| 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 |
|
/** |
| 50 |
|
#include "integrators/VelocityVerletIntegrator.hpp" |
| 51 |
|
#include "integrators/DLM.hpp" |
| 52 |
|
#include "utils/StringUtils.hpp" |
| 53 |
+ |
#include "utils/ProgressBar.hpp" |
| 54 |
|
|
| 55 |
< |
namespace oopse { |
| 55 |
> |
namespace OpenMD { |
| 56 |
|
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { |
| 57 |
|
dt2 = 0.5 * dt; |
| 58 |
|
rotAlgo = new DLM(); |
| 73 |
|
velocitizer_->removeComDrift(); |
| 74 |
|
|
| 75 |
|
// initialize the forces before the first step |
| 76 |
< |
calcForce(true, true); |
| 76 |
> |
calcForce(); |
| 77 |
|
|
| 78 |
|
// execute the constraint algorithm to make sure that the system is |
| 79 |
|
// constrained at the very beginning |
| 80 |
|
if (info_->getNGlobalConstraints() > 0) { |
| 81 |
|
rattle->constraintA(); |
| 82 |
< |
calcForce(true, true); |
| 82 |
> |
calcForce(); |
| 83 |
|
rattle->constraintB(); |
| 84 |
|
//copy the current snapshot to previous snapshot |
| 85 |
|
info_->getSnapshotManager()->advance(); |
| 95 |
|
|
| 96 |
|
dumpWriter->writeDumpAndEor(); |
| 97 |
|
|
| 98 |
+ |
progressBar = new ProgressBar(); |
| 99 |
+ |
|
| 100 |
|
//save statistics, before writeStat, we must save statistics |
| 101 |
|
thermo.saveStat(); |
| 102 |
|
saveConservedQuantity(); |
| 118 |
|
needStress = false; |
| 119 |
|
|
| 120 |
|
} |
| 121 |
< |
|
| 121 |
> |
|
| 122 |
|
void VelocityVerletIntegrator::doIntegrate() { |
| 123 |
|
|
| 124 |
|
|
| 131 |
|
integrateStep(); |
| 132 |
|
|
| 133 |
|
postStep(); |
| 134 |
< |
|
| 134 |
> |
|
| 135 |
|
} |
| 136 |
|
|
| 137 |
|
finalize(); |
| 142 |
|
void VelocityVerletIntegrator::preStep() { |
| 143 |
|
RealType difference = currentSnapshot_->getTime() + dt - currStatus; |
| 144 |
|
|
| 145 |
< |
if (difference > 0 || fabs(difference) < oopse::epsilon) { |
| 145 |
> |
if (difference > 0 || fabs(difference) < OpenMD::epsilon) { |
| 146 |
|
needPotential = true; |
| 147 |
|
needStress = true; |
| 148 |
|
} |
| 163 |
|
} |
| 164 |
|
} |
| 165 |
|
if (useRNEMD) { |
| 163 |
– |
rnemd_->collectData(); |
| 166 |
|
if (currentSnapshot_->getTime() >= currRNEMD) { |
| 167 |
|
rnemd_->doRNEMD(); |
| 168 |
|
currRNEMD += RNEMD_exchangeTime; |
| 169 |
|
} |
| 170 |
+ |
rnemd_->collectData(); |
| 171 |
|
} |
| 172 |
|
|
| 173 |
|
if (currentSnapshot_->getTime() >= currSample) { |
| 186 |
|
} |
| 187 |
|
|
| 188 |
|
statWriter->writeStat(currentSnapshot_->statData); |
| 189 |
< |
|
| 189 |
> |
|
| 190 |
> |
progressBar->setStatus(currentSnapshot_->getTime(), runTime); |
| 191 |
> |
progressBar->update(); |
| 192 |
> |
|
| 193 |
|
needPotential = false; |
| 194 |
|
needStress = false; |
| 195 |
|
currStatus += statusTime; |
| 216 |
|
void VelocityVerletIntegrator::integrateStep() { |
| 217 |
|
|
| 218 |
|
moveA(); |
| 219 |
< |
calcForce(needPotential, needStress); |
| 219 |
> |
calcForce(); |
| 220 |
|
moveB(); |
| 221 |
|
} |
| 222 |
|
|
| 223 |
|
|
| 224 |
< |
void VelocityVerletIntegrator::calcForce(bool needPotential, |
| 225 |
< |
bool needStress) { |
| 220 |
< |
forceMan_->calcForces(needPotential, needStress); |
| 224 |
> |
void VelocityVerletIntegrator::calcForce() { |
| 225 |
> |
forceMan_->calcForces(); |
| 226 |
|
} |
| 227 |
|
|
| 228 |
|
DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
| 281 |
|
} |
| 282 |
|
|
| 283 |
|
|
| 284 |
< |
} //end namespace oopse |
| 284 |
> |
} //end namespace OpenMD |
