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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 1513 by gezelter, Tue Oct 19 18:40:54 2010 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>
43		#include <fstream>
44		#include <string>
45
46	–	#include "applications/staticProps/StaticPropsCmd.h"
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	<	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	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
73	>	#include "applications/staticProps/Hxy.hpp"
74	>	#endif
75	>	#include "applications/staticProps/RhoR.hpp"
76
77	+	using namespace OpenMD;
78	+
79		int main(int argc, char* argv[]){
80
81	<	//register force fields
82	<	registerForceFields();
83	<
84	<	gengetopt_args_info args_info;
85	<
86	<	//parse the command line option
87	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
88	<	exit(1) ;
81	>	//register force fields
82	>	registerForceFields();
83	>
84	>	gengetopt_args_info args_info;
85	>
86	>	//parse the command line option
87	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
88	>	exit(1) ;
89	>	}
90	>
91	>	//get the dumpfile name
92	>	std::string dumpFileName = args_info.input_arg;
93	>	std::string sele1;
94	>	std::string sele2;
95	>	bool userSpecifiedSelect1;
96	>	bool userSpecifiedSelect2;
97	>
98	>	// check the first selection argument, or set it to the environment
99	>	// variable, or failing that, set it to "select all"
100	>
101	>	if (args_info.sele1_given) {
102	>	sele1 = args_info.sele1_arg;
103	>	} else {
104	>	char*  sele1Env= getenv("SELECTION1");
105	>	if (sele1Env) {
106	>	sele1 = sele1Env;
107	>	} else {
108	>	sele1 = "select all";
109		}
110	<
111	<
112	<	//get the dumpfile name and meta-data file name
113	<	std::string dumpFileName = args_info.input_arg;
114	<
115	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
116	<
117	<
118	<	//parse md file and set up the system
119	<	SimCreator creator;
120	<	SimInfo* info = creator.createSim(mdFileName, false);
121	<
122	<
79	<	std::string sele1;
80	<	std::string sele2;
81	<
82	<	if (args_info.sele1_given) {
83	<	sele1 = args_info.sele1_arg;
84	<	}else {
85	<
110	>	}
111	>
112	>	// check the second selection argument, or set it to the environment
113	>	// variable, or failing that, set it to "select all"
114	>
115	>	if (args_info.sele2_given) {
116	>	sele2 = args_info.sele2_arg;
117	>	} else {
118	>	char* sele2Env = getenv("SELECTION1");
119	>	if (sele2Env) {
120	>	sele2 = sele2Env;
121	>	} else {
122	>	sele2 = "select all";
123		}
124	<	if (args_info.sele1_given) {
125	<	sele1 = args_info.sele1_arg;
126	<	}else {
124	>	}
125	>
126	>
127	>	// Problems if sele1 wasn't specified, but
128	>	// if (!args_info.scd_given) {
129	>	//       sprintf( painCave.errMsg,
130	>	//                "neither --sele1 option nor $SELECTION1 is set");
131	>	//       painCave.severity = OPENMD_ERROR;
132	>	//       painCave.isFatal = 1;
133	>	//       simError();
134	>	//     }
135	>	//   }
136	>
137	>	// Problems if sele1 wasn't specified
138	>
139	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
140	>	//       sprintf( painCave.errMsg,
141	>	//                "neither --sele2 option nor $SELECTION1 is set");
142	>	//       painCave.severity = OPENMD_ERROR;
143	>	//       painCave.isFatal = 1;
144	>	//       simError();
145	>	//     }
146	>	//   }
147	>
148	>	bool batchMode;
149	>	if (args_info.scd_given){
150	>	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
151	>	batchMode = false;
152	>	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
153	>	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
154	>	sprintf( painCave.errMsg,
155	>	"below conditions are not satisfied:\n"
156	>	"0 <= begin && 0<= end && begin <= end-2\n");
157	>	painCave.severity = OPENMD_ERROR;
158	>	painCave.isFatal = 1;
159	>	simError();
160	>	}
161	>	batchMode = true;
162	>	} else{
163	>	sprintf( painCave.errMsg,
164	>	"either --sele1, --sele2, --sele3 are specified,"
165	>	" or --molname, --begin, --end are specified\n");
166	>	painCave.severity = OPENMD_ERROR;
167	>	painCave.isFatal = 1;
168	>	simError();
169	>
170	>	}
171	>	}
172	>
173	>	//parse md file and set up the system
174	>	SimCreator creator;
175	>	std::cout << "dumpFile = " << dumpFileName << "\n";
176	>	SimInfo* info = creator.createSim(dumpFileName);
177
178	+	RealType maxLen;
179	+	RealType zmaxLen;
180	+	if (args_info.length_given) {
181	+	maxLen = args_info.length_arg;
182	+	if (args_info.zlength_given){
183	+	zmaxLen = args_info.zlength_arg;
184		}
185	<
186	<	GofR rdf(info, dumpFileName, sele1, sele2, args_info.length_arg);
185	>	} else {
186	>	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
187	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
188	>	zmaxLen = hmat(2,2);
189	>	}
190
191	<	if (args_info.nbins_given) {
192	<	rdf.setNBins(args_info.nbins_arg);
191	>	StaticAnalyser* analyser;
192	>	if (args_info.gofr_given){
193	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
194	>	args_info.nbins_arg);
195	>	} else if (args_info.gofz_given) {
196	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
197	>	args_info.nbins_arg);
198	>	} else if (args_info.r_z_given) {
199	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
200	>	args_info.nbins_arg, args_info.nbins_z_arg);
201	>	} else if (args_info.r_theta_given) {
202	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
203	>	args_info.nbins_arg, args_info.nanglebins_arg);
204	>	} else if (args_info.r_omega_given) {
205	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
206	>	args_info.nbins_arg, args_info.nanglebins_arg);
207	>	} else if (args_info.theta_omega_given) {
208	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
209	>	args_info.nanglebins_arg);
210	>	} else if (args_info.gxyz_given) {
211	>	if (args_info.refsele_given) {
212	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
213	>	maxLen, args_info.nbins_arg);
214	>	} else {
215	>	sprintf( painCave.errMsg,
216	>	"--refsele must set when --gxyz is used");
217	>	painCave.severity = OPENMD_ERROR;
218	>	painCave.isFatal = 1;
219	>	simError();
220		}
221	+	} else if (args_info.twodgofr_given){
222	+	if (args_info.dz_given) {
223	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
224	+	args_info.dz_arg, args_info.nbins_arg);
225	+	} else {
226	+	sprintf( painCave.errMsg,
227	+	"A slab width (dz) must be specified when calculating TwoDGofR");
228	+	painCave.severity = OPENMD_ERROR;
229	+	painCave.isFatal = 1;
230	+	simError();
231	+	}
232	+	} else if (args_info.p2_given) {
233	+	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
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	+	} else if (args_info.bor_given){
249	+	if (args_info.rcut_given) {
250	+	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
251	+	args_info.nbins_arg, maxLen);
252	+	} else {
253	+	sprintf( painCave.errMsg,
254	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
255	+	painCave.severity = OPENMD_ERROR;
256	+	painCave.isFatal = 1;
257	+	simError();
258	+	}
259	+	} else if (args_info.bad_given){
260	+	if (args_info.rcut_given) {
261	+	analyser = new BondAngleDistribution(info, dumpFileName, sele1, 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 Bond Angle Distributions");
266	+	painCave.severity = OPENMD_ERROR;
267	+	painCave.isFatal = 1;
268	+	simError();
269	+	}
270	+	} else if (args_info.scd_given) {
271	+	if (batchMode) {
272	+	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
273	+	args_info.begin_arg, args_info.end_arg);
274	+	} else{
275	+	std::string sele3 = args_info.sele3_arg;
276	+	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
277	+	}
278	+	}else if (args_info.density_given) {
279	+	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
280	+	args_info.nbins_arg);
281	+	} else if (args_info.count_given) {
282	+	analyser = new ObjectCount(info, dumpFileName, sele1 );
283	+	} else if (args_info.slab_density_given) {
284	+	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
285	+	} else if (args_info.p_angle_given) {
286	+	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
287	+	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
288	+	}else if (args_info.hxy_given) {
289	+	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
290	+	args_info.nbins_y_arg, args_info.nbins_arg);
291	+	#endif
292	+	}else if (args_info.rho_r_given) {
293	+	if (args_info.radius_given){
294	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
295	+	}else{
296	+	sprintf( painCave.errMsg,
297	+	"A particle radius (radius) must be specified when calculating Rho(r)");
298	+	painCave.severity = OPENMD_ERROR;
299	+	painCave.isFatal = 1;
300	+	simError();
301	+	}
302	+	}else if (args_info.hullvol_given) {
303	+	analyser = new NanoVolume(info, dumpFileName, sele1);
304	+	}
305	+
306	+	if (args_info.output_given) {
307	+	analyser->setOutputName(args_info.output_arg);
308	+	}
309	+	if (args_info.step_given) {
310	+	analyser->setStep(args_info.step_arg);
311	+	}
312
313	<	rdf.process();
100	<
101	<	delete info;
313	>	analyser->process();
314
315	<	return 0;
315	>	delete analyser;
316	>	delete info;
317	>
318	>	return 0;
319		}
320

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 310 by tim, Thu Feb 10 18:14:03 2005 UTC vs.
Revision 1513 by gezelter, Tue Oct 19 18:40:54 2010 UTC

#	Line 0 | Line 1
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