| 6 |
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* 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
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|
| 42 |
– |
|
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– |
#include "restraints/ThermoIntegrationForceManager.hpp" |
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– |
|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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< |
namespace oopse { |
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> |
#include "restraints/ThermoIntegrationForceManager.hpp" |
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> |
|
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> |
namespace OpenMD { |
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|
|
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ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info): |
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RestraintForceManager(info){ |
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tIntLambda_ = 1.0; |
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sprintf(painCave.errMsg, |
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"ThermoIntegration error: the transformation parameter\n" |
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< |
"\t(lambda) was not specified. OOPSE will use a default\n" |
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> |
"\t(lambda) was not specified. OpenMD will use a default\n" |
| 64 |
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"\tvalue of %f. To set lambda, use the \n" |
| 65 |
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"\tthermodynamicIntegrationLambda variable.\n", |
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tIntLambda_); |
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tIntK_ = 1.0; |
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sprintf(painCave.errMsg, |
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"ThermoIntegration Warning: the tranformation parameter\n" |
| 78 |
< |
"\texponent (k) was not specified. OOPSE will use a default\n" |
| 78 |
> |
"\texponent (k) was not specified. OpenMD will use a default\n" |
| 79 |
|
"\tvalue of %f. To set k, use the thermodynamicIntegrationK\n" |
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"\tvariable.\n", |
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tIntK_); |
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ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){ |
| 91 |
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} |
| 92 |
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|
| 93 |
< |
void ThermoIntegrationForceManager::calcForces(bool needPotential, |
| 94 |
< |
bool needStress){ |
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> |
void ThermoIntegrationForceManager::calcForces(){ |
| 94 |
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Snapshot* curSnapshot; |
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SimInfo::MoleculeIterator mi; |
| 96 |
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Molecule* mol; |
| 97 |
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Molecule::IntegrableObjectIterator ii; |
| 98 |
< |
StuntDouble* integrableObject; |
| 98 |
> |
StuntDouble* sd; |
| 99 |
|
Vector3d frc; |
| 100 |
|
Vector3d trq; |
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Mat3x3d tempTau; |
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|
|
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|
// perform the standard calcForces first |
| 104 |
< |
ForceManager::calcForces(needPotential, needStress); |
| 104 |
> |
ForceManager::calcForces(); |
| 105 |
|
|
| 106 |
|
curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 107 |
|
|
| 108 |
< |
// now scale forces and torques of all the integrableObjects |
| 108 |
> |
// now scale forces and torques of all the sds |
| 109 |
|
|
| 110 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 111 |
|
mol = info_->nextMolecule(mi)) { |
| 112 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); |
| 113 |
< |
integrableObject != NULL; |
| 114 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 115 |
< |
frc = integrableObject->getFrc(); |
| 112 |
> |
|
| 113 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 114 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 115 |
> |
|
| 116 |
> |
frc = sd->getFrc(); |
| 117 |
|
frc *= factor_; |
| 118 |
< |
integrableObject->setFrc(frc); |
| 118 |
> |
sd->setFrc(frc); |
| 119 |
|
|
| 120 |
< |
if (integrableObject->isDirectional()){ |
| 121 |
< |
trq = integrableObject->getTrq(); |
| 120 |
> |
if (sd->isDirectional()){ |
| 121 |
> |
trq = sd->getTrq(); |
| 122 |
|
trq *= factor_; |
| 123 |
< |
integrableObject->setTrq(trq); |
| 123 |
> |
sd->setTrq(trq); |
| 124 |
|
} |
| 125 |
|
} |
| 126 |
|
} |
| 127 |
|
|
| 128 |
< |
// set vraw to be the unmodulated potential |
| 129 |
< |
lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL]; |
| 130 |
< |
curSnapshot->statData[Stats::VRAW] = lrPot_; |
| 128 |
> |
// set rawPotential to be the unmodulated potential |
| 129 |
> |
lrPot_ = curSnapshot->getLongRangePotential(); |
| 130 |
> |
curSnapshot->setRawPotential(lrPot_); |
| 131 |
|
|
| 132 |
|
// modulate the potential and update the snapshot |
| 133 |
|
lrPot_ *= factor_; |
| 134 |
< |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_; |
| 134 |
> |
curSnapshot->setLongRangePotential(lrPot_); |
| 135 |
|
|
| 136 |
|
// scale the pressure tensor |
| 137 |
< |
tempTau = curSnapshot->statData.getTau(); |
| 137 |
> |
tempTau = curSnapshot->getStressTensor(); |
| 138 |
|
tempTau *= factor_; |
| 139 |
< |
curSnapshot->statData.setTau(tempTau); |
| 139 |
> |
curSnapshot->setStressTensor(tempTau); |
| 140 |
|
|
| 141 |
|
// now, on to the applied restraining potentials (if needed): |
| 142 |
|
RealType restPot_local = 0.0; |
| 144 |
|
|
| 145 |
|
if (simParam->getUseRestraints()) { |
| 146 |
|
// do restraints from RestraintForceManager: |
| 147 |
– |
//restPot_local = doRestraints(1.0 - factor_); |
| 147 |
|
restPot_local = doRestraints(1.0 - factor_); |
| 148 |
|
vHarm_local = getUnscaledPotential(); |
| 149 |
|
} |
| 161 |
|
#endif |
| 162 |
|
|
| 163 |
|
// give the final values to stats |
| 164 |
< |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_; |
| 165 |
< |
curSnapshot->statData[Stats::VHARM] = vHarm_; |
| 164 |
> |
curSnapshot->setLongRangePotential(lrPot_); |
| 165 |
> |
curSnapshot->setRestraintPotential(vHarm_); |
| 166 |
|
} |
| 167 |
|
} |
