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"
#include "applications/dynamicProps/BondCorrFunc.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.bondcorr_given) {
    corrFunc = new BondCorrFunc(info, dumpFileName, sele1, 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:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 4 months ago) by gezelter
File size:	7755 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	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	gezelter	1953	#include "applications/dynamicProps/BondCorrFunc.hpp"
68	tim	321
69	gezelter	1390	using namespace OpenMD;
70	tim	321
71			int main(int argc, char* argv[]){
72
73	gezelter	507	gengetopt_args_info args_info;
74	tim	321
75	gezelter	507	//parse the command line option
76			if (cmdline_parser (argc, argv, &args_info) != 0) {
77			exit(1) ;
78			}
79	tim	321
80	gezelter	507	//get the dumpfile name and meta-data file name
81			std::string dumpFileName = args_info.input_arg;
82	tim	321
83	gezelter	507	std::string sele1;
84			std::string sele2;
85	gezelter	1937
86			// check the first selection argument, or set it to the environment
87			// variable, or failing that, set it to "select all"
88
89	gezelter	507	if (args_info.sele1_given) {
90			sele1 = args_info.sele1_arg;
91	gezelter	1937	} else {
92	gezelter	1390	char* sele1Env= getenv("SELECTION1");
93	gezelter	507	if (sele1Env) {
94			sele1 = sele1Env;
95	gezelter	1937	} else {
96			sele1 = "select all";
97	tim	321	}
98	gezelter	507	}
99	gezelter	1937
100			// check the second selection argument, or set it to the environment
101			// variable, or failing that, set it to the first selection
102
103	gezelter	507	if (args_info.sele2_given) {
104			sele2 = args_info.sele2_arg;
105	gezelter	1811	} else {
106	gezelter	1390	char* sele2Env = getenv("SELECTION2");
107	gezelter	507	if (sele2Env) {
108			sele2 = sele2Env;
109	gezelter	1937	} else {
110			//If sele2 is not specified, then the default behavior
111			//should be what is already intended for sele1
112	gezelter	507	sele2 = sele1;
113	tim	321	}
114	gezelter	507	}
115	tim	321
116	gezelter	1596	// use the memory string to figure out how much memory we can use:
117			char *end;
118			long long int memSize = memparse(args_info.memory_arg, &end);
119			sprintf( painCave.errMsg,
120			"Amount of memory being used: %llu bytes\n", memSize);
121			painCave.severity = OPENMD_INFO;
122			painCave.isFatal = 0;
123	gezelter	1782	simError();
124
125	gezelter	507	//parse md file and set up the system
126			SimCreator creator;
127	gezelter	1026	SimInfo* info = creator.createSim(dumpFileName, false);
128	tim	321
129	gezelter	507	TimeCorrFunc* corrFunc;
130	jmichalk	1604	if(args_info.sdcorr_given){
131			corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132	gezelter	1811	} else if (args_info.selecorr_given){
133			corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134	jmichalk	1604	} else if (args_info.dcorr_given){
135	gezelter	1596	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136	gezelter	507	} else if (args_info.rcorr_given) {
137	gezelter	1596	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138	chuckv	1098	} else if (args_info.r_rcorr_given) {
139	gezelter	1596	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140	chuckv	1112	} else if (args_info.thetacorr_given) {
141	gezelter	1596	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142	xsun	1183	} else if (args_info.drcorr_given) {
143	gezelter	1596	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
144	chuckv	1245	} else if (args_info.vcorr_given) {
145	gezelter	1596	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
146	gezelter	1953	} else if (args_info.bondcorr_given) {
147			corrFunc = new BondCorrFunc(info, dumpFileName, sele1, memSize);
148	chuckv	1245	} else if (args_info.helfandEcorr_given){
149	gezelter	1596	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
150	chuckv	1566	} else if (args_info.stresscorr_given){
151	gezelter	1596	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
152	gezelter	1615	} else if (args_info.momentum_given){
153			corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
154	tim	876	} else if (args_info.lcorr_given) {
155			int order;
156			if (args_info.order_given)
157			order = args_info.order_arg;
158			else {
159			sprintf( painCave.errMsg,
160	gezelter	1915	"--order must be set if --lcorr is set\n");
161	gezelter	1390	painCave.severity = OPENMD_ERROR;
162	tim	876	painCave.isFatal = 1;
163			simError();
164			}
165
166	gezelter	1596	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
167	gezelter	1915	} else if (args_info.lcorrZ_given) {
168			int order;
169			if (args_info.order_given)
170			order = args_info.order_arg;
171			else {
172			sprintf( painCave.errMsg,
173			"--order must be set if --lcorrZ is set\n");
174			painCave.severity = OPENMD_ERROR;
175			painCave.isFatal = 1;
176			simError();
177			}
178
179			corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
180
181	gezelter	1934	} else if (args_info.cohZ_given) {
182			int order;
183			if (args_info.order_given)
184			order = args_info.order_arg;
185			else {
186			sprintf( painCave.errMsg,
187			"--order must be set if --cohZ is set\n");
188			painCave.severity = OPENMD_ERROR;
189			painCave.isFatal = 1;
190			simError();
191			}
192
193			corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
194
195	gezelter	507	}
196	tim	321
197	gezelter	1934
198	gezelter	507	if (args_info.output_given) {
199			corrFunc->setOutputName(args_info.output_arg);
200			}
201	tim	321
202
203	gezelter	507	corrFunc->doCorrelate();
204	tim	321
205	gezelter	507	delete corrFunc;
206			delete info;
207	tim	321
208	gezelter	507	return 0;
209	tim	321	}
210
211