| 35 |
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* |
| 36 |
|
* [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 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 43 |
|
#include "brains/Snapshot.hpp" |
| 44 |
|
#include "integrators/Integrator.hpp" |
| 45 |
|
#include "integrators/DLM.hpp" |
| 46 |
< |
#include "integrators/FluctuatingChargeNVT.hpp" |
| 46 |
> |
#include "flucq/FluctuatingChargeLangevin.hpp" |
| 47 |
> |
#include "flucq/FluctuatingChargeNVT.hpp" |
| 48 |
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#include "utils/simError.h" |
| 49 |
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|
| 50 |
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namespace OpenMD { |
| 53 |
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needReset(false), velocitizer_(NULL), needVelocityScaling(false), |
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rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL), |
| 55 |
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rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info), |
| 56 |
< |
currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) { |
| 56 |
> |
snap(info->getSnapshotManager()->getCurrentSnapshot()) { |
| 57 |
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|
| 58 |
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simParams = info->getSimParams(); |
| 59 |
|
|
| 74 |
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painCave.isFatal = 1; |
| 75 |
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simError(); |
| 76 |
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} |
| 77 |
+ |
|
| 78 |
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// set the status, sample, and thermal kick times |
| 79 |
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if (simParams->haveSampleTime()){ |
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sampleTime = simParams->getSampleTime(); |
| 83 |
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sampleTime = simParams->getRunTime(); |
| 84 |
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statusTime = sampleTime; |
| 85 |
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} |
| 86 |
< |
|
| 86 |
> |
|
| 87 |
|
if (simParams->haveStatusTime()){ |
| 88 |
|
statusTime = simParams->getStatusTime(); |
| 89 |
|
} |
| 90 |
< |
|
| 90 |
> |
|
| 91 |
|
if (simParams->haveThermalTime()){ |
| 92 |
|
thermalTime = simParams->getThermalTime(); |
| 93 |
|
} else { |
| 94 |
|
thermalTime = simParams->getRunTime(); |
| 95 |
|
} |
| 96 |
< |
|
| 96 |
> |
|
| 97 |
|
if (!simParams->getUseInitalTime()) { |
| 98 |
< |
currentSnapshot_->setTime(0.0); |
| 98 |
> |
snap->setTime(0.0); |
| 99 |
|
} |
| 100 |
< |
|
| 100 |
> |
|
| 101 |
|
if (simParams->haveResetTime()) { |
| 102 |
|
needReset = true; |
| 103 |
|
resetTime = simParams->getResetTime(); |
| 104 |
|
} |
| 105 |
< |
|
| 105 |
> |
|
| 106 |
|
// Create a default ForceManager: If the subclass wants to use |
| 107 |
|
// a different ForceManager, use setForceManager |
| 106 |
– |
|
| 108 |
|
forceMan_ = new ForceManager(info); |
| 109 |
< |
|
| 109 |
> |
|
| 110 |
|
// check for the temperature set flag (velocity scaling) |
| 111 |
+ |
needVelocityScaling = false; |
| 112 |
|
if (simParams->haveTempSet()) { |
| 113 |
|
needVelocityScaling = simParams->getTempSet(); |
| 114 |
+ |
} |
| 115 |
|
|
| 116 |
+ |
if (needVelocityScaling) { |
| 117 |
|
if (simParams->haveTargetTemp()) { |
| 118 |
|
targetScalingTemp = simParams->getTargetTemp(); |
| 119 |
|
} |
| 120 |
|
else { |
| 121 |
|
sprintf(painCave.errMsg, |
| 122 |
< |
"Integrator Error: Target Temperature is not set\n"); |
| 122 |
> |
"Integrator Error: Target Temperature must be set to turn on tempSet\n"); |
| 123 |
|
painCave.isFatal = 1; |
| 124 |
|
simError(); |
| 125 |
|
|
| 126 |
|
} |
| 127 |
|
} |
| 128 |
< |
|
| 128 |
> |
|
| 129 |
|
// Create a default a velocitizer: If the subclass wants to use |
| 130 |
|
// a different velocitizer, use setVelocitizer |
| 131 |
|
velocitizer_ = new Velocitizer(info); |
| 132 |
< |
|
| 133 |
< |
if (simParams->haveUseRNEMD()) { |
| 134 |
< |
if (simParams->getUseRNEMD()) { |
| 132 |
> |
|
| 133 |
> |
if (simParams->getRNEMDParameters()->haveUseRNEMD()) { |
| 134 |
> |
if (simParams->getRNEMDParameters()->getUseRNEMD()) { |
| 135 |
|
// Create a default a RNEMD. |
| 136 |
|
rnemd_ = new RNEMD(info); |
| 137 |
< |
useRNEMD = simParams->getUseRNEMD(); |
| 138 |
< |
if (simParams->haveRNEMD_exchangeTime()) { |
| 139 |
< |
RNEMD_exchangeTime = simParams->getRNEMD_exchangeTime(); |
| 137 |
> |
useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD(); |
| 138 |
> |
if (simParams->getRNEMDParameters()->haveExchangeTime()) { |
| 139 |
> |
RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime(); |
| 140 |
|
} |
| 141 |
|
} |
| 142 |
|
} |
| 143 |
< |
|
| 143 |
> |
|
| 144 |
|
rotAlgo_ = new DLM(); |
| 145 |
|
rattle_ = new Rattle(info); |
| 146 |
< |
flucQ_ = new FluctuatingChargeNVT(info); |
| 146 |
> |
if (simParams->getFluctuatingChargeParameters()->havePropagator()) { |
| 147 |
> |
std::string prop = toUpperCopy(simParams->getFluctuatingChargeParameters()->getPropagator()); |
| 148 |
> |
if (prop.compare("NVT")==0){ |
| 149 |
> |
flucQ_ = new FluctuatingChargeNVT(info); |
| 150 |
> |
} else if (prop.compare("LANGEVIN")==0) { |
| 151 |
> |
flucQ_ = new FluctuatingChargeLangevin(info); |
| 152 |
> |
} else { |
| 153 |
> |
sprintf(painCave.errMsg, |
| 154 |
> |
"Integrator Error: Unknown Fluctuating Charge propagator (%s) requested\n", |
| 155 |
> |
simParams->getFluctuatingChargeParameters()->getPropagator().c_str()); |
| 156 |
> |
painCave.isFatal = 1; |
| 157 |
> |
} |
| 158 |
> |
} |
| 159 |
> |
flucQ_->setForceManager(forceMan_); |
| 160 |
|
} |
| 161 |
|
|
| 162 |
|
Integrator::~Integrator(){ |
