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. 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).
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "utils/StringUtils.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/DirectionalRCorrFunc.hpp"
#include "applications/dynamicProps/EnergyCorrFunc.hpp"
#include "applications/dynamicProps/StressCorrFunc.hpp"
#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
#include "applications/dynamicProps/MomentumCorrFunc.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;

  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  }else {
    char*  sele1Env= getenv("SELECTION1");
    if (sele1Env) {
      sele1 = sele1Env;
    }else {
      sprintf( painCave.errMsg,
               "neither --sele1 option nor $SELECTION1 is set");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  }
    
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  }else {
    char* sele2Env = getenv("SELECTION2");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else {
      sele2 = sele1;
    }
  }

  // use the memory string to figure out how much memory we can use:
  char *end;
  long long int memSize = memparse(args_info.memory_arg, &end);
  sprintf( painCave.errMsg,
           "Amount of memory being used: %llu bytes\n", memSize);
  painCave.severity = OPENMD_INFO;
  painCave.isFatal = 0;
  simError();     

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


  TimeCorrFunc* corrFunc;
  if(args_info.sdcorr_given){
    corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.dcorr_given){
    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.rcorr_given) {
    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.r_rcorr_given) {
    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.thetacorr_given) {
    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.drcorr_given) {
    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.vcorr_given) {
    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize); 
  } else if (args_info.helfandEcorr_given){
    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.stresscorr_given){
    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.momentum_given){
    corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } 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 = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
        
    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); 
  }

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


  corrFunc->doCorrelate();

  delete corrFunc;    
  delete info;

  return 0;   
}


Revision:	1725
Committed:	Sat May 26 18:13:43 2012 UTC (12 years, 11 months ago) by gezelter
File size:	6221 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	507	/*
2	tim	321	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	321	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	321	* 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	tim	321	*/
42
43			#include <iostream>
44			#include <fstream>
45			#include <string>
46
47			#include "brains/SimCreator.hpp"
48			#include "brains/SimInfo.hpp"
49	gezelter	1629	#include "utils/StringUtils.hpp"
50	tim	321	#include "utils/simError.h"
51
52			#include "applications/dynamicProps/DynamicPropsCmd.h"
53	tim	324	#include "applications/dynamicProps/DipoleCorrFunc.hpp"
54	tim	321	#include "applications/dynamicProps/RCorrFunc.hpp"
55			#include "applications/dynamicProps/VCorrFunc.hpp"
56	tim	876	#include "applications/dynamicProps/LegendreCorrFunc.hpp"
57	chuckv	1098	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
58	chuckv	1112	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
59	xsun	1183	#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
60	chuckv	1245	#include "applications/dynamicProps/EnergyCorrFunc.hpp"
61	gezelter	1629	#include "applications/dynamicProps/StressCorrFunc.hpp"
62			#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
63			#include "applications/dynamicProps/MomentumCorrFunc.hpp"
64	tim	321
65	tim	876
66	gezelter	1629
67	gezelter	1390	using namespace OpenMD;
68	tim	321
69			int main(int argc, char* argv[]){
70
71	gezelter	507	gengetopt_args_info args_info;
72	tim	321
73	gezelter	507	//parse the command line option
74			if (cmdline_parser (argc, argv, &args_info) != 0) {
75			exit(1) ;
76			}
77	tim	321
78
79	gezelter	507	//get the dumpfile name and meta-data file name
80			std::string dumpFileName = args_info.input_arg;
81	tim	321
82	gezelter	507	std::string sele1;
83			std::string sele2;
84	tim	321
85	gezelter	507	if (args_info.sele1_given) {
86			sele1 = args_info.sele1_arg;
87			}else {
88	gezelter	1390	char* sele1Env= getenv("SELECTION1");
89	gezelter	507	if (sele1Env) {
90			sele1 = sele1Env;
91	tim	321	}else {
92	gezelter	507	sprintf( painCave.errMsg,
93	gezelter	1390	"neither --sele1 option nor $SELECTION1 is set");
94			painCave.severity = OPENMD_ERROR;
95	gezelter	507	painCave.isFatal = 1;
96			simError();
97	tim	321	}
98	gezelter	507	}
99	tim	321
100	gezelter	507	if (args_info.sele2_given) {
101			sele2 = args_info.sele2_arg;
102			}else {
103	gezelter	1390	char* sele2Env = getenv("SELECTION2");
104	gezelter	507	if (sele2Env) {
105			sele2 = sele2Env;
106			} else {
107			sele2 = sele1;
108	tim	321	}
109	gezelter	507	}
110	tim	321
111	gezelter	1629	// use the memory string to figure out how much memory we can use:
112			char *end;
113			long long int memSize = memparse(args_info.memory_arg, &end);
114			sprintf( painCave.errMsg,
115			"Amount of memory being used: %llu bytes\n", memSize);
116			painCave.severity = OPENMD_INFO;
117			painCave.isFatal = 0;
118			simError();
119
120	gezelter	507	//parse md file and set up the system
121			SimCreator creator;
122	gezelter	1026	SimInfo* info = creator.createSim(dumpFileName, false);
123	tim	321
124
125	gezelter	507	TimeCorrFunc* corrFunc;
126	gezelter	1629	if(args_info.sdcorr_given){
127			corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
128			} else if (args_info.dcorr_given){
129			corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
130	gezelter	507	} else if (args_info.rcorr_given) {
131	gezelter	1629	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132	chuckv	1098	} else if (args_info.r_rcorr_given) {
133	gezelter	1629	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134	chuckv	1112	} else if (args_info.thetacorr_given) {
135	gezelter	1629	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136	xsun	1183	} else if (args_info.drcorr_given) {
137	gezelter	1629	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138	chuckv	1245	} else if (args_info.vcorr_given) {
139	gezelter	1629	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140	chuckv	1245	} else if (args_info.helfandEcorr_given){
141	gezelter	1629	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142			} else if (args_info.stresscorr_given){
143			corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
144			} else if (args_info.momentum_given){
145			corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
146	tim	876	} else if (args_info.lcorr_given) {
147			int order;
148			if (args_info.order_given)
149			order = args_info.order_arg;
150			else {
151			sprintf( painCave.errMsg,
152			"--order must be set if --lcoor is set\n");
153	gezelter	1390	painCave.severity = OPENMD_ERROR;
154	tim	876	painCave.isFatal = 1;
155			simError();
156			}
157
158	gezelter	1629	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
159	gezelter	507	}
160	tim	321
161	gezelter	507	if (args_info.output_given) {
162			corrFunc->setOutputName(args_info.output_arg);
163			}
164	tim	321
165
166	gezelter	507	corrFunc->doCorrelate();
167	tim	321
168	gezelter	507	delete corrFunc;
169			delete info;
170	tim	321
171	gezelter	507	return 0;
172	tim	321	}
173
174