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root/OpenMD/trunk/src/applications/dynamicProps/DynamicProps.cpp

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 321 by tim, Sun Feb 13 07:25:22 2005 UTC vs.
Revision 1566 by chuckv, Thu May 19 18:12:09 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
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	+	*
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		*/
41
42		#include <iostream>
#	Line 49 | Line 49
49		#include "utils/simError.h"
50
51		#include "applications/dynamicProps/DynamicPropsCmd.h"
52	<	#include "applications/dynamicProps/DCorrFunc.hpp"
52	>	#include "applications/dynamicProps/DipoleCorrFunc.hpp"
53		#include "applications/dynamicProps/RCorrFunc.hpp"
54		#include "applications/dynamicProps/VCorrFunc.hpp"
55	+	#include "applications/dynamicProps/LegendreCorrFunc.hpp"
56	+	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
57	+	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
58	+	#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
59	+	#include "applications/dynamicProps/EnergyCorrFunc.hpp"
60	+	#include "applications/dynamicProps/StressCorrFunc.hpp"
61
56	–	using namespace oopse;
62
63	+	using namespace OpenMD;
64	+
65		int main(int argc, char* argv[]){
66
67	<	//register force fields
68	<	registerForceFields();
67	>	//register force fields
68	>	registerForceFields();
69
70	<	gengetopt_args_info args_info;
70	>	gengetopt_args_info args_info;
71
72	<	//parse the command line option
73	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
74	<	exit(1) ;
75	<	}
72	>	//parse the command line option
73	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
74	>	exit(1) ;
75	>	}
76
77
78	<	//get the dumpfile name and meta-data file name
79	<	std::string dumpFileName = args_info.input_arg;
73	<
74	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
75	<
78	>	//get the dumpfile name and meta-data file name
79	>	std::string dumpFileName = args_info.input_arg;
80
81	<	std::string sele1;
82	<	std::string sele2;
81	>	std::string sele1;
82	>	std::string sele2;
83
84	<	if (args_info.sele1_given) {
85	<	sele1 = args_info.sele1_arg;
84	>	if (args_info.sele1_given) {
85	>	sele1 = args_info.sele1_arg;
86	>	}else {
87	>	char*  sele1Env= getenv("SELECTION1");
88	>	if (sele1Env) {
89	>	sele1 = sele1Env;
90		}else {
91	<	char*  sele1Env= getenv("OOPSE_SELE1");
92	<	if (sele1Env) {
93	<	sele1 = sele1Env;
94	<	}else {
95	<	sprintf( painCave.errMsg,
88	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
89	<	painCave.severity = OOPSE_ERROR;
90	<	painCave.isFatal = 1;
91	<	simError();
92	<	}
91	>	sprintf( painCave.errMsg,
92	>	"neither --sele1 option nor $SELECTION1 is set");
93	>	painCave.severity = OPENMD_ERROR;
94	>	painCave.isFatal = 1;
95	>	simError();
96		}
97	+	}
98
99	<	if (args_info.sele2_given) {
100	<	sele2 = args_info.sele2_arg;
101	<	}else {
102	<	char* sele2Env = getenv("OOPSE_SELE2");
103	<	if (sele2Env) {
104	<	sele2 = sele2Env;
105	<	} else {
106	<	sele2 = sele1;
103	<	}
99	>	if (args_info.sele2_given) {
100	>	sele2 = args_info.sele2_arg;
101	>	}else {
102	>	char* sele2Env = getenv("SELECTION2");
103	>	if (sele2Env) {
104	>	sele2 = sele2Env;
105	>	} else {
106	>	sele2 = sele1;
107		}
108	+	}
109
110	<	//parse md file and set up the system
111	<	SimCreator creator;
112	<	SimInfo* info = creator.createSim(mdFileName, false);
110	>	//parse md file and set up the system
111	>	SimCreator creator;
112	>	SimInfo* info = creator.createSim(dumpFileName, false);
113
114
115	<	CorrelationFunction* corrFunc;
116	<	if (args_info.dcorr_given){
117	<	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
118	<	} else if (args_info.rcorr_given) {
119	<	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
115	>	TimeCorrFunc* corrFunc;
116	>	if (args_info.dcorr_given){
117	>	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
118	>	} else if (args_info.rcorr_given) {
119	>	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
120	>	} else if (args_info.r_rcorr_given) {
121	>	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
122	>	} else if (args_info.thetacorr_given) {
123	>	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
124	>	} else if (args_info.drcorr_given) {
125	>	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
126	>	} else if (args_info.vcorr_given) {
127	>	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
128	>	} else if (args_info.helfandEcorr_given){
129	>	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2);
130	>	} else if (args_info.stresscorr_given){
131	>	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2);
132	>	} else if (args_info.lcorr_given) {
133	>	int order;
134	>	if (args_info.order_given)
135	>	order = args_info.order_arg;
136	>	else {
137	>	sprintf( painCave.errMsg,
138	>	"--order must be set if --lcoor is set\n");
139	>	painCave.severity = OPENMD_ERROR;
140	>	painCave.isFatal = 1;
141	>	simError();
142		}
143	<	else if (args_info.vcorr_given) {
144	<	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
145	<	}
143	>
144	>	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
145	>	}
146
147	<	if (args_info.output_given) {
148	<	corrFunc->setOutputName(args_info.output_arg);
149	<	}
147	>	if (args_info.output_given) {
148	>	corrFunc->setOutputName(args_info.output_arg);
149	>	}
150
151
152	<	corrFunc->doCorrelate();
152	>	corrFunc->doCorrelate();
153
154	<	delete corrFunc;
155	<	delete info;
154	>	delete corrFunc;
155	>	delete info;
156
157	<	return 0;
157	>	return 0;
158		}
159
160

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 321 by tim, Sun Feb 13 07:25:22 2005 UTC vs.
Revision 1566 by chuckv, Thu May 19 18:12:09 2011 UTC

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