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

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 333 by tim, Mon Feb 14 17:35:25 2005 UTC vs.
Revision 1615 by gezelter, Fri Aug 26 17:55:44 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 46 | Line 46
46		#include "brains/Register.hpp"
47		#include "brains/SimCreator.hpp"
48		#include "brains/SimInfo.hpp"
49	+	#include "utils/StringUtils.hpp"
50		#include "utils/simError.h"
51
52		#include "applications/dynamicProps/DynamicPropsCmd.h"
53		#include "applications/dynamicProps/DipoleCorrFunc.hpp"
54		#include "applications/dynamicProps/RCorrFunc.hpp"
55		#include "applications/dynamicProps/VCorrFunc.hpp"
56	+	#include "applications/dynamicProps/LegendreCorrFunc.hpp"
57	+	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
58	+	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
59	+	#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
60	+	#include "applications/dynamicProps/EnergyCorrFunc.hpp"
61	+	#include "applications/dynamicProps/StressCorrFunc.hpp"
62	+	#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
63	+	#include "applications/dynamicProps/MomentumCorrFunc.hpp"
64
56	–	using namespace oopse;
65
66	+	using namespace OpenMD;
67	+
68		int main(int argc, char* argv[]){
69
70	<	//register force fields
71	<	registerForceFields();
70	>	//register force fields
71	>	registerForceFields();
72
73	<	gengetopt_args_info args_info;
73	>	gengetopt_args_info args_info;
74
75	<	//parse the command line option
76	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
77	<	exit(1) ;
78	<	}
75	>	//parse the command line option
76	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
77	>	exit(1) ;
78	>	}
79
80
81	<	//get the dumpfile name and meta-data file name
82	<	std::string dumpFileName = args_info.input_arg;
73	<
74	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
75	<
81	>	//get the dumpfile name and meta-data file name
82	>	std::string dumpFileName = args_info.input_arg;
83
84	<	std::string sele1;
85	<	std::string sele2;
84	>	std::string sele1;
85	>	std::string sele2;
86
87	<	if (args_info.sele1_given) {
88	<	sele1 = args_info.sele1_arg;
87	>	if (args_info.sele1_given) {
88	>	sele1 = args_info.sele1_arg;
89	>	}else {
90	>	char*  sele1Env= getenv("SELECTION1");
91	>	if (sele1Env) {
92	>	sele1 = sele1Env;
93		}else {
94	<	char*  sele1Env= getenv("OOPSE_SELE1");
95	<	if (sele1Env) {
96	<	sele1 = sele1Env;
97	<	}else {
98	<	sprintf( painCave.errMsg,
88	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
89	<	painCave.severity = OOPSE_ERROR;
90	<	painCave.isFatal = 1;
91	<	simError();
92	<	}
94	>	sprintf( painCave.errMsg,
95	>	"neither --sele1 option nor $SELECTION1 is set");
96	>	painCave.severity = OPENMD_ERROR;
97	>	painCave.isFatal = 1;
98	>	simError();
99		}
100	+	}
101
102	<	if (args_info.sele2_given) {
103	<	sele2 = args_info.sele2_arg;
104	<	}else {
105	<	char* sele2Env = getenv("OOPSE_SELE2");
106	<	if (sele2Env) {
107	<	sele2 = sele2Env;
108	<	} else {
109	<	sele2 = sele1;
103	<	}
102	>	if (args_info.sele2_given) {
103	>	sele2 = args_info.sele2_arg;
104	>	}else {
105	>	char* sele2Env = getenv("SELECTION2");
106	>	if (sele2Env) {
107	>	sele2 = sele2Env;
108	>	} else {
109	>	sele2 = sele1;
110		}
111	+	}
112
113	<	//parse md file and set up the system
114	<	SimCreator creator;
115	<	SimInfo* info = creator.createSim(mdFileName, false);
113	>	// use the memory string to figure out how much memory we can use:
114	>	char *end;
115	>	long long int memSize = memparse(args_info.memory_arg, &end);
116	>	sprintf( painCave.errMsg,
117	>	"Amount of memory being used: %llu bytes\n", memSize);
118	>	painCave.severity = OPENMD_INFO;
119	>	painCave.isFatal = 0;
120	>	simError();
121	>
122	>	//parse md file and set up the system
123	>	SimCreator creator;
124	>	SimInfo* info = creator.createSim(dumpFileName, false);
125
126
127	<	TimeCorrFunc* corrFunc;
128	<	if (args_info.dcorr_given){
129	<	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
130	<	} else if (args_info.rcorr_given) {
131	<	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
127	>	TimeCorrFunc* corrFunc;
128	>	if(args_info.sdcorr_given){
129	>	corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
130	>	} else if (args_info.dcorr_given){
131	>	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132	>	} else if (args_info.rcorr_given) {
133	>	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134	>	} else if (args_info.r_rcorr_given) {
135	>	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136	>	} else if (args_info.thetacorr_given) {
137	>	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138	>	} else if (args_info.drcorr_given) {
139	>	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140	>	} else if (args_info.vcorr_given) {
141	>	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142	>	} else if (args_info.helfandEcorr_given){
143	>	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
144	>	} else if (args_info.stresscorr_given){
145	>	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
146	>	} else if (args_info.momentum_given){
147	>	corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
148	>	} else if (args_info.lcorr_given) {
149	>	int order;
150	>	if (args_info.order_given)
151	>	order = args_info.order_arg;
152	>	else {
153	>	sprintf( painCave.errMsg,
154	>	"--order must be set if --lcoor is set\n");
155	>	painCave.severity = OPENMD_ERROR;
156	>	painCave.isFatal = 1;
157	>	simError();
158		}
159	<	else if (args_info.vcorr_given) {
160	<	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
161	<	}
159	>
160	>	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
161	>	}
162
163	<	if (args_info.output_given) {
164	<	corrFunc->setOutputName(args_info.output_arg);
165	<	}
163	>	if (args_info.output_given) {
164	>	corrFunc->setOutputName(args_info.output_arg);
165	>	}
166
167
168	<	corrFunc->doCorrelate();
168	>	corrFunc->doCorrelate();
169
170	<	delete corrFunc;
171	<	delete info;
170	>	delete corrFunc;
171	>	delete info;
172
173	<	return 0;
173	>	return 0;
174		}
175
176

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 333 by tim, Mon Feb 14 17:35:25 2005 UTC vs.
Revision 1615 by gezelter, Fri Aug 26 17:55:44 2011 UTC

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