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root/OpenMD/branches/development/src/applications/dynamicProps/DynamicProps.cpp

Comparing:
trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents), Revision 324 by tim, Sun Feb 13 19:10:25 2005 UTC vs.
branches/development/src/applications/dynamicProps/DynamicProps.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <iostream>
#	Line 46 | Line 47
47		#include "brains/Register.hpp"
48		#include "brains/SimCreator.hpp"
49		#include "brains/SimInfo.hpp"
50	+	#include "utils/StringUtils.hpp"
51		#include "utils/simError.h"
52
53		#include "applications/dynamicProps/DynamicPropsCmd.h"
54		#include "applications/dynamicProps/DipoleCorrFunc.hpp"
55		#include "applications/dynamicProps/RCorrFunc.hpp"
56		#include "applications/dynamicProps/VCorrFunc.hpp"
57	+	#include "applications/dynamicProps/LegendreCorrFunc.hpp"
58	+	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
59	+	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
60	+	#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
61	+	#include "applications/dynamicProps/EnergyCorrFunc.hpp"
62	+	#include "applications/dynamicProps/StressCorrFunc.hpp"
63	+	#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
64	+	#include "applications/dynamicProps/MomentumCorrFunc.hpp"
65
56	–	using namespace oopse;
66
67	+
68	+	using namespace OpenMD;
69	+
70		int main(int argc, char* argv[]){
71
72	<	//register force fields
73	<	registerForceFields();
72	>	//register force fields
73	>	registerForceFields();
74
75	<	gengetopt_args_info args_info;
75	>	gengetopt_args_info args_info;
76
77	<	//parse the command line option
78	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
79	<	exit(1) ;
80	<	}
77	>	//parse the command line option
78	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
79	>	exit(1) ;
80	>	}
81
82
83	<	//get the dumpfile name and meta-data file name
84	<	std::string dumpFileName = args_info.input_arg;
73	<
74	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
75	<
83	>	//get the dumpfile name and meta-data file name
84	>	std::string dumpFileName = args_info.input_arg;
85
86	<	std::string sele1;
87	<	std::string sele2;
86	>	std::string sele1;
87	>	std::string sele2;
88
89	<	if (args_info.sele1_given) {
90	<	sele1 = args_info.sele1_arg;
89	>	if (args_info.sele1_given) {
90	>	sele1 = args_info.sele1_arg;
91	>	}else {
92	>	char*  sele1Env= getenv("SELECTION1");
93	>	if (sele1Env) {
94	>	sele1 = sele1Env;
95		}else {
96	<	char*  sele1Env= getenv("OOPSE_SELE1");
97	<	if (sele1Env) {
98	<	sele1 = sele1Env;
99	<	}else {
100	<	sprintf( painCave.errMsg,
88	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
89	<	painCave.severity = OOPSE_ERROR;
90	<	painCave.isFatal = 1;
91	<	simError();
92	<	}
96	>	sprintf( painCave.errMsg,
97	>	"neither --sele1 option nor $SELECTION1 is set");
98	>	painCave.severity = OPENMD_ERROR;
99	>	painCave.isFatal = 1;
100	>	simError();
101		}
102	+	}
103
104	<	if (args_info.sele2_given) {
105	<	sele2 = args_info.sele2_arg;
106	<	}else {
107	<	char* sele2Env = getenv("OOPSE_SELE2");
108	<	if (sele2Env) {
109	<	sele2 = sele2Env;
110	<	} else {
111	<	sele2 = sele1;
103	<	}
104	>	if (args_info.sele2_given) {
105	>	sele2 = args_info.sele2_arg;
106	>	}else {
107	>	char* sele2Env = getenv("SELECTION2");
108	>	if (sele2Env) {
109	>	sele2 = sele2Env;
110	>	} else {
111	>	sele2 = sele1;
112		}
113	+	}
114
115	<	//parse md file and set up the system
116	<	SimCreator creator;
117	<	SimInfo* info = creator.createSim(mdFileName, false);
115	>	// use the memory string to figure out how much memory we can use:
116	>	char *end;
117	>	long long int memSize = memparse(args_info.memory_arg, &end);
118	>	sprintf( painCave.errMsg,
119	>	"Amount of memory being used: %llu bytes\n", memSize);
120	>	painCave.severity = OPENMD_INFO;
121	>	painCave.isFatal = 0;
122	>	simError();
123
124	+	//parse md file and set up the system
125	+	SimCreator creator;
126	+	SimInfo* info = creator.createSim(dumpFileName, false);
127
111	–	CorrelationFunction* corrFunc;
112	–	if (args_info.dcorr_given){
113	–	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
114	–	} else if (args_info.rcorr_given) {
115	–	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
116	–	}
117	–	else if (args_info.vcorr_given) {
118	–	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
119	–	}
128
129	<	if (args_info.output_given) {
130	<	corrFunc->setOutputName(args_info.output_arg);
129	>	TimeCorrFunc* corrFunc;
130	>	if(args_info.sdcorr_given){
131	>	corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132	>	} else if (args_info.dcorr_given){
133	>	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134	>	} else if (args_info.rcorr_given) {
135	>	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136	>	} else if (args_info.r_rcorr_given) {
137	>	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138	>	} else if (args_info.thetacorr_given) {
139	>	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140	>	} else if (args_info.drcorr_given) {
141	>	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142	>	} else if (args_info.vcorr_given) {
143	>	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
144	>	} else if (args_info.helfandEcorr_given){
145	>	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
146	>	} else if (args_info.stresscorr_given){
147	>	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
148	>	} else if (args_info.momentum_given){
149	>	corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
150	>	} else if (args_info.lcorr_given) {
151	>	int order;
152	>	if (args_info.order_given)
153	>	order = args_info.order_arg;
154	>	else {
155	>	sprintf( painCave.errMsg,
156	>	"--order must be set if --lcoor is set\n");
157	>	painCave.severity = OPENMD_ERROR;
158	>	painCave.isFatal = 1;
159	>	simError();
160		}
161	+
162	+	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
163	+	}
164
165	+	if (args_info.output_given) {
166	+	corrFunc->setOutputName(args_info.output_arg);
167	+	}
168
126	–	corrFunc->doCorrelate();
169
170	<	delete corrFunc;
129	<	delete info;
170	>	corrFunc->doCorrelate();
171
172	<	return 0;
172	>	delete corrFunc;
173	>	delete info;
174	>
175	>	return 0;
176		}
177
178

Comparing:
trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords), Revision 324 by tim, Sun Feb 13 19:10:25 2005 UTC vs.
branches/development/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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