src/integrators/Integrator.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "brains/Snapshot.hpp"
#include "integrators/Integrator.hpp"
#include "integrators/DLM.hpp"
#include "flucq/FluctuatingChargeLangevin.hpp"
#include "flucq/FluctuatingChargeNVT.hpp"
#include "utils/simError.h"

namespace OpenMD {
  Integrator::Integrator(SimInfo* info) 
    : info_(info), forceMan_(NULL) , needPotential(false), needStress(false), 
      needReset(false), velocitizer_(NULL), needVelocityScaling(false), 
      rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL), 
      rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
      snap(info->getSnapshotManager()->getCurrentSnapshot()) {
    
    simParams = info->getSimParams();
    
    if (simParams->haveDt()) {
      dt = simParams->getDt();
    } else {
      sprintf(painCave.errMsg,
              "Integrator Error: dt is not set\n");
      painCave.isFatal = 1;
      simError();
    }
    
    if (simParams->haveRunTime()) {
      runTime = simParams->getRunTime();
    } else {
      sprintf(painCave.errMsg,
              "Integrator Error: runTime is not set\n");
      painCave.isFatal = 1;
      simError();
    }
    
    // set the status, sample, and thermal kick times
    if (simParams->haveSampleTime()){
      sampleTime = simParams->getSampleTime();
      statusTime = sampleTime;
    } else{
      sampleTime = simParams->getRunTime();
      statusTime = sampleTime;
    }
    
    if (simParams->haveStatusTime()){
      statusTime = simParams->getStatusTime();
    }
    
    if (simParams->haveThermalTime()){
      thermalTime = simParams->getThermalTime();
    } else {
      thermalTime = simParams->getRunTime();
    }
    
    if (!simParams->getUseInitalTime()) {
      snap->setTime(0.0);
    }
    
    if (simParams->haveResetTime()) {
      needReset = true;
      resetTime = simParams->getResetTime();
    }
    
    // Create a default ForceManager: If the subclass wants to use 
    // a different ForceManager, use setForceManager
    forceMan_ = new ForceManager(info);
    
    // check for the temperature set flag (velocity scaling)      
    needVelocityScaling = false;
    if (simParams->haveTempSet()) {
      needVelocityScaling = simParams->getTempSet();
    } 

    if (needVelocityScaling) {
      if (simParams->haveTargetTemp()) {
        targetScalingTemp = simParams->getTargetTemp();
      }
      else {
        sprintf(painCave.errMsg,
                "Integrator Error: Target Temperature must be set to turn on tempSet\n");
        painCave.isFatal = 1;
        simError();

      }
    }
    
    // Create a default a velocitizer: If the subclass wants to use 
    // a different velocitizer, use setVelocitizer
    velocitizer_ = new Velocitizer(info);
    
    if (simParams->getRNEMDParameters()->haveUseRNEMD()) {
      if (simParams->getRNEMDParameters()->getUseRNEMD()) {
        // Create a default a RNEMD.
        rnemd_ = new RNEMD(info);
        useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
        if (simParams->getRNEMDParameters()->haveExchangeTime()) {
          RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
        } 
      }
    }
    
    rotAlgo_ = new DLM();
    rattle_ = new Rattle(info);
    if (simParams->getFluctuatingChargeParameters()->havePropagator()) {
      std::string prop = toUpperCopy(simParams->getFluctuatingChargeParameters()->getPropagator());
      if (prop.compare("NVT")==0){
         flucQ_ = new FluctuatingChargeNVT(info);
      } else if (prop.compare("LANGEVIN")==0) {
         flucQ_ = new FluctuatingChargeLangevin(info);
      } else {
        sprintf(painCave.errMsg,
                "Integrator Error: Unknown Fluctuating Charge propagator (%s) requested\n",
                simParams->getFluctuatingChargeParameters()->getPropagator().c_str());
        painCave.isFatal = 1;
      }
    }
    flucQ_->setForceManager(forceMan_);
  }
  
  Integrator::~Integrator(){
    delete forceMan_;
    delete velocitizer_;
    delete rnemd_;
    delete flucQ_;
    delete rotAlgo_;
    delete rattle_;
    
    delete dumpWriter;
    delete statWriter;
  }
}

Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	6291 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#include "brains/Snapshot.hpp"
44	tim	3	#include "integrators/Integrator.hpp"
45	gezelter	1782	#include "integrators/DLM.hpp"
46			#include "flucq/FluctuatingChargeLangevin.hpp"
47			#include "flucq/FluctuatingChargeNVT.hpp"
48	tim	3	#include "utils/simError.h"
49	gezelter	1782
50	gezelter	1390	namespace OpenMD {
51	gezelter	507	Integrator::Integrator(SimInfo* info)
52	chrisfen	993	: info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
53			needReset(false), velocitizer_(NULL), needVelocityScaling(false),
54	gezelter	1782	rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL),
55			rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
56			snap(info->getSnapshotManager()->getCurrentSnapshot()) {
57	gezelter	246
58	gezelter	1782	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	gezelter	2
116	gezelter	1782	if (needVelocityScaling) {
117			if (simParams->haveTargetTemp()) {
118			targetScalingTemp = simParams->getTargetTemp();
119	gezelter	507	}
120	gezelter	1782	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	gezelter	2
126	gezelter	507	}
127	gezelter	1782	}
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	gezelter	507	}
142	gezelter	1782	}
143	gezelter	2
144	gezelter	1782	rotAlgo_ = new DLM();
145			rattle_ = new Rattle(info);
146	gezelter	1879	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	gezelter	1782	flucQ_->setForceManager(forceMan_);
160	gezelter	1343	}
161
162	gezelter	507	Integrator::~Integrator(){
163	gezelter	246	delete forceMan_;
164			delete velocitizer_;
165	skuang	1330	delete rnemd_;
166	gezelter	1782	delete flucQ_;
167			delete rotAlgo_;
168			delete rattle_;
169	gezelter	246
170			delete dumpWriter;
171			delete statWriter;
172	gezelter	507	}
173	gezelter	2	}
174