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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 1738 by gezelter, Tue Jun 5 17:58:01 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()) {
56 +    
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  
108 <      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 <      }
108 >    forceMan_ = new ForceManager(info);
109      
110 <      if (simParams->haveRunTime()) {
111 <        runTime = simParams->getRunTime();
112 <      } else {
67 <        sprintf(painCave.errMsg,
68 <                "Integrator Error: runTime is not set\n");
69 <        painCave.isFatal = 1;
70 <        simError();
71 <      }
72 <      // set the status, sample, and thermal kick times
73 <      if (simParams->haveSampleTime()){
74 <        sampleTime = simParams->getSampleTime();
75 <        statusTime = sampleTime;
76 <      } else{
77 <        sampleTime = simParams->getRunTime();
78 <        statusTime = sampleTime;
79 <      }
110 >    // check for the temperature set flag (velocity scaling)      
111 >    if (simParams->haveTempSet()) {
112 >      needVelocityScaling = simParams->getTempSet();
113  
114 <      if (simParams->haveStatusTime()){
115 <        statusTime = simParams->getStatusTime();
114 >      if (simParams->haveTargetTemp()) {
115 >        targetScalingTemp = simParams->getTargetTemp();
116        }
117 +      else {
118 +        sprintf(painCave.errMsg,
119 +                "Integrator Error: Target Temperature is not set\n");
120 +        painCave.isFatal = 1;
121 +        simError();
122  
85 –      if (simParams->haveThermalTime()){
86 –        thermalTime = simParams->getThermalTime();
87 –      } else {
88 –        thermalTime = simParams->getRunTime();
123        }
124 <
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);
124 >    }
125      
126 <      // check for the temperature set flag (velocity scaling)      
127 <      if (simParams->haveTempSet()) {
128 <        needVelocityScaling = simParams->getTempSet();
129 <
130 <        if (simParams->haveTargetTemp()) {
131 <          targetScalingTemp = simParams->getTargetTemp();
132 <        }
133 <        else {
134 <          sprintf(painCave.errMsg,
135 <                  "Integrator Error: Target Temperature is not set\n");
136 <          painCave.isFatal = 1;
137 <          simError();
116 <
117 <        }
126 >    // Create a default a velocitizer: If the subclass wants to use
127 >    // a different velocitizer, use setVelocitizer
128 >    velocitizer_ = new Velocitizer(info);
129 >    
130 >    if (simParams->getRNEMDParameters()->haveUseRNEMD()) {
131 >      if (simParams->getRNEMDParameters()->getUseRNEMD()) {
132 >        // Create a default a RNEMD.
133 >        rnemd_ = new RNEMD(info);
134 >        useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
135 >        if (simParams->getRNEMDParameters()->haveExchangeTime()) {
136 >          RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
137 >        }
138        }
139 <      
140 <      // Create a default a velocitizer: If the subclass wants to use
141 <      // a different velocitizer, use setVelocitizer
142 <      velocitizer_ = new Velocitizer(info);
143 <
144 <      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 <      }
139 >    }
140 >    
141 >    rotAlgo_ = new DLM();
142 >    rattle_ = new Rattle(info);
143 >    forceMan_->initialize();
144 >    flucQ_ = new FluctuatingChargeNVT(info, forceMan_);
145    }
146    
147    Integrator::~Integrator(){
148      delete forceMan_;
149      delete velocitizer_;
150      delete rnemd_;
151 +    delete flucQ_;
152 +    delete rotAlgo_;
153 +    delete rattle_;
154      
155      delete dumpWriter;
156      delete statWriter;
157    }
144 –
145 –
158   }
159  

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