| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
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* [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 |
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*/ |
| 42 |
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|
| 43 |
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/** |
| 67 |
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|
| 68 |
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void VelocityVerletIntegrator::initialize(){ |
| 69 |
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|
| 70 |
< |
forceMan_->init(); |
| 70 |
> |
forceMan_->initialize(); |
| 71 |
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|
| 72 |
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// remove center of mass drift velocity (in case we passed in a |
| 73 |
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// configuration that was drifting) |
| 74 |
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velocitizer_->removeComDrift(); |
| 75 |
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|
| 76 |
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// initialize the forces before the first step |
| 77 |
< |
calcForce(true, true); |
| 77 |
> |
calcForce(); |
| 78 |
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|
| 79 |
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// execute the constraint algorithm to make sure that the system is |
| 80 |
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// constrained at the very beginning |
| 81 |
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if (info_->getNGlobalConstraints() > 0) { |
| 82 |
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rattle->constraintA(); |
| 83 |
< |
calcForce(true, true); |
| 83 |
> |
calcForce(); |
| 84 |
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rattle->constraintB(); |
| 85 |
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//copy the current snapshot to previous snapshot |
| 86 |
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info_->getSnapshotManager()->advance(); |
| 217 |
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void VelocityVerletIntegrator::integrateStep() { |
| 218 |
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|
| 219 |
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moveA(); |
| 220 |
< |
calcForce(needPotential, needStress); |
| 220 |
> |
calcForce(); |
| 221 |
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moveB(); |
| 222 |
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} |
| 223 |
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| 224 |
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|
| 225 |
< |
void VelocityVerletIntegrator::calcForce(bool needPotential, |
| 226 |
< |
bool needStress) { |
| 226 |
< |
forceMan_->calcForces(needPotential, needStress); |
| 225 |
> |
void VelocityVerletIntegrator::calcForce() { |
| 226 |
> |
forceMan_->calcForces(); |
| 227 |
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} |
| 228 |
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| 229 |
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DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
