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

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 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	+	#include "applications/dynamicProps/BondCorrFunc.hpp"
68
69	+	using namespace OpenMD;
70
61	–	using namespace oopse;
62	–
71		int main(int argc, char* argv[]){
72
65	–	//register force fields
66	–	registerForceFields();
67	–
73		gengetopt_args_info args_info;
74
75		//parse the command line option
#	Line 72 | Line 77 | int main(int argc, char* argv[]){
77		exit(1) ;
78		}
79
75	–
80		//get the dumpfile name and meta-data file name
81		std::string dumpFileName = args_info.input_arg;
82
83		std::string sele1;
84		std::string sele2;
85	<
85	>
86	>	// check the first selection argument, or set it to the environment
87	>	// variable, or failing that, set it to "select all"
88	>
89		if (args_info.sele1_given) {
90		sele1 = args_info.sele1_arg;
91	<	}else {
92	<	char*  sele1Env= getenv("OOPSE_SELE1");
91	>	} else {
92	>	char*  sele1Env= getenv("SELECTION1");
93		if (sele1Env) {
94		sele1 = sele1Env;
95	<	}else {
96	<	sprintf( painCave.errMsg,
90	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
91	<	painCave.severity = OOPSE_ERROR;
92	<	painCave.isFatal = 1;
93	<	simError();
95	>	} else {
96	>	sele1 = "select all";
97		}
98		}
99	<
99	>
100	>	// check the second selection argument, or set it to the environment
101	>	// variable, or failing that, set it to the first selection
102	>
103		if (args_info.sele2_given) {
104		sele2 = args_info.sele2_arg;
105	<	}else {
106	<	char* sele2Env = getenv("OOPSE_SELE2");
105	>	} else {
106	>	char* sele2Env = getenv("SELECTION2");
107		if (sele2Env) {
108		sele2 = sele2Env;
109	<	} else {
109	>	} else {
110	>	//If sele2 is not specified, then the default behavior
111	>	//should be what is already intended for sele1
112		sele2 = sele1;
113		}
114		}
115
116	+	// use the memory string to figure out how much memory we can use:
117	+	char *end;
118	+	long long int memSize = memparse(args_info.memory_arg, &end);
119	+	sprintf( painCave.errMsg,
120	+	"Amount of memory being used: %llu bytes\n", memSize);
121	+	painCave.severity = OPENMD_INFO;
122	+	painCave.isFatal = 0;
123	+	simError();
124	+
125		//parse md file and set up the system
126		SimCreator creator;
127		SimInfo* info = creator.createSim(dumpFileName, false);
128
112	–
129		TimeCorrFunc* corrFunc;
130	<	if (args_info.dcorr_given){
131	<	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
130	>	if(args_info.sdcorr_given){
131	>	corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132	>	} else if (args_info.selecorr_given){
133	>	corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134	>	} else if (args_info.dcorr_given){
135	>	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136		} else if (args_info.rcorr_given) {
137	<	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
137	>	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138		} else if (args_info.r_rcorr_given) {
139	<	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
139	>	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140		} else if (args_info.thetacorr_given) {
141	<	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
141	>	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142		} else if (args_info.drcorr_given) {
143	<	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
144	<	}
145	<	else if (args_info.vcorr_given) {
146	<	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
143	>	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
144	>	} else if (args_info.vcorr_given) {
145	>	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
146	>	} else if (args_info.bondcorr_given) {
147	>	corrFunc = new BondCorrFunc(info, dumpFileName, sele1, memSize);
148	>	} else if (args_info.helfandEcorr_given){
149	>	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
150	>	} else if (args_info.stresscorr_given){
151	>	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
152	>	} else if (args_info.momentum_given){
153	>	corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
154		} else if (args_info.lcorr_given) {
155		int order;
156		if (args_info.order_given)
157		order = args_info.order_arg;
158		else {
159		sprintf( painCave.errMsg,
160	<	"--order must be set if --lcoor is set\n");
161	<	painCave.severity = OOPSE_ERROR;
160	>	"--order must be set if --lcorr is set\n");
161	>	painCave.severity = OPENMD_ERROR;
162		painCave.isFatal = 1;
163		simError();
164		}
165
166	<	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
166	>	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
167	>	} else if (args_info.lcorrZ_given) {
168	>	int order;
169	>	if (args_info.order_given)
170	>	order = args_info.order_arg;
171	>	else {
172	>	sprintf( painCave.errMsg,
173	>	"--order must be set if --lcorrZ is set\n");
174	>	painCave.severity = OPENMD_ERROR;
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>
179	>	corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
180	>
181	>	} else if (args_info.cohZ_given) {
182	>	int order;
183	>	if (args_info.order_given)
184	>	order = args_info.order_arg;
185	>	else {
186	>	sprintf( painCave.errMsg,
187	>	"--order must be set if --cohZ is set\n");
188	>	painCave.severity = OPENMD_ERROR;
189	>	painCave.isFatal = 1;
190	>	simError();
191	>	}
192	>
193	>	corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
194	>
195		}
196
197	+
198		if (args_info.output_given) {
199		corrFunc->setOutputName(args_info.output_arg);
200		}

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

#	Line 0 | Line 1
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