applications/recenter/recenter.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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

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

#include "applications/recenter/recenterCmd.h"
#include "brains/Thermo.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);

  //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);
  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();
  Vector3d COM;
  Vector3d pos;
  SimInfo::MoleculeIterator i;
  Molecule::IntegrableObjectIterator j;
  Molecule * mol;
  StuntDouble * sd;
  Thermo thermo(info);

  for (int istep = 0; istep < nFrames; istep++) {
    reader.readFrame(istep);
    COM = thermo.getCom();
    for( mol = info->beginMolecule(i); mol != NULL;
         mol = info->nextMolecule(i) ) {

      for( sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j) ) {

        pos = sd->getPos();
        sd->setPos(pos - COM);
        
      }
    }
    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:	1857
Committed:	Wed Apr 3 18:27:48 2013 UTC (12 years, 1 month ago) by kstocke1
File size:	4665 byte(s)
Log Message:	Added utility to recenter a simulation on the center of mass
#	User	Rev	Content
1	kstocke1	1857	/*
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, 234107 (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			#include <cstdlib>
44			#include <cstdio>
45			#include <cstring>
46			#include <cmath>
47			#include <iostream>
48			#include <string>
49			#include <map>
50			#include <fstream>
51
52			#include "applications/recenter/recenterCmd.h"
53			#include "brains/Thermo.hpp"
54			#include "brains/Register.hpp"
55			#include "brains/SimInfo.hpp"
56			#include "brains/SimCreator.hpp"
57			#include "io/DumpReader.hpp"
58			#include "io/DumpWriter.hpp"
59			#include "utils/StringUtils.hpp"
60
61			using namespace std;
62			using namespace OpenMD;
63
64			int main(int argc, char *argv []) {
65
66			registerLattice();
67
68			gengetopt_args_info args_info;
69			std::string inputFileName;
70			std::string outputFileName;
71			RealType temperature;
72
73			// parse command line arguments
74			if (cmdline_parser(argc, argv, &args_info) != 0)
75			exit(1);
76
77			//get input file name
78			if (args_info.inputs_num)
79			inputFileName = args_info.inputs[0];
80			else {
81			sprintf(painCave.errMsg, "No input file name was specified "
82			"on the command line");
83			painCave.isFatal = 1;
84			simError();
85			}
86
87			//parse md file and set up the system
88
89			SimCreator creator;
90			SimInfo* info = creator.createSim(inputFileName, false);
91			DumpReader reader(info, inputFileName);
92			// very important step:
93			info->update();
94
95			outputFileName = args_info.output_arg;
96
97			if (!outputFileName.compare(inputFileName)) {
98			sprintf(painCave.errMsg, "Input and Output File names should be different!");
99			painCave.isFatal = 1;
100			simError();
101			}
102
103			DumpWriter* writer = new DumpWriter(info, outputFileName);
104
105			if (writer == NULL) {
106			sprintf(painCave.errMsg, "error in creating DumpWriter");
107			painCave.isFatal = 1;
108			simError();
109			}
110
111			int nFrames = reader.getNFrames();
112			Vector3d COM;
113			Vector3d pos;
114			SimInfo::MoleculeIterator i;
115			Molecule::IntegrableObjectIterator j;
116			Molecule * mol;
117			StuntDouble * sd;
118			Thermo thermo(info);
119
120			for (int istep = 0; istep < nFrames; istep++) {
121			reader.readFrame(istep);
122			COM = thermo.getCom();
123			for( mol = info->beginMolecule(i); mol != NULL;
124			mol = info->nextMolecule(i) ) {
125
126			for( sd = mol->beginIntegrableObject(j); sd != NULL;
127			sd = mol->nextIntegrableObject(j) ) {
128
129			pos = sd->getPos();
130			sd->setPos(pos - COM);
131
132			}
133			}
134			writer->writeDump();
135			}
136
137			// deleting the writer will put the closing at the end of the dump file.
138
139			delete writer;
140
141			sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
142			"generated.\n", outputFileName.c_str());
143			painCave.isFatal = 0;
144			simError();
145			return 0;
146			}