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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 310 by tim, Thu Feb 10 18:14:03 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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 "applications/staticProps/StaticPropsCmd.h"
47	–	#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	<	using namespace oopse;
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/TetrahedralityParamXYZ.hpp"
81	>	#include "applications/staticProps/RNEMDStats.hpp"
82	>	#include "applications/staticProps/NitrileFrequencyMap.hpp"
83	>	#include "applications/staticProps/MultipoleSum.hpp"
84	>	#include "applications/staticProps/SurfaceDiffusion.hpp"
85	>	#include "applications/staticProps/HBondGeometric.hpp"
86
87	+	using namespace OpenMD;
88	+
89		int main(int argc, char* argv[]){
90
91	<	//register force fields
92	<	registerForceFields();
93	<
94	<	gengetopt_args_info args_info;
95	<
96	<	//parse the command line option
97	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
98	<	exit(1) ;
91	>
92	>	gengetopt_args_info args_info;
93	>
94	>	//parse the command line option
95	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
96	>	exit(1) ;
97	>	}
98	>
99	>	//get the dumpfile name
100	>	std::string dumpFileName = args_info.input_arg;
101	>	std::string sele1;
102	>	std::string sele2;
103	>	std::string sele3;
104	>
105	>	// check the first selection argument, or set it to the environment
106	>	// variable, or failing that, set it to "select all"
107	>
108	>	if (args_info.sele1_given) {
109	>	sele1 = args_info.sele1_arg;
110	>	} else {
111	>	char*  sele1Env= getenv("SELECTION1");
112	>	if (sele1Env) {
113	>	sele1 = sele1Env;
114	>	} else {
115	>	sele1 = "select all";
116		}
117	+	}
118	+
119	+	// check the second selection argument, or set it to the environment
120	+	// variable, or failing that, set it to the first selection
121	+
122	+	if (args_info.sele2_given) {
123	+	sele2 = args_info.sele2_arg;
124	+	} else {
125	+	char* sele2Env = getenv("SELECTION2");
126	+	if (sele2Env) {
127	+	sele2 = sele2Env;
128	+	} else {
129	+	//If sele2 is not specified, then the default behavior
130	+	//should be what is already intended for sele1
131	+	sele2 = sele1;
132	+	}
133	+	}
134
135	+	// check the third selection argument, which is only set if
136	+	// requested by the user
137
138	<	//get the dumpfile name and meta-data file name
69	<	std::string dumpFileName = args_info.input_arg;
138	>	if (args_info.sele3_given) sele3 = args_info.sele3_arg;
139
140	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
141	<
142	<
143	<	//parse md file and set up the system
144	<	SimCreator creator;
145	<	SimInfo* info = creator.createSim(mdFileName, false);
146	<
147	<
148	<	std::string sele1;
149	<	std::string sele2;
150	<
151	<	if (args_info.sele1_given) {
152	<	sele1 = args_info.sele1_arg;
153	<	}else {
154	<
140	>	bool batchMode(false);
141	>	if (args_info.scd_given){
142	>	if (args_info.sele1_given &&
143	>	args_info.sele2_given && args_info.sele3_given) {
144	>	batchMode = false;
145	>	} else if (args_info.molname_given &&
146	>	args_info.begin_given && args_info.end_given) {
147	>	if (args_info.begin_arg < 0 ||
148	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
149	>	sprintf( painCave.errMsg,
150	>	"below conditions are not satisfied:\n"
151	>	"0 <= begin && 0<= end && begin <= end-2\n");
152	>	painCave.severity = OPENMD_ERROR;
153	>	painCave.isFatal = 1;
154	>	simError();
155	>	}
156	>	batchMode = true;
157	>	} else{
158	>	sprintf( painCave.errMsg,
159	>	"either --sele1, --sele2, --sele3 are specified,"
160	>	" or --molname, --begin, --end are specified\n");
161	>	painCave.severity = OPENMD_ERROR;
162	>	painCave.isFatal = 1;
163	>	simError();
164		}
165	<	if (args_info.sele1_given) {
166	<	sele1 = args_info.sele1_arg;
167	<	}else {
165	>	}
166	>
167	>	//parse md file and set up the system
168	>	SimCreator creator;
169	>	SimInfo* info = creator.createSim(dumpFileName);
170
171	+	RealType maxLen;
172	+	RealType zmaxLen(0.0);
173	+	if (args_info.length_given) {
174	+	maxLen = args_info.length_arg;
175	+	if (args_info.zlength_given){
176	+	zmaxLen = args_info.zlength_arg;
177		}
178	<
179	<	GofR rdf(info, dumpFileName, sele1, sele2, args_info.length_arg);
178	>	} else {
179	>	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
180	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
181	>	zmaxLen = hmat(2,2);
182	>	}
183	>
184	>	StaticAnalyser* analyser;
185	>	if (args_info.gofr_given){
186	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
187	>	args_info.nbins_arg);
188	>	} else if (args_info.gofz_given) {
189	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
190	>	args_info.nbins_arg);
191	>	} else if (args_info.r_z_given) {
192	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
193	>	args_info.nbins_arg, args_info.nbins_z_arg);
194	>	} else if (args_info.r_theta_given) {
195	>	if (args_info.sele3_given)
196	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
197	>	args_info.nbins_arg, args_info.nanglebins_arg);
198	>	else
199	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
200	>	args_info.nbins_arg, args_info.nanglebins_arg);
201	>	} else if (args_info.r_omega_given) {
202	>	if (args_info.sele3_given)
203	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
204	>	args_info.nbins_arg, args_info.nanglebins_arg);
205	>	else
206	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
207	>	args_info.nbins_arg, args_info.nanglebins_arg);
208
209	<	if (args_info.nbins_given) {
210	<	rdf.setNBins(args_info.nbins_arg);
209	>	} else if (args_info.theta_omega_given) {
210	>	if (args_info.sele3_given)
211	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
212	>	args_info.nanglebins_arg);
213	>	else
214	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
215	>	args_info.nanglebins_arg);
216	>	} else if (args_info.gxyz_given) {
217	>	if (args_info.refsele_given) {
218	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
219	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
220	>	} else {
221	>	sprintf( painCave.errMsg,
222	>	"--refsele must set when --gxyz is used");
223	>	painCave.severity = OPENMD_ERROR;
224	>	painCave.isFatal = 1;
225	>	simError();
226		}
227	<
228	<	rdf.process();
229	<
230	<	delete info;
231	<
232	<	return 0;
227	>	} else if (args_info.twodgofr_given){
228	>	if (args_info.dz_given) {
229	>	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
230	>	args_info.dz_arg, args_info.nbins_arg);
231	>	} else {
232	>	sprintf( painCave.errMsg,
233	>	"A slab width (dz) must be specified when calculating TwoDGofR");
234	>	painCave.severity = OPENMD_ERROR;
235	>	painCave.isFatal = 1;
236	>	simError();
237	>	}
238	>	} else if (args_info.p2_given) {
239	>	if (args_info.sele1_given) {
240	>	if (args_info.sele2_given)
241	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
242	>	else
243	>	if (args_info.seleoffset_given)
244	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
245	>	args_info.seleoffset_arg);
246	>	else
247	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
248	>	} else {
249	>	sprintf( painCave.errMsg,
250	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
251	>	painCave.severity = OPENMD_ERROR;
252	>	painCave.isFatal = 1;
253	>	simError();
254	>	}
255	>	} else if (args_info.rp2_given){
256	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
257	>	} else if (args_info.bo_given){
258	>	if (args_info.rcut_given) {
259	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
260	>	args_info.rcut_arg,
261	>	args_info.nbins_arg);
262	>	} else {
263	>	sprintf( painCave.errMsg,
264	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
265	>	painCave.severity = OPENMD_ERROR;
266	>	painCave.isFatal = 1;
267	>	simError();
268	>	}
269	>	} else if (args_info.multipole_given){
270	>	analyser = new MultipoleSum(info, dumpFileName, sele1,
271	>	maxLen, args_info.nbins_arg);
272	>	} else if (args_info.tet_param_given) {
273	>	if (args_info.rcut_given) {
274	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
275	>	args_info.rcut_arg,
276	>	args_info.nbins_arg);
277	>	} else {
278	>	sprintf( painCave.errMsg,
279	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
280	>	painCave.severity = OPENMD_ERROR;
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	} else if (args_info.tet_param_z_given) {
285	>	if (args_info.rcut_given) {
286	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
287	>	args_info.rcut_arg,
288	>	args_info.nbins_arg);
289	>	} else {
290	>	sprintf( painCave.errMsg,
291	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
292	>	painCave.severity = OPENMD_ERROR;
293	>	painCave.isFatal = 1;
294	>	simError();
295	>	}
296	>	} else if (args_info.tet_param_xyz_given) {
297	>	if (!args_info.rcut_given) {
298	>	sprintf( painCave.errMsg,
299	>	"A cutoff radius (rcut) must be specified when calculating"
300	>	" Tetrahedrality Parameters");
301	>	painCave.severity = OPENMD_ERROR;
302	>	painCave.isFatal = 1;
303	>	simError();
304	>	}
305	>	if (!args_info.voxelSize_given) {
306	>	sprintf( painCave.errMsg,
307	>	"A voxel size must be specified when calculating"
308	>	" volume-resolved Tetrahedrality Parameters");
309	>	painCave.severity = OPENMD_ERROR;
310	>	painCave.isFatal = 1;
311	>	simError();
312	>	}
313	>	if (!args_info.gaussWidth_given) {
314	>	sprintf( painCave.errMsg,
315	>	"A gaussian width must be specified when calculating"
316	>	" volume-resolved Tetrahedrality Parameters");
317	>	painCave.severity = OPENMD_ERROR;
318	>	painCave.isFatal = 1;
319	>	simError();
320	>	}
321	>	analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
322	>	args_info.rcut_arg,
323	>	args_info.voxelSize_arg,
324	>	args_info.gaussWidth_arg);
325	>	} else if (args_info.ior_given){
326	>	if (args_info.rcut_given) {
327	>	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
328	>	args_info.rcut_arg,
329	>	args_info.nbins_arg, maxLen);
330	>	} else {
331	>	sprintf( painCave.errMsg,
332	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
333	>	painCave.severity = OPENMD_ERROR;
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	} else if (args_info.for_given){
338	>	if (args_info.rcut_given) {
339	>	analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
340	>	args_info.nbins_arg, maxLen);
341	>	} else {
342	>	sprintf( painCave.errMsg,
343	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
344	>	painCave.severity = OPENMD_ERROR;
345	>	painCave.isFatal = 1;
346	>	simError();
347	>	}
348	>	} else if (args_info.bad_given){
349	>	if (args_info.rcut_given) {
350	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
351	>	args_info.rcut_arg,
352	>	args_info.nbins_arg);
353	>	} else {
354	>	sprintf( painCave.errMsg,
355	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
356	>	painCave.severity = OPENMD_ERROR;
357	>	painCave.isFatal = 1;
358	>	simError();
359	>	}
360	>	} else if (args_info.scd_given) {
361	>	if (batchMode) {
362	>	analyser  = new SCDOrderParameter(info, dumpFileName,
363	>	args_info.molname_arg,
364	>	args_info.begin_arg, args_info.end_arg);
365	>	} else{
366	>	analyser  = new SCDOrderParameter(info, dumpFileName,
367	>	sele1, sele2, sele3);
368	>	}
369	>	}else if (args_info.density_given) {
370	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
371	>	args_info.nbins_arg);
372	>	} else if (args_info.count_given) {
373	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
374	>	} else if (args_info.slab_density_given) {
375	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
376	>	} else if (args_info.rnemdz_given) {
377	>	analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
378	>	} else if (args_info.rnemdr_given) {
379	>	analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
380	>	} else if (args_info.rnemdrt_given) {
381	>	analyser = new RNEMDRTheta(info, dumpFileName, sele1,
382	>	args_info.nbins_arg, args_info.nanglebins_arg);
383	>	} else if (args_info.nitrile_given) {
384	>	analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
385	>	args_info.nbins_arg);
386	>	} else if (args_info.p_angle_given) {
387	>	if (args_info.sele1_given) {
388	>	if (args_info.sele2_given)
389	>	analyser  = new pAngle(info, dumpFileName, sele1, sele2,
390	>	args_info.nbins_arg);
391	>	else
392	>	if (args_info.seleoffset_given) {
393	>	if (args_info.seleoffset2_given) {
394	>	analyser  = new pAngle(info, dumpFileName, sele1,
395	>	args_info.seleoffset_arg,
396	>	args_info.seleoffset2_arg,
397	>	args_info.nbins_arg);
398	>	} else {
399	>	analyser  = new pAngle(info, dumpFileName, sele1,
400	>	args_info.seleoffset_arg,
401	>	args_info.nbins_arg);
402	>	}
403	>	} else
404	>	analyser  = new pAngle(info, dumpFileName, sele1,
405	>	args_info.nbins_arg);
406	>	} else {
407	>	sprintf( painCave.errMsg,
408	>	"At least one selection script (--sele1) must be specified when "
409	>	"calculating P(angle) distributions");
410	>	painCave.severity = OPENMD_ERROR;
411	>	painCave.isFatal = 1;
412	>	simError();
413	>	}
414	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
415	>	}else if (args_info.hxy_given) {
416	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
417	>	args_info.nbins_y_arg, args_info.nbins_arg);
418	>	#endif
419	>	}else if (args_info.surfDiffusion_given){
420	>	analyser = new SurfaceDiffusion(info, dumpFileName, sele1, maxLen);
421	>	}else if (args_info.rho_r_given) {
422	>	if (args_info.radius_given){
423	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
424	>	}else{
425	>	sprintf( painCave.errMsg,
426	>	"A particle radius (radius) must be specified when calculating Rho(r)");
427	>	painCave.severity = OPENMD_ERROR;
428	>	painCave.isFatal = 1;
429	>	simError();
430	>	}
431	>	} else if (args_info.hullvol_given) {
432	>	analyser = new NanoVolume(info, dumpFileName, sele1);
433	>	} else if (args_info.rodlength_given) {
434	>	analyser = new NanoLength(info, dumpFileName, sele1);
435	>	} else if (args_info.angle_r_given) {
436	>	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
437	>	} else if (args_info.hbond_given){
438	>	if (args_info.rcut_given) {
439	>	if (args_info.thetacut_given) {
440	>
441	>	analyser = new HBondGeometric(info, dumpFileName, sele1, sele2,
442	>	args_info.rcut_arg,
443	>	args_info.thetacut_arg,
444	>	args_info.nbins_arg);
445	>	} else {
446	>	sprintf( painCave.errMsg,
447	>	"A cutoff angle (thetacut) must be specified when calculating Hydrogen Bonding Statistics");
448	>	painCave.severity = OPENMD_ERROR;
449	>	painCave.isFatal = 1;
450	>	simError();
451	>	}
452	>	} else {
453	>	sprintf( painCave.errMsg,
454	>	"A cutoff radius (rcut) must be specified when calculating Hydrogen Bonding Statistics");
455	>	painCave.severity = OPENMD_ERROR;
456	>	painCave.isFatal = 1;
457	>	simError();
458	>	}
459	>	}
460	>
461	>	if (args_info.output_given) {
462	>	analyser->setOutputName(args_info.output_arg);
463	>	}
464	>	if (args_info.step_given) {
465	>	analyser->setStep(args_info.step_arg);
466	>	}
467	>
468	>	analyser->process();
469	>
470	>	delete analyser;
471	>	delete info;
472	>
473	>	return 0;
474		}
105	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 310 by tim, Thu Feb 10 18:14:03 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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