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"
#include "applications/dynamicProps/SystemDipoleCorrFunc.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.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.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:	1604
Committed:	Mon Aug 8 18:53:40 2011 UTC (13 years, 8 months ago) by jmichalk
File size:	6059 byte(s)
Log Message:	This commit should allow EADM simulations to be run on the cluster. Main additions include EADM_FF.hpp/cpp as well as a system dipole correlation option in DynamicProps.
#	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	jmichalk	1604	#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
63	tim	321
64	tim	876
65	gezelter	1390	using namespace OpenMD;
66	tim	321
67			int main(int argc, char* argv[]){
68
69	gezelter	507	//register force fields
70			registerForceFields();
71	tim	321
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
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	tim	321
86	gezelter	507	if (args_info.sele1_given) {
87			sele1 = args_info.sele1_arg;
88			}else {
89	gezelter	1390	char* sele1Env= getenv("SELECTION1");
90	gezelter	507	if (sele1Env) {
91			sele1 = sele1Env;
92	tim	321	}else {
93	gezelter	507	sprintf( painCave.errMsg,
94	gezelter	1390	"neither --sele1 option nor $SELECTION1 is set");
95			painCave.severity = OPENMD_ERROR;
96	gezelter	507	painCave.isFatal = 1;
97			simError();
98	tim	321	}
99	gezelter	507	}
100	tim	321
101	gezelter	507	if (args_info.sele2_given) {
102			sele2 = args_info.sele2_arg;
103			}else {
104	gezelter	1390	char* sele2Env = getenv("SELECTION2");
105	gezelter	507	if (sele2Env) {
106			sele2 = sele2Env;
107			} else {
108			sele2 = sele1;
109	tim	321	}
110	gezelter	507	}
111	tim	321
112	gezelter	1596	// use the memory string to figure out how much memory we can use:
113			char *end;
114			long long int memSize = memparse(args_info.memory_arg, &end);
115			sprintf( painCave.errMsg,
116			"Amount of memory being used: %llu bytes\n", memSize);
117			painCave.severity = OPENMD_INFO;
118			painCave.isFatal = 0;
119			simError();
120
121	gezelter	507	//parse md file and set up the system
122			SimCreator creator;
123	gezelter	1026	SimInfo* info = creator.createSim(dumpFileName, false);
124	tim	321
125
126	gezelter	507	TimeCorrFunc* corrFunc;
127	jmichalk	1604	if(args_info.sdcorr_given){
128			corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
129			} else if (args_info.dcorr_given){
130	gezelter	1596	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
131	gezelter	507	} else if (args_info.rcorr_given) {
132	gezelter	1596	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133	chuckv	1098	} else if (args_info.r_rcorr_given) {
134	gezelter	1596	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135	chuckv	1112	} else if (args_info.thetacorr_given) {
136	gezelter	1596	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
137	xsun	1183	} else if (args_info.drcorr_given) {
138	gezelter	1596	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
139	chuckv	1245	} else if (args_info.vcorr_given) {
140	gezelter	1596	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
141	chuckv	1245	} else if (args_info.helfandEcorr_given){
142	gezelter	1596	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143	chuckv	1566	} else if (args_info.stresscorr_given){
144	gezelter	1596	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145	tim	876	} else if (args_info.lcorr_given) {
146			int order;
147			if (args_info.order_given)
148			order = args_info.order_arg;
149			else {
150			sprintf( painCave.errMsg,
151			"--order must be set if --lcoor is set\n");
152	gezelter	1390	painCave.severity = OPENMD_ERROR;
153	tim	876	painCave.isFatal = 1;
154			simError();
155			}
156
157	gezelter	1596	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
158	gezelter	507	}
159	tim	321
160	gezelter	507	if (args_info.output_given) {
161			corrFunc->setOutputName(args_info.output_arg);
162			}
163	tim	321
164
165	gezelter	507	corrFunc->doCorrelate();
166	tim	321
167	gezelter	507	delete corrFunc;
168			delete info;
169	tim	321
170	gezelter	507	return 0;
171	tim	321	}
172
173