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root/OpenMD/trunk/src/applications/staticProps/StaticProps.cpp

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 311 by tim, Thu Feb 10 22:37:21 2005 UTC vs.
Revision 1846 by gezelter, Thu Jan 31 15:55:47 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, 24107 (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 "io/DumpReader.hpp"
50		#include "utils/simError.h"
51
52		#include "applications/staticProps/StaticPropsCmd.h"
53	+	#include "applications/staticProps/StaticAnalyser.hpp"
54		#include "applications/staticProps/GofR.hpp"
55	+	#include "applications/staticProps/GofZ.hpp"
56	+	#include "applications/staticProps/GofRZ.hpp"
57		#include "applications/staticProps/GofRAngle.hpp"
58		#include "applications/staticProps/GofAngle2.hpp"
59		#include "applications/staticProps/GofXyz.hpp"
60	+	#include "applications/staticProps/TwoDGofR.hpp"
61	+	#include "applications/staticProps/P2OrderParameter.hpp"
62	+	#include "applications/staticProps/BondOrderParameter.hpp"
63	+	#include "applications/staticProps/BOPofR.hpp"
64	+	#include "applications/staticProps/RippleOP.hpp"
65	+	#include "applications/staticProps/SCDOrderParameter.hpp"
66	+	#include "applications/staticProps/DensityPlot.hpp"
67	+	#include "applications/staticProps/ObjectCount.hpp"
68	+	#include "applications/staticProps/RhoZ.hpp"
69	+	#include "applications/staticProps/pAngle.hpp"
70	+	#include "applications/staticProps/BondAngleDistribution.hpp"
71	+	#include "applications/staticProps/NanoVolume.hpp"
72	+	#include "applications/staticProps/NanoLength.hpp"
73	+	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
74	+	#include "applications/staticProps/Hxy.hpp"
75	+	#endif
76	+	#include "applications/staticProps/RhoR.hpp"
77	+	#include "applications/staticProps/AngleR.hpp"
78	+	#include "applications/staticProps/TetrahedralityParam.hpp"
79	+	#include "applications/staticProps/TetrahedralityParamZ.hpp"
80	+	using namespace OpenMD;
81
58	–	using namespace oopse;
59	–
82		int main(int argc, char* argv[]){
83
84	<	//register force fields
85	<	registerForceFields();
86	<
87	<	gengetopt_args_info args_info;
88	<
89	<	//parse the command line option
90	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
91	<	exit(1) ;
92	<	}
93	<
94	<
95	<	//get the dumpfile name and meta-data file name
96	<	std::string dumpFileName = args_info.input_arg;
97	<
98	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
99	<
100	<
101	<	std::string sele1;
102	<	std::string sele2;
103	<
104	<	if (args_info.sele1_given) {
105	<	sele1 = args_info.sele1_arg;
84	<	}else {
85	<	char*  sele1Env= getenv("OOPSE_SELE1");
86	<	if (sele1Env) {
87	<	sele1 = sele1Env;
88	<	}else {
89	<	sprintf( painCave.errMsg,
90	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
91	<	painCave.severity = OOPSE_ERROR;
92	<	painCave.isFatal = 1;
93	<	simError();
94	<	}
95	<	}
96	<
97	<	if (args_info.sele2_given) {
98	<	sele2 = args_info.sele2_arg;
99	<	}else {
100	<	char* sele2Env = getenv("OOPSE_SELE2");
101	<	if (sele2Env) {
102	<	sele2 = sele2Env;
103	<	} else {
104	<	sprintf( painCave.errMsg,
105	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
106	<	painCave.severity = OOPSE_ERROR;
107	<	painCave.isFatal = 1;
108	<	simError();
109	<	}
110	<	}
111	<
112	<	//parse md file and set up the system
113	<	SimCreator creator;
114	<	SimInfo* info = creator.createSim(mdFileName);
115	<
116	<	double maxLen;
117	<	if (args_info.length_given) {
118	<	maxLen = args_info.length_arg;
84	>
85	>	gengetopt_args_info args_info;
86	>
87	>	//parse the command line option
88	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
89	>	exit(1) ;
90	>	}
91	>
92	>	//get the dumpfile name
93	>	std::string dumpFileName = args_info.input_arg;
94	>	std::string sele1;
95	>	std::string sele2;
96	>
97	>	// check the first selection argument, or set it to the environment
98	>	// variable, or failing that, set it to "select all"
99	>
100	>	if (args_info.sele1_given) {
101	>	sele1 = args_info.sele1_arg;
102	>	} else {
103	>	char*  sele1Env= getenv("SELECTION1");
104	>	if (sele1Env) {
105	>	sele1 = sele1Env;
106		} else {
107	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
121	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2 ;
107	>	sele1 = "select all";
108		}
109	<
110	<
111	<	RadialDistrFunc* rdf;
112	<	if (args_info.gofr_given){
113	<	GofR* r = new GofR(info, dumpFileName, sele1, sele2);
114	<
115	<	r->setNRBins(args_info.nrbins_arg);
116	<	r->setLength(maxLen);
117	<
118	<	rdf = r;
119	<	} else if (args_info.r_theta_given) {
120	<	GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2);
121	<
122	<	rTheta->setNRBins(args_info.nrbins_arg);
123	<	rTheta->setLength(maxLen);
138	<	rTheta->setNAngleBins(args_info.nanglebins_arg);
139	<
140	<
141	<	rdf = rTheta;
109	>	}
110	>
111	>	// check the second selection argument, or set it to the environment
112	>	// variable, or failing that, set it to "select all"
113	>
114	>	if (args_info.sele2_given) {
115	>	sele2 = args_info.sele2_arg;
116	>	} else {
117	>	char* sele2Env = getenv("SELECTION1");
118	>	if (sele2Env) {
119	>	sele2 = sele2Env;
120	>	} else {
121	>	//If sele2 is not specified, then the default behavior
122	>	//should be what is already intended for sele1
123	>	sele2 = sele1;
124		}
125	<	else if (args_info.r_omega_given) {
144	<	GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2);
125	>	}
126
127	<
128	<	rOmega->setNRBins(args_info.nrbins_arg);
129	<	rOmega->setLength(maxLen);
130	<	rOmega->setNAngleBins(args_info.nanglebins_arg);
131	<
132	<	rdf = rOmega;
133	<	} else if (args_info.theta_omega_given) {
134	<	GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2);
135	<	rAngle2->setNAngleBins(args_info.nanglebins_arg);
136	<
137	<	rdf = rAngle2;
138	<	} else if (args_info.xyz_given) {
139	<
140	<	GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2);
141	<
142	<	xyz->setNRBins(args_info.nrbins_arg);
143	<	xyz->setLength(maxLen);
144	<
145	<
146	<	rdf = xyz;
147	<	}
148	<
149	<
150	<	if (args_info.output_given) {
170	<	rdf->setOutputName(args_info.output_arg);
171	<	}
172	<
173	<	if (args_info.step_given) {
174	<	rdf->setStep(args_info.step_arg);
127	>	bool batchMode;
128	>	if (args_info.scd_given){
129	>	if (args_info.sele1_given &&
130	>	args_info.sele2_given && args_info.sele3_given) {
131	>	batchMode = false;
132	>	} else if (args_info.molname_given &&
133	>	args_info.begin_given && args_info.end_given) {
134	>	if (args_info.begin_arg < 0 ||
135	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
136	>	sprintf( painCave.errMsg,
137	>	"below conditions are not satisfied:\n"
138	>	"0 <= begin && 0<= end && begin <= end-2\n");
139	>	painCave.severity = OPENMD_ERROR;
140	>	painCave.isFatal = 1;
141	>	simError();
142	>	}
143	>	batchMode = true;
144	>	} else{
145	>	sprintf( painCave.errMsg,
146	>	"either --sele1, --sele2, --sele3 are specified,"
147	>	" or --molname, --begin, --end are specified\n");
148	>	painCave.severity = OPENMD_ERROR;
149	>	painCave.isFatal = 1;
150	>	simError();
151		}
152	+	}
153	+
154	+	//parse md file and set up the system
155	+	SimCreator creator;
156	+	SimInfo* info = creator.createSim(dumpFileName);
157
158	<	rdf->process();
159	<
160	<	delete rdf;
161	<	delete info;
162	<
163	<	return 0;
158	>	RealType maxLen;
159	>	RealType zmaxLen;
160	>	if (args_info.length_given) {
161	>	maxLen = args_info.length_arg;
162	>	if (args_info.zlength_given){
163	>	zmaxLen = args_info.zlength_arg;
164	>	}
165	>	} else {
166	>	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
167	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
168	>	zmaxLen = hmat(2,2);
169	>	}
170	>
171	>	StaticAnalyser* analyser;
172	>	if (args_info.gofr_given){
173	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
174	>	args_info.nbins_arg);
175	>	} else if (args_info.gofz_given) {
176	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
177	>	args_info.nbins_arg);
178	>	} else if (args_info.r_z_given) {
179	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
180	>	args_info.nbins_arg, args_info.nbins_z_arg);
181	>	} else if (args_info.r_theta_given) {
182	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
183	>	args_info.nbins_arg, args_info.nanglebins_arg);
184	>	} else if (args_info.r_omega_given) {
185	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
186	>	args_info.nbins_arg, args_info.nanglebins_arg);
187	>	} else if (args_info.theta_omega_given) {
188	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
189	>	args_info.nanglebins_arg);
190	>	} else if (args_info.gxyz_given) {
191	>	if (args_info.refsele_given) {
192	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
193	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
194	>	} else {
195	>	sprintf( painCave.errMsg,
196	>	"--refsele must set when --gxyz is used");
197	>	painCave.severity = OPENMD_ERROR;
198	>	painCave.isFatal = 1;
199	>	simError();
200	>	}
201	>	} else if (args_info.twodgofr_given){
202	>	if (args_info.dz_given) {
203	>	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
204	>	args_info.dz_arg, args_info.nbins_arg);
205	>	} else {
206	>	sprintf( painCave.errMsg,
207	>	"A slab width (dz) must be specified when calculating TwoDGofR");
208	>	painCave.severity = OPENMD_ERROR;
209	>	painCave.isFatal = 1;
210	>	simError();
211	>	}
212	>	} else if (args_info.p2_given) {
213	>	if (args_info.sele1_given) {
214	>	if (args_info.sele2_given)
215	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
216	>	else
217	>	if (args_info.seleoffset_given)
218	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
219	>	args_info.seleoffset_arg);
220	>	else
221	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
222	>	} else {
223	>	sprintf( painCave.errMsg,
224	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
225	>	painCave.severity = OPENMD_ERROR;
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	} else if (args_info.rp2_given){
230	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
231	>	} else if (args_info.bo_given){
232	>	if (args_info.rcut_given) {
233	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
234	>	args_info.rcut_arg,
235	>	args_info.nbins_arg);
236	>	} else {
237	>	sprintf( painCave.errMsg,
238	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
239	>	painCave.severity = OPENMD_ERROR;
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243	>
244	>	} else if (args_info.tet_param_given) {
245	>	if (args_info.rcut_given) {
246	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
247	>	args_info.rcut_arg,
248	>	args_info.nbins_arg);
249	>	} else {
250	>	sprintf( painCave.errMsg,
251	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
252	>	painCave.severity = OPENMD_ERROR;
253	>	painCave.isFatal = 1;
254	>	simError();
255	>	}
256	>	} else if (args_info.tet_param_z_given) {
257	>	if (args_info.rcut_given) {
258	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
259	>	args_info.rcut_arg,
260	>	args_info.nbins_arg);
261	>	} else {
262	>	sprintf( painCave.errMsg,
263	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
264	>	painCave.severity = OPENMD_ERROR;
265	>	painCave.isFatal = 1;
266	>	simError();
267	>	}
268	>	} else if (args_info.bor_given){
269	>	if (args_info.rcut_given) {
270	>	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
271	>	args_info.nbins_arg, maxLen);
272	>	} else {
273	>	sprintf( painCave.errMsg,
274	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
275	>	painCave.severity = OPENMD_ERROR;
276	>	painCave.isFatal = 1;
277	>	simError();
278	>	}
279	>	} else if (args_info.bad_given){
280	>	if (args_info.rcut_given) {
281	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
282	>	args_info.rcut_arg,
283	>	args_info.nbins_arg);
284	>	} else {
285	>	sprintf( painCave.errMsg,
286	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
287	>	painCave.severity = OPENMD_ERROR;
288	>	painCave.isFatal = 1;
289	>	simError();
290	>	}
291	>	} else if (args_info.scd_given) {
292	>	if (batchMode) {
293	>	analyser  = new SCDOrderParameter(info, dumpFileName,
294	>	args_info.molname_arg,
295	>	args_info.begin_arg, args_info.end_arg);
296	>	} else{
297	>	std::string sele3 = args_info.sele3_arg;
298	>	analyser  = new SCDOrderParameter(info, dumpFileName,
299	>	sele1, sele2, sele3);
300	>	}
301	>	}else if (args_info.density_given) {
302	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
303	>	args_info.nbins_arg);
304	>	} else if (args_info.count_given) {
305	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
306	>	} else if (args_info.slab_density_given) {
307	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
308	>	} else if (args_info.p_angle_given) {
309	>	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
310	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
311	>	}else if (args_info.hxy_given) {
312	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
313	>	args_info.nbins_y_arg, args_info.nbins_arg);
314	>	#endif
315	>	}else if (args_info.rho_r_given) {
316	>	if (args_info.radius_given){
317	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
318	>	}else{
319	>	sprintf( painCave.errMsg,
320	>	"A particle radius (radius) must be specified when calculating Rho(r)");
321	>	painCave.severity = OPENMD_ERROR;
322	>	painCave.isFatal = 1;
323	>	simError();
324	>	}
325	>	} else if (args_info.hullvol_given) {
326	>	analyser = new NanoVolume(info, dumpFileName, sele1);
327	>	} else if (args_info.rodlength_given) {
328	>	analyser = new NanoLength(info, dumpFileName, sele1);
329	>	} else if (args_info.angle_r_given) {
330	>	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
331	>	}
332	>
333	>	if (args_info.output_given) {
334	>	analyser->setOutputName(args_info.output_arg);
335	>	}
336	>	if (args_info.step_given) {
337	>	analyser->setStep(args_info.step_arg);
338	>	}
339	>
340	>	analyser->process();
341	>
342	>	delete analyser;
343	>	delete info;
344	>
345	>	return 0;
346		}
184	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 311 by tim, Thu Feb 10 22:37:21 2005 UTC vs.
Revision 1846 by gezelter, Thu Jan 31 15:55:47 2013 UTC

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

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