applications/thermalizer/thermalizer.cpp

/*
 * Copyright (c) 2006 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).
 */

/**
 * @file thermalizer.cpp
 * @author Dan Gezelter
 * @date 09/20/2006
 * @version 1.0
 */

#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <cmath>
#include <iostream>
#include <string>
#include <map>
#include <fstream>

#include "applications/thermalizer/thermalizerCmd.h"
#include "integrators/Velocitizer.hpp"
#include "brains/Register.hpp"
#include "brains/SimInfo.hpp"
#include "brains/SimCreator.hpp"
#include "io/DumpReader.hpp"
#include "io/DumpWriter.hpp"
#include "utils/StringUtils.hpp"

using namespace std;
using namespace OpenMD;

int main(int argc, char *argv []) {

  registerLattice();
    
  gengetopt_args_info args_info;
  std::string inputFileName;
  std::string outputFileName;
  RealType temperature;

  // parse command line arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);

  temperature = args_info.temperature_arg;
    
  if (temperature < 0.0) {
    sprintf(painCave.errMsg, "Temperatures must be positive numbers.");
    painCave.isFatal = 1;
    simError();
  }

  //get input file name
  if (args_info.inputs_num)
    inputFileName = args_info.inputs[0];
  else {
    sprintf(painCave.errMsg, "No input file name was specified "
            "on the command line");
    painCave.isFatal = 1;
    simError();
  }
  
  //parse md file and set up the system

  SimCreator creator;
  SimInfo* info = creator.createSim(inputFileName, false);
  Velocitizer* veloSet = new Velocitizer(info);
  DumpReader reader(info, inputFileName);
  // very important step:
  info->update();

  outputFileName = args_info.output_arg;

  if (!outputFileName.compare(inputFileName)) {
    sprintf(painCave.errMsg, "Input and Output File names should be different!");
    painCave.isFatal = 1;
    simError();
  }

  DumpWriter* writer = new DumpWriter(info, outputFileName);
    
  if (writer == NULL) {
    sprintf(painCave.errMsg, "error in creating DumpWriter");
    painCave.isFatal = 1;
    simError();
  }

  int nFrames = reader.getNFrames();

  for (int istep = 0; istep < nFrames; istep++) {
    reader.readFrame(istep);
    veloSet->velocitize(temperature);
    writer->writeDump();
  }

  // deleting the writer will put the closing at the end of the dump file.

  delete writer;

  sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
          "generated.\n", outputFileName.c_str());
  painCave.isFatal = 0;
  simError();
  return 0;
}
Revision:	1725
Committed:	Sat May 26 18:13:43 2012 UTC (12 years, 11 months ago) by gezelter
File size:	4599 byte(s)
Log Message:	Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
#	User	Rev	Content
1	gezelter	1083	/*
2			* Copyright (c) 2006 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	1083	* 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	1083	* 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	1083	*/
42
43			/**
44			* @file thermalizer.cpp
45			* @author Dan Gezelter
46			* @date 09/20/2006
47			* @version 1.0
48			*/
49
50			#include <cstdlib>
51			#include <cstdio>
52			#include <cstring>
53			#include <cmath>
54			#include <iostream>
55			#include <string>
56			#include <map>
57			#include <fstream>
58
59			#include "applications/thermalizer/thermalizerCmd.h"
60			#include "integrators/Velocitizer.hpp"
61			#include "brains/Register.hpp"
62			#include "brains/SimInfo.hpp"
63			#include "brains/SimCreator.hpp"
64			#include "io/DumpReader.hpp"
65			#include "io/DumpWriter.hpp"
66			#include "utils/StringUtils.hpp"
67
68			using namespace std;
69	gezelter	1390	using namespace OpenMD;
70	gezelter	1083
71			int main(int argc, char *argv []) {
72
73			registerLattice();
74
75			gengetopt_args_info args_info;
76			std::string inputFileName;
77			std::string outputFileName;
78			RealType temperature;
79
80			// parse command line arguments
81			if (cmdline_parser(argc, argv, &args_info) != 0)
82			exit(1);
83
84			temperature = args_info.temperature_arg;
85
86			if (temperature < 0.0) {
87			sprintf(painCave.errMsg, "Temperatures must be positive numbers.");
88			painCave.isFatal = 1;
89			simError();
90			}
91
92			//get input file name
93			if (args_info.inputs_num)
94			inputFileName = args_info.inputs[0];
95			else {
96			sprintf(painCave.errMsg, "No input file name was specified "
97			"on the command line");
98			painCave.isFatal = 1;
99			simError();
100			}
101
102			//parse md file and set up the system
103
104			SimCreator creator;
105			SimInfo* info = creator.createSim(inputFileName, false);
106			Velocitizer* veloSet = new Velocitizer(info);
107			DumpReader reader(info, inputFileName);
108			// very important step:
109			info->update();
110
111			outputFileName = args_info.output_arg;
112
113			if (!outputFileName.compare(inputFileName)) {
114			sprintf(painCave.errMsg, "Input and Output File names should be different!");
115			painCave.isFatal = 1;
116			simError();
117			}
118
119			DumpWriter* writer = new DumpWriter(info, outputFileName);
120
121			if (writer == NULL) {
122			sprintf(painCave.errMsg, "error in creating DumpWriter");
123			painCave.isFatal = 1;
124			simError();
125			}
126
127			int nFrames = reader.getNFrames();
128
129			for (int istep = 0; istep < nFrames; istep++) {
130			reader.readFrame(istep);
131			veloSet->velocitize(temperature);
132			writer->writeDump();
133			}
134
135			// deleting the writer will put the closing at the end of the dump file.
136
137			delete writer;
138
139	gezelter	1390	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
140	gezelter	1083	"generated.\n", outputFileName.c_str());
141			painCave.isFatal = 0;
142			simError();
143			return 0;
144			}