221 |
} else { |
| 222 |
sprintf(painCave.errMsg, "BondAngleDistribution: unable to open %s\n", |
| 223 |
(getOutputFileName() + "q").c_str()); |
| 224 |
painCave.isFatal = 1; |
| 225 |
simError(); |
| 226 |
} |
| 227 |
|
| 228 |
} |
| 229 |
} |
