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, 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/dynamicProps/DynamicPropsCmd.h"
#include "applications/dynamicProps/SelectionCorrFunc.hpp"
#include "applications/dynamicProps/DipoleCorrFunc.hpp"
#include "applications/dynamicProps/RCorrFunc.hpp"
#include "applications/dynamicProps/VCorrFunc.hpp"
#include "applications/dynamicProps/LegendreCorrFunc.hpp"
#include "applications/dynamicProps/LegendreCorrFuncZ.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"
#include "applications/dynamicProps/cOHz.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;
    }
  }

  // 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.selecorr_given){
    corrFunc = new SelectionCorrFunc(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 --lcorr is set\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
        
    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); 
  } else if (args_info.lcorrZ_given) {
    int order;
    if (args_info.order_given)
        order = args_info.order_arg;
    else {
      sprintf( painCave.errMsg,
               "--order must be set if --lcorrZ is set\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
        
    corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); 

  } else if (args_info.cohZ_given) {
    int order;
    if (args_info.order_given)
        order = args_info.order_arg;
    else {
      sprintf( painCave.errMsg,
               "--order must be set if --cohZ is set\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
        
    corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); 

  }


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


  corrFunc->doCorrelate();

  delete corrFunc;    
  delete info;

  return 0;   
}


Revision:	1937
Committed:	Tue Oct 29 16:02:58 2013 UTC (11 years, 6 months ago) by gezelter
File size:	7590 byte(s)
Log Message:	Fixed a few bugs and added some sanity checks in the analysis codes.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	1596	#include "utils/StringUtils.hpp"
50	tim	321	#include "utils/simError.h"
51
52			#include "applications/dynamicProps/DynamicPropsCmd.h"
53	gezelter	1811	#include "applications/dynamicProps/SelectionCorrFunc.hpp"
54	tim	324	#include "applications/dynamicProps/DipoleCorrFunc.hpp"
55	tim	321	#include "applications/dynamicProps/RCorrFunc.hpp"
56			#include "applications/dynamicProps/VCorrFunc.hpp"
57	tim	876	#include "applications/dynamicProps/LegendreCorrFunc.hpp"
58	gezelter	1915	#include "applications/dynamicProps/LegendreCorrFuncZ.hpp"
59	chuckv	1098	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
60	chuckv	1112	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
61	xsun	1183	#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
62	chuckv	1245	#include "applications/dynamicProps/EnergyCorrFunc.hpp"
63	chuckv	1565	#include "applications/dynamicProps/StressCorrFunc.hpp"
64	jmichalk	1604	#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
65	gezelter	1615	#include "applications/dynamicProps/MomentumCorrFunc.hpp"
66	gezelter	1934	#include "applications/dynamicProps/cOHz.hpp"
67	tim	321
68	gezelter	1390	using namespace OpenMD;
69	tim	321
70			int main(int argc, char* argv[]){
71
72	gezelter	507	gengetopt_args_info args_info;
73	tim	321
74	gezelter	507	//parse the command line option
75			if (cmdline_parser (argc, argv, &args_info) != 0) {
76			exit(1) ;
77			}
78	tim	321
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	gezelter	1937
85			// check the first selection argument, or set it to the environment
86			// variable, or failing that, set it to "select all"
87
88	gezelter	507	if (args_info.sele1_given) {
89			sele1 = args_info.sele1_arg;
90	gezelter	1937	} else {
91	gezelter	1390	char* sele1Env= getenv("SELECTION1");
92	gezelter	507	if (sele1Env) {
93			sele1 = sele1Env;
94	gezelter	1937	} else {
95			sele1 = "select all";
96	tim	321	}
97	gezelter	507	}
98	gezelter	1937
99			// check the second selection argument, or set it to the environment
100			// variable, or failing that, set it to the first selection
101
102	gezelter	507	if (args_info.sele2_given) {
103			sele2 = args_info.sele2_arg;
104	gezelter	1811	} else {
105	gezelter	1390	char* sele2Env = getenv("SELECTION2");
106	gezelter	507	if (sele2Env) {
107			sele2 = sele2Env;
108	gezelter	1937	} else {
109			//If sele2 is not specified, then the default behavior
110			//should be what is already intended for sele1
111	gezelter	507	sele2 = sele1;
112	tim	321	}
113	gezelter	507	}
114	tim	321
115	gezelter	1596	// use the memory string to figure out how much memory we can use:
116			char *end;
117			long long int memSize = memparse(args_info.memory_arg, &end);
118			sprintf( painCave.errMsg,
119			"Amount of memory being used: %llu bytes\n", memSize);
120			painCave.severity = OPENMD_INFO;
121			painCave.isFatal = 0;
122	gezelter	1782	simError();
123
124	gezelter	507	//parse md file and set up the system
125			SimCreator creator;
126	gezelter	1026	SimInfo* info = creator.createSim(dumpFileName, false);
127	tim	321
128	gezelter	507	TimeCorrFunc* corrFunc;
129	jmichalk	1604	if(args_info.sdcorr_given){
130			corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
131	gezelter	1811	} else if (args_info.selecorr_given){
132			corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133	jmichalk	1604	} else if (args_info.dcorr_given){
134	gezelter	1596	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135	gezelter	507	} else if (args_info.rcorr_given) {
136	gezelter	1596	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
137	chuckv	1098	} else if (args_info.r_rcorr_given) {
138	gezelter	1596	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
139	chuckv	1112	} else if (args_info.thetacorr_given) {
140	gezelter	1596	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
141	xsun	1183	} else if (args_info.drcorr_given) {
142	gezelter	1596	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143	chuckv	1245	} else if (args_info.vcorr_given) {
144	gezelter	1596	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145	chuckv	1245	} else if (args_info.helfandEcorr_given){
146	gezelter	1596	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
147	chuckv	1566	} else if (args_info.stresscorr_given){
148	gezelter	1596	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
149	gezelter	1615	} else if (args_info.momentum_given){
150			corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
151	tim	876	} else if (args_info.lcorr_given) {
152			int order;
153			if (args_info.order_given)
154			order = args_info.order_arg;
155			else {
156			sprintf( painCave.errMsg,
157	gezelter	1915	"--order must be set if --lcorr is set\n");
158	gezelter	1390	painCave.severity = OPENMD_ERROR;
159	tim	876	painCave.isFatal = 1;
160			simError();
161			}
162
163	gezelter	1596	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
164	gezelter	1915	} else if (args_info.lcorrZ_given) {
165			int order;
166			if (args_info.order_given)
167			order = args_info.order_arg;
168			else {
169			sprintf( painCave.errMsg,
170			"--order must be set if --lcorrZ is set\n");
171			painCave.severity = OPENMD_ERROR;
172			painCave.isFatal = 1;
173			simError();
174			}
175
176			corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
177
178	gezelter	1934	} else if (args_info.cohZ_given) {
179			int order;
180			if (args_info.order_given)
181			order = args_info.order_arg;
182			else {
183			sprintf( painCave.errMsg,
184			"--order must be set if --cohZ is set\n");
185			painCave.severity = OPENMD_ERROR;
186			painCave.isFatal = 1;
187			simError();
188			}
189
190			corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
191
192	gezelter	507	}
193	tim	321
194	gezelter	1934
195	gezelter	507	if (args_info.output_given) {
196			corrFunc->setOutputName(args_info.output_arg);
197			}
198	tim	321
199
200	gezelter	507	corrFunc->doCorrelate();
201	tim	321
202	gezelter	507	delete corrFunc;
203			delete info;
204	tim	321
205	gezelter	507	return 0;
206	tim	321	}
207
208