applications/sequentialProps/SequentialProps.cpp

/*
 * Copyright (c) 2014 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 <iostream>
#include <fstream>
#include <string>

#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "utils/StringUtils.hpp"
#include "utils/simError.h"

#include "applications/sequentialProps/SequentialPropsCmd.h"
#include "applications/sequentialProps/SequentialAnalyzer.hpp"
#include "applications/sequentialProps/DensityAnalyzer.hpp"

using namespace OpenMD;

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

  //parse the command line option
  if (cmdline_parser (argc, argv, &args_info) != 0) {
    exit(1) ;
  }

  //get the dumpfile name and meta-data file name
  std::string dumpFileName = args_info.input_arg;
    
  std::string sele1;
  std::string sele2;
  
  // check the first selection argument, or set it to the environment
  // variable, or failing that, set it to "select all"
  
  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  } else {
    char*  sele1Env= getenv("SELECTION1");
    if (sele1Env) {
      sele1 = sele1Env;
    } else {
      sele1 = "select all";
    }
  }
  
  // check the second selection argument, or set it to the environment
  // variable, or failing that, set it to the first selection
  
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  } else {
    char* sele2Env = getenv("SELECTION2");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else { 
      //If sele2 is not specified, then the default behavior
      //should be what is already intended for sele1
      sele2 = sele1;
    }
  }

  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(dumpFileName, false);

  SequentialAnalyzer* analyzer;
  if(args_info.density_given){
    analyzer = new DensityAnalyzer(info, dumpFileName, sele1);
  }

  if (args_info.output_given) {
    analyzer->setOutputName(args_info.output_arg);
  }

  analyzer->doSequence();

  delete analyzer;    
  delete info;

  return 0;   
}


Revision:	2024
Committed:	Thu Oct 16 19:13:51 2014 UTC (10 years, 6 months ago) by gezelter
File size:	4144 byte(s)
Log Message:	Added Radial and Z-projected velocity autocorrelation functions Started to add SequentialProps program Mucking about with angular restraint potentials
#	User	Rev	Content
1	gezelter	2024	/*
2			* Copyright (c) 2014 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 <iostream>
44			#include <fstream>
45			#include <string>
46
47			#include "brains/SimCreator.hpp"
48			#include "brains/SimInfo.hpp"
49			#include "utils/StringUtils.hpp"
50			#include "utils/simError.h"
51
52			#include "applications/sequentialProps/SequentialPropsCmd.h"
53			#include "applications/sequentialProps/SequentialAnalyzer.hpp"
54			#include "applications/sequentialProps/DensityAnalyzer.hpp"
55
56			using namespace OpenMD;
57
58			int main(int argc, char* argv[]){
59
60			gengetopt_args_info args_info;
61
62			//parse the command line option
63			if (cmdline_parser (argc, argv, &args_info) != 0) {
64			exit(1) ;
65			}
66
67			//get the dumpfile name and meta-data file name
68			std::string dumpFileName = args_info.input_arg;
69
70			std::string sele1;
71			std::string sele2;
72
73			// check the first selection argument, or set it to the environment
74			// variable, or failing that, set it to "select all"
75
76			if (args_info.sele1_given) {
77			sele1 = args_info.sele1_arg;
78			} else {
79			char* sele1Env= getenv("SELECTION1");
80			if (sele1Env) {
81			sele1 = sele1Env;
82			} else {
83			sele1 = "select all";
84			}
85			}
86
87			// check the second selection argument, or set it to the environment
88			// variable, or failing that, set it to the first selection
89
90			if (args_info.sele2_given) {
91			sele2 = args_info.sele2_arg;
92			} else {
93			char* sele2Env = getenv("SELECTION2");
94			if (sele2Env) {
95			sele2 = sele2Env;
96			} else {
97			//If sele2 is not specified, then the default behavior
98			//should be what is already intended for sele1
99			sele2 = sele1;
100			}
101			}
102
103			//parse md file and set up the system
104			SimCreator creator;
105			SimInfo* info = creator.createSim(dumpFileName, false);
106
107			SequentialAnalyzer* analyzer;
108			if(args_info.density_given){
109			analyzer = new DensityAnalyzer(info, dumpFileName, sele1);
110			}
111
112			if (args_info.output_given) {
113			analyzer->setOutputName(args_info.output_arg);
114			}
115
116			analyzer->doSequence();
117
118			delete analyzer;
119			delete info;
120
121			return 0;
122			}
123
124