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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#include "brains/Snapshot.hpp"
#include "integrators/Integrator.hpp"
#include "utils/simError.h"
namespace oopse {
  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();
      }


     if (simParams->haveUseRNEMD()) {
        if (simParams->getUseRNEMD()) {
           useRNEMD = simParams->getUseRNEMD();
           if (simParams->haveRNEMD_swapTime()) {
              RNEMD_swapTime = simParams->getRNEMD_swapTime();
           } 
         }
      }
      
      // 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);
      // Create a default a RNEMD.
      rnemd_ = new RNEMD(info);
    
    }

  Integrator::~Integrator(){
    delete forceMan_;
    delete velocitizer_;
    delete rnemd_;
    
    delete dumpWriter;
    delete statWriter;
  }


}

Revision:	1330
Committed:	Thu Mar 19 21:03:36 2009 UTC (16 years, 1 month ago) by skuang
File size:	5043 byte(s)
Log Message:	Added handlers to Integrator to call RNEMD at the right times. Added initialization to RNEMD to make sure values from the MD file are available.
#	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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "brains/Snapshot.hpp"
43	tim	3	#include "integrators/Integrator.hpp"
44			#include "utils/simError.h"
45	gezelter	246	namespace oopse {
46	gezelter	507	Integrator::Integrator(SimInfo* info)
47	chrisfen	993	: info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
48			needReset(false), velocitizer_(NULL), needVelocityScaling(false),
49	gezelter	1329	rnemd_(NULL), useRNEMD(false),
50	chrisfen	993	dumpWriter(NULL), statWriter(NULL), thermo(info),
51	gezelter	246	currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
52	gezelter	2
53	gezelter	507	simParams = info->getSimParams();
54	gezelter	2
55	gezelter	507	if (simParams->haveDt()) {
56	gezelter	246	dt = simParams->getDt();
57	gezelter	507	} else {
58			sprintf(painCave.errMsg,
59			"Integrator Error: dt is not set\n");
60			painCave.isFatal = 1;
61			simError();
62			}
63	gezelter	246
64	gezelter	507	if (simParams->haveRunTime()) {
65	gezelter	246	runTime = simParams->getRunTime();
66	gezelter	507	} 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	gezelter	246	sampleTime = simParams->getSampleTime();
75			statusTime = sampleTime;
76	gezelter	507	} else{
77	gezelter	246	sampleTime = simParams->getRunTime();
78			statusTime = sampleTime;
79	gezelter	507	}
80	gezelter	2
81	gezelter	507	if (simParams->haveStatusTime()){
82	gezelter	246	statusTime = simParams->getStatusTime();
83	gezelter	507	}
84	gezelter	2
85	gezelter	507	if (simParams->haveThermalTime()){
86	gezelter	246	thermalTime = simParams->getThermalTime();
87	gezelter	507	} else {
88	gezelter	246	thermalTime = simParams->getRunTime();
89	gezelter	507	}
90	gezelter	2
91	tim	665	if (!simParams->getUseInitalTime()) {
92	gezelter	246	currentSnapshot_->setTime(0.0);
93	gezelter	507	}
94	tim	546
95			if (simParams->haveResetTime()) {
96			needReset = true;
97			resetTime = simParams->getResetTime();
98			}
99	skuang	1330
100
101			if (simParams->haveUseRNEMD()) {
102			if (simParams->getUseRNEMD()) {
103			useRNEMD = simParams->getUseRNEMD();
104			if (simParams->haveRNEMD_swapTime()) {
105			RNEMD_swapTime = simParams->getRNEMD_swapTime();
106			}
107			}
108			}
109	tim	546
110	chrisfen	993	// Create a default ForceManager: If the subclass wants to use
111			// a different ForceManager, use setForceManager
112	gezelter	507	forceMan_ = new ForceManager(info);
113	gezelter	2
114	gezelter	507	// check for the temperature set flag (velocity scaling)
115			if (simParams->haveTempSet()) {
116	gezelter	246	needVelocityScaling = simParams->getTempSet();
117	gezelter	2
118	gezelter	246	if (simParams->haveTargetTemp()) {
119	gezelter	507	targetScalingTemp = simParams->getTargetTemp();
120	gezelter	246	}
121			else {
122	gezelter	507	sprintf(painCave.errMsg,
123			"Integrator Error: Target Temperature is not set\n");
124			painCave.isFatal = 1;
125			simError();
126	gezelter	2
127			}
128	gezelter	507	}
129	gezelter	2
130	chrisfen	993	// Create a default a velocitizer: If the subclass wants to use
131			// a different velocitizer, use setVelocitizer
132	gezelter	507	velocitizer_ = new Velocitizer(info);
133	skuang	1330	// Create a default a RNEMD.
134			rnemd_ = new RNEMD(info);
135	gezelter	2
136	gezelter	507	}
137	gezelter	2
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