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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 369 by tim, Fri Feb 18 23:07:32 2005 UTC vs.
Revision 1585 by gezelter, Sun Jun 19 17:51:15 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <iostream>
#	Line 50 | Line 50
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/RhoAngleR.hpp"
79	+	#include "applications/staticProps/TetrahedralityParam.hpp"
80
81	<	using namespace oopse;
81	>	using namespace OpenMD;
82
83		int main(int argc, char* argv[]){
84
85	<	//register force fields
86	<	registerForceFields();
87	<
88	<	gengetopt_args_info args_info;
89	<
90	<	//parse the command line option
91	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
92	<	exit(1) ;
85	>	//register force fields
86	>	registerForceFields();
87	>
88	>	gengetopt_args_info args_info;
89	>
90	>	//parse the command line option
91	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
92	>	exit(1) ;
93	>	}
94	>
95	>	//get the dumpfile name
96	>	std::string dumpFileName = args_info.input_arg;
97	>	std::string sele1;
98	>	std::string sele2;
99	>	bool userSpecifiedSelect1;
100	>	bool userSpecifiedSelect2;
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	<	//get the dumpfile name and meta-data file name
117	<	std::string dumpFileName = args_info.input_arg;
118	<
119	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
120	<
121	<
122	<	std::string sele1;
123	<	std::string sele2;
124	<
125	<	if (args_info.sele1_given) {
126	<	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	<	}
114	>	}
115	>
116	>	// check the second selection argument, or set it to the environment
117	>	// variable, or failing that, set it to "select all"
118	>
119	>	if (args_info.sele2_given) {
120	>	sele2 = args_info.sele2_arg;
121	>	} else {
122	>	char* sele2Env = getenv("SELECTION1");
123	>	if (sele2Env) {
124	>	sele2 = sele2Env;
125	>	} else {
126	>	sele2 = "select all";
127		}
128	<
129	<	if (args_info.sele2_given) {
130	<	sele2 = args_info.sele2_arg;
131	<	}else {
132	<	char* sele2Env = getenv("OOPSE_SELE2");
133	<	if (sele2Env) {
134	<	sele2 = sele2Env;
135	<	} else {
136	<	sprintf( painCave.errMsg,
137	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
138	<	painCave.severity = OOPSE_ERROR;
139	<	painCave.isFatal = 1;
140	<	simError();
141	<	}
128	>	}
129	>
130	>
131	>	// Problems if sele1 wasn't specified, but
132	>	// if (!args_info.scd_given) {
133	>	//       sprintf( painCave.errMsg,
134	>	//                "neither --sele1 option nor $SELECTION1 is set");
135	>	//       painCave.severity = OPENMD_ERROR;
136	>	//       painCave.isFatal = 1;
137	>	//       simError();
138	>	//     }
139	>	//   }
140	>
141	>	// Problems if sele1 wasn't specified
142	>
143	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
144	>	//       sprintf( painCave.errMsg,
145	>	//                "neither --sele2 option nor $SELECTION1 is set");
146	>	//       painCave.severity = OPENMD_ERROR;
147	>	//       painCave.isFatal = 1;
148	>	//       simError();
149	>	//     }
150	>	//   }
151	>
152	>	bool batchMode;
153	>	if (args_info.scd_given){
154	>	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
155	>	batchMode = false;
156	>	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
157	>	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
158	>	sprintf( painCave.errMsg,
159	>	"below conditions are not satisfied:\n"
160	>	"0 <= begin && 0<= end && begin <= end-2\n");
161	>	painCave.severity = OPENMD_ERROR;
162	>	painCave.isFatal = 1;
163	>	simError();
164	>	}
165	>	batchMode = true;
166	>	} else{
167	>	sprintf( painCave.errMsg,
168	>	"either --sele1, --sele2, --sele3 are specified,"
169	>	" or --molname, --begin, --end are specified\n");
170	>	painCave.severity = OPENMD_ERROR;
171	>	painCave.isFatal = 1;
172	>	simError();
173	>
174		}
175	+	}
176	+
177	+	//parse md file and set up the system
178	+	SimCreator creator;
179	+	std::cout << "dumpFile = " << dumpFileName << "\n";
180	+	SimInfo* info = creator.createSim(dumpFileName);
181
182	<	//parse md file and set up the system
183	<	SimCreator creator;
184	<	SimInfo* info = creator.createSim(mdFileName);
185	<
186	<	double maxLen;
187	<	if (args_info.length_given) {
188	<	maxLen = args_info.length_arg;
182	>	RealType maxLen;
183	>	RealType zmaxLen;
184	>	if (args_info.length_given) {
185	>	maxLen = args_info.length_arg;
186	>	if (args_info.zlength_given){
187	>	zmaxLen = args_info.zlength_arg;
188	>	}
189	>	} else {
190	>	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
191	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
192	>	zmaxLen = hmat(2,2);
193	>	}
194	>
195	>	StaticAnalyser* analyser;
196	>	if (args_info.gofr_given){
197	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
198	>	args_info.nbins_arg);
199	>	} else if (args_info.gofz_given) {
200	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
201	>	args_info.nbins_arg);
202	>	} else if (args_info.r_z_given) {
203	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
204	>	args_info.nbins_arg, args_info.nbins_z_arg);
205	>	} else if (args_info.r_theta_given) {
206	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
207	>	args_info.nbins_arg, args_info.nanglebins_arg);
208	>	} else if (args_info.r_omega_given) {
209	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
210	>	args_info.nbins_arg, args_info.nanglebins_arg);
211	>	} else if (args_info.theta_omega_given) {
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	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
217	>	maxLen, args_info.nbins_arg);
218		} else {
219	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
220	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
219	>	sprintf( painCave.errMsg,
220	>	"--refsele must set when --gxyz is used");
221	>	painCave.severity = OPENMD_ERROR;
222	>	painCave.isFatal = 1;
223	>	simError();
224	>	}
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	<
237	<	RadialDistrFunc* rdf;
238	<	if (args_info.gofr_given){
239	<	rdf= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
240	<	} else if (args_info.r_theta_given) {
241	<	rdf  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
242	<	} else if (args_info.r_omega_given) {
243	<	rdf  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
244	<	} else if (args_info.theta_omega_given) {
245	<	rdf  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
246	<	} else if (args_info.gxyz_given) {
247	<	if (args_info.refsele_given) {
135	<	rdf= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
136	<	} else {
137	<	sprintf( painCave.errMsg,
138	<	"--refsele must set when --gxyz is used");
139	<	painCave.severity = OOPSE_ERROR;
140	<	painCave.isFatal = 1;
141	<	simError();
142	<	}
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	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
242	>	} else {
243	>	sprintf( painCave.errMsg,
244	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
245	>	painCave.severity = OPENMD_ERROR;
246	>	painCave.isFatal = 1;
247	>	simError();
248		}
249	+	} else if (args_info.rp2_given){
250	+	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
251	+	} else if (args_info.bo_given){
252	+	if (args_info.rcut_given) {
253	+	analyser = new BondOrderParameter(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 Bond Order Parameters");
259	+	painCave.severity = OPENMD_ERROR;
260	+	painCave.isFatal = 1;
261	+	simError();
262	+	}
263
264	<	if (args_info.output_given) {
265	<	rdf->setOutputName(args_info.output_arg);
264	>	} else if (args_info.tet_param_given) {
265	>	if (args_info.rcut_given) {
266	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
267	>	args_info.rcut_arg,
268	>	args_info.nbins_arg);
269	>	} else {
270	>	sprintf( painCave.errMsg,
271	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
272	>	painCave.severity = OPENMD_ERROR;
273	>	painCave.isFatal = 1;
274	>	simError();
275		}
276	<	if (args_info.step_given) {
277	<	rdf->setStep(args_info.step_arg);
276	>	} else if (args_info.bor_given){
277	>	if (args_info.rcut_given) {
278	>	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
279	>	args_info.nbins_arg, maxLen);
280	>	} else {
281	>	sprintf( painCave.errMsg,
282	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
283	>	painCave.severity = OPENMD_ERROR;
284	>	painCave.isFatal = 1;
285	>	simError();
286		}
287	+	} else if (args_info.bad_given){
288	+	if (args_info.rcut_given) {
289	+	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
290	+	args_info.nbins_arg);
291	+	} else {
292	+	sprintf( painCave.errMsg,
293	+	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
294	+	painCave.severity = OPENMD_ERROR;
295	+	painCave.isFatal = 1;
296	+	simError();
297	+	}
298	+	} else if (args_info.scd_given) {
299	+	if (batchMode) {
300	+	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
301	+	args_info.begin_arg, args_info.end_arg);
302	+	} else{
303	+	std::string sele3 = args_info.sele3_arg;
304	+	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
305	+	}
306	+	}else if (args_info.density_given) {
307	+	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
308	+	args_info.nbins_arg);
309	+	} else if (args_info.count_given) {
310	+	analyser = new ObjectCount(info, dumpFileName, sele1 );
311	+	} else if (args_info.slab_density_given) {
312	+	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
313	+	} else if (args_info.p_angle_given) {
314	+	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
315	+	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
316	+	}else if (args_info.hxy_given) {
317	+	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
318	+	args_info.nbins_y_arg, args_info.nbins_arg);
319	+	#endif
320	+	}else if (args_info.rho_r_given) {
321	+	if (args_info.radius_given){
322	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
323	+	}else{
324	+	sprintf( painCave.errMsg,
325	+	"A particle radius (radius) must be specified when calculating Rho(r)");
326	+	painCave.severity = OPENMD_ERROR;
327	+	painCave.isFatal = 1;
328	+	simError();
329	+	}
330	+	} else if (args_info.hullvol_given) {
331	+	analyser = new NanoVolume(info, dumpFileName, sele1);
332	+	} else if (args_info.rodlength_given) {
333	+	analyser = new NanoLength(info, dumpFileName, sele1);
334	+	} else if (args_info.angle_r_given) {
335	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
336	+	}
337	+
338	+	if (args_info.output_given) {
339	+	analyser->setOutputName(args_info.output_arg);
340	+	}
341	+	if (args_info.step_given) {
342	+	analyser->setStep(args_info.step_arg);
343	+	}
344	+
345	+	analyser->process();
346	+
347	+	delete analyser;
348	+	delete info;
349
350	<	rdf->process();
153	<
154	<	delete rdf;
155	<	delete info;
156	<
157	<	return 0;
350	>	return 0;
351		}
352

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 369 by tim, Fri Feb 18 23:07:32 2005 UTC vs.
Revision 1585 by gezelter, Sun Jun 19 17:51:15 2011 UTC

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

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