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

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 916 by tim, Fri Mar 24 16:49:09 2006 UTC vs.
Revision 1934 by gezelter, Mon Aug 26 14:15:09 2013 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"
53	–	#include "applications/dynamicProps/RMSD.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
68	+	using namespace OpenMD;
69
59	–	using namespace oopse;
60	–
70		int main(int argc, char* argv[]){
71
63	–	//register force fields
64	–	registerForceFields();
65	–
72		gengetopt_args_info args_info;
73
74		//parse the command line option
#	Line 73 | Line 79 | int main(int argc, char* argv[]){
79
80		//get the dumpfile name and meta-data file name
81		std::string dumpFileName = args_info.input_arg;
76	–
77	–	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
78	–
82
83		std::string sele1;
84		std::string sele2;
#	Line 83 | Line 86 | int main(int argc, char* argv[]){
86		if (args_info.sele1_given) {
87		sele1 = args_info.sele1_arg;
88		}else {
89	<	char*  sele1Env= getenv("OOPSE_SELE1");
89	>	char*  sele1Env= getenv("SELECTION1");
90		if (sele1Env) {
91		sele1 = sele1Env;
92		}else {
93		sprintf( painCave.errMsg,
94	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
95	<	painCave.severity = OOPSE_ERROR;
94	>	"neither --sele1 option nor $SELECTION1 is set");
95	>	painCave.severity = OPENMD_ERROR;
96		painCave.isFatal = 1;
97		simError();
98		}
#	Line 97 | Line 100 | int main(int argc, char* argv[]){
100
101		if (args_info.sele2_given) {
102		sele2 = args_info.sele2_arg;
103	<	}else {
104	<	char* sele2Env = getenv("OOPSE_SELE2");
103	>	} else {
104	>	char* sele2Env = getenv("SELECTION2");
105		if (sele2Env) {
106		sele2 = sele2Env;
107		} else {
#	Line 106 | Line 109 | int main(int argc, char* argv[]){
109		}
110		}
111
112	+	// use the memory string to figure out how much memory we can use:
113	+	char *end;
114	+	long long int memSize = memparse(args_info.memory_arg, &end);
115	+	sprintf( painCave.errMsg,
116	+	"Amount of memory being used: %llu bytes\n", memSize);
117	+	painCave.severity = OPENMD_INFO;
118	+	painCave.isFatal = 0;
119	+	simError();
120	+
121		//parse md file and set up the system
122		SimCreator creator;
123	<	SimInfo* info = creator.createSim(mdFileName, false);
123	>	SimInfo* info = creator.createSim(dumpFileName, false);
124
113	–
125		TimeCorrFunc* corrFunc;
126	<	if (args_info.rmsd_given) {
127	<	corrFunc = new RMSD(info, dumpFileName, sele1, sele2);
126	>	if(args_info.sdcorr_given){
127	>	corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
128	>	} else if (args_info.selecorr_given){
129	>	corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
130		} else if (args_info.dcorr_given){
131	<	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
131	>	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132		} else if (args_info.rcorr_given) {
133	<	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
134	<	}
135	<	else if (args_info.vcorr_given) {
136	<	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
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 = OOPSE_ERROR;
154	>	"--order must be set if --lcorr is set\n");
155	>	painCave.severity = OPENMD_ERROR;
156		painCave.isFatal = 1;
157		simError();
158		}
159
160	<	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
160	>	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
161	>	} else if (args_info.lcorrZ_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 --lcorrZ is set\n");
168	>	painCave.severity = OPENMD_ERROR;
169	>	painCave.isFatal = 1;
170	>	simError();
171	>	}
172	>
173	>	corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
174	>
175	>	} else if (args_info.cohZ_given) {
176	>	int order;
177	>	if (args_info.order_given)
178	>	order = args_info.order_arg;
179	>	else {
180	>	sprintf( painCave.errMsg,
181	>	"--order must be set if --cohZ is set\n");
182	>	painCave.severity = OPENMD_ERROR;
183	>	painCave.isFatal = 1;
184	>	simError();
185	>	}
186	>
187	>	corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
188	>
189		}
190
191	+
192	+
193		if (args_info.output_given) {
194		corrFunc->setOutputName(args_info.output_arg);
195		}

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 916 by tim, Fri Mar 24 16:49:09 2006 UTC vs.
Revision 1934 by gezelter, Mon Aug 26 14:15:09 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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