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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 1755 by gezelter, Thu Jun 14 01:58:35 2012 UTC

# Line 36 | Line 36
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).                        
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/FluctuatingChargeNVT.hpp"
47   #include "utils/simError.h"
48 +
49   namespace OpenMD {
50    Integrator::Integrator(SimInfo* info)
51      : info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
52        needReset(false), velocitizer_(NULL), needVelocityScaling(false),
53 <      rnemd_(NULL), useRNEMD(false),
54 <      dumpWriter(NULL), statWriter(NULL), thermo(info),
53 >      rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL),
54 >      rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
55        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 –      }
56      
57 <      if (simParams->haveRunTime()) {
58 <        runTime = simParams->getRunTime();
59 <      } else {
60 <        sprintf(painCave.errMsg,
61 <                "Integrator Error: runTime is not set\n");
62 <        painCave.isFatal = 1;
63 <        simError();
64 <      }
65 <      // set the status, sample, and thermal kick times
66 <      if (simParams->haveSampleTime()){
67 <        sampleTime = simParams->getSampleTime();
68 <        statusTime = sampleTime;
69 <      } else{
70 <        sampleTime = simParams->getRunTime();
71 <        statusTime = sampleTime;
72 <      }
57 >    simParams = info->getSimParams();
58 >    
59 >    if (simParams->haveDt()) {
60 >      dt = simParams->getDt();
61 >    } else {
62 >      sprintf(painCave.errMsg,
63 >              "Integrator Error: dt is not set\n");
64 >      painCave.isFatal = 1;
65 >      simError();
66 >    }
67 >    
68 >    if (simParams->haveRunTime()) {
69 >      runTime = simParams->getRunTime();
70 >    } else {
71 >      sprintf(painCave.errMsg,
72 >              "Integrator Error: runTime is not set\n");
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();
80 >      statusTime = sampleTime;
81 >    } else{
82 >      sampleTime = simParams->getRunTime();
83 >      statusTime = sampleTime;
84 >    }
85 >    
86 >    if (simParams->haveStatusTime()){
87 >      statusTime = simParams->getStatusTime();
88 >    }
89 >    
90 >    if (simParams->haveThermalTime()){
91 >      thermalTime = simParams->getThermalTime();
92 >    } else {
93 >      thermalTime = simParams->getRunTime();
94 >    }
95 >    
96 >    if (!simParams->getUseInitalTime()) {
97 >      currentSnapshot_->setTime(0.0);
98 >    }
99 >    
100 >    if (simParams->haveResetTime()) {
101 >      needReset = true;
102 >      resetTime = simParams->getResetTime();
103 >    }
104 >    
105 >    // Create a default ForceManager: If the subclass wants to use
106 >    // a different ForceManager, use setForceManager
107 >    forceMan_ = new ForceManager(info);
108 >    
109 >    // check for the temperature set flag (velocity scaling)      
110 >    if (simParams->haveTempSet()) {
111 >      needVelocityScaling = simParams->getTempSet();
112  
113 <      if (simParams->haveStatusTime()){
114 <        statusTime = simParams->getStatusTime();
113 >      if (simParams->haveTargetTemp()) {
114 >        targetScalingTemp = simParams->getTargetTemp();
115        }
116 +      else {
117 +        sprintf(painCave.errMsg,
118 +                "Integrator Error: Target Temperature is not set\n");
119 +        painCave.isFatal = 1;
120 +        simError();
121  
85 –      if (simParams->haveThermalTime()){
86 –        thermalTime = simParams->getThermalTime();
87 –      } else {
88 –        thermalTime = simParams->getRunTime();
122        }
123 <
91 <      if (!simParams->getUseInitalTime()) {
92 <        currentSnapshot_->setTime(0.0);
93 <      }
94 <
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);
123 >    }
124      
125 <      // check for the temperature set flag (velocity scaling)      
126 <      if (simParams->haveTempSet()) {
127 <        needVelocityScaling = simParams->getTempSet();
128 <
129 <        if (simParams->haveTargetTemp()) {
130 <          targetScalingTemp = simParams->getTargetTemp();
131 <        }
132 <        else {
133 <          sprintf(painCave.errMsg,
134 <                  "Integrator Error: Target Temperature is not set\n");
135 <          painCave.isFatal = 1;
136 <          simError();
116 <
117 <        }
125 >    // Create a default a velocitizer: If the subclass wants to use
126 >    // a different velocitizer, use setVelocitizer
127 >    velocitizer_ = new Velocitizer(info);
128 >    
129 >    if (simParams->getRNEMDParameters()->haveUseRNEMD()) {
130 >      if (simParams->getRNEMDParameters()->getUseRNEMD()) {
131 >        // Create a default a RNEMD.
132 >        rnemd_ = new RNEMD(info);
133 >        useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
134 >        if (simParams->getRNEMDParameters()->haveExchangeTime()) {
135 >          RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
136 >        }
137        }
138 <      
139 <      // Create a default a velocitizer: If the subclass wants to use
140 <      // a different velocitizer, use setVelocitizer
141 <      velocitizer_ = new Velocitizer(info);
142 <
143 <      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 <      }
138 >    }
139 >    
140 >    rotAlgo_ = new DLM();
141 >    rattle_ = new Rattle(info);
142 >    //forceMan_->initialize();
143 >    flucQ_ = new FluctuatingChargeNVT(info, forceMan_);
144    }
145    
146    Integrator::~Integrator(){
147      delete forceMan_;
148      delete velocitizer_;
149      delete rnemd_;
150 +    delete flucQ_;
151 +    delete rotAlgo_;
152 +    delete rattle_;
153      
154      delete dumpWriter;
155      delete statWriter;
156    }
144 –
145 –
157   }
158  

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