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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 354 by tim, Wed Feb 16 20:30:50 2005 UTC vs.
Revision 2015 by gezelter, Wed Aug 13 20:42:43 2014 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/TetrahedralityParamXYZ.hpp"
81	+	#include "applications/staticProps/RNEMDStats.hpp"
82	+	#include "applications/staticProps/NitrileFrequencyMap.hpp"
83	+	#include "applications/staticProps/MultipoleSum.hpp"
84
85	<	using namespace oopse;
85	>	using namespace OpenMD;
86
87		int main(int argc, char* argv[]){
88
89	<	//register force fields
90	<	registerForceFields();
89	>
90	>	gengetopt_args_info args_info;
91	>
92	>	//parse the command line option
93	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
94	>	exit(1) ;
95	>	}
96	>
97	>	//get the dumpfile name
98	>	std::string dumpFileName = args_info.input_arg;
99	>	std::string sele1;
100	>	std::string sele2;
101	>
102	>	// check the first selection argument, or set it to the environment
103	>	// variable, or failing that, set it to "select all"
104	>
105	>	if (args_info.sele1_given) {
106	>	sele1 = args_info.sele1_arg;
107	>	} else {
108	>	char*  sele1Env= getenv("SELECTION1");
109	>	if (sele1Env) {
110	>	sele1 = sele1Env;
111	>	} else {
112	>	sele1 = "select all";
113	>	}
114	>	}
115	>
116	>	// check the second selection argument, or set it to the environment
117	>	// variable, or failing that, set it to the first selection
118	>
119	>	if (args_info.sele2_given) {
120	>	sele2 = args_info.sele2_arg;
121	>	} else {
122	>	char* sele2Env = getenv("SELECTION2");
123	>	if (sele2Env) {
124	>	sele2 = sele2Env;
125	>	} else {
126	>	//If sele2 is not specified, then the default behavior
127	>	//should be what is already intended for sele1
128	>	sele2 = sele1;
129	>	}
130	>	}
131
132	<	gengetopt_args_info args_info;
133	<
134	<	//parse the command line option
135	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
136	<	exit(1) ;
132	>	bool batchMode;
133	>	if (args_info.scd_given){
134	>	if (args_info.sele1_given &&
135	>	args_info.sele2_given && args_info.sele3_given) {
136	>	batchMode = false;
137	>	} else if (args_info.molname_given &&
138	>	args_info.begin_given && args_info.end_given) {
139	>	if (args_info.begin_arg < 0 ||
140	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
141	>	sprintf( painCave.errMsg,
142	>	"below conditions are not satisfied:\n"
143	>	"0 <= begin && 0<= end && begin <= end-2\n");
144	>	painCave.severity = OPENMD_ERROR;
145	>	painCave.isFatal = 1;
146	>	simError();
147	>	}
148	>	batchMode = true;
149	>	} else{
150	>	sprintf( painCave.errMsg,
151	>	"either --sele1, --sele2, --sele3 are specified,"
152	>	" or --molname, --begin, --end are specified\n");
153	>	painCave.severity = OPENMD_ERROR;
154	>	painCave.isFatal = 1;
155	>	simError();
156		}
157	+	}
158	+
159	+	//parse md file and set up the system
160	+	SimCreator creator;
161	+	SimInfo* info = creator.createSim(dumpFileName);
162
163	<
164	<	//get the dumpfile name and meta-data file name
165	<	std::string dumpFileName = args_info.input_arg;
166	<
167	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
168	<
78	<
79	<	std::string sele1;
80	<	std::string sele2;
81	<
82	<	if (args_info.sele1_given) {
83	<	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	<	}
163	>	RealType maxLen;
164	>	RealType zmaxLen;
165	>	if (args_info.length_given) {
166	>	maxLen = args_info.length_arg;
167	>	if (args_info.zlength_given){
168	>	zmaxLen = args_info.zlength_arg;
169		}
170	<
171	<	if (args_info.sele2_given) {
172	<	sele2 = args_info.sele2_arg;
173	<	}else {
174	<	char* sele2Env = getenv("OOPSE_SELE2");
175	<	if (sele2Env) {
176	<	sele2 = sele2Env;
177	<	} else {
178	<	sprintf( painCave.errMsg,
179	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
180	<	painCave.severity = OOPSE_ERROR;
181	<	painCave.isFatal = 1;
182	<	simError();
183	<	}
170	>	} else {
171	>	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
172	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
173	>	zmaxLen = hmat(2,2);
174	>	}
175	>
176	>	StaticAnalyser* analyser;
177	>	if (args_info.gofr_given){
178	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
179	>	args_info.nbins_arg);
180	>	} else if (args_info.gofz_given) {
181	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
182	>	args_info.nbins_arg);
183	>	} else if (args_info.r_z_given) {
184	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
185	>	args_info.nbins_arg, args_info.nbins_z_arg);
186	>	} else if (args_info.r_theta_given) {
187	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
188	>	args_info.nbins_arg, args_info.nanglebins_arg);
189	>	} else if (args_info.r_omega_given) {
190	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
191	>	args_info.nbins_arg, args_info.nanglebins_arg);
192	>	} else if (args_info.theta_omega_given) {
193	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
194	>	args_info.nanglebins_arg);
195	>	} else if (args_info.gxyz_given) {
196	>	if (args_info.refsele_given) {
197	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
198	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
199	>	} else {
200	>	sprintf( painCave.errMsg,
201	>	"--refsele must set when --gxyz is used");
202	>	painCave.severity = OPENMD_ERROR;
203	>	painCave.isFatal = 1;
204	>	simError();
205		}
206	<
207	<	//parse md file and set up the system
208	<	SimCreator creator;
209	<	SimInfo* info = creator.createSim(mdFileName);
115	<
116	<	double maxLen;
117	<	if (args_info.length_given) {
118	<	maxLen = args_info.length_arg;
206	>	} else if (args_info.twodgofr_given){
207	>	if (args_info.dz_given) {
208	>	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
209	>	args_info.dz_arg, args_info.nbins_arg);
210		} else {
211	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
212	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
211	>	sprintf( painCave.errMsg,
212	>	"A slab width (dz) must be specified when calculating TwoDGofR");
213	>	painCave.severity = OPENMD_ERROR;
214	>	painCave.isFatal = 1;
215	>	simError();
216		}
217	<
218	<	RadialDistrFunc* rdf;
219	<	if (args_info.gofr_given){
220	<	rdf= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
221	<	} else if (args_info.r_theta_given) {
222	<	rdf  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
223	<	} else if (args_info.r_omega_given) {
224	<	rdf  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
225	<	} else if (args_info.theta_omega_given) {
226	<	rdf  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
227	<	} else if (args_info.xyz_given) {
228	<	rdf= new GofXyz(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
217	>	} else if (args_info.p2_given) {
218	>	if (args_info.sele1_given) {
219	>	if (args_info.sele2_given)
220	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
221	>	else
222	>	if (args_info.seleoffset_given)
223	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
224	>	args_info.seleoffset_arg);
225	>	else
226	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
227	>	} else {
228	>	sprintf( painCave.errMsg,
229	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
230	>	painCave.severity = OPENMD_ERROR;
231	>	painCave.isFatal = 1;
232	>	simError();
233		}
234	<
235	<	if (args_info.output_given) {
236	<	rdf->setOutputName(args_info.output_arg);
234	>	} else if (args_info.rp2_given){
235	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
236	>	} else if (args_info.bo_given){
237	>	if (args_info.rcut_given) {
238	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
239	>	args_info.rcut_arg,
240	>	args_info.nbins_arg);
241	>	} else {
242	>	sprintf( painCave.errMsg,
243	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
244	>	painCave.severity = OPENMD_ERROR;
245	>	painCave.isFatal = 1;
246	>	simError();
247		}
248	<	if (args_info.step_given) {
249	<	rdf->setStep(args_info.step_arg);
248	>	} else if (args_info.multipole_given){
249	>	analyser = new MultipoleSum(info, dumpFileName, sele1,
250	>	maxLen, args_info.nbins_arg);
251	>	} else if (args_info.tet_param_given) {
252	>	if (args_info.rcut_given) {
253	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
254	>	args_info.rcut_arg,
255	>	args_info.nbins_arg);
256	>	} else {
257	>	sprintf( painCave.errMsg,
258	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
259	>	painCave.severity = OPENMD_ERROR;
260	>	painCave.isFatal = 1;
261	>	simError();
262		}
263	<
264	<	rdf->process();
265	<
266	<	delete rdf;
267	<	delete info;
268	<
269	<	return 0;
263	>	} else if (args_info.tet_param_z_given) {
264	>	if (args_info.rcut_given) {
265	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
266	>	args_info.rcut_arg,
267	>	args_info.nbins_arg);
268	>	} else {
269	>	sprintf( painCave.errMsg,
270	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
271	>	painCave.severity = OPENMD_ERROR;
272	>	painCave.isFatal = 1;
273	>	simError();
274	>	}
275	>	} else if (args_info.tet_param_xyz_given) {
276	>	if (!args_info.rcut_given) {
277	>	sprintf( painCave.errMsg,
278	>	"A cutoff radius (rcut) must be specified when calculating"
279	>	" Tetrahedrality Parameters");
280	>	painCave.severity = OPENMD_ERROR;
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	if (!args_info.voxelSize_given) {
285	>	sprintf( painCave.errMsg,
286	>	"A voxel size must be specified when calculating"
287	>	" volume-resolved Tetrahedrality Parameters");
288	>	painCave.severity = OPENMD_ERROR;
289	>	painCave.isFatal = 1;
290	>	simError();
291	>	}
292	>	if (!args_info.gaussWidth_given) {
293	>	sprintf( painCave.errMsg,
294	>	"A gaussian width must be specified when calculating"
295	>	" volume-resolved Tetrahedrality Parameters");
296	>	painCave.severity = OPENMD_ERROR;
297	>	painCave.isFatal = 1;
298	>	simError();
299	>	}
300	>	analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
301	>	args_info.rcut_arg,
302	>	args_info.voxelSize_arg,
303	>	args_info.gaussWidth_arg);
304	>	} else if (args_info.ior_given){
305	>	if (args_info.rcut_given) {
306	>	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
307	>	args_info.rcut_arg,
308	>	args_info.nbins_arg, maxLen);
309	>	} else {
310	>	sprintf( painCave.errMsg,
311	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
312	>	painCave.severity = OPENMD_ERROR;
313	>	painCave.isFatal = 1;
314	>	simError();
315	>	}
316	>	} else if (args_info.for_given){
317	>	if (args_info.rcut_given) {
318	>	analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
319	>	args_info.nbins_arg, maxLen);
320	>	} else {
321	>	sprintf( painCave.errMsg,
322	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
323	>	painCave.severity = OPENMD_ERROR;
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>	} else if (args_info.bad_given){
328	>	if (args_info.rcut_given) {
329	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
330	>	args_info.rcut_arg,
331	>	args_info.nbins_arg);
332	>	} else {
333	>	sprintf( painCave.errMsg,
334	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
335	>	painCave.severity = OPENMD_ERROR;
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339	>	} else if (args_info.scd_given) {
340	>	if (batchMode) {
341	>	analyser  = new SCDOrderParameter(info, dumpFileName,
342	>	args_info.molname_arg,
343	>	args_info.begin_arg, args_info.end_arg);
344	>	} else{
345	>	std::string sele3 = args_info.sele3_arg;
346	>	analyser  = new SCDOrderParameter(info, dumpFileName,
347	>	sele1, sele2, sele3);
348	>	}
349	>	}else if (args_info.density_given) {
350	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
351	>	args_info.nbins_arg);
352	>	} else if (args_info.count_given) {
353	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
354	>	} else if (args_info.slab_density_given) {
355	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
356	>	} else if (args_info.rnemdz_given) {
357	>	analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
358	>	} else if (args_info.rnemdr_given) {
359	>	analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
360	>	} else if (args_info.rnemdrt_given) {
361	>	analyser = new RNEMDRTheta(info, dumpFileName, sele1,
362	>	args_info.nbins_arg, args_info.nanglebins_arg);
363	>	} else if (args_info.nitrile_given) {
364	>	analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
365	>	args_info.nbins_arg);
366	>	} else if (args_info.p_angle_given) {
367	>	if (args_info.sele1_given) {
368	>	if (args_info.sele2_given)
369	>	analyser  = new pAngle(info, dumpFileName, sele1, sele2,
370	>	args_info.nbins_arg);
371	>	else
372	>	if (args_info.seleoffset_given) {
373	>	if (args_info.seleoffset2_given) {
374	>	analyser  = new pAngle(info, dumpFileName, sele1,
375	>	args_info.seleoffset_arg,
376	>	args_info.seleoffset2_arg,
377	>	args_info.nbins_arg);
378	>	} else {
379	>	analyser  = new pAngle(info, dumpFileName, sele1,
380	>	args_info.seleoffset_arg,
381	>	args_info.nbins_arg);
382	>	}
383	>	} else
384	>	analyser  = new pAngle(info, dumpFileName, sele1,
385	>	args_info.nbins_arg);
386	>	} else {
387	>	sprintf( painCave.errMsg,
388	>	"At least one selection script (--sele1) must be specified when "
389	>	"calculating P(angle) distributions");
390	>	painCave.severity = OPENMD_ERROR;
391	>	painCave.isFatal = 1;
392	>	simError();
393	>	}
394	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
395	>	}else if (args_info.hxy_given) {
396	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
397	>	args_info.nbins_y_arg, args_info.nbins_arg);
398	>	#endif
399	>	}else if (args_info.rho_r_given) {
400	>	if (args_info.radius_given){
401	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
402	>	}else{
403	>	sprintf( painCave.errMsg,
404	>	"A particle radius (radius) must be specified when calculating Rho(r)");
405	>	painCave.severity = OPENMD_ERROR;
406	>	painCave.isFatal = 1;
407	>	simError();
408	>	}
409	>	} else if (args_info.hullvol_given) {
410	>	analyser = new NanoVolume(info, dumpFileName, sele1);
411	>	} else if (args_info.rodlength_given) {
412	>	analyser = new NanoLength(info, dumpFileName, sele1);
413	>	} else if (args_info.angle_r_given) {
414	>	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
415	>	}
416	>
417	>	if (args_info.output_given) {
418	>	analyser->setOutputName(args_info.output_arg);
419	>	}
420	>	if (args_info.step_given) {
421	>	analyser->setStep(args_info.step_arg);
422	>	}
423	>
424	>	analyser->process();
425	>
426	>	delete analyser;
427	>	delete info;
428	>
429	>	return 0;
430		}
151	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 354 by tim, Wed Feb 16 20:30:50 2005 UTC vs.
Revision 2015 by gezelter, Wed Aug 13 20:42:43 2014 UTC

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