| 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/RippleOP.hpp" |
| 45 |
|
#include "io/DumpReader.hpp" |
| 46 |
|
#include "primitives/Molecule.hpp" |
| 47 |
|
#include "utils/NumericConstant.hpp" |
| 48 |
< |
namespace oopse { |
| 48 |
> |
namespace OpenMD { |
| 49 |
|
|
| 50 |
|
|
| 51 |
|
RippleOP::RippleOP(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
| 63 |
|
}else { |
| 64 |
|
sprintf( painCave.errMsg, |
| 65 |
|
"--sele1 must be static selection\n"); |
| 66 |
< |
painCave.severity = OOPSE_ERROR; |
| 66 |
> |
painCave.severity = OPENMD_ERROR; |
| 67 |
|
painCave.isFatal = 1; |
| 68 |
|
simError(); |
| 69 |
|
} |
| 73 |
|
}else { |
| 74 |
|
sprintf( painCave.errMsg, |
| 75 |
|
"--sele2 must be static selection\n"); |
| 76 |
< |
painCave.severity = OOPSE_ERROR; |
| 76 |
> |
painCave.severity = OPENMD_ERROR; |
| 77 |
|
painCave.isFatal = 1; |
| 78 |
|
simError(); |
| 79 |
|
} |
| 81 |
|
if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
| 82 |
|
sprintf( painCave.errMsg, |
| 83 |
|
"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n"); |
| 84 |
< |
painCave.severity = OOPSE_ERROR; |
| 84 |
> |
painCave.severity = OPENMD_ERROR; |
| 85 |
|
painCave.isFatal = 1; |
| 86 |
|
simError(); |
| 87 |
|
|
| 105 |
|
RigidBody* rb; |
| 106 |
|
SimInfo::MoleculeIterator mi; |
| 107 |
|
Molecule::RigidBodyIterator rbIter; |
| 108 |
+ |
|
| 109 |
+ |
StuntDouble* j1; |
| 110 |
+ |
StuntDouble* j2; |
| 111 |
+ |
StuntDouble* sd3; |
| 112 |
|
|
| 113 |
|
DumpReader reader(info_, dumpFilename_); |
| 114 |
|
int nFrames = reader.getNFrames(); |
| 115 |
< |
|
| 115 |
> |
|
| 116 |
|
for (int i = 0; i < nFrames; i += step_) { |
| 117 |
|
reader.readFrame(i); |
| 118 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 119 |
+ |
int nMolecules = info_->getNGlobalMolecules(); |
| 120 |
+ |
int i1; |
| 121 |
+ |
int nUpper=0; |
| 122 |
+ |
int nLower=0; |
| 123 |
+ |
int nTail=0; |
| 124 |
+ |
RealType sumZ = 0.0; |
| 125 |
|
|
| 115 |
– |
|
| 126 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 127 |
|
//change the positions of atoms which belong to the rigidbodies |
| 128 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 129 |
|
rb->updateAtoms(); |
| 130 |
|
} |
| 131 |
|
} |
| 132 |
+ |
|
| 133 |
+ |
for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; sd3 = seleMan2_.nextSelected(i1)) { |
| 134 |
+ |
Vector3d pos1 = sd3->getPos(); |
| 135 |
+ |
if (usePeriodicBoundaryConditions_) |
| 136 |
+ |
currentSnapshot_->wrapVector(pos1); |
| 137 |
+ |
sd3->setPos(pos1); |
| 138 |
+ |
} |
| 139 |
+ |
|
| 140 |
+ |
for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; sd3 = seleMan2_.nextSelected(i1)) { |
| 141 |
+ |
Vector3d pos1 = sd3->getPos(); |
| 142 |
+ |
sumZ += pos1.z(); |
| 143 |
+ |
} |
| 144 |
+ |
RealType avgZ = sumZ / (RealType) nMolecules; |
| 145 |
|
|
| 146 |
< |
Mat3x3d orderTensorHead(0.0), orderTensorTail(0.0); |
| 147 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 148 |
< |
Vector3d vecHead = j->first->getElectroFrame().getColumn(2); |
| 149 |
< |
Vector3d vecTail = j->second->getA().getColumn(2); |
| 150 |
< |
orderTensorHead +=outProduct(vecHead, vecHead); |
| 146 |
> |
Mat3x3d orderTensorHeadUpper(0.0), orderTensorTail(0.0), orderTensorHeadLower(0.0); |
| 147 |
> |
// for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 148 |
> |
for (j1 = seleMan1_.beginSelected(i1); j1 != NULL; j1 = seleMan1_.nextSelected(i1)) { |
| 149 |
> |
Vector3d pos = j1->getPos(); |
| 150 |
> |
if (usePeriodicBoundaryConditions_) |
| 151 |
> |
currentSnapshot_->wrapVector(pos); |
| 152 |
> |
Vector3d vecHeadUpper; |
| 153 |
> |
if (pos.z() >= avgZ){ |
| 154 |
> |
vecHeadUpper = j1->getElectroFrame().getColumn(2); |
| 155 |
> |
nUpper++; |
| 156 |
> |
} |
| 157 |
> |
Vector3d vecHeadLower; |
| 158 |
> |
if (pos.z() <= avgZ){ |
| 159 |
> |
vecHeadLower = j1->getElectroFrame().getColumn(2); |
| 160 |
> |
nLower++; |
| 161 |
> |
} |
| 162 |
> |
orderTensorHeadUpper +=outProduct(vecHeadUpper, vecHeadUpper); |
| 163 |
> |
orderTensorHeadLower +=outProduct(vecHeadLower, vecHeadLower); |
| 164 |
> |
} |
| 165 |
> |
for (j2 = seleMan2_.beginSelected(i1); j2 != NULL; j2 = seleMan2_.nextSelected(i1)) { |
| 166 |
> |
// The lab frame vector corresponding to the body-fixed |
| 167 |
> |
// z-axis is simply the second column of A.transpose() |
| 168 |
> |
// or, identically, the second row of A itself. |
| 169 |
> |
|
| 170 |
> |
Vector3d vecTail = j2->getA().getRow(2); |
| 171 |
|
orderTensorTail +=outProduct(vecTail, vecTail); |
| 172 |
+ |
nTail++; |
| 173 |
|
} |
| 130 |
– |
|
| 131 |
– |
orderTensorHead /= sdPairs_.size(); |
| 132 |
– |
orderTensorHead -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
| 174 |
|
|
| 175 |
< |
orderTensorTail /= sdPairs_.size(); |
| 175 |
> |
orderTensorHeadUpper /= (RealType) nUpper; |
| 176 |
> |
orderTensorHeadLower /= (RealType) nLower; |
| 177 |
> |
orderTensorHeadUpper -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
| 178 |
> |
orderTensorHeadLower -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
| 179 |
> |
|
| 180 |
> |
orderTensorTail /= (RealType) nTail; |
| 181 |
|
orderTensorTail -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
| 182 |
|
|
| 183 |
< |
Vector3d eigenvaluesHead, eigenvaluesTail; |
| 184 |
< |
Mat3x3d eigenvectorsHead, eigenvectorsTail; |
| 185 |
< |
Mat3x3d::diagonalize(orderTensorHead, eigenvaluesHead, eigenvectorsHead); |
| 183 |
> |
Vector3d eigenvaluesHeadUpper, eigenvaluesHeadLower, eigenvaluesTail; |
| 184 |
> |
Mat3x3d eigenvectorsHeadUpper, eigenvectorsHeadLower, eigenvectorsTail; |
| 185 |
> |
Mat3x3d::diagonalize(orderTensorHeadUpper, eigenvaluesHeadUpper, eigenvectorsHeadUpper); |
| 186 |
> |
Mat3x3d::diagonalize(orderTensorHeadLower, eigenvaluesHeadLower, eigenvectorsHeadLower); |
| 187 |
|
Mat3x3d::diagonalize(orderTensorTail, eigenvaluesTail, eigenvectorsTail); |
| 188 |
|
|
| 189 |
< |
int which; |
| 190 |
< |
RealType maxEval = 0.0; |
| 189 |
> |
int whichUpper, whichLower, whichTail; |
| 190 |
> |
RealType maxEvalUpper = 0.0; |
| 191 |
> |
RealType maxEvalLower = 0.0; |
| 192 |
> |
RealType maxEvalTail = 0.0; |
| 193 |
|
for(int k = 0; k< 3; k++){ |
| 194 |
< |
if(fabs(eigenvaluesHead[k]) > maxEval){ |
| 195 |
< |
which = k; |
| 196 |
< |
maxEval = fabs(eigenvaluesHead[k]); |
| 194 |
> |
if(fabs(eigenvaluesHeadUpper[k]) > maxEvalUpper){ |
| 195 |
> |
whichUpper = k; |
| 196 |
> |
maxEvalUpper = fabs(eigenvaluesHeadUpper[k]); |
| 197 |
|
} |
| 198 |
|
} |
| 199 |
< |
RealType p2Head = 1.5 * maxEval; |
| 151 |
< |
maxEval = 0.0; |
| 199 |
> |
RealType p2HeadUpper = 1.5 * maxEvalUpper; |
| 200 |
|
for(int k = 0; k< 3; k++){ |
| 201 |
< |
if(fabs(eigenvaluesTail[k]) > maxEval){ |
| 202 |
< |
which = k; |
| 203 |
< |
maxEval = fabs(eigenvaluesTail[k]); |
| 201 |
> |
if(fabs(eigenvaluesHeadLower[k]) > maxEvalLower){ |
| 202 |
> |
whichLower = k; |
| 203 |
> |
maxEvalLower = fabs(eigenvaluesHeadLower[k]); |
| 204 |
|
} |
| 205 |
|
} |
| 206 |
< |
RealType p2Tail = 1.5 * maxEval; |
| 206 |
> |
RealType p2HeadLower = 1.5 * maxEvalLower; |
| 207 |
> |
for(int k = 0; k< 3; k++){ |
| 208 |
> |
if(fabs(eigenvaluesTail[k]) > maxEvalTail){ |
| 209 |
> |
whichTail = k; |
| 210 |
> |
maxEvalTail = fabs(eigenvaluesTail[k]); |
| 211 |
> |
} |
| 212 |
> |
} |
| 213 |
> |
RealType p2Tail = 1.5 * maxEvalTail; |
| 214 |
|
|
| 215 |
|
//the eigen vector is already normalized in SquareMatrix3::diagonalize |
| 216 |
< |
Vector3d directorHead = eigenvectorsHead.getColumn(which); |
| 217 |
< |
if (directorHead[0] < 0) { |
| 218 |
< |
directorHead.negate(); |
| 216 |
> |
Vector3d directorHeadUpper = eigenvectorsHeadUpper.getColumn(whichUpper); |
| 217 |
> |
if (directorHeadUpper[0] < 0) { |
| 218 |
> |
directorHeadUpper.negate(); |
| 219 |
|
} |
| 220 |
< |
Vector3d directorTail = eigenvectorsTail.getColumn(which); |
| 220 |
> |
Vector3d directorHeadLower = eigenvectorsHeadLower.getColumn(whichLower); |
| 221 |
> |
if (directorHeadLower[0] < 0) { |
| 222 |
> |
directorHeadLower.negate(); |
| 223 |
> |
} |
| 224 |
> |
Vector3d directorTail = eigenvectorsTail.getColumn(whichTail); |
| 225 |
|
if (directorTail[0] < 0) { |
| 226 |
|
directorTail.negate(); |
| 227 |
|
} |
| 228 |
|
|
| 229 |
< |
OrderParam paramHead, paramTail; |
| 230 |
< |
paramHead.p2 = p2Head; |
| 231 |
< |
paramHead.director = directorHead; |
| 229 |
> |
OrderParam paramHeadUpper, paramHeadLower, paramTail; |
| 230 |
> |
paramHeadUpper.p2 = p2HeadUpper; |
| 231 |
> |
paramHeadUpper.director = directorHeadUpper; |
| 232 |
> |
paramHeadLower.p2 = p2HeadLower; |
| 233 |
> |
paramHeadLower.director = directorHeadLower; |
| 234 |
|
paramTail.p2 = p2Tail; |
| 235 |
|
paramTail.director = directorTail; |
| 236 |
|
|
| 237 |
< |
orderParamsHead_.push_back(paramHead); |
| 237 |
> |
orderParamsHeadUpper_.push_back(paramHeadUpper); |
| 238 |
> |
orderParamsHeadLower_.push_back(paramHeadLower); |
| 239 |
|
orderParamsTail_.push_back(paramTail); |
| 240 |
|
|
| 241 |
|
} |
| 242 |
|
|
| 243 |
< |
OrderParam sumOPHead, errsumOPHead; |
| 243 |
> |
OrderParam sumOPHeadUpper, errsumOPHeadUpper; |
| 244 |
> |
OrderParam sumOPHeadLower, errsumOPHeadLower; |
| 245 |
|
OrderParam sumOPTail, errsumOPTail; |
| 246 |
|
|
| 247 |
< |
sumOPHead.p2 = 0.0; |
| 248 |
< |
errsumOPHead.p2 = 0.0; |
| 249 |
< |
for (std::size_t i = 0; i < orderParamsHead_.size(); ++i) { |
| 250 |
< |
sumOPHead.p2 += orderParamsHead_[i].p2; |
| 251 |
< |
sumOPHead.director[0] += orderParamsHead_[i].director[0]; |
| 252 |
< |
sumOPHead.director[1] += orderParamsHead_[i].director[1]; |
| 253 |
< |
sumOPHead.director[2] += orderParamsHead_[i].director[2]; |
| 247 |
> |
sumOPHeadUpper.p2 = 0.0; |
| 248 |
> |
errsumOPHeadUpper.p2 = 0.0; |
| 249 |
> |
sumOPHeadLower.p2 = 0.0; |
| 250 |
> |
errsumOPHeadLower.p2 = 0.0; |
| 251 |
> |
for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) { |
| 252 |
> |
sumOPHeadUpper.p2 += orderParamsHeadUpper_[i].p2; |
| 253 |
> |
sumOPHeadUpper.director[0] += orderParamsHeadUpper_[i].director[0]; |
| 254 |
> |
sumOPHeadUpper.director[1] += orderParamsHeadUpper_[i].director[1]; |
| 255 |
> |
sumOPHeadUpper.director[2] += orderParamsHeadUpper_[i].director[2]; |
| 256 |
|
} |
| 257 |
|
|
| 258 |
< |
avgOPHead.p2 = sumOPHead.p2 / (RealType)orderParamsHead_.size(); |
| 259 |
< |
avgOPHead.director[0] = sumOPHead.director[0] / (RealType)orderParamsHead_.size(); |
| 260 |
< |
avgOPHead.director[1] = sumOPHead.director[1] / (RealType)orderParamsHead_.size(); |
| 261 |
< |
avgOPHead.director[2] = sumOPHead.director[2] / (RealType)orderParamsHead_.size(); |
| 262 |
< |
for (std::size_t i = 0; i < orderParamsHead_.size(); ++i) { |
| 263 |
< |
errsumOPHead.p2 += pow((orderParamsHead_[i].p2 - avgOPHead.p2), 2); |
| 258 |
> |
avgOPHeadUpper.p2 = sumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size(); |
| 259 |
> |
avgOPHeadUpper.director[0] = sumOPHeadUpper.director[0] / (RealType)orderParamsHeadUpper_.size(); |
| 260 |
> |
avgOPHeadUpper.director[1] = sumOPHeadUpper.director[1] / (RealType)orderParamsHeadUpper_.size(); |
| 261 |
> |
avgOPHeadUpper.director[2] = sumOPHeadUpper.director[2] / (RealType)orderParamsHeadUpper_.size(); |
| 262 |
> |
for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) { |
| 263 |
> |
errsumOPHeadUpper.p2 += pow((orderParamsHeadUpper_[i].p2 - avgOPHeadUpper.p2), 2); |
| 264 |
|
} |
| 265 |
< |
errOPHead.p2 = sqrt(errsumOPHead.p2 / (RealType)orderParamsHead_.size()); |
| 265 |
> |
errOPHeadUpper.p2 = sqrt(errsumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size()); |
| 266 |
> |
for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) { |
| 267 |
> |
sumOPHeadLower.p2 += orderParamsHeadLower_[i].p2; |
| 268 |
> |
sumOPHeadLower.director[0] += orderParamsHeadLower_[i].director[0]; |
| 269 |
> |
sumOPHeadLower.director[1] += orderParamsHeadLower_[i].director[1]; |
| 270 |
> |
sumOPHeadLower.director[2] += orderParamsHeadLower_[i].director[2]; |
| 271 |
> |
} |
| 272 |
|
|
| 273 |
+ |
avgOPHeadLower.p2 = sumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size(); |
| 274 |
+ |
avgOPHeadLower.director[0] = sumOPHeadLower.director[0] / (RealType)orderParamsHeadLower_.size(); |
| 275 |
+ |
avgOPHeadLower.director[1] = sumOPHeadLower.director[1] / (RealType)orderParamsHeadLower_.size(); |
| 276 |
+ |
avgOPHeadLower.director[2] = sumOPHeadLower.director[2] / (RealType)orderParamsHeadLower_.size(); |
| 277 |
+ |
for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) { |
| 278 |
+ |
errsumOPHeadLower.p2 += pow((orderParamsHeadLower_[i].p2 - avgOPHeadLower.p2), 2); |
| 279 |
+ |
} |
| 280 |
+ |
errOPHeadLower.p2 = sqrt(errsumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size()); |
| 281 |
+ |
|
| 282 |
|
sumOPTail.p2 = 0.0; |
| 283 |
|
errsumOPTail.p2 = 0.0; |
| 284 |
|
for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) { |
| 307 |
|
os<< "#selection1: (" << selectionScript1_ << ")\n"; |
| 308 |
|
os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n"; |
| 309 |
|
|
| 310 |
< |
os << avgOPHead.p2 << "\t" |
| 311 |
< |
<< errOPHead.p2 << "\t" |
| 312 |
< |
<< avgOPHead.director[0] << "\t" |
| 313 |
< |
<< avgOPHead.director[1] << "\t" |
| 314 |
< |
<< avgOPHead.director[2] << "\n"; |
| 310 |
> |
os << avgOPHeadUpper.p2 << "\t" |
| 311 |
> |
<< errOPHeadUpper.p2 << "\t" |
| 312 |
> |
<< avgOPHeadUpper.director[0] << "\t" |
| 313 |
> |
<< avgOPHeadUpper.director[1] << "\t" |
| 314 |
> |
<< avgOPHeadUpper.director[2] << "\n"; |
| 315 |
> |
|
| 316 |
> |
os << avgOPHeadLower.p2 << "\t" |
| 317 |
> |
<< errOPHeadLower.p2 << "\t" |
| 318 |
> |
<< avgOPHeadLower.director[0] << "\t" |
| 319 |
> |
<< avgOPHeadLower.director[1] << "\t" |
| 320 |
> |
<< avgOPHeadLower.director[2] << "\n"; |
| 321 |
|
|
| 322 |
|
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 323 |
|
os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n"; |
