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Comparing branches/development/src/integrators/Integrator.cpp (file contents):
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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).          
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()) {
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 >    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 <      simParams = info->getSimParams();
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  
56 –      if (simParams->haveDt()) {
57 –        dt = simParams->getDt();
58 –      } else {
59 –        sprintf(painCave.errMsg,
60 –                "Integrator Error: dt is not set\n");
61 –        painCave.isFatal = 1;
62 –        simError();
126        }
127 +    }
128      
129 <      if (simParams->haveRunTime()) {
130 <        runTime = simParams->getRunTime();
131 <      } else {
132 <        sprintf(painCave.errMsg,
133 <                "Integrator Error: runTime is not set\n");
134 <        painCave.isFatal = 1;
135 <        simError();
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 <      // set the status, sample, and thermal kick times
143 <      if (simParams->haveSampleTime()){
144 <        sampleTime = simParams->getSampleTime();
145 <        statusTime = sampleTime;
146 <      } else{
147 <        sampleTime = simParams->getRunTime();
148 <        statusTime = sampleTime;
149 <      }
150 <
151 <      if (simParams->haveStatusTime()){
83 <        statusTime = simParams->getStatusTime();
84 <      }
85 <
86 <      if (simParams->haveThermalTime()){
87 <        thermalTime = simParams->getThermalTime();
142 >    }
143 >    
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 <        thermalTime = simParams->getRunTime();
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 <      if (!simParams->getUseInitalTime()) {
93 <        currentSnapshot_->setTime(0.0);
94 <      }
95 <
96 <      if (simParams->haveResetTime()) {
97 <        needReset = true;
98 <        resetTime = simParams->getResetTime();
99 <      }
100 <      
101 <      // Create a default ForceManager: If the subclass wants to use
102 <      // a different ForceManager, use setForceManager
103 <
104 <      forceMan_ = new ForceManager(info);
105 <    
106 <      // check for the temperature set flag (velocity scaling)      
107 <      if (simParams->haveTempSet()) {
108 <        needVelocityScaling = simParams->getTempSet();
109 <
110 <        if (simParams->haveTargetTemp()) {
111 <          targetScalingTemp = simParams->getTargetTemp();
112 <        }
113 <        else {
114 <          sprintf(painCave.errMsg,
115 <                  "Integrator Error: Target Temperature is not set\n");
116 <          painCave.isFatal = 1;
117 <          simError();
118 <
119 <        }
120 <      }
121 <      
122 <      // Create a default a velocitizer: If the subclass wants to use
123 <      // a different velocitizer, use setVelocitizer
124 <      velocitizer_ = new Velocitizer(info);
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 <      }
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    }
146 –
147 –
173   }
174  

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