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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: |
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* |
| 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 |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
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* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
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* 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 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
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* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
| 32 |
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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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include <cmath> |
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#include "constraints/ZconstraintForceManager.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "utils/simError.h" |
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#include "utils/OOPSEConstant.hpp" |
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> |
#include "utils/PhysicalConstants.hpp" |
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#include "utils/StringUtils.hpp" |
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namespace oopse { |
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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 OpenMD { |
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ZconstraintForceManager::ZconstraintForceManager(SimInfo* info): ForceManager(info), infiniteTime(1e31) { |
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currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Globals* simParam = info_->getSimParams(); |
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zconsTol_ = 0.01; |
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sprintf(painCave.errMsg, |
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"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
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"\tOOPSE will use a default value of %f.\n" |
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> |
"\tOpenMD will use a default value of %f.\n" |
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"\tTo set the tolerance, use the zconsTol variable.\n", |
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zconsTol_); |
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painCave.isFatal = 0; |
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} else { |
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targetTemp = 298.0; |
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} |
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< |
RealType zforceConstant = OOPSEConstant::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox); |
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> |
RealType zforceConstant = PhysicalConstants::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox); |
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|
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int nZconstraints = simParam->getNZconsStamps(); |
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std::vector<ZConsStamp*> stamp = simParam->getZconsStamps(); |
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currZconsTime_ = currSnapshot_->getTime(); |
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} |
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|
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< |
void ZconstraintForceManager::calcForces(bool needPotential, bool needStress){ |
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< |
ForceManager::calcForces(needPotential, needStress); |
| 248 |
> |
void ZconstraintForceManager::calcForces(){ |
| 249 |
> |
ForceManager::calcForces(); |
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|
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if (usingZconsGap_){ |
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updateZPos(); |
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Vector3d force(0.0); |
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Vector3d com; |
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RealType totalFZ_local = 0; |
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+ |
RealType lrPot; |
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std::list<ZconstraintMol>::iterator i; |
| 441 |
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StuntDouble* integrableObject; |
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Molecule::IntegrableObjectIterator ii; |
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RealType resPos = usingSMD_? i->cantPos : i->param.zTargetPos; |
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RealType diff = com[whichDirection] - resPos; |
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|
RealType harmonicU = 0.5 * i->param.kz * diff * diff; |
| 450 |
< |
currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU; |
| 450 |
> |
lrPot = currSnapshot_->getLongRangePotential(); |
| 451 |
> |
lrPot += harmonicU; |
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> |
currSnapshot_->setLongRangePotential(lrPot); |
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RealType harmonicF = -i->param.kz * diff; |
| 454 |
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totalFZ_local += harmonicF; |
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|
|
