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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 354 by tim, Wed Feb 16 20:30:50 2005 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 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	+	#include "applications/staticProps/TetrahedralityParamZ.hpp"
80	+	using namespace OpenMD;
81
58	–	using namespace oopse;
59	–
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) ;
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	>
97	>	// check the first selection argument, or set it to the environment
98	>	// variable, or failing that, set it to "select all"
99	>
100	>	if (args_info.sele1_given) {
101	>	sele1 = args_info.sele1_arg;
102	>	} else {
103	>	char*  sele1Env= getenv("SELECTION1");
104	>	if (sele1Env) {
105	>	sele1 = sele1Env;
106	>	} else {
107	>	sele1 = "select all";
108		}
109	<
110	<
111	<	//get the dumpfile name and meta-data file name
112	<	std::string dumpFileName = args_info.input_arg;
113	<
114	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
115	<
116	<
117	<	std::string sele1;
118	<	std::string sele2;
119	<
120	<	if (args_info.sele1_given) {
121	<	sele1 = args_info.sele1_arg;
122	<	}else {
123	<	char*  sele1Env= getenv("OOPSE_SELE1");
124	<	if (sele1Env) {
125	<	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	<	}
109	>	}
110	>
111	>	// check the second selection argument, or set it to the environment
112	>	// variable, or failing that, set it to "select all"
113	>
114	>	if (args_info.sele2_given) {
115	>	sele2 = args_info.sele2_arg;
116	>	} else {
117	>	char* sele2Env = getenv("SELECTION1");
118	>	if (sele2Env) {
119	>	sele2 = sele2Env;
120	>	} else {
121	>	//It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior
122	>	//should not be 'select all' but rather what is already intended for sele1
123	>	//JRM 8/22/12
124	>	sele2 = sele1;
125	>	//sele2 = "select all";
126		}
127	<
128	<	if (args_info.sele2_given) {
129	<	sele2 = args_info.sele2_arg;
130	<	}else {
131	<	char* sele2Env = getenv("OOPSE_SELE2");
132	<	if (sele2Env) {
133	<	sele2 = sele2Env;
134	<	} else {
135	<	sprintf( painCave.errMsg,
136	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
137	<	painCave.severity = OOPSE_ERROR;
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
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	<	//parse md file and set up the system
182	<	SimCreator creator;
183	<	SimInfo* info = creator.createSim(mdFileName);
184	<
185	<	double maxLen;
186	<	if (args_info.length_given) {
187	<	maxLen = args_info.length_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	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
219	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
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	<
236	<	RadialDistrFunc* rdf;
237	<	if (args_info.gofr_given){
238	<	rdf= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
239	<	} else if (args_info.r_theta_given) {
240	<	rdf  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
241	<	} else if (args_info.r_omega_given) {
242	<	rdf  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
243	<	} else if (args_info.theta_omega_given) {
244	<	rdf  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
245	<	} else if (args_info.xyz_given) {
246	<	rdf= new GofXyz(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
235	>	} else if (args_info.p2_given) {
236	>	if (args_info.sele1_given) {
237	>	if (args_info.sele2_given)
238	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
239	>	else
240	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
241	>	} else {
242	>	sprintf( painCave.errMsg,
243	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
244	>	painCave.severity = OPENMD_ERROR;
245	>	painCave.isFatal = 1;
246	>	simError();
247		}
248	+	} else if (args_info.rp2_given){
249	+	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
250	+	} else if (args_info.bo_given){
251	+	if (args_info.rcut_given) {
252	+	analyser = new BondOrderParameter(info, dumpFileName, sele1,
253	+	args_info.rcut_arg,
254	+	args_info.nbins_arg);
255	+	} else {
256	+	sprintf( painCave.errMsg,
257	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
258	+	painCave.severity = OPENMD_ERROR;
259	+	painCave.isFatal = 1;
260	+	simError();
261	+	}
262
263	<	if (args_info.output_given) {
264	<	rdf->setOutputName(args_info.output_arg);
263	>	} else if (args_info.tet_param_given) {
264	>	if (args_info.rcut_given) {
265	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
266	>	args_info.rcut_arg,
267	>	args_info.nbins_arg);
268	>	} else {
269	>	sprintf( painCave.errMsg,
270	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
271	>	painCave.severity = OPENMD_ERROR;
272	>	painCave.isFatal = 1;
273	>	simError();
274		}
275	<	if (args_info.step_given) {
276	<	rdf->setStep(args_info.step_arg);
275	>	} else if (args_info.tet_param_z_given) {
276	>	if (args_info.rcut_given) {
277	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
278	>	args_info.rcut_arg,
279	>	args_info.nbins_arg);
280	>	} else {
281	>	sprintf( painCave.errMsg,
282	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
283	>	painCave.severity = OPENMD_ERROR;
284	>	painCave.isFatal = 1;
285	>	simError();
286		}
287	+	} else if (args_info.bor_given){
288	+	if (args_info.rcut_given) {
289	+	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
290	+	args_info.nbins_arg, maxLen);
291	+	} else {
292	+	sprintf( painCave.errMsg,
293	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
294	+	painCave.severity = OPENMD_ERROR;
295	+	painCave.isFatal = 1;
296	+	simError();
297	+	}
298	+	} else if (args_info.bad_given){
299	+	if (args_info.rcut_given) {
300	+	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
301	+	args_info.nbins_arg);
302	+	} else {
303	+	sprintf( painCave.errMsg,
304	+	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
305	+	painCave.severity = OPENMD_ERROR;
306	+	painCave.isFatal = 1;
307	+	simError();
308	+	}
309	+	} else if (args_info.scd_given) {
310	+	if (batchMode) {
311	+	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
312	+	args_info.begin_arg, args_info.end_arg);
313	+	} else{
314	+	std::string sele3 = args_info.sele3_arg;
315	+	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
316	+	}
317	+	}else if (args_info.density_given) {
318	+	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
319	+	args_info.nbins_arg);
320	+	} else if (args_info.count_given) {
321	+	analyser = new ObjectCount(info, dumpFileName, sele1 );
322	+	} else if (args_info.slab_density_given) {
323	+	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
324	+	} else if (args_info.p_angle_given) {
325	+	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
326	+	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
327	+	}else if (args_info.hxy_given) {
328	+	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
329	+	args_info.nbins_y_arg, args_info.nbins_arg);
330	+	#endif
331	+	}else if (args_info.rho_r_given) {
332	+	if (args_info.radius_given){
333	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
334	+	}else{
335	+	sprintf( painCave.errMsg,
336	+	"A particle radius (radius) must be specified when calculating Rho(r)");
337	+	painCave.severity = OPENMD_ERROR;
338	+	painCave.isFatal = 1;
339	+	simError();
340	+	}
341	+	} else if (args_info.hullvol_given) {
342	+	analyser = new NanoVolume(info, dumpFileName, sele1);
343	+	} else if (args_info.rodlength_given) {
344	+	analyser = new NanoLength(info, dumpFileName, sele1);
345	+	} else if (args_info.angle_r_given) {
346	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
347	+	}
348	+
349	+	if (args_info.output_given) {
350	+	analyser->setOutputName(args_info.output_arg);
351	+	}
352	+	if (args_info.step_given) {
353	+	analyser->setStep(args_info.step_arg);
354	+	}
355	+
356	+	analyser->process();
357	+
358	+	delete analyser;
359	+	delete info;
360
361	<	rdf->process();
145	<
146	<	delete rdf;
147	<	delete info;
148	<
149	<	return 0;
361	>	return 0;
362		}
363

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 354 by tim, Wed Feb 16 20:30:50 2005 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

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

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