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root/OpenMD/trunk/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.
Revision 1915 by gezelter, Mon Jul 29 17:55:17 2013 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, 234107 (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>
44		#include <fstream>
45		#include <string>
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/SelectionCorrFunc.hpp"
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/LegendreCorrFuncZ.hpp"
59	+	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
60	+	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
61	+	#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
62	+	#include "applications/dynamicProps/EnergyCorrFunc.hpp"
63	+	#include "applications/dynamicProps/StressCorrFunc.hpp"
64	+	#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
65	+	#include "applications/dynamicProps/MomentumCorrFunc.hpp"
66
67	<	using namespace oopse;
67	>	using namespace OpenMD;
68
69		int main(int argc, char* argv[]){
70
71	<	//register force fields
61	<	registerForceFields();
71	>	gengetopt_args_info args_info;
72
73	<	gengetopt_args_info args_info;
73	>	//parse the command line option
74	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
75	>	exit(1) ;
76	>	}
77
65	–	//parse the command line option
66	–	if (cmdline_parser (argc, argv, &args_info) != 0) {
67	–	exit(1) ;
68	–	}
78
79	<
80	<	//get the dumpfile name and meta-data file name
72	<	std::string dumpFileName = args_info.input_arg;
73	<
74	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
75	<
79	>	//get the dumpfile name and meta-data file name
80	>	std::string dumpFileName = args_info.input_arg;
81
82	<	std::string sele1;
83	<	std::string sele2;
82	>	std::string sele1;
83	>	std::string sele2;
84
85	<	if (args_info.sele1_given) {
86	<	sele1 = args_info.sele1_arg;
85	>	if (args_info.sele1_given) {
86	>	sele1 = args_info.sele1_arg;
87	>	}else {
88	>	char*  sele1Env= getenv("SELECTION1");
89	>	if (sele1Env) {
90	>	sele1 = sele1Env;
91		}else {
92	<	char*  sele1Env= getenv("OOPSE_SELE1");
93	<	if (sele1Env) {
94	<	sele1 = sele1Env;
95	<	}else {
96	<	sprintf( painCave.errMsg,
88	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
89	<	painCave.severity = OOPSE_ERROR;
90	<	painCave.isFatal = 1;
91	<	simError();
92	<	}
92	>	sprintf( painCave.errMsg,
93	>	"neither --sele1 option nor $SELECTION1 is set");
94	>	painCave.severity = OPENMD_ERROR;
95	>	painCave.isFatal = 1;
96	>	simError();
97		}
98	+	}
99
100	<	if (args_info.sele2_given) {
101	<	sele2 = args_info.sele2_arg;
102	<	}else {
103	<	char* sele2Env = getenv("OOPSE_SELE2");
104	<	if (sele2Env) {
105	<	sele2 = sele2Env;
106	<	} else {
107	<	sele2 = sele1;
103	<	}
100	>	if (args_info.sele2_given) {
101	>	sele2 = args_info.sele2_arg;
102	>	} else {
103	>	char* sele2Env = getenv("SELECTION2");
104	>	if (sele2Env) {
105	>	sele2 = sele2Env;
106	>	} else {
107	>	sele2 = sele1;
108		}
109	+	}
110
111	<	//parse md file and set up the system
112	<	SimCreator creator;
113	<	SimInfo* info = creator.createSim(mdFileName, false);
111	>	// 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	+	//parse md file and set up the system
121	+	SimCreator creator;
122	+	SimInfo* info = creator.createSim(dumpFileName, false);
123
124	<	CorrelationFunction* corrFunc;
125	<	if (args_info.dcorr_given){
126	<	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
127	<	} else if (args_info.rcorr_given) {
128	<	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
124	>	TimeCorrFunc* corrFunc;
125	>	if(args_info.sdcorr_given){
126	>	corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
127	>	} else if (args_info.selecorr_given){
128	>	corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
129	>	} else if (args_info.dcorr_given){
130	>	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
131	>	} else if (args_info.rcorr_given) {
132	>	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133	>	} else if (args_info.r_rcorr_given) {
134	>	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135	>	} else if (args_info.thetacorr_given) {
136	>	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
137	>	} else if (args_info.drcorr_given) {
138	>	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
139	>	} else if (args_info.vcorr_given) {
140	>	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
141	>	} else if (args_info.helfandEcorr_given){
142	>	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143	>	} else if (args_info.stresscorr_given){
144	>	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145	>	} else if (args_info.momentum_given){
146	>	corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
147	>	} else if (args_info.lcorr_given) {
148	>	int order;
149	>	if (args_info.order_given)
150	>	order = args_info.order_arg;
151	>	else {
152	>	sprintf( painCave.errMsg,
153	>	"--order must be set if --lcorr is set\n");
154	>	painCave.severity = OPENMD_ERROR;
155	>	painCave.isFatal = 1;
156	>	simError();
157		}
158	<	else if (args_info.vcorr_given) {
159	<	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
158	>
159	>	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
160	>	} else if (args_info.lcorrZ_given) {
161	>	int order;
162	>	if (args_info.order_given)
163	>	order = args_info.order_arg;
164	>	else {
165	>	sprintf( painCave.errMsg,
166	>	"--order must be set if --lcorrZ is set\n");
167	>	painCave.severity = OPENMD_ERROR;
168	>	painCave.isFatal = 1;
169	>	simError();
170		}
171	+
172	+	corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
173
174	<	if (args_info.output_given) {
122	<	corrFunc->setOutputName(args_info.output_arg);
123	<	}
174	>	}
175
176	+	if (args_info.output_given) {
177	+	corrFunc->setOutputName(args_info.output_arg);
178	+	}
179
126	–	corrFunc->doCorrelate();
180
181	<	delete corrFunc;
129	<	delete info;
181	>	corrFunc->doCorrelate();
182
183	<	return 0;
183	>	delete corrFunc;
184	>	delete info;
185	>
186	>	return 0;
187		}
188
189

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 324 by tim, Sun Feb 13 19:10:25 2005 UTC vs.
Revision 1915 by gezelter, Mon Jul 29 17:55:17 2013 UTC

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