src/integrators/RNEMD.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 "integrators/RNEMD.hpp"
#include "math/SquareMatrix3.hpp"
#include "primitives/Molecule.hpp"
#include "primitives/StuntDouble.hpp"

#ifndef IS_MPI
#include "math/SeqRandNumGen.hpp"
#else
#include "math/ParallelRandNumGen.hpp"
#endif

/* Remove me after testing*/
/*
#include <cstdio>
#include <iostream>
*/
/*End remove me*/

namespace oopse {
  
  RNEMD::RNEMD(SimInfo* info) : info_(info) {
    
    int seedValue;
    Globals * simParams = info->getSimParams();

    stringToEnumMap_["Kinetic"] = rnemdKinetic;
    stringToEnumMap_["Px"] = rnemdPx;
    stringToEnumMap_["Py"] = rnemdPy;
    stringToEnumMap_["Pz"] = rnemdPz;
    stringToEnumMap_["Unknown"] = rnemdUnknown;

    const std::string st = simParams->getRNEMD_swapType();

    std::map<std::string, RNEMDTypeEnum>::iterator i;
    i = stringToEnumMap_.find(st);
    rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;


    set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
    set_RNEMD_nBins(simParams->getRNEMD_nBins());
    exchangeSum_ = 0.0;
    
#ifndef IS_MPI
    if (simParams->haveSeed()) {
      seedValue = simParams->getSeed();
      randNumGen_ = new SeqRandNumGen(seedValue);
    }else {
      randNumGen_ = new SeqRandNumGen();
    }    
#else
    if (simParams->haveSeed()) {
      seedValue = simParams->getSeed();
      randNumGen_ = new ParallelRandNumGen(seedValue);
    }else {
      randNumGen_ = new ParallelRandNumGen();
    }    
#endif 
  }
  
  RNEMD::~RNEMD() {
    delete randNumGen_;
  }

  void RNEMD::doSwap() {
    std::cerr << "in RNEMD!\n";   
    std::cerr << "nBins = " << nBins_ << "\n";
    std::cerr << "swapTime = " << swapTime_ << "\n";
    std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
    std::cerr << "swapType = " << rnemdType_ << "\n";
  }   
}
Revision:	1330
Committed:	Thu Mar 19 21:03:36 2009 UTC (16 years, 1 month ago) by skuang
File size:	3879 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.
#	Content
1	/*
2	* 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 "integrators/RNEMD.hpp"
43	#include "math/SquareMatrix3.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "primitives/StuntDouble.hpp"
46
47	#ifndef IS_MPI
48	#include "math/SeqRandNumGen.hpp"
49	#else
50	#include "math/ParallelRandNumGen.hpp"
51	#endif
52
53	/* Remove me after testing*/
54	/*
55	#include <cstdio>
56	#include <iostream>
57	*/
58	/End remove me/
59
60	namespace oopse {
61
62	RNEMD::RNEMD(SimInfo* info) : info_(info) {
63
64	int seedValue;
65	Globals * simParams = info->getSimParams();
66
67	stringToEnumMap_["Kinetic"] = rnemdKinetic;
68	stringToEnumMap_["Px"] = rnemdPx;
69	stringToEnumMap_["Py"] = rnemdPy;
70	stringToEnumMap_["Pz"] = rnemdPz;
71	stringToEnumMap_["Unknown"] = rnemdUnknown;
72
73	const std::string st = simParams->getRNEMD_swapType();
74
75	std::map<std::string, RNEMDTypeEnum>::iterator i;
76	i = stringToEnumMap_.find(st);
77	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
78
79
80	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
81	set_RNEMD_nBins(simParams->getRNEMD_nBins());
82	exchangeSum_ = 0.0;
83
84	#ifndef IS_MPI
85	if (simParams->haveSeed()) {
86	seedValue = simParams->getSeed();
87	randNumGen_ = new SeqRandNumGen(seedValue);
88	}else {
89	randNumGen_ = new SeqRandNumGen();
90	}
91	#else
92	if (simParams->haveSeed()) {
93	seedValue = simParams->getSeed();
94	randNumGen_ = new ParallelRandNumGen(seedValue);
95	}else {
96	randNumGen_ = new ParallelRandNumGen();
97	}
98	#endif
99	}
100
101	RNEMD::~RNEMD() {
102	delete randNumGen_;
103	}
104
105	void RNEMD::doSwap() {
106	std::cerr << "in RNEMD!\n";
107	std::cerr << "nBins = " << nBins_ << "\n";
108	std::cerr << "swapTime = " << swapTime_ << "\n";
109	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
110	std::cerr << "swapType = " << rnemdType_ << "\n";
111	}
112	}