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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 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 "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
63	<	registerForceFields();
64	<
89	>
90		gengetopt_args_info args_info;
91	<
91	>
92		//parse the command line option
93		if (cmdline_parser (argc, argv, &args_info) != 0) {
94		exit(1) ;
95		}
96	<
97	<
73	<	//get the dumpfile name and meta-data file name
96	>
97	>	//get the dumpfile name
98		std::string dumpFileName = args_info.input_arg;
75	–
76	–	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
77	–
78	–
99		std::string sele1;
100		std::string sele2;
101	<
101	>	std::string sele3;
102	>
103	>	// check the first selection argument, or set it to the environment
104	>	// variable, or failing that, set it to "select all"
105	>
106		if (args_info.sele1_given) {
107		sele1 = args_info.sele1_arg;
108	<	}else {
109	<	char*  sele1Env= getenv("OOPSE_SELE1");
108	>	} else {
109	>	char*  sele1Env= getenv("SELECTION1");
110		if (sele1Env) {
111		sele1 = sele1Env;
112	<	}else {
113	<	sprintf( painCave.errMsg,
90	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
91	<	painCave.severity = OOPSE_ERROR;
92	<	painCave.isFatal = 1;
93	<	simError();
112	>	} else {
113	>	sele1 = "select all";
114		}
115		}
116	<
116	>
117	>	// check the second selection argument, or set it to the environment
118	>	// variable, or failing that, set it to the first selection
119	>
120		if (args_info.sele2_given) {
121		sele2 = args_info.sele2_arg;
122	<	}else {
123	<	char* sele2Env = getenv("OOPSE_SELE2");
122	>	} else {
123	>	char* sele2Env = getenv("SELECTION2");
124		if (sele2Env) {
125		sele2 = sele2Env;
126	<	} else {
126	>	} else {
127	>	//If sele2 is not specified, then the default behavior
128	>	//should be what is already intended for sele1
129	>	sele2 = sele1;
130	>	}
131	>	}
132	>
133	>	// check the third selection argument, which is only set if
134	>	// requested by the user
135	>
136	>	if (args_info.sele3_given) sele3 = args_info.sele3_arg;
137	>
138	>	bool batchMode;
139	>	if (args_info.scd_given){
140	>	if (args_info.sele1_given &&
141	>	args_info.sele2_given && args_info.sele3_given) {
142	>	batchMode = false;
143	>	} else if (args_info.molname_given &&
144	>	args_info.begin_given && args_info.end_given) {
145	>	if (args_info.begin_arg < 0 ||
146	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
147	>	sprintf( painCave.errMsg,
148	>	"below conditions are not satisfied:\n"
149	>	"0 <= begin && 0<= end && begin <= end-2\n");
150	>	painCave.severity = OPENMD_ERROR;
151	>	painCave.isFatal = 1;
152	>	simError();
153	>	}
154	>	batchMode = true;
155	>	} else{
156		sprintf( painCave.errMsg,
157	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
158	<	painCave.severity = OOPSE_ERROR;
157	>	"either --sele1, --sele2, --sele3 are specified,"
158	>	" or --molname, --begin, --end are specified\n");
159	>	painCave.severity = OPENMD_ERROR;
160		painCave.isFatal = 1;
161	<	simError();
161	>	simError();
162		}
163		}
164	<
164	>
165		//parse md file and set up the system
166		SimCreator creator;
167	<	SimInfo* info = creator.createSim(mdFileName);
167	>	SimInfo* info = creator.createSim(dumpFileName);
168
169	<	double maxLen;
169	>	RealType maxLen;
170	>	RealType zmaxLen;
171		if (args_info.length_given) {
172		maxLen = args_info.length_arg;
173	+	if (args_info.zlength_given){
174	+	zmaxLen = args_info.zlength_arg;
175	+	}
176		} else {
177		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
178	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
178	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
179	>	zmaxLen = hmat(2,2);
180		}
181	<
182	<	RadialDistrFunc* rdf;
181	>
182	>	StaticAnalyser* analyser;
183		if (args_info.gofr_given){
184	<	rdf= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
184	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
185	>	args_info.nbins_arg);
186	>	} else if (args_info.gofz_given) {
187	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
188	>	args_info.nbins_arg);
189	>	} else if (args_info.r_z_given) {
190	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
191	>	args_info.nbins_arg, args_info.nbins_z_arg);
192		} else if (args_info.r_theta_given) {
193	<	rdf  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
193	>	if (args_info.sele3_given)
194	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
195	>	args_info.nbins_arg, args_info.nanglebins_arg);
196	>	else
197	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
198	>	args_info.nbins_arg, args_info.nanglebins_arg);
199		} else if (args_info.r_omega_given) {
200	<	rdf  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
200	>	if (args_info.sele3_given)
201	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
202	>	args_info.nbins_arg, args_info.nanglebins_arg);
203	>	else
204	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
205	>	args_info.nbins_arg, args_info.nanglebins_arg);
206	>
207		} else if (args_info.theta_omega_given) {
208	<	rdf  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
208	>	if (args_info.sele3_given)
209	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
210	>	args_info.nanglebins_arg);
211	>	else
212	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
213	>	args_info.nanglebins_arg);
214		} else if (args_info.gxyz_given) {
215		if (args_info.refsele_given) {
216	<	rdf= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
216	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
217	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
218		} else {
219		sprintf( painCave.errMsg,
220	<	"--refsele must set when --gxyz is used");
221	<	painCave.severity = OOPSE_ERROR;
220	>	"--refsele must set when --gxyz is used");
221	>	painCave.severity = OPENMD_ERROR;
222		painCave.isFatal = 1;
223		simError();
224		}
225	<	}
226	<
227	<	if (args_info.output_given) {
228	<	rdf->setOutputName(args_info.output_arg);
225	>	} else if (args_info.twodgofr_given){
226	>	if (args_info.dz_given) {
227	>	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
228	>	args_info.dz_arg, args_info.nbins_arg);
229	>	} else {
230	>	sprintf( painCave.errMsg,
231	>	"A slab width (dz) must be specified when calculating TwoDGofR");
232	>	painCave.severity = OPENMD_ERROR;
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236	>	} else if (args_info.p2_given) {
237	>	if (args_info.sele1_given) {
238	>	if (args_info.sele2_given)
239	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
240	>	else
241	>	if (args_info.seleoffset_given)
242	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
243	>	args_info.seleoffset_arg);
244	>	else
245	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
246	>	} else {
247	>	sprintf( painCave.errMsg,
248	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
249	>	painCave.severity = OPENMD_ERROR;
250	>	painCave.isFatal = 1;
251	>	simError();
252	>	}
253	>	} else if (args_info.rp2_given){
254	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
255	>	} else if (args_info.bo_given){
256	>	if (args_info.rcut_given) {
257	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
258	>	args_info.rcut_arg,
259	>	args_info.nbins_arg);
260	>	} else {
261	>	sprintf( painCave.errMsg,
262	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
263	>	painCave.severity = OPENMD_ERROR;
264	>	painCave.isFatal = 1;
265	>	simError();
266	>	}
267	>	} else if (args_info.multipole_given){
268	>	analyser = new MultipoleSum(info, dumpFileName, sele1,
269	>	maxLen, args_info.nbins_arg);
270	>	} else if (args_info.tet_param_given) {
271	>	if (args_info.rcut_given) {
272	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
273	>	args_info.rcut_arg,
274	>	args_info.nbins_arg);
275	>	} else {
276	>	sprintf( painCave.errMsg,
277	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
278	>	painCave.severity = OPENMD_ERROR;
279	>	painCave.isFatal = 1;
280	>	simError();
281	>	}
282	>	} else if (args_info.tet_param_z_given) {
283	>	if (args_info.rcut_given) {
284	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
285	>	args_info.rcut_arg,
286	>	args_info.nbins_arg);
287	>	} else {
288	>	sprintf( painCave.errMsg,
289	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
290	>	painCave.severity = OPENMD_ERROR;
291	>	painCave.isFatal = 1;
292	>	simError();
293	>	}
294	>	} else if (args_info.tet_param_xyz_given) {
295	>	if (!args_info.rcut_given) {
296	>	sprintf( painCave.errMsg,
297	>	"A cutoff radius (rcut) must be specified when calculating"
298	>	" Tetrahedrality Parameters");
299	>	painCave.severity = OPENMD_ERROR;
300	>	painCave.isFatal = 1;
301	>	simError();
302	>	}
303	>	if (!args_info.voxelSize_given) {
304	>	sprintf( painCave.errMsg,
305	>	"A voxel size must be specified when calculating"
306	>	" volume-resolved Tetrahedrality Parameters");
307	>	painCave.severity = OPENMD_ERROR;
308	>	painCave.isFatal = 1;
309	>	simError();
310	>	}
311	>	if (!args_info.gaussWidth_given) {
312	>	sprintf( painCave.errMsg,
313	>	"A gaussian width must be specified when calculating"
314	>	" volume-resolved Tetrahedrality Parameters");
315	>	painCave.severity = OPENMD_ERROR;
316	>	painCave.isFatal = 1;
317	>	simError();
318	>	}
319	>	analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
320	>	args_info.rcut_arg,
321	>	args_info.voxelSize_arg,
322	>	args_info.gaussWidth_arg);
323	>	} else if (args_info.ior_given){
324	>	if (args_info.rcut_given) {
325	>	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
326	>	args_info.rcut_arg,
327	>	args_info.nbins_arg, maxLen);
328	>	} else {
329	>	sprintf( painCave.errMsg,
330	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
331	>	painCave.severity = OPENMD_ERROR;
332	>	painCave.isFatal = 1;
333	>	simError();
334	>	}
335	>	} else if (args_info.for_given){
336	>	if (args_info.rcut_given) {
337	>	analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
338	>	args_info.nbins_arg, maxLen);
339	>	} else {
340	>	sprintf( painCave.errMsg,
341	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
342	>	painCave.severity = OPENMD_ERROR;
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346	>	} else if (args_info.bad_given){
347	>	if (args_info.rcut_given) {
348	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
349	>	args_info.rcut_arg,
350	>	args_info.nbins_arg);
351	>	} else {
352	>	sprintf( painCave.errMsg,
353	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
354	>	painCave.severity = OPENMD_ERROR;
355	>	painCave.isFatal = 1;
356	>	simError();
357	>	}
358	>	} else if (args_info.scd_given) {
359	>	if (batchMode) {
360	>	analyser  = new SCDOrderParameter(info, dumpFileName,
361	>	args_info.molname_arg,
362	>	args_info.begin_arg, args_info.end_arg);
363	>	} else{
364	>	analyser  = new SCDOrderParameter(info, dumpFileName,
365	>	sele1, sele2, sele3);
366	>	}
367	>	}else if (args_info.density_given) {
368	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
369	>	args_info.nbins_arg);
370	>	} else if (args_info.count_given) {
371	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
372	>	} else if (args_info.slab_density_given) {
373	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
374	>	} else if (args_info.rnemdz_given) {
375	>	analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
376	>	} else if (args_info.rnemdr_given) {
377	>	analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
378	>	} else if (args_info.rnemdrt_given) {
379	>	analyser = new RNEMDRTheta(info, dumpFileName, sele1,
380	>	args_info.nbins_arg, args_info.nanglebins_arg);
381	>	} else if (args_info.nitrile_given) {
382	>	analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
383	>	args_info.nbins_arg);
384	>	} else if (args_info.p_angle_given) {
385	>	if (args_info.sele1_given) {
386	>	if (args_info.sele2_given)
387	>	analyser  = new pAngle(info, dumpFileName, sele1, sele2,
388	>	args_info.nbins_arg);
389	>	else
390	>	if (args_info.seleoffset_given) {
391	>	if (args_info.seleoffset2_given) {
392	>	analyser  = new pAngle(info, dumpFileName, sele1,
393	>	args_info.seleoffset_arg,
394	>	args_info.seleoffset2_arg,
395	>	args_info.nbins_arg);
396	>	} else {
397	>	analyser  = new pAngle(info, dumpFileName, sele1,
398	>	args_info.seleoffset_arg,
399	>	args_info.nbins_arg);
400	>	}
401	>	} else
402	>	analyser  = new pAngle(info, dumpFileName, sele1,
403	>	args_info.nbins_arg);
404	>	} else {
405	>	sprintf( painCave.errMsg,
406	>	"At least one selection script (--sele1) must be specified when "
407	>	"calculating P(angle) distributions");
408	>	painCave.severity = OPENMD_ERROR;
409	>	painCave.isFatal = 1;
410	>	simError();
411	>	}
412	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
413	>	}else if (args_info.hxy_given) {
414	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
415	>	args_info.nbins_y_arg, args_info.nbins_arg);
416	>	#endif
417	>	}else if (args_info.rho_r_given) {
418	>	if (args_info.radius_given){
419	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
420	>	}else{
421	>	sprintf( painCave.errMsg,
422	>	"A particle radius (radius) must be specified when calculating Rho(r)");
423	>	painCave.severity = OPENMD_ERROR;
424	>	painCave.isFatal = 1;
425	>	simError();
426	>	}
427	>	} else if (args_info.hullvol_given) {
428	>	analyser = new NanoVolume(info, dumpFileName, sele1);
429	>	} else if (args_info.rodlength_given) {
430	>	analyser = new NanoLength(info, dumpFileName, sele1);
431	>	} else if (args_info.angle_r_given) {
432	>	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
433		}
434	+
435	+	if (args_info.output_given) {
436	+	analyser->setOutputName(args_info.output_arg);
437	+	}
438		if (args_info.step_given) {
439	<	rdf->setStep(args_info.step_arg);
439	>	analyser->setStep(args_info.step_arg);
440		}
441	<
442	<	rdf->process();
443	<
444	<	delete rdf;
441	>
442	>	analyser->process();
443	>
444	>	delete analyser;
445		delete info;
446	<
446	>
447		return 0;
448		}
159	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 UTC

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