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Comparing branches/development/src/integrators/Integrator.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1870 by gezelter, Tue May 7 19:09:54 2013 UTC

# Line 35 | Line 35
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]  Vardeman & Gezelter, in progress (2009).                        
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   */
42  
43   #include "brains/Snapshot.hpp"
44   #include "integrators/Integrator.hpp"
45 + #include "integrators/DLM.hpp"
46 + #include "flucq/FluctuatingChargeLangevin.hpp"
47 + #include "flucq/FluctuatingChargeNVT.hpp"
48   #include "utils/simError.h"
49 +
50   namespace OpenMD {
51    Integrator::Integrator(SimInfo* info)
52      : info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
53        needReset(false), velocitizer_(NULL), needVelocityScaling(false),
54 <      rnemd_(NULL), useRNEMD(false),
55 <      dumpWriter(NULL), statWriter(NULL), thermo(info),
56 <      currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
52 <
53 <      simParams = info->getSimParams();
54 <
55 <      if (simParams->haveDt()) {
56 <        dt = simParams->getDt();
57 <      } else {
58 <        sprintf(painCave.errMsg,
59 <                "Integrator Error: dt is not set\n");
60 <        painCave.isFatal = 1;
61 <        simError();
62 <      }
54 >      rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL),
55 >      rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
56 >      snap(info->getSnapshotManager()->getCurrentSnapshot()) {
57      
58 <      if (simParams->haveRunTime()) {
59 <        runTime = simParams->getRunTime();
60 <      } else {
61 <        sprintf(painCave.errMsg,
62 <                "Integrator Error: runTime is not set\n");
63 <        painCave.isFatal = 1;
64 <        simError();
65 <      }
66 <      // set the status, sample, and thermal kick times
67 <      if (simParams->haveSampleTime()){
68 <        sampleTime = simParams->getSampleTime();
69 <        statusTime = sampleTime;
70 <      } else{
71 <        sampleTime = simParams->getRunTime();
72 <        statusTime = sampleTime;
73 <      }
58 >    simParams = info->getSimParams();
59 >    
60 >    if (simParams->haveDt()) {
61 >      dt = simParams->getDt();
62 >    } else {
63 >      sprintf(painCave.errMsg,
64 >              "Integrator Error: dt is not set\n");
65 >      painCave.isFatal = 1;
66 >      simError();
67 >    }
68 >    
69 >    if (simParams->haveRunTime()) {
70 >      runTime = simParams->getRunTime();
71 >    } else {
72 >      sprintf(painCave.errMsg,
73 >              "Integrator Error: runTime is not set\n");
74 >      painCave.isFatal = 1;
75 >      simError();
76 >    }
77 >    
78 >    // set the status, sample, and thermal kick times
79 >    if (simParams->haveSampleTime()){
80 >      sampleTime = simParams->getSampleTime();
81 >      statusTime = sampleTime;
82 >    } else{
83 >      sampleTime = simParams->getRunTime();
84 >      statusTime = sampleTime;
85 >    }
86 >    
87 >    if (simParams->haveStatusTime()){
88 >      statusTime = simParams->getStatusTime();
89 >    }
90 >    
91 >    if (simParams->haveThermalTime()){
92 >      thermalTime = simParams->getThermalTime();
93 >    } else {
94 >      thermalTime = simParams->getRunTime();
95 >    }
96 >    
97 >    if (!simParams->getUseInitalTime()) {
98 >      snap->setTime(0.0);
99 >    }
100 >    
101 >    if (simParams->haveResetTime()) {
102 >      needReset = true;
103 >      resetTime = simParams->getResetTime();
104 >    }
105 >    
106 >    // Create a default ForceManager: If the subclass wants to use
107 >    // a different ForceManager, use setForceManager
108 >    forceMan_ = new ForceManager(info);
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 (simParams->haveStatusTime()){
117 <        statusTime = simParams->getStatusTime();
116 >    if (needVelocityScaling) {
117 >      if (simParams->haveTargetTemp()) {
118 >        targetScalingTemp = simParams->getTargetTemp();
119        }
120 +      else {
121 +        sprintf(painCave.errMsg,
122 +                "Integrator Error: Target Temperature must be set to turn on tempSet\n");
123 +        painCave.isFatal = 1;
124 +        simError();
125  
85 –      if (simParams->haveThermalTime()){
86 –        thermalTime = simParams->getThermalTime();
87 –      } else {
88 –        thermalTime = simParams->getRunTime();
126        }
127 <
128 <      if (!simParams->getUseInitalTime()) {
129 <        currentSnapshot_->setTime(0.0);
127 >    }
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->getRNEMDParameters()->haveUseRNEMD()) {
134 >      if (simParams->getRNEMDParameters()->getUseRNEMD()) {
135 >        // Create a default a RNEMD.
136 >        rnemd_ = new RNEMD(info);
137 >        useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
138 >        if (simParams->getRNEMDParameters()->haveExchangeTime()) {
139 >          RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
140 >        }
141        }
142 <
95 <      if (simParams->haveResetTime()) {
96 <        needReset = true;
97 <        resetTime = simParams->getResetTime();
98 <      }
99 <      
100 <      // Create a default ForceManager: If the subclass wants to use
101 <      // a different ForceManager, use setForceManager
102 <      forceMan_ = new ForceManager(info);
142 >    }
143      
144 <      // check for the temperature set flag (velocity scaling)      
145 <      if (simParams->haveTempSet()) {
146 <        needVelocityScaling = simParams->getTempSet();
147 <
148 <        if (simParams->haveTargetTemp()) {
149 <          targetScalingTemp = simParams->getTargetTemp();
150 <        }
151 <        else {
152 <          sprintf(painCave.errMsg,
153 <                  "Integrator Error: Target Temperature is not set\n");
154 <          painCave.isFatal = 1;
155 <          simError();
156 <
117 <        }
144 >    rotAlgo_ = new DLM();
145 >    rattle_ = new Rattle(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 <      // Create a default a velocitizer: If the subclass wants to use
121 <      // a different velocitizer, use setVelocitizer
122 <      velocitizer_ = new Velocitizer(info);
123 <
124 <      if (simParams->haveUseRNEMD()) {
125 <        if (simParams->getUseRNEMD()) {
126 <          // Create a default a RNEMD.
127 <          rnemd_ = new RNEMD(info);
128 <          useRNEMD = simParams->getUseRNEMD();
129 <          if (simParams->haveRNEMD_exchangeTime()) {
130 <            RNEMD_exchangeTime = simParams->getRNEMD_exchangeTime();
131 <          }
132 <        }
133 <      }
158 >    }
159 >    flucQ_->setForceManager(forceMan_);
160    }
161    
162    Integrator::~Integrator(){
163      delete forceMan_;
164      delete velocitizer_;
165      delete rnemd_;
166 +    delete flucQ_;
167 +    delete rotAlgo_;
168 +    delete rattle_;
169      
170      delete dumpWriter;
171      delete statWriter;
172    }
144 –
145 –
173   }
174  

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