| 1 |
< |
/* |
| 1 |
> |
/* |
| 2 |
|
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
|
* |
| 4 |
|
* The University of Notre Dame grants you ("Licensee") a |
| 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, 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 |
|
*/ |
| 42 |
|
|
| 43 |
< |
#include <cmath> |
| 43 |
> |
#ifdef IS_MPI |
| 44 |
> |
#include <mpi.h> |
| 45 |
> |
#endif |
| 46 |
> |
|
| 47 |
|
#include "restraints/ThermoIntegrationForceManager.hpp" |
| 44 |
– |
#include "integrators/Integrator.hpp" |
| 45 |
– |
#include "primitives/Molecule.hpp" |
| 46 |
– |
#include "utils/simError.h" |
| 47 |
– |
#include "utils/OOPSEConstant.hpp" |
| 48 |
– |
#include "utils/StringUtils.hpp" |
| 48 |
|
|
| 49 |
< |
namespace oopse { |
| 49 |
> |
namespace OpenMD { |
| 50 |
|
|
| 51 |
|
ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info): |
| 52 |
< |
ForceManager(info){ |
| 52 |
> |
RestraintForceManager(info){ |
| 53 |
|
currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 54 |
|
simParam = info_->getSimParams(); |
| 55 |
|
|
| 56 |
< |
if (simParam->haveThermIntLambda()){ |
| 57 |
< |
tIntLambda_ = simParam->getThermIntLambda(); |
| 56 |
> |
if (simParam->haveThermodynamicIntegrationLambda()){ |
| 57 |
> |
tIntLambda_ = simParam->getThermodynamicIntegrationLambda(); |
| 58 |
|
} |
| 59 |
|
else{ |
| 60 |
|
tIntLambda_ = 1.0; |
| 61 |
|
sprintf(painCave.errMsg, |
| 62 |
< |
"ThermoIntegration error: the transformation parameter (lambda) was\n" |
| 63 |
< |
"\tnot specified. OOPSE will use a default value of %f. To set\n" |
| 64 |
< |
"\tlambda, use the thermodynamicIntegrationLambda variable.\n", |
| 62 |
> |
"ThermoIntegration error: the transformation parameter\n" |
| 63 |
> |
"\t(lambda) was not specified. OpenMD will use a default\n" |
| 64 |
> |
"\tvalue of %f. To set lambda, use the \n" |
| 65 |
> |
"\tthermodynamicIntegrationLambda variable.\n", |
| 66 |
|
tIntLambda_); |
| 67 |
|
painCave.isFatal = 0; |
| 68 |
|
simError(); |
| 69 |
|
} |
| 70 |
|
|
| 71 |
< |
if (simParam->haveThermIntK()){ |
| 72 |
< |
tIntK_ = simParam->getThermIntK(); |
| 71 |
> |
if (simParam->haveThermodynamicIntegrationK()){ |
| 72 |
> |
tIntK_ = simParam->getThermodynamicIntegrationK(); |
| 73 |
|
} |
| 74 |
|
else{ |
| 75 |
|
tIntK_ = 1.0; |
| 76 |
|
sprintf(painCave.errMsg, |
| 77 |
< |
"ThermoIntegration Warning: the tranformation parameter exponent\n" |
| 78 |
< |
"\t(k) was not specified. OOPSE will use a default value of %f.\n" |
| 79 |
< |
"\tTo set k, use the thermodynamicIntegrationK variable.\n", |
| 77 |
> |
"ThermoIntegration Warning: the tranformation parameter\n" |
| 78 |
> |
"\texponent (k) was not specified. OpenMD will use a default\n" |
| 79 |
> |
"\tvalue of %f. To set k, use the thermodynamicIntegrationK\n" |
| 80 |
> |
"\tvariable.\n", |
| 81 |
|
tIntK_); |
| 82 |
|
painCave.isFatal = 0; |
| 83 |
|
simError(); |
| 84 |
|
} |
| 85 |
|
|
| 85 |
– |
if (simParam->getUseSolidThermInt()) { |
| 86 |
– |
// build a restraint object |
| 87 |
– |
restraint_ = new Restraints(info_, tIntLambda_, tIntK_); |
| 88 |
– |
|
| 89 |
– |
} |
| 90 |
– |
|
| 86 |
|
// build the scaling factor used to modulate the forces and torques |
| 87 |
|
factor_ = pow(tIntLambda_, tIntK_); |
| 93 |
– |
|
| 88 |
|
} |
| 89 |
|
|
| 90 |
|
ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){ |
| 91 |
|
} |
| 92 |
|
|
| 93 |
< |
void ThermoIntegrationForceManager::calcForces(bool needPotential, |
| 100 |
< |
bool needStress){ |
| 93 |
> |
void ThermoIntegrationForceManager::calcForces(){ |
| 94 |
|
Snapshot* curSnapshot; |
| 95 |
|
SimInfo::MoleculeIterator mi; |
| 96 |
|
Molecule* mol; |
| 97 |
|
Molecule::IntegrableObjectIterator ii; |
| 98 |
< |
StuntDouble* integrableObject; |
| 98 |
> |
StuntDouble* sd; |
| 99 |
|
Vector3d frc; |
| 100 |
|
Vector3d trq; |
| 101 |
+ |
Mat3x3d tempTau; |
| 102 |
|
|
| 109 |
– |
curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 110 |
– |
|
| 103 |
|
// perform the standard calcForces first |
| 104 |
< |
ForceManager::calcForces(needPotential, needStress); |
| 104 |
> |
ForceManager::calcForces(); |
| 105 |
|
|
| 106 |
< |
// now scale forces and torques of all the integrableObjects |
| 106 |
> |
curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 107 |
> |
|
| 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 |
|
} |
| 131 |
– |
|
| 132 |
– |
// set vraw to be the unmodulated potential |
| 133 |
– |
lrPot_ = curSnapshot->statData[Stats::POTENTIAL_ENERGY]; |
| 134 |
– |
curSnapshot->statData[Stats::VRAW] = lrPot_; |
| 135 |
– |
|
| 136 |
– |
// modulate the potential and update the snapshot |
| 137 |
– |
lrPot_ *= factor_; |
| 138 |
– |
curSnapshot->statData[Stats::POTENTIAL_ENERGY] = lrPot_; |
| 126 |
|
} |
| 127 |
|
|
| 128 |
< |
// do crystal restraint forces for thermodynamic integration |
| 129 |
< |
if (simParam->getUseSolidThermInt()) { |
| 130 |
< |
|
| 144 |
< |
lrPot_ += restraint_->Calc_Restraint_Forces(); |
| 145 |
< |
curSnapshot->statData[Stats::POTENTIAL_ENERGY] = lrPot_; |
| 146 |
< |
|
| 147 |
< |
vHarm_ = restraint_->getVharm(); |
| 148 |
< |
curSnapshot->statData[Stats::VHARM] = vHarm_; |
| 149 |
< |
} |
| 128 |
> |
// set rawPotential to be the unmodulated potential |
| 129 |
> |
lrPot_ = curSnapshot->getLongRangePotential(); |
| 130 |
> |
curSnapshot->setRawPotential(lrPot_); |
| 131 |
|
|
| 132 |
< |
} |
| 133 |
< |
|
| 132 |
> |
// modulate the potential and update the snapshot |
| 133 |
> |
lrPot_ *= factor_; |
| 134 |
> |
curSnapshot->setLongRangePotential(lrPot_); |
| 135 |
> |
|
| 136 |
> |
// scale the pressure tensor |
| 137 |
> |
tempTau = curSnapshot->getStressTensor(); |
| 138 |
> |
tempTau *= factor_; |
| 139 |
> |
curSnapshot->setStressTensor(tempTau); |
| 140 |
> |
|
| 141 |
> |
// now, on to the applied restraining potentials (if needed): |
| 142 |
> |
RealType restPot_local = 0.0; |
| 143 |
> |
RealType vHarm_local = 0.0; |
| 144 |
> |
|
| 145 |
> |
if (simParam->getUseRestraints()) { |
| 146 |
> |
// do restraints from RestraintForceManager: |
| 147 |
> |
restPot_local = doRestraints(1.0 - factor_); |
| 148 |
> |
vHarm_local = getUnscaledPotential(); |
| 149 |
> |
} |
| 150 |
> |
|
| 151 |
> |
#ifdef IS_MPI |
| 152 |
> |
RealType restPot; |
| 153 |
> |
MPI_Allreduce(&restPot_local, &restPot, 1, |
| 154 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 155 |
> |
MPI_Allreduce(&vHarm_local, &vHarm_, 1, |
| 156 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 157 |
> |
lrPot_ += restPot; |
| 158 |
> |
#else |
| 159 |
> |
lrPot_ += restPot_local; |
| 160 |
> |
vHarm_ = vHarm_local; |
| 161 |
> |
#endif |
| 162 |
> |
|
| 163 |
> |
// give the final values to stats |
| 164 |
> |
curSnapshot->setLongRangePotential(lrPot_); |
| 165 |
> |
curSnapshot->setRestraintPotential(vHarm_); |
| 166 |
> |
} |
| 167 |
|
} |
