| 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). |
| 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 |
|
/** |
| 54 |
|
#include "utils/ProgressBar.hpp" |
| 55 |
|
|
| 56 |
|
namespace OpenMD { |
| 57 |
< |
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { |
| 57 |
> |
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) { |
| 58 |
|
dt2 = 0.5 * dt; |
| 58 |
– |
rotAlgo = new DLM(); |
| 59 |
– |
rattle = new Rattle(info); |
| 59 |
|
} |
| 60 |
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|
| 61 |
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VelocityVerletIntegrator::~VelocityVerletIntegrator() { |
| 63 |
– |
delete rotAlgo; |
| 64 |
– |
delete rattle; |
| 62 |
|
} |
| 63 |
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|
| 64 |
|
void VelocityVerletIntegrator::initialize(){ |
| 65 |
|
|
| 66 |
< |
forceMan_->init(); |
| 66 |
> |
forceMan_->initialize(); |
| 67 |
|
|
| 68 |
|
// remove center of mass drift velocity (in case we passed in a |
| 69 |
|
// configuration that was drifting) |
| 70 |
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velocitizer_->removeComDrift(); |
| 71 |
+ |
|
| 72 |
+ |
// find the initial fluctuating charges. |
| 73 |
+ |
flucQ_->initialize(); |
| 74 |
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|
| 75 |
|
// initialize the forces before the first step |
| 76 |
< |
calcForce(true, true); |
| 76 |
> |
calcForce(); |
| 77 |
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|
| 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); |
| 83 |
< |
rattle->constraintB(); |
| 81 |
> |
rattle_->constraintA(); |
| 82 |
> |
calcForce(); |
| 83 |
> |
rattle_->constraintB(); |
| 84 |
|
//copy the current snapshot to previous snapshot |
| 85 |
|
info_->getSnapshotManager()->advance(); |
| 86 |
|
} |
| 121 |
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|
| 122 |
|
void VelocityVerletIntegrator::doIntegrate() { |
| 123 |
|
|
| 124 |
– |
|
| 124 |
|
initialize(); |
| 125 |
|
|
| 126 |
< |
while (currentSnapshot_->getTime() < runTime) { |
| 127 |
< |
|
| 128 |
< |
preStep(); |
| 129 |
< |
|
| 130 |
< |
integrateStep(); |
| 132 |
< |
|
| 133 |
< |
postStep(); |
| 134 |
< |
|
| 135 |
< |
} |
| 136 |
< |
|
| 126 |
> |
while (currentSnapshot_->getTime() < runTime) { |
| 127 |
> |
preStep(); |
| 128 |
> |
integrateStep(); |
| 129 |
> |
postStep(); |
| 130 |
> |
} |
| 131 |
|
finalize(); |
| 138 |
– |
|
| 132 |
|
} |
| 133 |
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|
| 134 |
|
|
| 203 |
|
|
| 204 |
|
dumpWriter = NULL; |
| 205 |
|
statWriter = NULL; |
| 213 |
– |
|
| 206 |
|
} |
| 207 |
|
|
| 208 |
|
void VelocityVerletIntegrator::integrateStep() { |
| 209 |
|
|
| 210 |
|
moveA(); |
| 211 |
< |
calcForce(needPotential, needStress); |
| 211 |
> |
calcForce(); |
| 212 |
|
moveB(); |
| 213 |
|
} |
| 214 |
|
|
| 215 |
|
|
| 216 |
< |
void VelocityVerletIntegrator::calcForce(bool needPotential, |
| 217 |
< |
bool needStress) { |
| 226 |
< |
forceMan_->calcForces(needPotential, needStress); |
| 216 |
> |
void VelocityVerletIntegrator::calcForce() { |
| 217 |
> |
forceMan_->calcForces(); |
| 218 |
|
} |
| 219 |
|
|
| 220 |
|
DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
