| 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 "applications/staticProps/P2OrderParameter.hpp"
|
| 43 |
#include "utils/simError.h"
|
| 44 |
#include "io/DumpReader.hpp"
|
| 45 |
#include "primitives/Molecule.hpp"
|
| 46 |
#include "utils/NumericConstant.hpp"
|
| 47 |
namespace oopse {
|
| 48 |
|
| 49 |
|
| 50 |
P2OrderParameter::P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
|
| 51 |
: StaticAnalyser(info, filename),
|
| 52 |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
|
| 53 |
seleMan1_(info), seleMan2_(info){
|
| 54 |
|
| 55 |
setOutputName(getPrefix(filename) + ".p2");
|
| 56 |
|
| 57 |
evaluator1_.loadScriptString(sele1);
|
| 58 |
evaluator2_.loadScriptString(sele2);
|
| 59 |
|
| 60 |
if (!evaluator1_.isDynamic()) {
|
| 61 |
seleMan1_.setSelectionSet(evaluator1_.evaluate());
|
| 62 |
}else {
|
| 63 |
sprintf( painCave.errMsg,
|
| 64 |
"--sele1 must be static selection\n");
|
| 65 |
painCave.severity = OOPSE_ERROR;
|
| 66 |
painCave.isFatal = 1;
|
| 67 |
simError();
|
| 68 |
}
|
| 69 |
|
| 70 |
if (!evaluator2_.isDynamic()) {
|
| 71 |
seleMan2_.setSelectionSet(evaluator2_.evaluate());
|
| 72 |
}else {
|
| 73 |
sprintf( painCave.errMsg,
|
| 74 |
"--sele2 must be static selection\n");
|
| 75 |
painCave.severity = OOPSE_ERROR;
|
| 76 |
painCave.isFatal = 1;
|
| 77 |
simError();
|
| 78 |
}
|
| 79 |
|
| 80 |
if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
|
| 81 |
sprintf( painCave.errMsg,
|
| 82 |
"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
|
| 83 |
painCave.severity = OOPSE_ERROR;
|
| 84 |
painCave.isFatal = 1;
|
| 85 |
simError();
|
| 86 |
|
| 87 |
}
|
| 88 |
|
| 89 |
int i;
|
| 90 |
int j;
|
| 91 |
StuntDouble* sd1;
|
| 92 |
StuntDouble* sd2;
|
| 93 |
for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
|
| 94 |
sd1 != NULL && sd2 != NULL;
|
| 95 |
sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
|
| 96 |
|
| 97 |
sdPairs_.push_back(std::make_pair(sd1, sd2));
|
| 98 |
}
|
| 99 |
|
| 100 |
|
| 101 |
}
|
| 102 |
|
| 103 |
void P2OrderParameter::process() {
|
| 104 |
Molecule* mol;
|
| 105 |
RigidBody* rb;
|
| 106 |
SimInfo::MoleculeIterator mi;
|
| 107 |
Molecule::RigidBodyIterator rbIter;
|
| 108 |
|
| 109 |
DumpReader reader(info_, dumpFilename_);
|
| 110 |
int nFrames = reader.getNFrames();
|
| 111 |
|
| 112 |
for (int i = 0; i < nFrames; i += step_) {
|
| 113 |
reader.readFrame(i);
|
| 114 |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
|
| 115 |
|
| 116 |
|
| 117 |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
|
| 118 |
//change the positions of atoms which belong to the rigidbodies
|
| 119 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
|
| 120 |
rb->updateAtoms();
|
| 121 |
}
|
| 122 |
|
| 123 |
}
|
| 124 |
|
| 125 |
Mat3x3d orderTensor(0.0);
|
| 126 |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
|
| 127 |
Vector3d vec = j->first->getPos() - j->second->getPos();
|
| 128 |
currentSnapshot_->wrapVector(vec);
|
| 129 |
vec.normalize();
|
| 130 |
orderTensor +=outProduct(vec, vec);
|
| 131 |
}
|
| 132 |
|
| 133 |
orderTensor /= sdPairs_.size();
|
| 134 |
orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
|
| 135 |
|
| 136 |
Vector3d eigenvalues;
|
| 137 |
Mat3x3d eigenvectors;
|
| 138 |
Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
|
| 139 |
|
| 140 |
int which;
|
| 141 |
RealType maxEval = 0.0;
|
| 142 |
for(int k = 0; k< 3; k++){
|
| 143 |
if(fabs(eigenvalues[k]) > maxEval){
|
| 144 |
which = k;
|
| 145 |
maxEval = fabs(eigenvalues[k]);
|
| 146 |
}
|
| 147 |
}
|
| 148 |
RealType p2 = 1.5 * maxEval;
|
| 149 |
|
| 150 |
//the eigen vector is already normalized in SquareMatrix3::diagonalize
|
| 151 |
Vector3d director = eigenvectors.getColumn(which);
|
| 152 |
if (director[0] < 0) {
|
| 153 |
director.negate();
|
| 154 |
}
|
| 155 |
|
| 156 |
RealType angle = 0.0;
|
| 157 |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
|
| 158 |
Vector3d vec = j->first->getPos() - j->second->getPos();
|
| 159 |
currentSnapshot_->wrapVector(vec);
|
| 160 |
vec.normalize();
|
| 161 |
|
| 162 |
angle += acos(dot(vec, director)) ;
|
| 163 |
}
|
| 164 |
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0;
|
| 165 |
|
| 166 |
OrderParam param;
|
| 167 |
param.p2 = p2;
|
| 168 |
param.director = director;
|
| 169 |
param.angle = angle;
|
| 170 |
|
| 171 |
orderParams_.push_back(param);
|
| 172 |
|
| 173 |
}
|
| 174 |
|
| 175 |
writeP2();
|
| 176 |
|
| 177 |
}
|
| 178 |
|
| 179 |
void P2OrderParameter::writeP2() {
|
| 180 |
|
| 181 |
std::ofstream os(getOutputFileName().c_str());
|
| 182 |
os << "#radial distribution function\n";
|
| 183 |
os<< "#selection1: (" << selectionScript1_ << ")\t";
|
| 184 |
os << "selection2: (" << selectionScript2_ << ")\n";
|
| 185 |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
|
| 186 |
|
| 187 |
for (std::size_t i = 0; i < orderParams_.size(); ++i) {
|
| 188 |
os << orderParams_[i].p2 << "\t"
|
| 189 |
<< orderParams_[i].director[0] << "\t"
|
| 190 |
<< orderParams_[i].director[1] << "\t"
|
| 191 |
<< orderParams_[i].director[2] << "\t"
|
| 192 |
<< orderParams_[i].angle << "\n";
|
| 193 |
|
| 194 |
}
|
| 195 |
|
| 196 |
}
|
| 197 |
|
| 198 |
}
|
| 199 |
|
