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root/OpenMD/branches/development/src/applications/staticProps/StaticProps.cpp

Comparing:
trunk/src/applications/staticProps/StaticProps.cpp (file contents), Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
branches/development/src/applications/staticProps/StaticProps.cpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 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]  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
80	<	using namespace oopse;
80	>	using namespace OpenMD;
81
82		int main(int argc, char* argv[]){
83
84	<	//register force fields
85	<	registerForceFields();
86	<
87	<	gengetopt_args_info args_info;
88	<
89	<	//parse the command line option
90	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
91	<	exit(1) ;
92	<	}
93	<
94	<
95	<	//get the dumpfile name and meta-data file name
96	<	std::string dumpFileName = args_info.input_arg;
97	<
98	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
99	<
100	<
101	<	std::string sele1;
102	<	std::string sele2;
103	<
104	<	if (args_info.sele1_given) {
105	<	sele1 = args_info.sele1_arg;
106	<	}else {
107	<	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	<	}
95	<	}
96	<
97	<	if (args_info.sele2_given) {
98	<	sele2 = args_info.sele2_arg;
99	<	}else {
100	<	char* sele2Env = getenv("OOPSE_SELE2");
101	<	if (sele2Env) {
102	<	sele2 = sele2Env;
103	<	} else {
104	<	sprintf( painCave.errMsg,
105	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
106	<	painCave.severity = OOPSE_ERROR;
107	<	painCave.isFatal = 1;
108	<	simError();
109	<	}
110	<	}
111	<
112	<	//parse md file and set up the system
113	<	SimCreator creator;
114	<	SimInfo* info = creator.createSim(mdFileName, false);
115	<
116	<	double maxLen;
117	<	if (args_info.length_given) {
118	<	maxLen = args_info.length_arg;
84	>
85	>	gengetopt_args_info args_info;
86	>
87	>	//parse the command line option
88	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
89	>	exit(1) ;
90	>	}
91	>
92	>	//get the dumpfile name
93	>	std::string dumpFileName = args_info.input_arg;
94	>	std::string sele1;
95	>	std::string sele2;
96	>	bool userSpecifiedSelect1;
97	>	bool userSpecifiedSelect2;
98	>
99	>	// check the first selection argument, or set it to the environment
100	>	// variable, or failing that, set it to "select all"
101	>
102	>	if (args_info.sele1_given) {
103	>	sele1 = args_info.sele1_arg;
104	>	} else {
105	>	char*  sele1Env= getenv("SELECTION1");
106	>	if (sele1Env) {
107	>	sele1 = sele1Env;
108		} else {
109	<	double rcut;
121	<	double rsw;
122	<	info->getCutoff(rcut, rsw);
123	<	maxLen = rcut + rsw;
109	>	sele1 = "select all";
110		}
111	<
112	<
113	<	RadialDistrFunc* rdf;
114	<	if (args_info.gofr_given){
115	<	GofR* r = new GofR(info, dumpFileName, sele1, sele2);
116	<
117	<	r->setNRBins(args_info.nrbins_arg);
118	<	r->setLength(maxLen);
119	<
120	<	rdf = r;
121	<	} else if (args_info.r_theta_given) {
122	<	GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2);
123	<
138	<	rTheta->setNRBins(args_info.nrbins_arg);
139	<	rTheta->setLength(maxLen);
140	<	rTheta->setNAngleBins(args_info.nanglebins_arg);
141	<
142	<
143	<	rdf = rTheta;
111	>	}
112	>
113	>	// check the second selection argument, or set it to the environment
114	>	// variable, or failing that, set it to "select all"
115	>
116	>	if (args_info.sele2_given) {
117	>	sele2 = args_info.sele2_arg;
118	>	} else {
119	>	char* sele2Env = getenv("SELECTION1");
120	>	if (sele2Env) {
121	>	sele2 = sele2Env;
122	>	} else {
123	>	sele2 = "select all";
124		}
125	<	else if (args_info.r_omega_given) {
126	<	GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2);
127	<
128	<
129	<	rOmega->setNRBins(args_info.nrbins_arg);
130	<	rOmega->setLength(maxLen);
131	<	rOmega->setNAngleBins(args_info.nanglebins_arg);
132	<
133	<	rdf = rOmega;
134	<	} else if (args_info.theta_omega_given) {
135	<	GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2);
136	<	rAngle2->setNAngleBins(args_info.nanglebins_arg);
137	<
138	<	rdf = rAngle2;
139	<	} else if (args_info.xyz_given) {
140	<
141	<	GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2);
142	<
143	<	xyz->setNRBins(args_info.nrbins_arg);
144	<	xyz->setLength(maxLen);
145	<
146	<
147	<	rdf = xyz;
148	<	}
149	<
150	<
151	<	if (args_info.output_given) {
152	<	rdf->setOutputName(args_info.output_arg);
125	>	}
126	>
127	>
128	>	// Problems if sele1 wasn't specified, but
129	>	// if (!args_info.scd_given) {
130	>	//       sprintf( painCave.errMsg,
131	>	//                "neither --sele1 option nor $SELECTION1 is set");
132	>	//       painCave.severity = OPENMD_ERROR;
133	>	//       painCave.isFatal = 1;
134	>	//       simError();
135	>	//     }
136	>	//   }
137	>
138	>	// Problems if sele1 wasn't specified
139	>
140	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
141	>	//       sprintf( painCave.errMsg,
142	>	//                "neither --sele2 option nor $SELECTION1 is set");
143	>	//       painCave.severity = OPENMD_ERROR;
144	>	//       painCave.isFatal = 1;
145	>	//       simError();
146	>	//     }
147	>	//   }
148	>
149	>	bool batchMode;
150	>	if (args_info.scd_given){
151	>	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
152	>	batchMode = false;
153	>	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
154	>	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
155	>	sprintf( painCave.errMsg,
156	>	"below conditions are not satisfied:\n"
157	>	"0 <= begin && 0<= end && begin <= end-2\n");
158	>	painCave.severity = OPENMD_ERROR;
159	>	painCave.isFatal = 1;
160	>	simError();
161	>	}
162	>	batchMode = true;
163	>	} else{
164	>	sprintf( painCave.errMsg,
165	>	"either --sele1, --sele2, --sele3 are specified,"
166	>	" or --molname, --begin, --end are specified\n");
167	>	painCave.severity = OPENMD_ERROR;
168	>	painCave.isFatal = 1;
169	>	simError();
170	>
171		}
172	+	}
173	+
174	+	//parse md file and set up the system
175	+	SimCreator creator;
176	+	std::cout << "dumpFile = " << dumpFileName << "\n";
177	+	SimInfo* info = creator.createSim(dumpFileName);
178
179	<	if (args_info.step_given) {
180	<	rdf->setStep(args_info.step_arg);
179	>	RealType maxLen;
180	>	RealType zmaxLen;
181	>	if (args_info.length_given) {
182	>	maxLen = args_info.length_arg;
183	>	if (args_info.zlength_given){
184	>	zmaxLen = args_info.zlength_arg;
185		}
186	+	} else {
187	+	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
188	+	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
189	+	zmaxLen = hmat(2,2);
190	+	}
191	+
192	+	StaticAnalyser* analyser;
193	+	if (args_info.gofr_given){
194	+	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
195	+	args_info.nbins_arg);
196	+	} else if (args_info.gofz_given) {
197	+	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
198	+	args_info.nbins_arg);
199	+	} else if (args_info.r_z_given) {
200	+	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
201	+	args_info.nbins_arg, args_info.nbins_z_arg);
202	+	} else if (args_info.r_theta_given) {
203	+	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
204	+	args_info.nbins_arg, args_info.nanglebins_arg);
205	+	} else if (args_info.r_omega_given) {
206	+	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
207	+	args_info.nbins_arg, args_info.nanglebins_arg);
208	+	} else if (args_info.theta_omega_given) {
209	+	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
210	+	args_info.nanglebins_arg);
211	+	} else if (args_info.gxyz_given) {
212	+	if (args_info.refsele_given) {
213	+	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
214	+	maxLen, args_info.nbins_arg);
215	+	} else {
216	+	sprintf( painCave.errMsg,
217	+	"--refsele must set when --gxyz is used");
218	+	painCave.severity = OPENMD_ERROR;
219	+	painCave.isFatal = 1;
220	+	simError();
221	+	}
222	+	} else if (args_info.twodgofr_given){
223	+	if (args_info.dz_given) {
224	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
225	+	args_info.dz_arg, args_info.nbins_arg);
226	+	} else {
227	+	sprintf( painCave.errMsg,
228	+	"A slab width (dz) must be specified when calculating TwoDGofR");
229	+	painCave.severity = OPENMD_ERROR;
230	+	painCave.isFatal = 1;
231	+	simError();
232	+	}
233	+	} else if (args_info.p2_given) {
234	+	if (args_info.sele1_given) {
235	+	if (args_info.sele2_given)
236	+	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
237	+	else
238	+	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
239	+	} else {
240	+	sprintf( painCave.errMsg,
241	+	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
242	+	painCave.severity = OPENMD_ERROR;
243	+	painCave.isFatal = 1;
244	+	simError();
245	+	}
246	+	} else if (args_info.rp2_given){
247	+	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
248	+	} else if (args_info.bo_given){
249	+	if (args_info.rcut_given) {
250	+	analyser = new BondOrderParameter(info, dumpFileName, sele1,
251	+	args_info.rcut_arg,
252	+	args_info.nbins_arg);
253	+	} else {
254	+	sprintf( painCave.errMsg,
255	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
256	+	painCave.severity = OPENMD_ERROR;
257	+	painCave.isFatal = 1;
258	+	simError();
259	+	}
260	+
261	+	} else if (args_info.tet_param_given) {
262	+	if (args_info.rcut_given) {
263	+	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
264	+	args_info.rcut_arg,
265	+	args_info.nbins_arg);
266	+	} else {
267	+	sprintf( painCave.errMsg,
268	+	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
269	+	painCave.severity = OPENMD_ERROR;
270	+	painCave.isFatal = 1;
271	+	simError();
272	+	}
273	+	} else if (args_info.bor_given){
274	+	if (args_info.rcut_given) {
275	+	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
276	+	args_info.nbins_arg, maxLen);
277	+	} else {
278	+	sprintf( painCave.errMsg,
279	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
280	+	painCave.severity = OPENMD_ERROR;
281	+	painCave.isFatal = 1;
282	+	simError();
283	+	}
284	+	} else if (args_info.bad_given){
285	+	if (args_info.rcut_given) {
286	+	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
287	+	args_info.nbins_arg);
288	+	} else {
289	+	sprintf( painCave.errMsg,
290	+	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
291	+	painCave.severity = OPENMD_ERROR;
292	+	painCave.isFatal = 1;
293	+	simError();
294	+	}
295	+	} else if (args_info.scd_given) {
296	+	if (batchMode) {
297	+	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
298	+	args_info.begin_arg, args_info.end_arg);
299	+	} else{
300	+	std::string sele3 = args_info.sele3_arg;
301	+	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
302	+	}
303	+	}else if (args_info.density_given) {
304	+	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
305	+	args_info.nbins_arg);
306	+	} else if (args_info.count_given) {
307	+	analyser = new ObjectCount(info, dumpFileName, sele1 );
308	+	} else if (args_info.slab_density_given) {
309	+	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
310	+	} else if (args_info.p_angle_given) {
311	+	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
312	+	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
313	+	}else if (args_info.hxy_given) {
314	+	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
315	+	args_info.nbins_y_arg, args_info.nbins_arg);
316	+	#endif
317	+	}else if (args_info.rho_r_given) {
318	+	if (args_info.radius_given){
319	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
320	+	}else{
321	+	sprintf( painCave.errMsg,
322	+	"A particle radius (radius) must be specified when calculating Rho(r)");
323	+	painCave.severity = OPENMD_ERROR;
324	+	painCave.isFatal = 1;
325	+	simError();
326	+	}
327	+	} else if (args_info.hullvol_given) {
328	+	analyser = new NanoVolume(info, dumpFileName, sele1);
329	+	} else if (args_info.rodlength_given) {
330	+	analyser = new NanoLength(info, dumpFileName, sele1);
331	+	} else if (args_info.angle_r_given) {
332	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
333	+	}
334	+
335	+	if (args_info.output_given) {
336	+	analyser->setOutputName(args_info.output_arg);
337	+	}
338	+	if (args_info.step_given) {
339	+	analyser->setStep(args_info.step_arg);
340	+	}
341	+
342	+	analyser->process();
343	+
344	+	delete analyser;
345	+	delete info;
346
347	<	rdf->process();
180	<
181	<	delete rdf;
182	<	delete info;
183	<
184	<	return 0;
347	>	return 0;
348		}
349

Comparing:
trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords), Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
branches/development/src/applications/staticProps/StaticProps.cpp (property svn:keywords), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

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