| 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
/** |
| 50 |
|
#include "brains/ForceManager.hpp" |
| 51 |
|
#include "primitives/Molecule.hpp" |
| 52 |
|
#include "UseTheForce/doForces_interface.h" |
| 53 |
< |
#define __C |
| 53 |
> |
#define __OPENMD_C |
| 54 |
|
#include "UseTheForce/DarkSide/fInteractionMap.h" |
| 55 |
|
#include "utils/simError.h" |
| 56 |
< |
namespace oopse { |
| 56 |
> |
#include "primitives/Bond.hpp" |
| 57 |
> |
#include "primitives/Bend.hpp" |
| 58 |
> |
#include "primitives/Torsion.hpp" |
| 59 |
> |
#include "primitives/Inversion.hpp" |
| 60 |
|
|
| 61 |
< |
void ForceManager::calcForces(bool needPotential, bool needStress) { |
| 61 |
> |
namespace OpenMD { |
| 62 |
> |
|
| 63 |
> |
ForceManager::ForceManager(SimInfo * info) : info_(info), |
| 64 |
> |
NBforcesInitialized_(false) { |
| 65 |
> |
} |
| 66 |
> |
|
| 67 |
> |
void ForceManager::calcForces() { |
| 68 |
> |
|
| 69 |
|
|
| 70 |
|
if (!info_->isFortranInitialized()) { |
| 71 |
|
info_->update(); |
| 72 |
+ |
nbiMan_->setSimInfo(info_); |
| 73 |
+ |
nbiMan_->initialize(); |
| 74 |
+ |
info_->setupFortran(); |
| 75 |
|
} |
| 76 |
< |
|
| 76 |
> |
|
| 77 |
|
preCalculation(); |
| 78 |
|
|
| 79 |
|
calcShortRangeInteraction(); |
| 80 |
|
|
| 81 |
< |
calcLongRangeInteraction(needPotential, needStress); |
| 81 |
> |
calcLongRangeInteraction(); |
| 82 |
|
|
| 83 |
|
postCalculation(); |
| 84 |
< |
|
| 84 |
> |
|
| 85 |
|
} |
| 86 |
< |
|
| 86 |
> |
|
| 87 |
|
void ForceManager::preCalculation() { |
| 88 |
|
SimInfo::MoleculeIterator mi; |
| 89 |
|
Molecule* mol; |
| 94 |
|
|
| 95 |
|
// forces are zeroed here, before any are accumulated. |
| 96 |
|
// NOTE: do not rezero the forces in Fortran. |
| 97 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 97 |
> |
|
| 98 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 99 |
> |
mol = info_->nextMolecule(mi)) { |
| 100 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 101 |
|
atom->zeroForcesAndTorques(); |
| 102 |
|
} |
| 103 |
< |
|
| 103 |
> |
|
| 104 |
|
//change the positions of atoms which belong to the rigidbodies |
| 105 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 105 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 106 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 107 |
|
rb->zeroForcesAndTorques(); |
| 108 |
|
} |
| 109 |
+ |
|
| 110 |
|
} |
| 111 |
|
|
| 112 |
+ |
// Zero out the stress tensor |
| 113 |
+ |
tau *= 0.0; |
| 114 |
+ |
|
| 115 |
|
} |
| 116 |
< |
|
| 116 |
> |
|
| 117 |
|
void ForceManager::calcShortRangeInteraction() { |
| 118 |
|
Molecule* mol; |
| 119 |
|
RigidBody* rb; |
| 120 |
|
Bond* bond; |
| 121 |
|
Bend* bend; |
| 122 |
|
Torsion* torsion; |
| 123 |
+ |
Inversion* inversion; |
| 124 |
|
SimInfo::MoleculeIterator mi; |
| 125 |
|
Molecule::RigidBodyIterator rbIter; |
| 126 |
|
Molecule::BondIterator bondIter;; |
| 127 |
|
Molecule::BendIterator bendIter; |
| 128 |
|
Molecule::TorsionIterator torsionIter; |
| 129 |
+ |
Molecule::InversionIterator inversionIter; |
| 130 |
+ |
RealType bondPotential = 0.0; |
| 131 |
+ |
RealType bendPotential = 0.0; |
| 132 |
+ |
RealType torsionPotential = 0.0; |
| 133 |
+ |
RealType inversionPotential = 0.0; |
| 134 |
|
|
| 135 |
|
//calculate short range interactions |
| 136 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 136 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 137 |
> |
mol = info_->nextMolecule(mi)) { |
| 138 |
|
|
| 139 |
|
//change the positions of atoms which belong to the rigidbodies |
| 140 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 141 |
< |
rb->updateAtoms(); |
| 140 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 141 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 142 |
> |
rb->updateAtoms(); |
| 143 |
|
} |
| 144 |
|
|
| 145 |
< |
for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
| 146 |
< |
bond->calcForce(); |
| 145 |
> |
for (bond = mol->beginBond(bondIter); bond != NULL; |
| 146 |
> |
bond = mol->nextBond(bondIter)) { |
| 147 |
> |
bond->calcForce(); |
| 148 |
> |
bondPotential += bond->getPotential(); |
| 149 |
|
} |
| 150 |
|
|
| 151 |
< |
for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
| 152 |
< |
bend->calcForce(); |
| 151 |
> |
for (bend = mol->beginBend(bendIter); bend != NULL; |
| 152 |
> |
bend = mol->nextBend(bendIter)) { |
| 153 |
> |
|
| 154 |
> |
RealType angle; |
| 155 |
> |
bend->calcForce(angle); |
| 156 |
> |
RealType currBendPot = bend->getPotential(); |
| 157 |
> |
|
| 158 |
> |
bendPotential += bend->getPotential(); |
| 159 |
> |
std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend); |
| 160 |
> |
if (i == bendDataSets.end()) { |
| 161 |
> |
BendDataSet dataSet; |
| 162 |
> |
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 163 |
> |
dataSet.prev.potential = dataSet.curr.potential = currBendPot; |
| 164 |
> |
dataSet.deltaV = 0.0; |
| 165 |
> |
bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet)); |
| 166 |
> |
}else { |
| 167 |
> |
i->second.prev.angle = i->second.curr.angle; |
| 168 |
> |
i->second.prev.potential = i->second.curr.potential; |
| 169 |
> |
i->second.curr.angle = angle; |
| 170 |
> |
i->second.curr.potential = currBendPot; |
| 171 |
> |
i->second.deltaV = fabs(i->second.curr.potential - |
| 172 |
> |
i->second.prev.potential); |
| 173 |
> |
} |
| 174 |
|
} |
| 175 |
+ |
|
| 176 |
+ |
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
| 177 |
+ |
torsion = mol->nextTorsion(torsionIter)) { |
| 178 |
+ |
RealType angle; |
| 179 |
+ |
torsion->calcForce(angle); |
| 180 |
+ |
RealType currTorsionPot = torsion->getPotential(); |
| 181 |
+ |
torsionPotential += torsion->getPotential(); |
| 182 |
+ |
std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion); |
| 183 |
+ |
if (i == torsionDataSets.end()) { |
| 184 |
+ |
TorsionDataSet dataSet; |
| 185 |
+ |
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 186 |
+ |
dataSet.prev.potential = dataSet.curr.potential = currTorsionPot; |
| 187 |
+ |
dataSet.deltaV = 0.0; |
| 188 |
+ |
torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet)); |
| 189 |
+ |
}else { |
| 190 |
+ |
i->second.prev.angle = i->second.curr.angle; |
| 191 |
+ |
i->second.prev.potential = i->second.curr.potential; |
| 192 |
+ |
i->second.curr.angle = angle; |
| 193 |
+ |
i->second.curr.potential = currTorsionPot; |
| 194 |
+ |
i->second.deltaV = fabs(i->second.curr.potential - |
| 195 |
+ |
i->second.prev.potential); |
| 196 |
+ |
} |
| 197 |
+ |
} |
| 198 |
|
|
| 199 |
< |
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
| 200 |
< |
torsion->calcForce(); |
| 201 |
< |
} |
| 202 |
< |
|
| 199 |
> |
for (inversion = mol->beginInversion(inversionIter); |
| 200 |
> |
inversion != NULL; |
| 201 |
> |
inversion = mol->nextInversion(inversionIter)) { |
| 202 |
> |
RealType angle; |
| 203 |
> |
inversion->calcForce(angle); |
| 204 |
> |
RealType currInversionPot = inversion->getPotential(); |
| 205 |
> |
inversionPotential += inversion->getPotential(); |
| 206 |
> |
std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion); |
| 207 |
> |
if (i == inversionDataSets.end()) { |
| 208 |
> |
InversionDataSet dataSet; |
| 209 |
> |
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 210 |
> |
dataSet.prev.potential = dataSet.curr.potential = currInversionPot; |
| 211 |
> |
dataSet.deltaV = 0.0; |
| 212 |
> |
inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet)); |
| 213 |
> |
}else { |
| 214 |
> |
i->second.prev.angle = i->second.curr.angle; |
| 215 |
> |
i->second.prev.potential = i->second.curr.potential; |
| 216 |
> |
i->second.curr.angle = angle; |
| 217 |
> |
i->second.curr.potential = currInversionPot; |
| 218 |
> |
i->second.deltaV = fabs(i->second.curr.potential - |
| 219 |
> |
i->second.prev.potential); |
| 220 |
> |
} |
| 221 |
> |
} |
| 222 |
|
} |
| 223 |
|
|
| 224 |
< |
double shortRangePotential = 0.0; |
| 225 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 133 |
< |
shortRangePotential += mol->getPotential(); |
| 134 |
< |
} |
| 135 |
< |
|
| 224 |
> |
RealType shortRangePotential = bondPotential + bendPotential + |
| 225 |
> |
torsionPotential + inversionPotential; |
| 226 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 227 |
|
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
| 228 |
+ |
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 229 |
+ |
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
| 230 |
+ |
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
| 231 |
+ |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 232 |
+ |
|
| 233 |
|
} |
| 234 |
< |
|
| 235 |
< |
void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) { |
| 234 |
> |
|
| 235 |
> |
void ForceManager::calcLongRangeInteraction() { |
| 236 |
|
Snapshot* curSnapshot; |
| 237 |
|
DataStorage* config; |
| 238 |
< |
double* frc; |
| 239 |
< |
double* pos; |
| 240 |
< |
double* trq; |
| 241 |
< |
double* A; |
| 242 |
< |
double* electroFrame; |
| 243 |
< |
double* rc; |
| 238 |
> |
RealType* frc; |
| 239 |
> |
RealType* pos; |
| 240 |
> |
RealType* trq; |
| 241 |
> |
RealType* A; |
| 242 |
> |
RealType* electroFrame; |
| 243 |
> |
RealType* rc; |
| 244 |
> |
RealType* particlePot; |
| 245 |
|
|
| 246 |
|
//get current snapshot from SimInfo |
| 247 |
|
curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 248 |
< |
|
| 248 |
> |
|
| 249 |
|
//get array pointers |
| 250 |
|
config = &(curSnapshot->atomData); |
| 251 |
|
frc = config->getArrayPointer(DataStorage::dslForce); |
| 253 |
|
trq = config->getArrayPointer(DataStorage::dslTorque); |
| 254 |
|
A = config->getArrayPointer(DataStorage::dslAmat); |
| 255 |
|
electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 256 |
+ |
particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 257 |
|
|
| 258 |
|
//calculate the center of mass of cutoff group |
| 259 |
|
SimInfo::MoleculeIterator mi; |
| 262 |
|
CutoffGroup* cg; |
| 263 |
|
Vector3d com; |
| 264 |
|
std::vector<Vector3d> rcGroup; |
| 265 |
< |
|
| 265 |
> |
|
| 266 |
|
if(info_->getNCutoffGroups() > 0){ |
| 267 |
< |
|
| 268 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 269 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 267 |
> |
|
| 268 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 269 |
> |
mol = info_->nextMolecule(mi)) { |
| 270 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 271 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 272 |
|
cg->getCOM(com); |
| 273 |
|
rcGroup.push_back(com); |
| 274 |
|
} |
| 276 |
|
|
| 277 |
|
rc = rcGroup[0].getArrayPointer(); |
| 278 |
|
} else { |
| 279 |
< |
// center of mass of the group is the same as position of the atom if cutoff group does not exist |
| 279 |
> |
// center of mass of the group is the same as position of the atom |
| 280 |
> |
// if cutoff group does not exist |
| 281 |
|
rc = pos; |
| 282 |
|
} |
| 183 |
– |
|
| 184 |
– |
//initialize data before passing to fortran |
| 185 |
– |
double longRangePotential[LR_POT_TYPES]; |
| 186 |
– |
double lrPot = 0.0; |
| 283 |
|
|
| 284 |
< |
Mat3x3d tau; |
| 285 |
< |
short int passedCalcPot = needPotential; |
| 286 |
< |
short int passedCalcStress = needStress; |
| 284 |
> |
//initialize data before passing to fortran |
| 285 |
> |
RealType longRangePotential[LR_POT_TYPES]; |
| 286 |
> |
RealType lrPot = 0.0; |
| 287 |
|
int isError = 0; |
| 288 |
|
|
| 289 |
|
for (int i=0; i<LR_POT_TYPES;i++){ |
| 290 |
|
longRangePotential[i]=0.0; //Initialize array |
| 291 |
|
} |
| 292 |
< |
|
| 293 |
< |
|
| 294 |
< |
|
| 295 |
< |
doForceLoop( pos, |
| 296 |
< |
rc, |
| 297 |
< |
A, |
| 298 |
< |
electroFrame, |
| 299 |
< |
frc, |
| 300 |
< |
trq, |
| 301 |
< |
tau.getArrayPointer(), |
| 302 |
< |
longRangePotential, |
| 303 |
< |
&passedCalcPot, |
| 208 |
< |
&passedCalcStress, |
| 209 |
< |
&isError ); |
| 210 |
< |
|
| 292 |
> |
|
| 293 |
> |
doForceLoop(pos, |
| 294 |
> |
rc, |
| 295 |
> |
A, |
| 296 |
> |
electroFrame, |
| 297 |
> |
frc, |
| 298 |
> |
trq, |
| 299 |
> |
tau.getArrayPointer(), |
| 300 |
> |
longRangePotential, |
| 301 |
> |
particlePot, |
| 302 |
> |
&isError ); |
| 303 |
> |
|
| 304 |
|
if( isError ){ |
| 305 |
|
sprintf( painCave.errMsg, |
| 306 |
|
"Error returned from the fortran force calculation.\n" ); |
| 310 |
|
for (int i=0; i<LR_POT_TYPES;i++){ |
| 311 |
|
lrPot += longRangePotential[i]; //Quick hack |
| 312 |
|
} |
| 313 |
< |
|
| 313 |
> |
|
| 314 |
|
//store the tau and long range potential |
| 315 |
|
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 316 |
< |
// curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential; |
| 317 |
< |
curSnapshot->statData.setTau(tau); |
| 316 |
> |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT]; |
| 317 |
> |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT]; |
| 318 |
|
} |
| 319 |
|
|
| 320 |
< |
|
| 320 |
> |
|
| 321 |
|
void ForceManager::postCalculation() { |
| 322 |
|
SimInfo::MoleculeIterator mi; |
| 323 |
|
Molecule* mol; |
| 324 |
|
Molecule::RigidBodyIterator rbIter; |
| 325 |
|
RigidBody* rb; |
| 326 |
+ |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 327 |
|
|
| 328 |
|
// collect the atomic forces onto rigid bodies |
| 329 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 330 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 331 |
< |
rb->calcForcesAndTorques(); |
| 329 |
> |
|
| 330 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 331 |
> |
mol = info_->nextMolecule(mi)) { |
| 332 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 333 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 334 |
> |
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 335 |
> |
tau += rbTau; |
| 336 |
|
} |
| 337 |
|
} |
| 338 |
< |
|
| 338 |
> |
|
| 339 |
> |
#ifdef IS_MPI |
| 340 |
> |
Mat3x3d tmpTau(tau); |
| 341 |
> |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 342 |
> |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 343 |
> |
#endif |
| 344 |
> |
curSnapshot->statData.setTau(tau); |
| 345 |
|
} |
| 346 |
|
|
| 347 |
< |
} //end namespace oopse |
| 347 |
> |
} //end namespace OpenMD |
