| 6 |
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* 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 |
|
*/ |
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|
|
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|
#include "brains/Snapshot.hpp" |
| 44 |
|
#include "integrators/Integrator.hpp" |
| 45 |
|
#include "utils/simError.h" |
| 46 |
< |
namespace oopse { |
| 46 |
> |
namespace OpenMD { |
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|
Integrator::Integrator(SimInfo* info) |
| 48 |
< |
: info_(info), forceMan_(NULL) , needPotential(false), needStress(false), needReset(false), velocitizer_(NULL), |
| 49 |
< |
needVelocityScaling(false), dumpWriter(NULL), statWriter(NULL), thermo(info) |
| 48 |
> |
: info_(info), forceMan_(NULL) , needPotential(false), needStress(false), |
| 49 |
> |
needReset(false), velocitizer_(NULL), needVelocityScaling(false), |
| 50 |
> |
rnemd_(NULL), useRNEMD(false), |
| 51 |
> |
dumpWriter(NULL), statWriter(NULL), thermo(info), |
| 52 |
|
currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) { |
| 53 |
|
|
| 54 |
|
simParams = info->getSimParams(); |
| 89 |
|
thermalTime = simParams->getRunTime(); |
| 90 |
|
} |
| 91 |
|
|
| 92 |
< |
if (!simParams->getUseInitTime()) { |
| 92 |
> |
if (!simParams->getUseInitalTime()) { |
| 93 |
|
currentSnapshot_->setTime(0.0); |
| 94 |
|
} |
| 95 |
|
|
| 98 |
|
resetTime = simParams->getResetTime(); |
| 99 |
|
} |
| 100 |
|
|
| 101 |
< |
//create a default ForceManager |
| 102 |
< |
//if the subclass wants to use a different ForceManager, use setForceManager |
| 101 |
> |
// Create a default ForceManager: If the subclass wants to use |
| 102 |
> |
// a different ForceManager, use setForceManager |
| 103 |
> |
|
| 104 |
|
forceMan_ = new ForceManager(info); |
| 105 |
< |
|
| 102 |
< |
//set the force manager for thermodynamic integration if specified |
| 103 |
< |
if (simParams->getUseSolidThermInt() || simParams->getUseLiquidThermInt()){ |
| 104 |
< |
ThermoIntegrationForceManager* thermoForce_ |
| 105 |
< |
= new ThermoIntegrationForceManager(info); |
| 106 |
< |
setForceManager(thermoForce_); |
| 107 |
< |
} |
| 108 |
< |
|
| 105 |
> |
|
| 106 |
|
// check for the temperature set flag (velocity scaling) |
| 107 |
|
if (simParams->haveTempSet()) { |
| 108 |
|
needVelocityScaling = simParams->getTempSet(); |
| 118 |
|
|
| 119 |
|
} |
| 120 |
|
} |
| 121 |
< |
|
| 122 |
< |
//create a default a velocitizer |
| 123 |
< |
//if the subclass want to using different velocitizer, use setVelocitizer |
| 121 |
> |
|
| 122 |
> |
// Create a default a velocitizer: If the subclass wants to use |
| 123 |
> |
// a different velocitizer, use setVelocitizer |
| 124 |
|
velocitizer_ = new Velocitizer(info); |
| 128 |
– |
|
| 129 |
– |
} |
| 125 |
|
|
| 126 |
+ |
if (simParams->haveUseRNEMD()) { |
| 127 |
+ |
if (simParams->getUseRNEMD()) { |
| 128 |
+ |
// Create a default a RNEMD. |
| 129 |
+ |
rnemd_ = new RNEMD(info); |
| 130 |
+ |
useRNEMD = simParams->getUseRNEMD(); |
| 131 |
+ |
if (simParams->haveRNEMD_exchangeTime()) { |
| 132 |
+ |
RNEMD_exchangeTime = simParams->getRNEMD_exchangeTime(); |
| 133 |
+ |
} |
| 134 |
+ |
} |
| 135 |
+ |
} |
| 136 |
+ |
} |
| 137 |
+ |
|
| 138 |
|
Integrator::~Integrator(){ |
| 139 |
|
delete forceMan_; |
| 140 |
|
delete velocitizer_; |
| 141 |
+ |
delete rnemd_; |
| 142 |
|
|
| 143 |
|
delete dumpWriter; |
| 144 |
|
delete statWriter; |
