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 "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),
      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->haveUseRNEMD()) {
        if (simParams->getUseRNEMD()) {
          // Create a default a RNEMD.
          rnemd_ = new RNEMD(info);
          useRNEMD = simParams->getUseRNEMD();
          if (simParams->haveRNEMD_exchangeTime()) {
            RNEMD_exchangeTime = simParams->getRNEMD_exchangeTime();
          } 
        }
      }
  }
  
  Integrator::~Integrator(){
    delete forceMan_;
    delete velocitizer_;
    delete rnemd_;
    
    delete dumpWriter;
    delete statWriter;
  }


}

Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	5164 byte(s)
Log Message:	updated copyright notices
#	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			#include "utils/simError.h"
46	gezelter	1390	namespace OpenMD {
47	gezelter	507	Integrator::Integrator(SimInfo* info)
48	chrisfen	993	: info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
49			needReset(false), velocitizer_(NULL), needVelocityScaling(false),
50	gezelter	1329	rnemd_(NULL), useRNEMD(false),
51	chrisfen	993	dumpWriter(NULL), statWriter(NULL), thermo(info),
52	gezelter	246	currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
53	gezelter	2
54	gezelter	507	simParams = info->getSimParams();
55	gezelter	2
56	gezelter	507	if (simParams->haveDt()) {
57	gezelter	246	dt = simParams->getDt();
58	gezelter	507	} else {
59			sprintf(painCave.errMsg,
60			"Integrator Error: dt is not set\n");
61			painCave.isFatal = 1;
62			simError();
63			}
64	gezelter	246
65	gezelter	507	if (simParams->haveRunTime()) {
66	gezelter	246	runTime = simParams->getRunTime();
67	gezelter	507	} else {
68			sprintf(painCave.errMsg,
69			"Integrator Error: runTime is not set\n");
70			painCave.isFatal = 1;
71			simError();
72			}
73			// set the status, sample, and thermal kick times
74			if (simParams->haveSampleTime()){
75	gezelter	246	sampleTime = simParams->getSampleTime();
76			statusTime = sampleTime;
77	gezelter	507	} else{
78	gezelter	246	sampleTime = simParams->getRunTime();
79			statusTime = sampleTime;
80	gezelter	507	}
81	gezelter	2
82	gezelter	507	if (simParams->haveStatusTime()){
83	gezelter	246	statusTime = simParams->getStatusTime();
84	gezelter	507	}
85	gezelter	2
86	gezelter	507	if (simParams->haveThermalTime()){
87	gezelter	246	thermalTime = simParams->getThermalTime();
88	gezelter	507	} else {
89	gezelter	246	thermalTime = simParams->getRunTime();
90	gezelter	507	}
91	gezelter	2
92	tim	665	if (!simParams->getUseInitalTime()) {
93	gezelter	246	currentSnapshot_->setTime(0.0);
94	gezelter	507	}
95	tim	546
96			if (simParams->haveResetTime()) {
97			needReset = true;
98			resetTime = simParams->getResetTime();
99			}
100
101	chrisfen	993	// Create a default ForceManager: If the subclass wants to use
102			// a different ForceManager, use setForceManager
103	gezelter	1469
104	gezelter	507	forceMan_ = new ForceManager(info);
105	gezelter	1469
106	gezelter	507	// check for the temperature set flag (velocity scaling)
107			if (simParams->haveTempSet()) {
108	gezelter	246	needVelocityScaling = simParams->getTempSet();
109	gezelter	2
110	gezelter	246	if (simParams->haveTargetTemp()) {
111	gezelter	507	targetScalingTemp = simParams->getTargetTemp();
112	gezelter	246	}
113			else {
114	gezelter	507	sprintf(painCave.errMsg,
115			"Integrator Error: Target Temperature is not set\n");
116			painCave.isFatal = 1;
117			simError();
118	gezelter	2
119			}
120	gezelter	507	}
121	gezelter	1343
122	chrisfen	993	// Create a default a velocitizer: If the subclass wants to use
123			// a different velocitizer, use setVelocitizer
124	gezelter	507	velocitizer_ = new Velocitizer(info);
125	gezelter	2
126	gezelter	1343	if (simParams->haveUseRNEMD()) {
127			if (simParams->getUseRNEMD()) {
128			// Create a default a RNEMD.
129			rnemd_ = new RNEMD(info);
130			useRNEMD = simParams->getUseRNEMD();
131	skuang	1368	if (simParams->haveRNEMD_exchangeTime()) {
132			RNEMD_exchangeTime = simParams->getRNEMD_exchangeTime();
133	gezelter	1343	}
134			}
135			}
136			}
137
138	gezelter	507	Integrator::~Integrator(){
139	gezelter	246	delete forceMan_;
140			delete velocitizer_;
141	skuang	1330	delete rnemd_;
142	gezelter	246
143			delete dumpWriter;
144			delete statWriter;
145	gezelter	507	}
146	gezelter	2
147
148			}
149