applications/dynamicProps/DynamicProps.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 <iostream>
#include <fstream>
#include <string>

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

#include "applications/dynamicProps/DynamicPropsCmd.h"
#include "applications/dynamicProps/DipoleCorrFunc.hpp"
#include "applications/dynamicProps/RCorrFunc.hpp"
#include "applications/dynamicProps/VCorrFunc.hpp"
#include "applications/dynamicProps/LegendreCorrFunc.hpp"
#include "applications/dynamicProps/RadialRCorrFunc.hpp"
#include "applications/dynamicProps/ThetaCorrFunc.hpp"
#include "applications/dynamicProps/ActionCorrFunc.hpp"
#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"


using namespace oopse;

int main(int argc, char* argv[]){
  
  //register force fields
  registerForceFields();

  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;

  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  }else {
    char*  sele1Env= getenv("OOPSE_SELE1");
    if (sele1Env) {
      sele1 = sele1Env;
    }else {
      sprintf( painCave.errMsg,
               "neither --sele1 option nor $OOPSE_SELE1 is set");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  }
    
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  }else {
    char* sele2Env = getenv("OOPSE_SELE2");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else {
      sele2 = sele1;
    }
  }

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


  TimeCorrFunc* corrFunc;
  if (args_info.dcorr_given){
    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
  } else if (args_info.rcorr_given) {
    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
  } else if (args_info.r_rcorr_given) {
    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
  } else if (args_info.thetacorr_given) {
    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
  } else if (args_info.actioncorr_given) {
    corrFunc = new ActionCorrFunc(info, dumpFileName, sele1, sele2);
  } else if (args_info.drcorr_given) {
    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
  }
  else if (args_info.vcorr_given) {
    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2); 
  } else if (args_info.lcorr_given) {
    int order;
    if (args_info.order_given)
        order = args_info.order_arg;
    else {
      sprintf( painCave.errMsg,
               "--order must be set if --lcoor is set\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    }
        
    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order); 
  }

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


  corrFunc->doCorrelate();

  delete corrFunc;    
  delete info;

  return 0;   
}


Revision:	3235
Committed:	Tue Oct 2 12:05:25 2007 UTC (16 years, 11 months ago) by xsun
File size:	5236 byte(s)
Log Message:	Added: Action Correlation function (for viscosity), Directional RCorr (for non-spherical bodies) Modified: LCorr (for multiple axes)
#	User	Rev	Content
1	gezelter	2204	/*
2	tim	2005	* 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 <iostream>
43			#include <fstream>
44			#include <string>
45
46			#include "brains/Register.hpp"
47			#include "brains/SimCreator.hpp"
48			#include "brains/SimInfo.hpp"
49			#include "utils/simError.h"
50
51			#include "applications/dynamicProps/DynamicPropsCmd.h"
52	tim	2008	#include "applications/dynamicProps/DipoleCorrFunc.hpp"
53	tim	2005	#include "applications/dynamicProps/RCorrFunc.hpp"
54			#include "applications/dynamicProps/VCorrFunc.hpp"
55	tim	2576	#include "applications/dynamicProps/LegendreCorrFunc.hpp"
56	chuckv	3084	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
57	chuckv	3110	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
58	xsun	3235	#include "applications/dynamicProps/ActionCorrFunc.hpp"
59			#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
60	tim	2005
61	tim	2576
62	tim	2005	using namespace oopse;
63
64			int main(int argc, char* argv[]){
65
66	gezelter	2204	//register force fields
67			registerForceFields();
68	tim	2005
69	gezelter	2204	gengetopt_args_info args_info;
70	tim	2005
71	gezelter	2204	//parse the command line option
72			if (cmdline_parser (argc, argv, &args_info) != 0) {
73			exit(1) ;
74			}
75	tim	2005
76
77	gezelter	2204	//get the dumpfile name and meta-data file name
78			std::string dumpFileName = args_info.input_arg;
79	tim	2005
80	gezelter	2204	std::string sele1;
81			std::string sele2;
82	tim	2005
83	gezelter	2204	if (args_info.sele1_given) {
84			sele1 = args_info.sele1_arg;
85			}else {
86			char* sele1Env= getenv("OOPSE_SELE1");
87			if (sele1Env) {
88			sele1 = sele1Env;
89	tim	2005	}else {
90	gezelter	2204	sprintf( painCave.errMsg,
91	tim	2005	"neither --sele1 option nor $OOPSE_SELE1 is set");
92	gezelter	2204	painCave.severity = OOPSE_ERROR;
93			painCave.isFatal = 1;
94			simError();
95	tim	2005	}
96	gezelter	2204	}
97	tim	2005
98	gezelter	2204	if (args_info.sele2_given) {
99			sele2 = args_info.sele2_arg;
100			}else {
101			char* sele2Env = getenv("OOPSE_SELE2");
102			if (sele2Env) {
103			sele2 = sele2Env;
104			} else {
105			sele2 = sele1;
106	tim	2005	}
107	gezelter	2204	}
108	tim	2005
109	gezelter	2204	//parse md file and set up the system
110			SimCreator creator;
111	gezelter	2984	SimInfo* info = creator.createSim(dumpFileName, false);
112	tim	2005
113
114	gezelter	2204	TimeCorrFunc* corrFunc;
115	tim	2671	if (args_info.dcorr_given){
116	gezelter	2204	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
117			} else if (args_info.rcorr_given) {
118			corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
119	chuckv	3084	} else if (args_info.r_rcorr_given) {
120			corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
121	chuckv	3110	} else if (args_info.thetacorr_given) {
122			corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
123	xsun	3235	} else if (args_info.actioncorr_given) {
124			corrFunc = new ActionCorrFunc(info, dumpFileName, sele1, sele2);
125			} else if (args_info.drcorr_given) {
126			corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
127	gezelter	2204	}
128			else if (args_info.vcorr_given) {
129			corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
130	tim	2576	} else if (args_info.lcorr_given) {
131			int order;
132			if (args_info.order_given)
133			order = args_info.order_arg;
134			else {
135			sprintf( painCave.errMsg,
136			"--order must be set if --lcoor is set\n");
137			painCave.severity = OOPSE_ERROR;
138			painCave.isFatal = 1;
139			simError();
140			}
141
142			corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
143	gezelter	2204	}
144	tim	2005
145	gezelter	2204	if (args_info.output_given) {
146			corrFunc->setOutputName(args_info.output_arg);
147			}
148	tim	2005
149
150	gezelter	2204	corrFunc->doCorrelate();
151	tim	2005
152	gezelter	2204	delete corrFunc;
153			delete info;
154	tim	2005
155	gezelter	2204	return 0;
156	tim	2005	}
157
158