| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include <math.h> |
| 47 |
|
#include "integrators/NPT.hpp" |
| 48 |
|
#include "math/SquareMatrix3.hpp" |
| 49 |
|
#include "primitives/Molecule.hpp" |
| 50 |
< |
#include "utils/OOPSEConstant.hpp" |
| 50 |
> |
#include "utils/PhysicalConstants.hpp" |
| 51 |
|
#include "utils/simError.h" |
| 52 |
|
|
| 53 |
|
// Basic isotropic thermostating and barostating via the Melchionna |
| 60 |
|
// |
| 61 |
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 62 |
|
|
| 63 |
< |
namespace oopse { |
| 63 |
> |
namespace OpenMD { |
| 64 |
|
|
| 65 |
|
NPT::NPT(SimInfo* info) : |
| 66 |
|
VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6), maxIterNum_(4) { |
| 77 |
|
if (!simParams->haveTargetTemp()) { |
| 78 |
|
sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n"); |
| 79 |
|
painCave.isFatal = 1; |
| 80 |
< |
painCave.severity = OOPSE_ERROR; |
| 80 |
> |
painCave.severity = OPENMD_ERROR; |
| 81 |
|
simError(); |
| 82 |
|
} else { |
| 83 |
|
targetTemp = simParams->getTargetTemp(); |
| 86 |
|
// We must set tauThermostat |
| 87 |
|
if (!simParams->haveTauThermostat()) { |
| 88 |
|
sprintf(painCave.errMsg, "If you use the constant temperature\n" |
| 89 |
< |
"\tintegrator, you must set tauThermostat_.\n"); |
| 89 |
> |
"\tintegrator, you must set tauThermostat.\n"); |
| 90 |
|
|
| 91 |
< |
painCave.severity = OOPSE_ERROR; |
| 91 |
> |
painCave.severity = OPENMD_ERROR; |
| 92 |
|
painCave.isFatal = 1; |
| 93 |
|
simError(); |
| 94 |
|
} else { |
| 108 |
|
if (!simParams->haveTauBarostat()) { |
| 109 |
|
sprintf(painCave.errMsg, |
| 110 |
|
"If you use the NPT integrator, you must set tauBarostat.\n"); |
| 111 |
< |
painCave.severity = OOPSE_ERROR; |
| 111 |
> |
painCave.severity = OPENMD_ERROR; |
| 112 |
|
painCave.isFatal = 1; |
| 113 |
|
simError(); |
| 114 |
|
} else { |
| 151 |
|
|
| 152 |
|
instaTemp =thermo.getTemperature(); |
| 153 |
|
press = thermo.getPressureTensor(); |
| 154 |
< |
instaPress = OOPSEConstant::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0; |
| 154 |
> |
instaPress = PhysicalConstants::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0; |
| 155 |
|
instaVol =thermo.getVolume(); |
| 156 |
|
|
| 157 |
|
Vector3d COM = info_->getCom(); |
| 172 |
|
getVelScaleA(sc, vel); |
| 173 |
|
|
| 174 |
|
// velocity half step (use chi from previous step here): |
| 175 |
< |
//vel[j] += dt2 * ((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]); |
| 176 |
< |
vel += dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc; |
| 175 |
> |
//vel[j] += dt2 * ((frc[j] / mass) * PhysicalConstants::energyConvert - sc[j]); |
| 176 |
> |
vel += dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc; |
| 177 |
|
integrableObject->setVel(vel); |
| 178 |
|
|
| 179 |
|
if (integrableObject->isDirectional()) { |
| 186 |
|
|
| 187 |
|
ji = integrableObject->getJ(); |
| 188 |
|
|
| 189 |
< |
//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi); |
| 190 |
< |
ji += dt2*OOPSEConstant::energyConvert * Tb - dt2*chi* ji; |
| 189 |
> |
//ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi); |
| 190 |
> |
ji += dt2*PhysicalConstants::energyConvert * Tb - dt2*chi* ji; |
| 191 |
|
|
| 192 |
|
rotAlgo->rotate(integrableObject, ji, dt); |
| 193 |
|
|
| 307 |
|
getVelScaleB(sc, index); |
| 308 |
|
|
| 309 |
|
// velocity half step |
| 310 |
< |
//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]); |
| 311 |
< |
vel = oldVel[index] + dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc; |
| 310 |
> |
//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * PhysicalConstants::energyConvert - sc[j]); |
| 311 |
> |
vel = oldVel[index] + dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc; |
| 312 |
|
integrableObject->setVel(vel); |
| 313 |
|
|
| 314 |
|
if (integrableObject->isDirectional()) { |
| 315 |
|
// get and convert the torque to body frame |
| 316 |
|
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 317 |
|
|
| 318 |
< |
//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi[3*i+j]*chi); |
| 319 |
< |
ji = oldJi[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi*oldJi[index]; |
| 318 |
> |
//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi[3*i+j]*chi); |
| 319 |
> |
ji = oldJi[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi*oldJi[index]; |
| 320 |
|
integrableObject->setJ(ji); |
| 321 |
|
} |
| 322 |
|
|
