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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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< |
* 1. Acknowledgement of the program authors must be made in any |
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< |
* publication of scientific results based in part on use of the |
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< |
* 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 |
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< |
* 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 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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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 "brains/SimInfo.hpp" |
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#include "integrators/IntegratorCreator.hpp" |
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#include "integrators/NPrT.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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> |
#include "utils/PhysicalConstants.hpp" |
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#include "utils/simError.h" |
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|
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namespace oopse { |
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> |
namespace OpenMD { |
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NPrT::NPrT(SimInfo* info) : NPT(info) { |
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Globals* simParams = info_->getSimParams(); |
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if (!simParams->haveSurfaceTension()) { |
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sprintf(painCave.errMsg, |
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"If you use the NPT integrator, you must set tauBarostat.\n"); |
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< |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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surfaceTension= simParams->getSurfaceTension()* OOPSEConstant::surfaceTensorConvert * OOPSEConstant::energyConvert; |
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> |
surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert; |
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} |
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|
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} |
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void NPrT::evolveEtaA() { |
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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> |
Mat3x3d hmat = snap->getHmat(); |
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RealType hz = hmat(2, 2); |
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RealType Axy = hmat(0,0) * hmat(1, 1); |
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< |
RealType sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert); |
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< |
RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert); |
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> |
RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert); |
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> |
RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert); |
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eta(0,0) -= dt2* Axy * (sx - surfaceTension) / (NkBT*tb2); |
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eta(1,1) -= dt2* Axy * (sy - surfaceTension) / (NkBT*tb2); |
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< |
eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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> |
eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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oldEta = eta; |
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} |
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|
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void NPrT::evolveEtaB() { |
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< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
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> |
Mat3x3d hmat = snap->getHmat(); |
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RealType hz = hmat(2, 2); |
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RealType Axy = hmat(0,0) * hmat(1, 1); |
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prevEta = eta; |
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< |
RealType sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert); |
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< |
RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert); |
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> |
RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert); |
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> |
RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert); |
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eta(0,0) = oldEta(0, 0) - dt2 * Axy * (sx -surfaceTension) / (NkBT*tb2); |
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eta(1,1) = oldEta(1, 1) - dt2 * Axy * (sy -surfaceTension) / (NkBT*tb2); |
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eta(2,2) = oldEta(2, 2) + dt2 * instaVol * |
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< |
(press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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> |
(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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} |
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|
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void NPrT::calcVelScale(){ |
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vScale(i, j) = eta(i, j); |
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|
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if (i == j) { |
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< |
vScale(i, j) += chi; |
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> |
vScale(i, j) += thermostat.first; |
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} |
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} |
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} |
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scaleMat(0, 0) = exp(dt*eta(0, 0)); |
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scaleMat(1, 1) = exp(dt*eta(1, 1)); |
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scaleMat(2, 2) = exp(dt*eta(2, 2)); |
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< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
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> |
Mat3x3d hmat = snap->getHmat(); |
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hmat = hmat *scaleMat; |
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< |
currentSnapshot_->setHmat(hmat); |
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> |
snap->setHmat(hmat); |
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|
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} |
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|
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} |
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|
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RealType NPrT::calcConservedQuantity(){ |
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< |
|
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< |
chi= currentSnapshot_->getChi(); |
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< |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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> |
thermostat = snap->getThermostat(); |
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loadEta(); |
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|
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// We need NkBT a lot, so just set it here: This is the RAW number |
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// of integrableObjects, so no subtraction or addition of constraints or |
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// orientational degrees of freedom: |
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< |
NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp; |
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> |
NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp; |
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|
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// fkBT is used because the thermostat operates on more degrees of freedom |
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// than the barostat (when there are particles with orientational degrees |
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// of freedom). |
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< |
fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; |
| 156 |
> |
fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp; |
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|
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|
|
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< |
RealType totalEnergy = thermo.getTotalE(); |
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> |
RealType totalEnergy = thermo.getTotalEnergy(); |
| 160 |
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|
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< |
RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
| 161 |
> |
RealType thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /(2.0 * PhysicalConstants::energyConvert); |
| 162 |
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|
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< |
RealType thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
| 163 |
> |
RealType thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert; |
| 164 |
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|
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SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
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RealType trEta = tmp.trace(); |
| 167 |
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|
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< |
RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
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> |
RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert); |
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|
|
| 170 |
< |
RealType barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
| 170 |
> |
RealType barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert; |
| 171 |
|
|
| 172 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 172 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 173 |
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RealType hz = hmat(2, 2); |
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RealType area = hmat(0,0) * hmat(1, 1); |
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|
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RealType conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 177 |
< |
barostat_kinetic + barostat_potential - surfaceTension * area/ OOPSEConstant::energyConvert; |
| 177 |
> |
barostat_kinetic + barostat_potential - surfaceTension * area/ PhysicalConstants::energyConvert; |
| 178 |
|
|
| 179 |
|
return conservedQuantity; |
| 180 |
|
|
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} |
| 182 |
|
|
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|
void NPrT::loadEta() { |
| 184 |
< |
eta= currentSnapshot_->getEta(); |
| 184 |
> |
eta= snap->getBarostat(); |
| 185 |
|
|
| 186 |
|
//if (!eta.isDiagonal()) { |
| 187 |
|
// sprintf( painCave.errMsg, |
| 192 |
|
} |
| 193 |
|
|
| 194 |
|
void NPrT::saveEta() { |
| 195 |
< |
currentSnapshot_->setEta(eta); |
| 195 |
> |
snap->setBarostat(eta); |
| 196 |
|
} |
| 197 |
|
|
| 198 |
|
} |
