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, 24107 (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/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),
      currentSnapshot_(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()) {
      currentSnapshot_->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)      
    if (simParams->haveTempSet()) {
      needVelocityScaling = simParams->getTempSet();

      if (simParams->haveTargetTemp()) {
        targetScalingTemp = simParams->getTargetTemp();
      }
      else {
        sprintf(painCave.errMsg,
                "Integrator Error: Target Temperature is not set\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);
    flucQ_ = new FluctuatingChargeNVT(info);
  }
  
  Integrator::~Integrator(){
    delete forceMan_;
    delete velocitizer_;
    delete rnemd_;
    delete flucQ_;
    delete rotAlgo_;
    delete rattle_;
    
    delete dumpWriter;
    delete statWriter;
  }
}

Revision:	1731
Committed:	Thu May 31 12:25:30 2012 UTC (12 years, 11 months ago) by gezelter
File size:	5526 byte(s)
Log Message:	Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [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	1715	#include "integrators/DLM.hpp"
46	gezelter	1731	#include "flucq/FluctuatingChargeNVT.hpp"
47	tim	3	#include "utils/simError.h"
48	gezelter	1715
49	gezelter	1390	namespace OpenMD {
50	gezelter	507	Integrator::Integrator(SimInfo* info)
51	chrisfen	993	: info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
52			needReset(false), velocitizer_(NULL), needVelocityScaling(false),
53	gezelter	1715	rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL),
54			rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
55	gezelter	246	currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
56
57	gezelter	1715	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			// set the status, sample, and thermal kick times
77			if (simParams->haveSampleTime()){
78			sampleTime = simParams->getSampleTime();
79			statusTime = sampleTime;
80			} else{
81			sampleTime = simParams->getRunTime();
82			statusTime = sampleTime;
83			}
84	gezelter	2
85	gezelter	1715	if (simParams->haveStatusTime()){
86			statusTime = simParams->getStatusTime();
87			}
88	gezelter	2
89	gezelter	1715	if (simParams->haveThermalTime()){
90			thermalTime = simParams->getThermalTime();
91			} else {
92			thermalTime = simParams->getRunTime();
93			}
94	gezelter	2
95	gezelter	1715	if (!simParams->getUseInitalTime()) {
96			currentSnapshot_->setTime(0.0);
97			}
98	tim	546
99	gezelter	1715	if (simParams->haveResetTime()) {
100			needReset = true;
101			resetTime = simParams->getResetTime();
102			}
103	tim	546
104	gezelter	1715	// Create a default ForceManager: If the subclass wants to use
105			// a different ForceManager, use setForceManager
106	gezelter	1469
107	gezelter	1715	forceMan_ = new ForceManager(info);
108	gezelter	1469
109	gezelter	1715	// check for the temperature set flag (velocity scaling)
110			if (simParams->haveTempSet()) {
111			needVelocityScaling = simParams->getTempSet();
112	gezelter	2
113	gezelter	1715	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	gezelter	2
122	gezelter	507	}
123	gezelter	1715	}
124	gezelter	1343
125	gezelter	1715	// Create a default a velocitizer: If the subclass wants to use
126			// a different velocitizer, use setVelocitizer
127			velocitizer_ = new Velocitizer(info);
128	gezelter	2
129	gezelter	1731	if (simParams->getRNEMDParameters()->haveUseRNEMD()) {
130			if (simParams->getRNEMDParameters()->getUseRNEMD()) {
131	gezelter	1715	// Create a default a RNEMD.
132			rnemd_ = new RNEMD(info);
133	gezelter	1731	useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
134			if (simParams->getRNEMDParameters()->haveExchangeTime()) {
135			RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
136	gezelter	1715	}
137	gezelter	1343	}
138	gezelter	1715	}
139
140			rotAlgo_ = new DLM();
141			rattle_ = new Rattle(info);
142			flucQ_ = new FluctuatingChargeNVT(info);
143	gezelter	1343	}
144
145	gezelter	507	Integrator::~Integrator(){
146	gezelter	246	delete forceMan_;
147			delete velocitizer_;
148	skuang	1330	delete rnemd_;
149	gezelter	1715	delete flucQ_;
150			delete rotAlgo_;
151			delete rattle_;
152	gezelter	246
153			delete dumpWriter;
154			delete statWriter;
155	gezelter	507	}
156	gezelter	2	}
157