ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 1026 by gezelter, Wed Aug 30 21:04:04 2006 UTC vs.
Revision 1937 by gezelter, Tue Oct 29 16:02:58 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"
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
58	–	using namespace oopse;
59	–
70		int main(int argc, char* argv[]){
71
62	–	//register force fields
63	–	registerForceFields();
64	–
72		gengetopt_args_info args_info;
73
74		//parse the command line option
#	Line 69 | Line 76 | int main(int argc, char* argv[]){
76		exit(1) ;
77		}
78
72	–
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;
84	<
84	>
85	>	// check the first selection argument, or set it to the environment
86	>	// variable, or failing that, set it to "select all"
87	>
88		if (args_info.sele1_given) {
89		sele1 = args_info.sele1_arg;
90	<	}else {
91	<	char*  sele1Env= getenv("OOPSE_SELE1");
90	>	} else {
91	>	char*  sele1Env= getenv("SELECTION1");
92		if (sele1Env) {
93		sele1 = sele1Env;
94	<	}else {
95	<	sprintf( painCave.errMsg,
87	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
88	<	painCave.severity = OOPSE_ERROR;
89	<	painCave.isFatal = 1;
90	<	simError();
94	>	} else {
95	>	sele1 = "select all";
96		}
97		}
98	<
98	>
99	>	// check the second selection argument, or set it to the environment
100	>	// variable, or failing that, set it to the first selection
101	>
102		if (args_info.sele2_given) {
103		sele2 = args_info.sele2_arg;
104	<	}else {
105	<	char* sele2Env = getenv("OOPSE_SELE2");
104	>	} else {
105	>	char* sele2Env = getenv("SELECTION2");
106		if (sele2Env) {
107		sele2 = sele2Env;
108	<	} else {
108	>	} else {
109	>	//If sele2 is not specified, then the default behavior
110	>	//should be what is already intended for sele1
111		sele2 = sele1;
112		}
113		}
114
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
109	–
128		TimeCorrFunc* corrFunc;
129	<	if (args_info.dcorr_given){
130	<	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
129	>	if(args_info.sdcorr_given){
130	>	corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
131	>	} else if (args_info.selecorr_given){
132	>	corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133	>	} else if (args_info.dcorr_given){
134	>	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135		} else if (args_info.rcorr_given) {
136	<	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
137	<	}
138	<	else if (args_info.vcorr_given) {
139	<	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
136	>	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
137	>	} else if (args_info.r_rcorr_given) {
138	>	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
139	>	} else if (args_info.thetacorr_given) {
140	>	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
141	>	} else if (args_info.drcorr_given) {
142	>	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143	>	} else if (args_info.vcorr_given) {
144	>	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145	>	} else if (args_info.helfandEcorr_given){
146	>	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
147	>	} else if (args_info.stresscorr_given){
148	>	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
149	>	} else if (args_info.momentum_given){
150	>	corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
151		} else if (args_info.lcorr_given) {
152		int order;
153		if (args_info.order_given)
154		order = args_info.order_arg;
155		else {
156		sprintf( painCave.errMsg,
157	<	"--order must be set if --lcoor is set\n");
158	<	painCave.severity = OOPSE_ERROR;
157	>	"--order must be set if --lcorr is set\n");
158	>	painCave.severity = OPENMD_ERROR;
159		painCave.isFatal = 1;
160		simError();
161		}
162
163	<	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
163	>	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
164	>	} else if (args_info.lcorrZ_given) {
165	>	int order;
166	>	if (args_info.order_given)
167	>	order = args_info.order_arg;
168	>	else {
169	>	sprintf( painCave.errMsg,
170	>	"--order must be set if --lcorrZ is set\n");
171	>	painCave.severity = OPENMD_ERROR;
172	>	painCave.isFatal = 1;
173	>	simError();
174	>	}
175	>
176	>	corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
177	>
178	>	} else if (args_info.cohZ_given) {
179	>	int order;
180	>	if (args_info.order_given)
181	>	order = args_info.order_arg;
182	>	else {
183	>	sprintf( painCave.errMsg,
184	>	"--order must be set if --cohZ is set\n");
185	>	painCave.severity = OPENMD_ERROR;
186	>	painCave.isFatal = 1;
187	>	simError();
188	>	}
189	>
190	>	corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
191	>
192		}
193
194	+
195		if (args_info.output_given) {
196		corrFunc->setOutputName(args_info.output_arg);
197		}

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 1026 by gezelter, Wed Aug 30 21:04:04 2006 UTC vs.
Revision 1937 by gezelter, Tue Oct 29 16:02:58 2013 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines