| 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 |
|
#include "primitives/Bond.hpp" |
| 57 |
|
#include "primitives/Bend.hpp" |
| 58 |
< |
namespace oopse { |
| 58 |
> |
#include "primitives/Torsion.hpp" |
| 59 |
> |
#include "primitives/Inversion.hpp" |
| 60 |
> |
namespace OpenMD { |
| 61 |
|
|
| 62 |
|
void ForceManager::calcForces(bool needPotential, bool needStress) { |
| 63 |
|
|
| 85 |
|
|
| 86 |
|
// forces are zeroed here, before any are accumulated. |
| 87 |
|
// NOTE: do not rezero the forces in Fortran. |
| 88 |
< |
|
| 88 |
> |
|
| 89 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 90 |
|
mol = info_->nextMolecule(mi)) { |
| 91 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 92 |
|
atom->zeroForcesAndTorques(); |
| 93 |
|
} |
| 94 |
< |
|
| 94 |
> |
|
| 95 |
|
//change the positions of atoms which belong to the rigidbodies |
| 96 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 97 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 98 |
|
rb->zeroForcesAndTorques(); |
| 99 |
|
} |
| 100 |
+ |
|
| 101 |
|
} |
| 102 |
|
|
| 103 |
|
// Zero out the stress tensor |
| 111 |
|
Bond* bond; |
| 112 |
|
Bend* bend; |
| 113 |
|
Torsion* torsion; |
| 114 |
+ |
Inversion* inversion; |
| 115 |
|
SimInfo::MoleculeIterator mi; |
| 116 |
|
Molecule::RigidBodyIterator rbIter; |
| 117 |
|
Molecule::BondIterator bondIter;; |
| 118 |
|
Molecule::BendIterator bendIter; |
| 119 |
|
Molecule::TorsionIterator torsionIter; |
| 120 |
+ |
Molecule::InversionIterator inversionIter; |
| 121 |
|
RealType bondPotential = 0.0; |
| 122 |
|
RealType bendPotential = 0.0; |
| 123 |
|
RealType torsionPotential = 0.0; |
| 124 |
+ |
RealType inversionPotential = 0.0; |
| 125 |
|
|
| 126 |
|
//calculate short range interactions |
| 127 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 145 |
|
RealType angle; |
| 146 |
|
bend->calcForce(angle); |
| 147 |
|
RealType currBendPot = bend->getPotential(); |
| 148 |
+ |
|
| 149 |
|
bendPotential += bend->getPotential(); |
| 150 |
|
std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend); |
| 151 |
|
if (i == bendDataSets.end()) { |
| 186 |
|
i->second.prev.potential); |
| 187 |
|
} |
| 188 |
|
} |
| 189 |
+ |
|
| 190 |
+ |
for (inversion = mol->beginInversion(inversionIter); |
| 191 |
+ |
inversion != NULL; |
| 192 |
+ |
inversion = mol->nextInversion(inversionIter)) { |
| 193 |
+ |
RealType angle; |
| 194 |
+ |
inversion->calcForce(angle); |
| 195 |
+ |
RealType currInversionPot = inversion->getPotential(); |
| 196 |
+ |
inversionPotential += inversion->getPotential(); |
| 197 |
+ |
std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion); |
| 198 |
+ |
if (i == inversionDataSets.end()) { |
| 199 |
+ |
InversionDataSet dataSet; |
| 200 |
+ |
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 201 |
+ |
dataSet.prev.potential = dataSet.curr.potential = currInversionPot; |
| 202 |
+ |
dataSet.deltaV = 0.0; |
| 203 |
+ |
inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet)); |
| 204 |
+ |
}else { |
| 205 |
+ |
i->second.prev.angle = i->second.curr.angle; |
| 206 |
+ |
i->second.prev.potential = i->second.curr.potential; |
| 207 |
+ |
i->second.curr.angle = angle; |
| 208 |
+ |
i->second.curr.potential = currInversionPot; |
| 209 |
+ |
i->second.deltaV = fabs(i->second.curr.potential - |
| 210 |
+ |
i->second.prev.potential); |
| 211 |
+ |
} |
| 212 |
+ |
} |
| 213 |
|
} |
| 214 |
|
|
| 215 |
|
RealType shortRangePotential = bondPotential + bendPotential + |
| 216 |
< |
torsionPotential; |
| 216 |
> |
torsionPotential + inversionPotential; |
| 217 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 218 |
|
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
| 219 |
|
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 220 |
|
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
| 221 |
|
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
| 222 |
+ |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 223 |
|
|
| 224 |
|
} |
| 225 |
|
|
| 233 |
|
RealType* A; |
| 234 |
|
RealType* electroFrame; |
| 235 |
|
RealType* rc; |
| 236 |
+ |
RealType* particlePot; |
| 237 |
|
|
| 238 |
|
//get current snapshot from SimInfo |
| 239 |
|
curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 245 |
|
trq = config->getArrayPointer(DataStorage::dslTorque); |
| 246 |
|
A = config->getArrayPointer(DataStorage::dslAmat); |
| 247 |
|
electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 248 |
+ |
particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 249 |
|
|
| 250 |
|
//calculate the center of mass of cutoff group |
| 251 |
|
SimInfo::MoleculeIterator mi; |
| 293 |
|
trq, |
| 294 |
|
tau.getArrayPointer(), |
| 295 |
|
longRangePotential, |
| 296 |
< |
&passedCalcPot, |
| 296 |
> |
particlePot, |
| 297 |
> |
&passedCalcPot, |
| 298 |
|
&passedCalcStress, |
| 299 |
|
&isError ); |
| 300 |
|
|
| 356 |
|
} |
| 357 |
|
} |
| 358 |
|
|
| 359 |
< |
} //end namespace oopse |
| 359 |
> |
} //end namespace OpenMD |
