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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 311 by tim, Thu Feb 10 22:37:21 2005 UTC vs.
Revision 1522 by kstocke1, Fri Nov 19 20:26:36 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>
#	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	+	#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	+	#include "applications/staticProps/AngleR.hpp"
77	+	#include "applications/staticProps/RhoAngleR.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");
108	<	if (sele1Env) {
109	<	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);
115	<
116	<	double maxLen;
117	<	if (args_info.length_given) {
118	<	maxLen = args_info.length_arg;
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	>	//get the dumpfile name
95	>	std::string dumpFileName = args_info.input_arg;
96	>	std::string sele1;
97	>	std::string sele2;
98	>	bool userSpecifiedSelect1;
99	>	bool userSpecifiedSelect2;
100	>
101	>	// check the first selection argument, or set it to the environment
102	>	// variable, or failing that, set it to "select all"
103	>
104	>	if (args_info.sele1_given) {
105	>	sele1 = args_info.sele1_arg;
106	>	} else {
107	>	char*  sele1Env= getenv("SELECTION1");
108	>	if (sele1Env) {
109	>	sele1 = sele1Env;
110		} else {
111	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
121	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2 ;
111	>	sele1 = "select all";
112		}
113	<
114	<
115	<	RadialDistrFunc* rdf;
116	<	if (args_info.gofr_given){
117	<	GofR* r = new GofR(info, dumpFileName, sele1, sele2);
118	<
119	<	r->setNRBins(args_info.nrbins_arg);
120	<	r->setLength(maxLen);
121	<
122	<	rdf = r;
123	<	} else if (args_info.r_theta_given) {
124	<	GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2);
125	<
136	<	rTheta->setNRBins(args_info.nrbins_arg);
137	<	rTheta->setLength(maxLen);
138	<	rTheta->setNAngleBins(args_info.nanglebins_arg);
139	<
140	<
141	<	rdf = rTheta;
113	>	}
114	>
115	>	// check the second selection argument, or set it to the environment
116	>	// variable, or failing that, set it to "select all"
117	>
118	>	if (args_info.sele2_given) {
119	>	sele2 = args_info.sele2_arg;
120	>	} else {
121	>	char* sele2Env = getenv("SELECTION1");
122	>	if (sele2Env) {
123	>	sele2 = sele2Env;
124	>	} else {
125	>	sele2 = "select all";
126		}
127	<	else if (args_info.r_omega_given) {
128	<	GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2);
129	<
130	<
131	<	rOmega->setNRBins(args_info.nrbins_arg);
132	<	rOmega->setLength(maxLen);
133	<	rOmega->setNAngleBins(args_info.nanglebins_arg);
134	<
135	<	rdf = rOmega;
136	<	} else if (args_info.theta_omega_given) {
137	<	GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2);
138	<	rAngle2->setNAngleBins(args_info.nanglebins_arg);
139	<
140	<	rdf = rAngle2;
141	<	} else if (args_info.xyz_given) {
142	<
143	<	GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2);
144	<
145	<	xyz->setNRBins(args_info.nrbins_arg);
146	<	xyz->setLength(maxLen);
147	<
148	<
149	<	rdf = xyz;
150	<	}
151	<
152	<
153	<	if (args_info.output_given) {
154	<	rdf->setOutputName(args_info.output_arg);
127	>	}
128	>
129	>
130	>	// Problems if sele1 wasn't specified, but
131	>	// if (!args_info.scd_given) {
132	>	//       sprintf( painCave.errMsg,
133	>	//                "neither --sele1 option nor $SELECTION1 is set");
134	>	//       painCave.severity = OPENMD_ERROR;
135	>	//       painCave.isFatal = 1;
136	>	//       simError();
137	>	//     }
138	>	//   }
139	>
140	>	// Problems if sele1 wasn't specified
141	>
142	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
143	>	//       sprintf( painCave.errMsg,
144	>	//                "neither --sele2 option nor $SELECTION1 is set");
145	>	//       painCave.severity = OPENMD_ERROR;
146	>	//       painCave.isFatal = 1;
147	>	//       simError();
148	>	//     }
149	>	//   }
150	>
151	>	bool batchMode;
152	>	if (args_info.scd_given){
153	>	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
154	>	batchMode = false;
155	>	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
156	>	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
157	>	sprintf( painCave.errMsg,
158	>	"below conditions are not satisfied:\n"
159	>	"0 <= begin && 0<= end && begin <= end-2\n");
160	>	painCave.severity = OPENMD_ERROR;
161	>	painCave.isFatal = 1;
162	>	simError();
163	>	}
164	>	batchMode = true;
165	>	} else{
166	>	sprintf( painCave.errMsg,
167	>	"either --sele1, --sele2, --sele3 are specified,"
168	>	" or --molname, --begin, --end are specified\n");
169	>	painCave.severity = OPENMD_ERROR;
170	>	painCave.isFatal = 1;
171	>	simError();
172	>
173		}
174	+	}
175	+
176	+	//parse md file and set up the system
177	+	SimCreator creator;
178	+	std::cout << "dumpFile = " << dumpFileName << "\n";
179	+	SimInfo* info = creator.createSim(dumpFileName);
180
181	<	if (args_info.step_given) {
182	<	rdf->setStep(args_info.step_arg);
181	>	RealType maxLen;
182	>	RealType zmaxLen;
183	>	if (args_info.length_given) {
184	>	maxLen = args_info.length_arg;
185	>	if (args_info.zlength_given){
186	>	zmaxLen = args_info.zlength_arg;
187		}
188	+	} else {
189	+	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
190	+	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
191	+	zmaxLen = hmat(2,2);
192	+	}
193	+
194	+	StaticAnalyser* analyser;
195	+	if (args_info.gofr_given){
196	+	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
197	+	args_info.nbins_arg);
198	+	} else if (args_info.gofz_given) {
199	+	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
200	+	args_info.nbins_arg);
201	+	} else if (args_info.r_z_given) {
202	+	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
203	+	args_info.nbins_arg, args_info.nbins_z_arg);
204	+	} else if (args_info.r_theta_given) {
205	+	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
206	+	args_info.nbins_arg, args_info.nanglebins_arg);
207	+	} else if (args_info.r_omega_given) {
208	+	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
209	+	args_info.nbins_arg, args_info.nanglebins_arg);
210	+	} else if (args_info.theta_omega_given) {
211	+	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
212	+	args_info.nanglebins_arg);
213	+	} else if (args_info.gxyz_given) {
214	+	if (args_info.refsele_given) {
215	+	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
216	+	maxLen, args_info.nbins_arg);
217	+	} else {
218	+	sprintf( painCave.errMsg,
219	+	"--refsele must set when --gxyz is used");
220	+	painCave.severity = OPENMD_ERROR;
221	+	painCave.isFatal = 1;
222	+	simError();
223	+	}
224	+	} else if (args_info.twodgofr_given){
225	+	if (args_info.dz_given) {
226	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
227	+	args_info.dz_arg, args_info.nbins_arg);
228	+	} else {
229	+	sprintf( painCave.errMsg,
230	+	"A slab width (dz) must be specified when calculating TwoDGofR");
231	+	painCave.severity = OPENMD_ERROR;
232	+	painCave.isFatal = 1;
233	+	simError();
234	+	}
235	+	} else if (args_info.p2_given) {
236	+	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
237	+	} else if (args_info.rp2_given){
238	+	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
239	+	} else if (args_info.bo_given){
240	+	if (args_info.rcut_given) {
241	+	analyser = new BondOrderParameter(info, dumpFileName, sele1,
242	+	args_info.rcut_arg,
243	+	args_info.nbins_arg);
244	+	} else {
245	+	sprintf( painCave.errMsg,
246	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
247	+	painCave.severity = OPENMD_ERROR;
248	+	painCave.isFatal = 1;
249	+	simError();
250	+	}
251	+
252	+	} else if (args_info.tet_param_given) {
253	+	if (args_info.rcut_given) {
254	+	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
255	+	args_info.rcut_arg,
256	+	args_info.nbins_arg);
257	+	} else {
258	+	sprintf( painCave.errMsg,
259	+	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
260	+	painCave.severity = OPENMD_ERROR;
261	+	painCave.isFatal = 1;
262	+	simError();
263	+	}
264	+	} else if (args_info.bor_given){
265	+	if (args_info.rcut_given) {
266	+	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
267	+	args_info.nbins_arg, maxLen);
268	+	} else {
269	+	sprintf( painCave.errMsg,
270	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
271	+	painCave.severity = OPENMD_ERROR;
272	+	painCave.isFatal = 1;
273	+	simError();
274	+	}
275	+	} else if (args_info.bad_given){
276	+	if (args_info.rcut_given) {
277	+	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
278	+	args_info.nbins_arg);
279	+	} else {
280	+	sprintf( painCave.errMsg,
281	+	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
282	+	painCave.severity = OPENMD_ERROR;
283	+	painCave.isFatal = 1;
284	+	simError();
285	+	}
286	+	} else if (args_info.scd_given) {
287	+	if (batchMode) {
288	+	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
289	+	args_info.begin_arg, args_info.end_arg);
290	+	} else{
291	+	std::string sele3 = args_info.sele3_arg;
292	+	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
293	+	}
294	+	}else if (args_info.density_given) {
295	+	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
296	+	args_info.nbins_arg);
297	+	} else if (args_info.count_given) {
298	+	analyser = new ObjectCount(info, dumpFileName, sele1 );
299	+	} else if (args_info.slab_density_given) {
300	+	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
301	+	} else if (args_info.p_angle_given) {
302	+	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
303	+	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
304	+	}else if (args_info.hxy_given) {
305	+	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
306	+	args_info.nbins_y_arg, args_info.nbins_arg);
307	+	#endif
308	+	}else if (args_info.rho_r_given) {
309	+	if (args_info.radius_given){
310	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
311	+	}else{
312	+	sprintf( painCave.errMsg,
313	+	"A particle radius (radius) must be specified when calculating Rho(r)");
314	+	painCave.severity = OPENMD_ERROR;
315	+	painCave.isFatal = 1;
316	+	simError();
317	+	}
318	+	} else if (args_info.hullvol_given) {
319	+	analyser = new NanoVolume(info, dumpFileName, sele1);
320	+	} else if (args_info.angle_r_given) {
321	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
322	+	}
323	+
324	+	if (args_info.output_given) {
325	+	analyser->setOutputName(args_info.output_arg);
326	+	}
327	+	if (args_info.step_given) {
328	+	analyser->setStep(args_info.step_arg);
329	+	}
330	+
331	+	analyser->process();
332	+
333	+	delete analyser;
334	+	delete info;
335
336	<	rdf->process();
178	<
179	<	delete rdf;
180	<	delete info;
181	<
182	<	return 0;
336	>	return 0;
337		}
338

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 311 by tim, Thu Feb 10 22:37:21 2005 UTC vs.
Revision 1522 by kstocke1, Fri Nov 19 20:26:36 2010 UTC

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

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