| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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 "applications/staticProps/P2OrderParameter.hpp" |
| 45 |
|
#include "io/DumpReader.hpp" |
| 46 |
|
#include "primitives/Molecule.hpp" |
| 47 |
|
#include "utils/NumericConstant.hpp" |
| 47 |
– |
namespace oopse { |
| 48 |
|
|
| 49 |
+ |
using namespace std; |
| 50 |
+ |
namespace OpenMD { |
| 51 |
|
|
| 52 |
< |
P2OrderParameter::P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
| 53 |
< |
: StaticAnalyser(info, filename), |
| 54 |
< |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
| 55 |
< |
seleMan1_(info), seleMan2_(info){ |
| 56 |
< |
|
| 52 |
> |
P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
| 53 |
> |
const string& sele1) |
| 54 |
> |
: StaticAnalyser(info, filename), doVect_(true), |
| 55 |
> |
selectionScript1_(sele1), evaluator1_(info), |
| 56 |
> |
evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
| 57 |
> |
|
| 58 |
|
setOutputName(getPrefix(filename) + ".p2"); |
| 59 |
< |
|
| 59 |
> |
|
| 60 |
|
evaluator1_.loadScriptString(sele1); |
| 61 |
< |
evaluator2_.loadScriptString(sele2); |
| 61 |
> |
} |
| 62 |
|
|
| 63 |
< |
if (!evaluator1_.isDynamic()) { |
| 64 |
< |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 65 |
< |
}else { |
| 66 |
< |
sprintf( painCave.errMsg, |
| 67 |
< |
"--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 |
< |
|
| 63 |
> |
P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
| 64 |
> |
const string& sele1, const string& sele2) |
| 65 |
> |
: StaticAnalyser(info, filename), doVect_(false), |
| 66 |
> |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), |
| 67 |
> |
evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
| 68 |
|
|
| 69 |
+ |
setOutputName(getPrefix(filename) + ".p2"); |
| 70 |
+ |
|
| 71 |
+ |
evaluator1_.loadScriptString(sele1); |
| 72 |
+ |
evaluator2_.loadScriptString(sele2); |
| 73 |
|
} |
| 74 |
|
|
| 75 |
|
void P2OrderParameter::process() { |
| 77 |
|
RigidBody* rb; |
| 78 |
|
SimInfo::MoleculeIterator mi; |
| 79 |
|
Molecule::RigidBodyIterator rbIter; |
| 80 |
< |
|
| 80 |
> |
StuntDouble* sd1; |
| 81 |
> |
StuntDouble* sd2; |
| 82 |
> |
int ii; |
| 83 |
> |
int jj; |
| 84 |
> |
int vecCount; |
| 85 |
> |
|
| 86 |
|
DumpReader reader(info_, dumpFilename_); |
| 87 |
|
int nFrames = reader.getNFrames(); |
| 88 |
|
|
| 89 |
|
for (int i = 0; i < nFrames; i += step_) { |
| 90 |
|
reader.readFrame(i); |
| 91 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 92 |
< |
|
| 93 |
< |
|
| 94 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 92 |
> |
|
| 93 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 94 |
> |
mol = info_->nextMolecule(mi)) { |
| 95 |
|
//change the positions of atoms which belong to the rigidbodies |
| 96 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 96 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 97 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 98 |
|
rb->updateAtoms(); |
| 99 |
< |
} |
| 122 |
< |
|
| 99 |
> |
} |
| 100 |
|
} |
| 101 |
|
|
| 102 |
|
Mat3x3d orderTensor(0.0); |
| 103 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 104 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 105 |
< |
if (usePeriodicBoundaryConditions_) |
| 106 |
< |
currentSnapshot_->wrapVector(vec); |
| 107 |
< |
vec.normalize(); |
| 108 |
< |
orderTensor +=outProduct(vec, vec); |
| 103 |
> |
vecCount = 0; |
| 104 |
> |
|
| 105 |
> |
if (evaluator1_.isDynamic()) |
| 106 |
> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 107 |
> |
|
| 108 |
> |
if (doVect_) { |
| 109 |
> |
|
| 110 |
> |
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
| 111 |
> |
sd1 = seleMan1_.nextSelected(ii)) { |
| 112 |
> |
if (sd1->isDirectional()) { |
| 113 |
> |
Vector3d vec = sd1->getA().getColumn(2); |
| 114 |
> |
vec.normalize(); |
| 115 |
> |
orderTensor += outProduct(vec, vec); |
| 116 |
> |
vecCount++; |
| 117 |
> |
} |
| 118 |
> |
} |
| 119 |
> |
|
| 120 |
> |
orderTensor /= vecCount; |
| 121 |
> |
|
| 122 |
> |
} else { |
| 123 |
> |
|
| 124 |
> |
if (evaluator2_.isDynamic()) |
| 125 |
> |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
| 126 |
> |
|
| 127 |
> |
if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
| 128 |
> |
sprintf( painCave.errMsg, |
| 129 |
> |
"In frame %d, the number of selected StuntDoubles are not\n" |
| 130 |
> |
"\tthe same in --sele1 and sele2\n", i); |
| 131 |
> |
painCave.severity = OPENMD_INFO; |
| 132 |
> |
painCave.isFatal = 0; |
| 133 |
> |
simError(); |
| 134 |
> |
} |
| 135 |
> |
|
| 136 |
> |
for (sd1 = seleMan1_.beginSelected(ii), |
| 137 |
> |
sd2 = seleMan2_.beginSelected(jj); |
| 138 |
> |
sd1 != NULL && sd2 != NULL; |
| 139 |
> |
sd1 = seleMan1_.nextSelected(ii), |
| 140 |
> |
sd2 = seleMan2_.nextSelected(jj)) { |
| 141 |
> |
|
| 142 |
> |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 143 |
> |
|
| 144 |
> |
if (usePeriodicBoundaryConditions_) |
| 145 |
> |
currentSnapshot_->wrapVector(vec); |
| 146 |
> |
|
| 147 |
> |
vec.normalize(); |
| 148 |
> |
|
| 149 |
> |
orderTensor +=outProduct(vec, vec); |
| 150 |
> |
vecCount++; |
| 151 |
> |
} |
| 152 |
> |
|
| 153 |
> |
orderTensor /= vecCount; |
| 154 |
|
} |
| 155 |
|
|
| 156 |
< |
orderTensor /= sdPairs_.size(); |
| 156 |
> |
if (vecCount == 0) { |
| 157 |
> |
sprintf( painCave.errMsg, |
| 158 |
> |
"In frame %d, the number of selected vectors was zero.\n" |
| 159 |
> |
"\tThis will not give a meaningful order parameter.", i); |
| 160 |
> |
painCave.severity = OPENMD_ERROR; |
| 161 |
> |
painCave.isFatal = 1; |
| 162 |
> |
simError(); |
| 163 |
> |
} |
| 164 |
> |
|
| 165 |
|
orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
| 166 |
|
|
| 167 |
|
Vector3d eigenvalues; |
| 168 |
|
Mat3x3d eigenvectors; |
| 169 |
+ |
|
| 170 |
|
Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); |
| 171 |
|
|
| 172 |
|
int which; |
| 186 |
|
} |
| 187 |
|
|
| 188 |
|
RealType angle = 0.0; |
| 189 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 190 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 191 |
< |
if (usePeriodicBoundaryConditions_) |
| 192 |
< |
currentSnapshot_->wrapVector(vec); |
| 193 |
< |
vec.normalize(); |
| 194 |
< |
|
| 195 |
< |
angle += acos(dot(vec, director)) ; |
| 189 |
> |
vecCount = 0; |
| 190 |
> |
|
| 191 |
> |
if (doVect_) { |
| 192 |
> |
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
| 193 |
> |
sd1 = seleMan1_.nextSelected(ii)) { |
| 194 |
> |
if (sd1->isDirectional()) { |
| 195 |
> |
Vector3d vec = sd1->getA().getColumn(2); |
| 196 |
> |
vec.normalize(); |
| 197 |
> |
angle += acos(dot(vec, director)); |
| 198 |
> |
vecCount++; |
| 199 |
> |
} |
| 200 |
> |
} |
| 201 |
> |
angle = angle/(vecCount*NumericConstant::PI)*180.0; |
| 202 |
> |
|
| 203 |
> |
} else { |
| 204 |
> |
for (sd1 = seleMan1_.beginSelected(ii), |
| 205 |
> |
sd2 = seleMan2_.beginSelected(jj); |
| 206 |
> |
sd1 != NULL && sd2 != NULL; |
| 207 |
> |
sd1 = seleMan1_.nextSelected(ii), |
| 208 |
> |
sd2 = seleMan2_.nextSelected(jj)) { |
| 209 |
> |
|
| 210 |
> |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 211 |
> |
if (usePeriodicBoundaryConditions_) |
| 212 |
> |
currentSnapshot_->wrapVector(vec); |
| 213 |
> |
vec.normalize(); |
| 214 |
> |
angle += acos(dot(vec, director)) ; |
| 215 |
> |
vecCount++; |
| 216 |
> |
} |
| 217 |
> |
angle = angle / (vecCount * NumericConstant::PI) * 180.0; |
| 218 |
|
} |
| 166 |
– |
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
| 219 |
|
|
| 220 |
|
OrderParam param; |
| 221 |
|
param.p2 = p2; |
| 225 |
|
orderParams_.push_back(param); |
| 226 |
|
|
| 227 |
|
} |
| 228 |
< |
|
| 228 |
> |
|
| 229 |
|
writeP2(); |
| 230 |
< |
|
| 230 |
> |
|
| 231 |
|
} |
| 232 |
|
|
| 233 |
|
void P2OrderParameter::writeP2() { |
| 234 |
|
|
| 235 |
< |
std::ofstream os(getOutputFileName().c_str()); |
| 235 |
> |
ofstream os(getOutputFileName().c_str()); |
| 236 |
|
os << "#radial distribution function\n"; |
| 237 |
|
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
| 238 |
< |
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 238 |
> |
if (!doVect_) { |
| 239 |
> |
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 240 |
> |
} |
| 241 |
|
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
| 242 |
|
|
| 243 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
| 243 |
> |
for (size_t i = 0; i < orderParams_.size(); ++i) { |
| 244 |
|
os << orderParams_[i].p2 << "\t" |
| 245 |
|
<< orderParams_[i].director[0] << "\t" |
| 246 |
|
<< orderParams_[i].director[1] << "\t" |
