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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include "brains/Snapshot.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "integrators/DLM.hpp" |
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#include "flucq/FluctuatingChargeLangevin.hpp" |
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#include "flucq/FluctuatingChargeNVT.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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Integrator::Integrator(SimInfo* info) |
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: info_(info), forceMan_(NULL) , needPotential(false), needStress(false), velocitizer_(NULL), |
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needVelocityScaling(false), dumpWriter(NULL), eorWriter(NULL), statWriter(NULL), thermo(info), |
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currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) { |
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Globals* simParams = info->getSimParams(); |
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|
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namespace OpenMD { |
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Integrator::Integrator(SimInfo* info) |
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: info_(info), forceMan_(NULL) , needPotential(false), needStress(false), |
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needReset(false), velocitizer_(NULL), needVelocityScaling(false), |
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rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL), |
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rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info), |
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snap(info->getSnapshotManager()->getCurrentSnapshot()) { |
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|
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simParams = info->getSimParams(); |
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|
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if (simParams->haveDt()) { |
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dt = simParams->getDt(); |
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dt = simParams->getDt(); |
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} else { |
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sprintf(painCave.errMsg, |
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"Integrator Error: dt is not set\n"); |
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painCave.isFatal = 1; |
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simError(); |
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sprintf(painCave.errMsg, |
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"Integrator Error: dt is not set\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (simParams->haveRunTime()) { |
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runTime = simParams->getRunTime(); |
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runTime = simParams->getRunTime(); |
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} else { |
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sprintf(painCave.errMsg, |
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"Integrator Error: runTime is not set\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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// set the status, sample, and thermal kick times |
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if (simParams->haveSampleTime()){ |
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sampleTime = simParams->getSampleTime(); |
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statusTime = sampleTime; |
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sampleTime = simParams->getSampleTime(); |
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statusTime = sampleTime; |
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} else{ |
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sampleTime = simParams->getRunTime(); |
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statusTime = sampleTime; |
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sampleTime = simParams->getRunTime(); |
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statusTime = sampleTime; |
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} |
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|
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if (simParams->haveStatusTime()){ |
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statusTime = simParams->getStatusTime(); |
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statusTime = simParams->getStatusTime(); |
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} |
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|
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if (simParams->haveThermalTime()){ |
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thermalTime = simParams->getThermalTime(); |
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thermalTime = simParams->getThermalTime(); |
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} else { |
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thermalTime = simParams->getRunTime(); |
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thermalTime = simParams->getRunTime(); |
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} |
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if (!simParams->getUseInitTime()) { |
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currentSnapshot_->setTime(0.0); |
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if (!simParams->getUseInitalTime()) { |
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snap->setTime(0.0); |
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} |
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//create a default a ForceManager |
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//if the subclass want to using different ForceManager, use setForceManager |
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if (simParams->haveResetTime()) { |
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needReset = true; |
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resetTime = simParams->getResetTime(); |
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} |
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// Create a default ForceManager: If the subclass wants to use |
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// a different ForceManager, use setForceManager |
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forceMan_ = new ForceManager(info); |
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// check for the temperature set flag (velocity scaling) |
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needVelocityScaling = false; |
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if (simParams->haveTempSet()) { |
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needVelocityScaling = simParams->getTempSet(); |
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needVelocityScaling = simParams->getTempSet(); |
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} |
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if (simParams->haveTargetTemp()) { |
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targetScalingTemp = simParams->getTargetTemp(); |
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} |
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else { |
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sprintf(painCave.errMsg, |
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"Integrator Error: Target Temperature is not set\n"); |
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painCave.isFatal = 1; |
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simError(); |
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if (needVelocityScaling) { |
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if (simParams->haveTargetTemp()) { |
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targetScalingTemp = simParams->getTargetTemp(); |
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} |
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else { |
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sprintf(painCave.errMsg, |
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"Integrator Error: Target Temperature must be set to turn on tempSet\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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//create a default a velocitizer |
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//if the subclass want to using different velocitizer, use setVelocitizer |
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// Create a default a velocitizer: If the subclass wants to use |
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// a different velocitizer, use setVelocitizer |
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velocitizer_ = new Velocitizer(info); |
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} |
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Integrator::~Integrator(){ |
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if (simParams->getRNEMDParameters()->haveUseRNEMD()) { |
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if (simParams->getRNEMDParameters()->getUseRNEMD()) { |
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// Create a default a RNEMD. |
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rnemd_ = new RNEMD(info); |
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useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD(); |
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if (simParams->getRNEMDParameters()->haveExchangeTime()) { |
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RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime(); |
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} |
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} |
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} |
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|
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rotAlgo_ = new DLM(); |
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rattle_ = new Rattle(info); |
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if (simParams->getFluctuatingChargeParameters()->havePropagator()) { |
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std::string prop = toUpperCopy(simParams->getFluctuatingChargeParameters()->getPropagator()); |
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if (prop.compare("NVT")==0){ |
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flucQ_ = new FluctuatingChargeNVT(info); |
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} else if (prop.compare("LANGEVIN")==0) { |
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flucQ_ = new FluctuatingChargeLangevin(info); |
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} else { |
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sprintf(painCave.errMsg, |
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"Integrator Error: Unknown Fluctuating Charge propagator (%s) requested\n", |
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simParams->getFluctuatingChargeParameters()->getPropagator().c_str()); |
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painCave.isFatal = 1; |
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} |
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} |
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flucQ_->setForceManager(forceMan_); |
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} |
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|
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Integrator::~Integrator(){ |
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delete forceMan_; |
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delete velocitizer_; |
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delete rnemd_; |
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delete flucQ_; |
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delete rotAlgo_; |
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delete rattle_; |
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delete dumpWriter; |
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delete eorWriter; |
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delete statWriter; |
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} |
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} |
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} |
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