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.
#	Content
1	/*
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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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	using namespace OpenMD;
70
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	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
140	"generated.\n", outputFileName.c_str());
141	painCave.isFatal = 0;
142	simError();
143	return 0;
144	}