| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
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* 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 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* 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 |
|
*/ |
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|
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/** |
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#include "brains/ForceManager.hpp" |
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|
#include "primitives/Molecule.hpp" |
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#include "UseTheForce/doForces_interface.h" |
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< |
#define __OOPSE_C |
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> |
#define __OPENMD_C |
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#include "UseTheForce/DarkSide/fInteractionMap.h" |
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#include "utils/simError.h" |
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#include "primitives/Bond.hpp" |
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#include "primitives/Bend.hpp" |
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#include "primitives/Torsion.hpp" |
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#include "primitives/Inversion.hpp" |
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– |
namespace oopse { |
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|
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< |
void ForceManager::calcForces(bool needPotential, bool needStress) { |
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> |
namespace OpenMD { |
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> |
|
| 63 |
> |
ForceManager::ForceManager(SimInfo * info) : info_(info), |
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> |
NBforcesInitialized_(false) { |
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> |
} |
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> |
|
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> |
void ForceManager::calcForces() { |
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|
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+ |
|
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if (!info_->isFortranInitialized()) { |
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info_->update(); |
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+ |
nbiMan_->setSimInfo(info_); |
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+ |
nbiMan_->initialize(); |
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+ |
info_->setupFortran(); |
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} |
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|
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preCalculation(); |
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|
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calcShortRangeInteraction(); |
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|
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< |
calcLongRangeInteraction(needPotential, needStress); |
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> |
calcLongRangeInteraction(); |
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|
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< |
postCalculation(needStress); |
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> |
postCalculation(); |
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|
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} |
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|
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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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+ |
Molecule::CutoffGroupIterator ci; |
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CutoffGroup* cg; |
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|
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// forces are zeroed here, before any are accumulated. |
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// NOTE: do not rezero the forces in Fortran. |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->zeroForcesAndTorques(); |
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} |
| 111 |
< |
|
| 111 |
> |
|
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> |
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
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> |
std::cerr << "should not see me \n"; |
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> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
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> |
cg = mol->nextCutoffGroup(ci)) { |
| 116 |
> |
//calculate the center of mass of cutoff group |
| 117 |
> |
cg->updateCOM(); |
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> |
} |
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> |
} |
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} |
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< |
|
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> |
|
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// Zero out the stress tensor |
| 123 |
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tau *= 0.0; |
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|
| 164 |
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RealType angle; |
| 165 |
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bend->calcForce(angle); |
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RealType currBendPot = bend->getPotential(); |
| 167 |
+ |
|
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bendPotential += bend->getPotential(); |
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std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend); |
| 170 |
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if (i == bendDataSets.end()) { |
| 242 |
|
|
| 243 |
|
} |
| 244 |
|
|
| 245 |
< |
void ForceManager::calcLongRangeInteraction(bool needPotential, |
| 226 |
< |
bool needStress) { |
| 245 |
> |
void ForceManager::calcLongRangeInteraction() { |
| 246 |
|
Snapshot* curSnapshot; |
| 247 |
|
DataStorage* config; |
| 248 |
+ |
DataStorage* cgConfig; |
| 249 |
|
RealType* frc; |
| 250 |
|
RealType* pos; |
| 251 |
|
RealType* trq; |
| 259 |
|
|
| 260 |
|
//get array pointers |
| 261 |
|
config = &(curSnapshot->atomData); |
| 262 |
+ |
cgConfig = &(curSnapshot->cgData); |
| 263 |
|
frc = config->getArrayPointer(DataStorage::dslForce); |
| 264 |
|
pos = config->getArrayPointer(DataStorage::dslPosition); |
| 265 |
|
trq = config->getArrayPointer(DataStorage::dslTorque); |
| 267 |
|
electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 268 |
|
particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 269 |
|
|
| 270 |
< |
//calculate the center of mass of cutoff group |
| 271 |
< |
SimInfo::MoleculeIterator mi; |
| 272 |
< |
Molecule* mol; |
| 252 |
< |
Molecule::CutoffGroupIterator ci; |
| 253 |
< |
CutoffGroup* cg; |
| 254 |
< |
Vector3d com; |
| 255 |
< |
std::vector<Vector3d> rcGroup; |
| 256 |
< |
|
| 257 |
< |
if(info_->getNCutoffGroups() > 0){ |
| 258 |
< |
|
| 259 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 260 |
< |
mol = info_->nextMolecule(mi)) { |
| 261 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 262 |
< |
cg = mol->nextCutoffGroup(ci)) { |
| 263 |
< |
cg->getCOM(com); |
| 264 |
< |
rcGroup.push_back(com); |
| 265 |
< |
} |
| 266 |
< |
}// end for (mol) |
| 267 |
< |
|
| 268 |
< |
rc = rcGroup[0].getArrayPointer(); |
| 270 |
> |
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
| 271 |
> |
std::cerr << "should not see me \n"; |
| 272 |
> |
rc = cgConfig->getArrayPointer(DataStorage::dslPosition); |
| 273 |
|
} else { |
| 274 |
|
// center of mass of the group is the same as position of the atom |
| 275 |
|
// if cutoff group does not exist |
| 279 |
|
//initialize data before passing to fortran |
| 280 |
|
RealType longRangePotential[LR_POT_TYPES]; |
| 281 |
|
RealType lrPot = 0.0; |
| 278 |
– |
Vector3d totalDipole; |
| 279 |
– |
short int passedCalcPot = needPotential; |
| 280 |
– |
short int passedCalcStress = needStress; |
| 282 |
|
int isError = 0; |
| 283 |
|
|
| 284 |
|
for (int i=0; i<LR_POT_TYPES;i++){ |
| 294 |
|
tau.getArrayPointer(), |
| 295 |
|
longRangePotential, |
| 296 |
|
particlePot, |
| 296 |
– |
&passedCalcPot, |
| 297 |
– |
&passedCalcStress, |
| 297 |
|
&isError ); |
| 298 |
|
|
| 299 |
|
if( isError ){ |
| 305 |
|
for (int i=0; i<LR_POT_TYPES;i++){ |
| 306 |
|
lrPot += longRangePotential[i]; //Quick hack |
| 307 |
|
} |
| 308 |
< |
|
| 310 |
< |
// grab the simulation box dipole moment if specified |
| 311 |
< |
if (info_->getCalcBoxDipole()){ |
| 312 |
< |
getAccumulatedBoxDipole(totalDipole.getArrayPointer()); |
| 313 |
< |
|
| 314 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0); |
| 315 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
| 316 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
| 317 |
< |
} |
| 318 |
< |
|
| 308 |
> |
|
| 309 |
|
//store the tau and long range potential |
| 310 |
|
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 311 |
|
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT]; |
| 313 |
|
} |
| 314 |
|
|
| 315 |
|
|
| 316 |
< |
void ForceManager::postCalculation(bool needStress) { |
| 316 |
> |
void ForceManager::postCalculation() { |
| 317 |
|
SimInfo::MoleculeIterator mi; |
| 318 |
|
Molecule* mol; |
| 319 |
|
Molecule::RigidBodyIterator rbIter; |
| 326 |
|
mol = info_->nextMolecule(mi)) { |
| 327 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 328 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 329 |
< |
if (needStress) { |
| 330 |
< |
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 341 |
< |
tau += rbTau; |
| 342 |
< |
} else{ |
| 343 |
< |
rb->calcForcesAndTorques(); |
| 344 |
< |
} |
| 329 |
> |
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 330 |
> |
tau += rbTau; |
| 331 |
|
} |
| 332 |
|
} |
| 333 |
< |
|
| 348 |
< |
if (needStress) { |
| 333 |
> |
|
| 334 |
|
#ifdef IS_MPI |
| 335 |
< |
Mat3x3d tmpTau(tau); |
| 336 |
< |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 337 |
< |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 335 |
> |
Mat3x3d tmpTau(tau); |
| 336 |
> |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 337 |
> |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 338 |
|
#endif |
| 339 |
< |
curSnapshot->statData.setTau(tau); |
| 355 |
< |
} |
| 339 |
> |
curSnapshot->statData.setTau(tau); |
| 340 |
|
} |
| 341 |
|
|
| 342 |
< |
} //end namespace oopse |
| 342 |
> |
} //end namespace OpenMD |
