| 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, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include "brains/SimInfo.hpp" |
| 44 |
|
#include "integrators/IntegratorCreator.hpp" |
| 45 |
|
#include "integrators/NgammaT.hpp" |
| 46 |
|
#include "primitives/Molecule.hpp" |
| 47 |
< |
#include "utils/OOPSEConstant.hpp" |
| 47 |
> |
#include "utils/PhysicalConstants.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
|
|
| 50 |
< |
namespace oopse { |
| 50 |
> |
namespace OpenMD { |
| 51 |
|
NgammaT::NgammaT(SimInfo* info) : NPT(info) { |
| 52 |
|
Globals* simParams = info_->getSimParams(); |
| 53 |
|
if (!simParams->haveSurfaceTension()) { |
| 54 |
|
sprintf(painCave.errMsg, |
| 55 |
|
"If you use the NgammaT integrator, you must set a surface tension.\n"); |
| 56 |
< |
painCave.severity = OOPSE_ERROR; |
| 56 |
> |
painCave.severity = OPENMD_ERROR; |
| 57 |
|
painCave.isFatal = 1; |
| 58 |
|
simError(); |
| 59 |
|
} else { |
| 60 |
< |
surfaceTension= simParams->getSurfaceTension()* OOPSEConstant::surfaceTensionConvert * OOPSEConstant::energyConvert; |
| 60 |
> |
surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert; |
| 61 |
|
} |
| 62 |
|
|
| 63 |
|
} |
| 65 |
|
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 66 |
|
RealType hz = hmat(2, 2); |
| 67 |
|
RealType Axy = hmat(0,0) * hmat(1, 1); |
| 68 |
< |
RealType sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert); |
| 69 |
< |
RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert); |
| 68 |
> |
RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert); |
| 69 |
> |
RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert); |
| 70 |
|
eta(0,0) -= dt2* Axy * (sx - surfaceTension) / (NkBT*tb2); |
| 71 |
|
eta(1,1) -= dt2* Axy * (sy - surfaceTension) / (NkBT*tb2); |
| 72 |
|
eta(2,2) = 0.0; |
| 78 |
|
RealType hz = hmat(2, 2); |
| 79 |
|
RealType Axy = hmat(0,0) * hmat(1, 1); |
| 80 |
|
prevEta = eta; |
| 81 |
< |
RealType sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert); |
| 82 |
< |
RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert); |
| 81 |
> |
RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert); |
| 82 |
> |
RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert); |
| 83 |
|
eta(0,0) = oldEta(0, 0) - dt2 * Axy * (sx -surfaceTension) / (NkBT*tb2); |
| 84 |
|
eta(1,1) = oldEta(1, 1) - dt2 * Axy * (sy -surfaceTension) / (NkBT*tb2); |
| 85 |
|
eta(2,2) = 0.0; |
| 148 |
|
// We need NkBT a lot, so just set it here: This is the RAW number |
| 149 |
|
// of integrableObjects, so no subtraction or addition of constraints or |
| 150 |
|
// orientational degrees of freedom: |
| 151 |
< |
NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp; |
| 151 |
> |
NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp; |
| 152 |
|
|
| 153 |
|
// fkBT is used because the thermostat operates on more degrees of freedom |
| 154 |
|
// than the barostat (when there are particles with orientational degrees |
| 155 |
|
// of freedom). |
| 156 |
< |
fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; |
| 156 |
> |
fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp; |
| 157 |
|
|
| 158 |
|
|
| 159 |
|
RealType totalEnergy = thermo.getTotalE(); |
| 160 |
|
|
| 161 |
< |
RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
| 161 |
> |
RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert); |
| 162 |
|
|
| 163 |
< |
RealType thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
| 163 |
> |
RealType thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert; |
| 164 |
|
|
| 165 |
|
SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 166 |
|
RealType trEta = tmp.trace(); |
| 167 |
|
|
| 168 |
< |
RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
| 168 |
> |
RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert); |
| 169 |
|
|
| 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(); |
| 173 |
|
RealType hz = hmat(2, 2); |
| 174 |
|
RealType area = hmat(0,0) * hmat(1, 1); |
| 175 |
|
|
| 176 |
|
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 |
|
|
