| 73 |
|
painCave.isFatal = 1; |
| 74 |
|
simError(); |
| 75 |
|
} |
| 76 |
+ |
|
| 77 |
|
// set the status, sample, and thermal kick times |
| 78 |
|
if (simParams->haveSampleTime()){ |
| 79 |
|
sampleTime = simParams->getSampleTime(); |
| 82 |
|
sampleTime = simParams->getRunTime(); |
| 83 |
|
statusTime = sampleTime; |
| 84 |
|
} |
| 85 |
< |
|
| 85 |
> |
|
| 86 |
|
if (simParams->haveStatusTime()){ |
| 87 |
|
statusTime = simParams->getStatusTime(); |
| 88 |
|
} |
| 89 |
< |
|
| 89 |
> |
|
| 90 |
|
if (simParams->haveThermalTime()){ |
| 91 |
|
thermalTime = simParams->getThermalTime(); |
| 92 |
|
} else { |
| 93 |
|
thermalTime = simParams->getRunTime(); |
| 94 |
|
} |
| 95 |
< |
|
| 95 |
> |
|
| 96 |
|
if (!simParams->getUseInitalTime()) { |
| 97 |
|
currentSnapshot_->setTime(0.0); |
| 98 |
|
} |
| 99 |
< |
|
| 99 |
> |
|
| 100 |
|
if (simParams->haveResetTime()) { |
| 101 |
|
needReset = true; |
| 102 |
|
resetTime = simParams->getResetTime(); |
| 103 |
|
} |
| 104 |
< |
|
| 104 |
> |
|
| 105 |
|
// Create a default ForceManager: If the subclass wants to use |
| 106 |
|
// a different ForceManager, use setForceManager |
| 106 |
– |
|
| 107 |
|
forceMan_ = new ForceManager(info); |
| 108 |
< |
|
| 108 |
> |
|
| 109 |
|
// check for the temperature set flag (velocity scaling) |
| 110 |
+ |
needVelocityScaling = false; |
| 111 |
|
if (simParams->haveTempSet()) { |
| 112 |
|
needVelocityScaling = simParams->getTempSet(); |
| 113 |
+ |
} |
| 114 |
|
|
| 115 |
+ |
if (needVelocityScaling) { |
| 116 |
|
if (simParams->haveTargetTemp()) { |
| 117 |
|
targetScalingTemp = simParams->getTargetTemp(); |
| 118 |
|
} |
| 119 |
|
else { |
| 120 |
|
sprintf(painCave.errMsg, |
| 121 |
< |
"Integrator Error: Target Temperature is not set\n"); |
| 121 |
> |
"Integrator Error: Target Temperature must be set to turn on tempSet\n"); |
| 122 |
|
painCave.isFatal = 1; |
| 123 |
|
simError(); |
| 124 |
|
|
| 125 |
|
} |
| 126 |
|
} |
| 127 |
< |
|
| 127 |
> |
|
| 128 |
|
// Create a default a velocitizer: If the subclass wants to use |
| 129 |
|
// a different velocitizer, use setVelocitizer |
| 130 |
|
velocitizer_ = new Velocitizer(info); |
| 131 |
< |
|
| 131 |
> |
|
| 132 |
|
if (simParams->getRNEMDParameters()->haveUseRNEMD()) { |
| 133 |
|
if (simParams->getRNEMDParameters()->getUseRNEMD()) { |
| 134 |
|
// Create a default a RNEMD. |
| 139 |
|
} |
| 140 |
|
} |
| 141 |
|
} |
| 142 |
< |
|
| 142 |
> |
|
| 143 |
|
rotAlgo_ = new DLM(); |
| 144 |
|
rattle_ = new Rattle(info); |
| 145 |
< |
flucQ_ = new FluctuatingChargeNVT(info); |
| 145 |
> |
//forceMan_->initialize(); |
| 146 |
> |
flucQ_ = new FluctuatingChargeNVT(info, forceMan_); |
| 147 |
|
} |
| 148 |
|
|
| 149 |
|
Integrator::~Integrator(){ |
