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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 |
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< |
* 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," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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< |
* 2. Redistributions of source code must retain the above copyright |
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> |
* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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> |
* 2. Redistributions in binary form must reproduce the above copyright |
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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 |
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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. |
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+ |
* |
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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). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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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/NPTf.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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|
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// Basic non-isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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for(i = 0; i < 3; i ++){ |
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for(j = 0; j < 3; j++){ |
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if( i == j) { |
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< |
eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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> |
eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2); |
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} |
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for(j = 0; j < 3; j++){ |
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if( i == j) { |
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eta(i, j) = oldEta(i, j) + dt2 * instaVol * |
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< |
(press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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> |
(press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2); |
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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). |
| 259 |
< |
fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; |
| 259 |
> |
fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp; |
| 260 |
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|
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RealType conservedQuantity; |
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|
RealType totalEnergy; |
| 268 |
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|
| 269 |
|
totalEnergy = thermo.getTotalE(); |
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|
|
| 271 |
< |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
| 271 |
> |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert); |
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|
|
| 273 |
< |
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
| 273 |
> |
thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert; |
| 274 |
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|
| 275 |
|
SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 276 |
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trEta = tmp.trace(); |
| 277 |
|
|
| 278 |
< |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
| 278 |
> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert); |
| 279 |
|
|
| 280 |
< |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
| 280 |
> |
barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert; |
| 281 |
|
|
| 282 |
|
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 283 |
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barostat_kinetic + barostat_potential; |
