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

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2024 by gezelter, Thu Oct 16 19:13:51 2014 UTC

#	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	+	#include "applications/dynamicProps/cOHz.hpp"
67	+	#include "applications/dynamicProps/BondCorrFunc.hpp"
68	+	#include "applications/dynamicProps/FreqFlucCorrFunc.hpp"
69
70	<	using namespace oopse;
70	>	using namespace OpenMD;
71
72		int main(int argc, char* argv[]){
73
60	–	//register force fields
61	–	registerForceFields();
62	–
74		gengetopt_args_info args_info;
75
76		//parse the command line option
#	Line 67 | Line 78 | int main(int argc, char* argv[]){
78		exit(1) ;
79		}
80
70	–
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	–
83
84		std::string sele1;
85		std::string sele2;
86	<
86	>
87	>	// check the first selection argument, or set it to the environment
88	>	// variable, or failing that, set it to "select all"
89	>
90		if (args_info.sele1_given) {
91		sele1 = args_info.sele1_arg;
92	<	}else {
93	<	char*  sele1Env= getenv("OOPSE_SELE1");
92	>	} else {
93	>	char*  sele1Env= getenv("SELECTION1");
94		if (sele1Env) {
95		sele1 = sele1Env;
96	<	}else {
97	<	sprintf( painCave.errMsg,
88	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
89	<	painCave.severity = OOPSE_ERROR;
90	<	painCave.isFatal = 1;
91	<	simError();
96	>	} else {
97	>	sele1 = "select all";
98		}
99		}
100	<
100	>
101	>	// check the second selection argument, or set it to the environment
102	>	// variable, or failing that, set it to the first selection
103	>
104		if (args_info.sele2_given) {
105		sele2 = args_info.sele2_arg;
106	<	}else {
107	<	char* sele2Env = getenv("OOPSE_SELE2");
106	>	} else {
107	>	char* sele2Env = getenv("SELECTION2");
108		if (sele2Env) {
109		sele2 = sele2Env;
110	<	} else {
110	>	} else {
111	>	//If sele2 is not specified, then the default behavior
112	>	//should be what is already intended for sele1
113		sele2 = sele1;
114		}
115		}
116
117	+	// use the memory string to figure out how much memory we can use:
118	+	char *end;
119	+	long long int memSize = memparse(args_info.memory_arg, &end);
120	+	sprintf( painCave.errMsg,
121	+	"Amount of memory being used: %llu bytes\n", memSize);
122	+	painCave.severity = OPENMD_INFO;
123	+	painCave.isFatal = 0;
124	+	simError();
125	+
126		//parse md file and set up the system
127		SimCreator creator;
128	<	SimInfo* info = creator.createSim(mdFileName, false);
128	>	SimInfo* info = creator.createSim(dumpFileName, false);
129
110	–
130		TimeCorrFunc* corrFunc;
131	<	if (args_info.dcorr_given){
132	<	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
131	>	if(args_info.sdcorr_given){
132	>	corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133	>	} else if (args_info.selecorr_given){
134	>	corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135	>	} else if (args_info.dcorr_given){
136	>	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
137		} else if (args_info.rcorr_given) {
138	<	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
138	>	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
139	>	} else if (args_info.r_rcorr_given) {
140	>	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
141	>	} else if (args_info.thetacorr_given) {
142	>	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143	>	} else if (args_info.drcorr_given) {
144	>	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145	>	} else if (args_info.vcorr_given) {
146	>	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
147	>	} else if (args_info.vcorrZ_given) {
148	>	corrFunc = new VCorrFuncZ(info, dumpFileName, sele1, sele2, memSize);
149	>	} else if (args_info.vcorrR_given) {
150	>	corrFunc = new VCorrFuncR(info, dumpFileName, sele1, sele2, memSize);
151	>	} else if (args_info.bondcorr_given) {
152	>	corrFunc = new BondCorrFunc(info, dumpFileName, sele1, memSize);
153	>	} else if (args_info.helfandEcorr_given){
154	>	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
155	>	} else if (args_info.stresscorr_given){
156	>	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
157	>	} else if (args_info.momentum_given){
158	>	corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
159	>	} else if (args_info.freqfluccorr_given){
160	>	corrFunc = new FreqFlucCorrFunc(info, dumpFileName, sele1, sele2, memSize);
161	>	} else if (args_info.lcorr_given) {
162	>	int order;
163	>	if (args_info.order_given)
164	>	order = args_info.order_arg;
165	>	else {
166	>	sprintf( painCave.errMsg,
167	>	"--order must be set if --lcorr is set\n");
168	>	painCave.severity = OPENMD_ERROR;
169	>	painCave.isFatal = 1;
170	>	simError();
171	>	}
172	>
173	>	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
174	>	} else if (args_info.lcorrZ_given) {
175	>	int order;
176	>	if (args_info.order_given)
177	>	order = args_info.order_arg;
178	>	else {
179	>	sprintf( painCave.errMsg,
180	>	"--order must be set if --lcorrZ is set\n");
181	>	painCave.severity = OPENMD_ERROR;
182	>	painCave.isFatal = 1;
183	>	simError();
184	>	}
185	>
186	>	corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
187	>
188	>	} else if (args_info.cohZ_given) {
189	>	int order;
190	>	if (args_info.order_given)
191	>	order = args_info.order_arg;
192	>	else {
193	>	sprintf( painCave.errMsg,
194	>	"--order must be set if --cohZ is set\n");
195	>	painCave.severity = OPENMD_ERROR;
196	>	painCave.isFatal = 1;
197	>	simError();
198	>	}
199	>
200	>	corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
201	>
202		}
117	–	else if (args_info.vcorr_given) {
118	–	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
119	–	}
203
204	+
205		if (args_info.output_given) {
206		corrFunc->setOutputName(args_info.output_arg);
207		}

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2024 by gezelter, Thu Oct 16 19:13:51 2014 UTC

#	Line 0 | Line 1
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