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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 1764 by gezelter, Tue Jul 3 18:32:27 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),
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 <      }
53 >      rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL),
54 >      rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
55 >      snap(info->getSnapshotManager()->getCurrentSnapshot()) {
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 >      snap->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 >    needVelocityScaling = false;
111 >    if (simParams->haveTempSet()) {
112 >      needVelocityScaling = simParams->getTempSet();
113 >    }
114  
115 <      if (simParams->haveStatusTime()){
116 <        statusTime = simParams->getStatusTime();
115 >    if (needVelocityScaling) {
116 >      if (simParams->haveTargetTemp()) {
117 >        targetScalingTemp = simParams->getTargetTemp();
118        }
119 +      else {
120 +        sprintf(painCave.errMsg,
121 +                "Integrator Error: Target Temperature must be set to turn on tempSet\n");
122 +        painCave.isFatal = 1;
123 +        simError();
124  
85 –      if (simParams->haveThermalTime()){
86 –        thermalTime = simParams->getThermalTime();
87 –      } else {
88 –        thermalTime = simParams->getRunTime();
125        }
126 <
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);
126 >    }
127      
128 <      // check for the temperature set flag (velocity scaling)      
129 <      if (simParams->haveTempSet()) {
130 <        needVelocityScaling = simParams->getTempSet();
131 <
132 <        if (simParams->haveTargetTemp()) {
133 <          targetScalingTemp = simParams->getTargetTemp();
134 <        }
135 <        else {
136 <          sprintf(painCave.errMsg,
137 <                  "Integrator Error: Target Temperature is not set\n");
138 <          painCave.isFatal = 1;
139 <          simError();
116 <
117 <        }
128 >    // Create a default a velocitizer: If the subclass wants to use
129 >    // a different velocitizer, use setVelocitizer
130 >    velocitizer_ = new Velocitizer(info);
131 >    
132 >    if (simParams->getRNEMDParameters()->haveUseRNEMD()) {
133 >      if (simParams->getRNEMDParameters()->getUseRNEMD()) {
134 >        // Create a default a RNEMD.
135 >        rnemd_ = new RNEMD(info);
136 >        useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
137 >        if (simParams->getRNEMDParameters()->haveExchangeTime()) {
138 >          RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
139 >        }
140        }
141 <      
142 <      // Create a default a velocitizer: If the subclass wants to use
143 <      // a different velocitizer, use setVelocitizer
144 <      velocitizer_ = new Velocitizer(info);
145 <
146 <      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 <      }
141 >    }
142 >    
143 >    rotAlgo_ = new DLM();
144 >    rattle_ = new Rattle(info);
145 >    flucQ_ = new FluctuatingChargeNVT(info);
146 >    flucQ_->setForceManager(forceMan_);
147    }
148    
149    Integrator::~Integrator(){
150      delete forceMan_;
151      delete velocitizer_;
152      delete rnemd_;
153 +    delete flucQ_;
154 +    delete rotAlgo_;
155 +    delete rattle_;
156      
157      delete dumpWriter;
158      delete statWriter;
159    }
144 –
145 –
160   }
161  

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