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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "brains/Register.hpp"
#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"


using namespace OpenMD;

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("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.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.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:	1596
Committed:	Mon Jul 25 17:30:53 2011 UTC (13 years, 9 months ago) by gezelter
File size:	5876 byte(s)
Log Message:	Updated the BlockSnapshotManager to use a specified memory footprint in constructor and not to rely on physmem and residentMem to figure out free memory. DynamicProps is the only program that uses the BlockSnapshotManager, so substantial changes were needed there as well.
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	321	*/
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	gezelter	1596	#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	chuckv	1565	#include "applications/dynamicProps/StressCorrFunc.hpp"
62	tim	321
63	tim	876
64	gezelter	1390	using namespace OpenMD;
65	tim	321
66			int main(int argc, char* argv[]){
67
68	gezelter	507	//register force fields
69			registerForceFields();
70	tim	321
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	1596	// 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	tim	917	if (args_info.dcorr_given){
127	gezelter	1596	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
128	gezelter	507	} else if (args_info.rcorr_given) {
129	gezelter	1596	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
130	chuckv	1098	} else if (args_info.r_rcorr_given) {
131	gezelter	1596	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132	chuckv	1112	} else if (args_info.thetacorr_given) {
133	gezelter	1596	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134	xsun	1183	} else if (args_info.drcorr_given) {
135	gezelter	1596	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136	chuckv	1245	} else if (args_info.vcorr_given) {
137	gezelter	1596	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138	chuckv	1245	} else if (args_info.helfandEcorr_given){
139	gezelter	1596	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140	chuckv	1566	} else if (args_info.stresscorr_given){
141	gezelter	1596	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142	tim	876	} else if (args_info.lcorr_given) {
143			int order;
144			if (args_info.order_given)
145			order = args_info.order_arg;
146			else {
147			sprintf( painCave.errMsg,
148			"--order must be set if --lcoor is set\n");
149	gezelter	1390	painCave.severity = OPENMD_ERROR;
150	tim	876	painCave.isFatal = 1;
151			simError();
152			}
153
154	gezelter	1596	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
155	gezelter	507	}
156	tim	321
157	gezelter	507	if (args_info.output_given) {
158			corrFunc->setOutputName(args_info.output_arg);
159			}
160	tim	321
161
162	gezelter	507	corrFunc->doCorrelate();
163	tim	321
164	gezelter	507	delete corrFunc;
165			delete info;
166	tim	321
167	gezelter	507	return 0;
168	tim	321	}
169
170