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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
Revision 1937 by gezelter, Tue Oct 29 16:02:58 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, 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 "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	+	#include "applications/staticProps/RNEMDStats.hpp"
81
82	<	using namespace oopse;
82	>	using namespace OpenMD;
83
84		int main(int argc, char* argv[]){
85
86	<	//register force fields
87	<	registerForceFields();
88	<
89	<	gengetopt_args_info args_info;
90	<
91	<	//parse the command line option
92	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
93	<	exit(1) ;
94	<	}
95	<
96	<
97	<	//get the dumpfile name and meta-data file name
98	<	std::string dumpFileName = args_info.input_arg;
99	<
100	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
101	<
102	<
103	<	std::string sele1;
104	<	std::string sele2;
105	<
106	<	if (args_info.sele1_given) {
107	<	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, false);
115	<
116	<	double maxLen;
117	<	if (args_info.length_given) {
118	<	maxLen = args_info.length_arg;
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	>	//get the dumpfile name
95	>	std::string dumpFileName = args_info.input_arg;
96	>	std::string sele1;
97	>	std::string sele2;
98	>
99	>	// check the first selection argument, or set it to the environment
100	>	// variable, or failing that, set it to "select all"
101	>
102	>	if (args_info.sele1_given) {
103	>	sele1 = args_info.sele1_arg;
104	>	} else {
105	>	char*  sele1Env= getenv("SELECTION1");
106	>	if (sele1Env) {
107	>	sele1 = sele1Env;
108		} else {
109	<	double rcut;
121	<	double rsw;
122	<	info->getCutoff(rcut, rsw);
123	<	maxLen = rcut + rsw;
109	>	sele1 = "select all";
110		}
111	<
112	<
113	<	RadialDistrFunc* rdf;
114	<	if (args_info.gofr_given){
115	<	GofR* r = new GofR(info, dumpFileName, sele1, sele2);
116	<
117	<	r->setNRBins(args_info.nrbins_arg);
118	<	r->setLength(maxLen);
119	<
120	<	rdf = r;
121	<	} else if (args_info.r_theta_given) {
122	<	GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2);
123	<
124	<	rTheta->setNRBins(args_info.nrbins_arg);
125	<	rTheta->setLength(maxLen);
140	<	rTheta->setNAngleBins(args_info.nanglebins_arg);
141	<
142	<
143	<	rdf = rTheta;
111	>	}
112	>
113	>	// check the second selection argument, or set it to the environment
114	>	// variable, or failing that, set it to the first selection
115	>
116	>	if (args_info.sele2_given) {
117	>	sele2 = args_info.sele2_arg;
118	>	} else {
119	>	char* sele2Env = getenv("SELECTION2");
120	>	if (sele2Env) {
121	>	sele2 = sele2Env;
122	>	} else {
123	>	//If sele2 is not specified, then the default behavior
124	>	//should be what is already intended for sele1
125	>	sele2 = sele1;
126		}
127	<	else if (args_info.r_omega_given) {
146	<	GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2);
127	>	}
128
129	<
130	<	rOmega->setNRBins(args_info.nrbins_arg);
131	<	rOmega->setLength(maxLen);
132	<	rOmega->setNAngleBins(args_info.nanglebins_arg);
133	<
134	<	rdf = rOmega;
135	<	} else if (args_info.theta_omega_given) {
136	<	GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2);
137	<	rAngle2->setNAngleBins(args_info.nanglebins_arg);
138	<
139	<	rdf = rAngle2;
140	<	} else if (args_info.xyz_given) {
141	<
142	<	GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2);
143	<
144	<	xyz->setNRBins(args_info.nrbins_arg);
145	<	xyz->setLength(maxLen);
146	<
147	<
148	<	rdf = xyz;
149	<	}
150	<
151	<
152	<	if (args_info.output_given) {
172	<	rdf->setOutputName(args_info.output_arg);
173	<	}
174	<
175	<	if (args_info.step_given) {
176	<	rdf->setStep(args_info.step_arg);
129	>	bool batchMode;
130	>	if (args_info.scd_given){
131	>	if (args_info.sele1_given &&
132	>	args_info.sele2_given && args_info.sele3_given) {
133	>	batchMode = false;
134	>	} else if (args_info.molname_given &&
135	>	args_info.begin_given && args_info.end_given) {
136	>	if (args_info.begin_arg < 0 ||
137	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
138	>	sprintf( painCave.errMsg,
139	>	"below conditions are not satisfied:\n"
140	>	"0 <= begin && 0<= end && begin <= end-2\n");
141	>	painCave.severity = OPENMD_ERROR;
142	>	painCave.isFatal = 1;
143	>	simError();
144	>	}
145	>	batchMode = true;
146	>	} else{
147	>	sprintf( painCave.errMsg,
148	>	"either --sele1, --sele2, --sele3 are specified,"
149	>	" or --molname, --begin, --end are specified\n");
150	>	painCave.severity = OPENMD_ERROR;
151	>	painCave.isFatal = 1;
152	>	simError();
153		}
154	+	}
155	+
156	+	//parse md file and set up the system
157	+	SimCreator creator;
158	+	SimInfo* info = creator.createSim(dumpFileName);
159
160	<	rdf->process();
161	<
162	<	delete rdf;
163	<	delete info;
164	<
165	<	return 0;
160	>	RealType maxLen;
161	>	RealType zmaxLen;
162	>	if (args_info.length_given) {
163	>	maxLen = args_info.length_arg;
164	>	if (args_info.zlength_given){
165	>	zmaxLen = args_info.zlength_arg;
166	>	}
167	>	} else {
168	>	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
169	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
170	>	zmaxLen = hmat(2,2);
171	>	}
172	>
173	>	StaticAnalyser* analyser;
174	>	if (args_info.gofr_given){
175	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
176	>	args_info.nbins_arg);
177	>	} else if (args_info.gofz_given) {
178	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
179	>	args_info.nbins_arg);
180	>	} else if (args_info.r_z_given) {
181	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
182	>	args_info.nbins_arg, args_info.nbins_z_arg);
183	>	} else if (args_info.r_theta_given) {
184	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
185	>	args_info.nbins_arg, args_info.nanglebins_arg);
186	>	} else if (args_info.r_omega_given) {
187	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
188	>	args_info.nbins_arg, args_info.nanglebins_arg);
189	>	} else if (args_info.theta_omega_given) {
190	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
191	>	args_info.nanglebins_arg);
192	>	} else if (args_info.gxyz_given) {
193	>	if (args_info.refsele_given) {
194	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
195	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
196	>	} else {
197	>	sprintf( painCave.errMsg,
198	>	"--refsele must set when --gxyz is used");
199	>	painCave.severity = OPENMD_ERROR;
200	>	painCave.isFatal = 1;
201	>	simError();
202	>	}
203	>	} else if (args_info.twodgofr_given){
204	>	if (args_info.dz_given) {
205	>	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
206	>	args_info.dz_arg, args_info.nbins_arg);
207	>	} else {
208	>	sprintf( painCave.errMsg,
209	>	"A slab width (dz) must be specified when calculating TwoDGofR");
210	>	painCave.severity = OPENMD_ERROR;
211	>	painCave.isFatal = 1;
212	>	simError();
213	>	}
214	>	} else if (args_info.p2_given) {
215	>	if (args_info.sele1_given) {
216	>	if (args_info.sele2_given)
217	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
218	>	else
219	>	if (args_info.seleoffset_given)
220	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
221	>	args_info.seleoffset_arg);
222	>	else
223	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
224	>	} else {
225	>	sprintf( painCave.errMsg,
226	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
227	>	painCave.severity = OPENMD_ERROR;
228	>	painCave.isFatal = 1;
229	>	simError();
230	>	}
231	>	} else if (args_info.rp2_given){
232	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
233	>	} else if (args_info.bo_given){
234	>	if (args_info.rcut_given) {
235	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
236	>	args_info.rcut_arg,
237	>	args_info.nbins_arg);
238	>	} else {
239	>	sprintf( painCave.errMsg,
240	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
241	>	painCave.severity = OPENMD_ERROR;
242	>	painCave.isFatal = 1;
243	>	simError();
244	>	}
245	>
246	>	} else if (args_info.tet_param_given) {
247	>	if (args_info.rcut_given) {
248	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
249	>	args_info.rcut_arg,
250	>	args_info.nbins_arg);
251	>	} else {
252	>	sprintf( painCave.errMsg,
253	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
254	>	painCave.severity = OPENMD_ERROR;
255	>	painCave.isFatal = 1;
256	>	simError();
257	>	}
258	>	} else if (args_info.tet_param_z_given) {
259	>	if (args_info.rcut_given) {
260	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
261	>	args_info.rcut_arg,
262	>	args_info.nbins_arg);
263	>	} else {
264	>	sprintf( painCave.errMsg,
265	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
266	>	painCave.severity = OPENMD_ERROR;
267	>	painCave.isFatal = 1;
268	>	simError();
269	>	}
270	>	} else if (args_info.bor_given){
271	>	if (args_info.rcut_given) {
272	>	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
273	>	args_info.nbins_arg, maxLen);
274	>	} else {
275	>	sprintf( painCave.errMsg,
276	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
277	>	painCave.severity = OPENMD_ERROR;
278	>	painCave.isFatal = 1;
279	>	simError();
280	>	}
281	>	} else if (args_info.bad_given){
282	>	if (args_info.rcut_given) {
283	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
284	>	args_info.rcut_arg,
285	>	args_info.nbins_arg);
286	>	} else {
287	>	sprintf( painCave.errMsg,
288	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
289	>	painCave.severity = OPENMD_ERROR;
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293	>	} else if (args_info.scd_given) {
294	>	if (batchMode) {
295	>	analyser  = new SCDOrderParameter(info, dumpFileName,
296	>	args_info.molname_arg,
297	>	args_info.begin_arg, args_info.end_arg);
298	>	} else{
299	>	std::string sele3 = args_info.sele3_arg;
300	>	analyser  = new SCDOrderParameter(info, dumpFileName,
301	>	sele1, sele2, sele3);
302	>	}
303	>	}else if (args_info.density_given) {
304	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
305	>	args_info.nbins_arg);
306	>	} else if (args_info.count_given) {
307	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
308	>	} else if (args_info.slab_density_given) {
309	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
310	>	} else if (args_info.rnemdz_given) {
311	>	analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
312	>	} else if (args_info.rnemdr_given) {
313	>	analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
314	>	} else if (args_info.p_angle_given) {
315	>	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
316	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
317	>	}else if (args_info.hxy_given) {
318	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
319	>	args_info.nbins_y_arg, args_info.nbins_arg);
320	>	#endif
321	>	}else if (args_info.rho_r_given) {
322	>	if (args_info.radius_given){
323	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
324	>	}else{
325	>	sprintf( painCave.errMsg,
326	>	"A particle radius (radius) must be specified when calculating Rho(r)");
327	>	painCave.severity = OPENMD_ERROR;
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	} else if (args_info.hullvol_given) {
332	>	analyser = new NanoVolume(info, dumpFileName, sele1);
333	>	} else if (args_info.rodlength_given) {
334	>	analyser = new NanoLength(info, dumpFileName, sele1);
335	>	} else if (args_info.angle_r_given) {
336	>	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
337	>	}
338	>
339	>	if (args_info.output_given) {
340	>	analyser->setOutputName(args_info.output_arg);
341	>	}
342	>	if (args_info.step_given) {
343	>	analyser->setStep(args_info.step_arg);
344	>	}
345	>
346	>	analyser->process();
347	>
348	>	delete analyser;
349	>	delete info;
350	>
351	>	return 0;
352		}
186	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
Revision 1937 by gezelter, Tue Oct 29 16:02:58 2013 UTC

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

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