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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1091 by chuckv, Fri Nov 10 18:45:29 2006 UTC vs.
Revision 1994 by gezelter, Wed Apr 30 18:50:45 2014 UTC

#	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, 234107 (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"
#	Line 52 | Line 52
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	+	#include "applications/staticProps/RNEMDStats.hpp"
81	+	#include "applications/staticProps/NitrileFrequencyMap.hpp"
82
83	<	using namespace oopse;
83	>	using namespace OpenMD;
84
85		int main(int argc, char* argv[]){
86
87	<	//register force fields
74	<	registerForceFields();
75	<
87	>
88		gengetopt_args_info args_info;
89	<
89	>
90		//parse the command line option
91		if (cmdline_parser (argc, argv, &args_info) != 0) {
92		exit(1) ;
93		}
94	<
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;
88	<	bool userSpecifiedSelect2;
89	<
99	>
100		// check the first selection argument, or set it to the environment
101		// variable, or failing that, set it to "select all"
102	<
102	>
103		if (args_info.sele1_given) {
104		sele1 = args_info.sele1_arg;
105		} else {
106	<	char*  sele1Env= getenv("OOPSE_SELE1");
106	>	char*  sele1Env= getenv("SELECTION1");
107		if (sele1Env) {
108		sele1 = sele1Env;
109		} else {
110		sele1 = "select all";
111		}
112		}
113	<
113	>
114		// check the second selection argument, or set it to the environment
115	<	// variable, or failing that, set it to "select all"
115	>	// variable, or failing that, set it to the first selection
116
117		if (args_info.sele2_given) {
118		sele2 = args_info.sele2_arg;
119		} else {
120	<	char* sele2Env = getenv("OOPSE_SELE2");
120	>	char* sele2Env = getenv("SELECTION2");
121		if (sele2Env) {
122		sele2 = sele2Env;
123		} else {
124	<	sele2 = "select all";
124	>	//If sele2 is not specified, then the default behavior
125	>	//should be what is already intended for sele1
126	>	sele2 = sele1;
127		}
128		}
129
118	–
119	–	// Problems if sele1 wasn't specified, but
120	–	// if (!args_info.scd_given) {
121	–	//       sprintf( painCave.errMsg,
122	–	//                "neither --sele1 option nor $OOPSE_SELE1 is set");
123	–	//       painCave.severity = OOPSE_ERROR;
124	–	//       painCave.isFatal = 1;
125	–	//       simError();
126	–	//     }
127	–	//   }
128	–
129	–	// Problems if sele1 wasn't specified
130	–
131	–	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
132	–	//       sprintf( painCave.errMsg,
133	–	//                "neither --sele2 option nor $OOPSE_SELE2 is set");
134	–	//       painCave.severity = OOPSE_ERROR;
135	–	//       painCave.isFatal = 1;
136	–	//       simError();
137	–	//     }
138	–	//   }
139	–
130		bool batchMode;
131		if (args_info.scd_given){
132	<	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
132	>	if (args_info.sele1_given &&
133	>	args_info.sele2_given && args_info.sele3_given) {
134		batchMode = false;
135	<	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
136	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
135	>	} else if (args_info.molname_given &&
136	>	args_info.begin_given && args_info.end_given) {
137	>	if (args_info.begin_arg < 0 ||
138	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
139		sprintf( painCave.errMsg,
140		"below conditions are not satisfied:\n"
141		"0 <= begin && 0<= end && begin <= end-2\n");
142	<	painCave.severity = OOPSE_ERROR;
142	>	painCave.severity = OPENMD_ERROR;
143		painCave.isFatal = 1;
144		simError();
145		}
#	Line 155 | Line 148 | int main(int argc, char* argv[]){
148		sprintf( painCave.errMsg,
149		"either --sele1, --sele2, --sele3 are specified,"
150		" or --molname, --begin, --end are specified\n");
151	<	painCave.severity = OOPSE_ERROR;
151	>	painCave.severity = OPENMD_ERROR;
152		painCave.isFatal = 1;
153	<	simError();
161	<
153	>	simError();
154		}
155		}
156	<
156	>
157		//parse md file and set up the system
158		SimCreator creator;
167	–	std::cout << "dumpFile = " << dumpFileName << "\n";
159		SimInfo* info = creator.createSim(dumpFileName);
160
161		RealType maxLen;
162	+	RealType zmaxLen;
163		if (args_info.length_given) {
164		maxLen = args_info.length_arg;
165	+	if (args_info.zlength_given){
166	+	zmaxLen = args_info.zlength_arg;
167	+	}
168		} else {
169		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
170	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
170	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
171	>	zmaxLen = hmat(2,2);
172		}
173	<
173	>
174		StaticAnalyser* analyser;
175		if (args_info.gofr_given){
176		analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
177	<	args_info.nbins_arg);
177	>	args_info.nbins_arg);
178	>	} else if (args_info.gofz_given) {
179	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
180	>	args_info.nbins_arg);
181	>	} else if (args_info.r_z_given) {
182	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
183	>	args_info.nbins_arg, args_info.nbins_z_arg);
184		} else if (args_info.r_theta_given) {
185		analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
186	<	args_info.nbins_arg, args_info.nanglebins_arg);
186	>	args_info.nbins_arg, args_info.nanglebins_arg);
187		} else if (args_info.r_omega_given) {
188		analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
189	<	args_info.nbins_arg, args_info.nanglebins_arg);
189	>	args_info.nbins_arg, args_info.nanglebins_arg);
190		} else if (args_info.theta_omega_given) {
191		analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
192	<	args_info.nanglebins_arg);
192	>	args_info.nanglebins_arg);
193		} else if (args_info.gxyz_given) {
194		if (args_info.refsele_given) {
195	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
196	<	maxLen, args_info.nbins_arg);
195	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
196	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
197		} else {
198		sprintf( painCave.errMsg,
199	<	"--refsele must set when --gxyz is used");
200	<	painCave.severity = OOPSE_ERROR;
199	>	"--refsele must set when --gxyz is used");
200	>	painCave.severity = OPENMD_ERROR;
201		painCave.isFatal = 1;
202		simError();
203		}
204	+	} else if (args_info.twodgofr_given){
205	+	if (args_info.dz_given) {
206	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
207	+	args_info.dz_arg, args_info.nbins_arg);
208	+	} else {
209	+	sprintf( painCave.errMsg,
210	+	"A slab width (dz) must be specified when calculating TwoDGofR");
211	+	painCave.severity = OPENMD_ERROR;
212	+	painCave.isFatal = 1;
213	+	simError();
214	+	}
215		} else if (args_info.p2_given) {
216	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
216	>	if (args_info.sele1_given) {
217	>	if (args_info.sele2_given)
218	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
219	>	else
220	>	if (args_info.seleoffset_given)
221	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
222	>	args_info.seleoffset_arg);
223	>	else
224	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
225	>	} else {
226	>	sprintf( painCave.errMsg,
227	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
228	>	painCave.severity = OPENMD_ERROR;
229	>	painCave.isFatal = 1;
230	>	simError();
231	>	}
232		} else if (args_info.rp2_given){
233		analyser = new RippleOP(info, dumpFileName, sele1, sele2);
234		} else if (args_info.bo_given){
235		if (args_info.rcut_given) {
236		analyser = new BondOrderParameter(info, dumpFileName, sele1,
237	<	args_info.rcut_arg,
238	<	args_info.nbins_arg);
237	>	args_info.rcut_arg,
238	>	args_info.nbins_arg);
239		} else {
240		sprintf( painCave.errMsg,
241	<	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
242	<	painCave.severity = OOPSE_ERROR;
241	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
242	>	painCave.severity = OPENMD_ERROR;
243		painCave.isFatal = 1;
244		simError();
245		}
246	+
247	+	} else if (args_info.tet_param_given) {
248	+	if (args_info.rcut_given) {
249	+	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
250	+	args_info.rcut_arg,
251	+	args_info.nbins_arg);
252	+	} else {
253	+	sprintf( painCave.errMsg,
254	+	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
255	+	painCave.severity = OPENMD_ERROR;
256	+	painCave.isFatal = 1;
257	+	simError();
258	+	}
259	+	} else if (args_info.tet_param_z_given) {
260	+	if (args_info.rcut_given) {
261	+	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
262	+	args_info.rcut_arg,
263	+	args_info.nbins_arg);
264	+	} else {
265	+	sprintf( painCave.errMsg,
266	+	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
267	+	painCave.severity = OPENMD_ERROR;
268	+	painCave.isFatal = 1;
269	+	simError();
270	+	}
271	+	} else if (args_info.ior_given){
272	+	if (args_info.rcut_given) {
273	+	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
274	+	args_info.rcut_arg,
275	+	args_info.nbins_arg, maxLen);
276	+	} else {
277	+	sprintf( painCave.errMsg,
278	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
279	+	painCave.severity = OPENMD_ERROR;
280	+	painCave.isFatal = 1;
281	+	simError();
282	+	}
283	+	} else if (args_info.for_given){
284	+	if (args_info.rcut_given) {
285	+	analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
286	+	args_info.nbins_arg, maxLen);
287	+	} else {
288	+	sprintf( painCave.errMsg,
289	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
290	+	painCave.severity = OPENMD_ERROR;
291	+	painCave.isFatal = 1;
292	+	simError();
293	+	}
294	+	} else if (args_info.bad_given){
295	+	if (args_info.rcut_given) {
296	+	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
297	+	args_info.rcut_arg,
298	+	args_info.nbins_arg);
299	+	} else {
300	+	sprintf( painCave.errMsg,
301	+	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
302	+	painCave.severity = OPENMD_ERROR;
303	+	painCave.isFatal = 1;
304	+	simError();
305	+	}
306		} else if (args_info.scd_given) {
307		if (batchMode) {
308	<	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
309	<	args_info.begin_arg, args_info.end_arg);
308	>	analyser  = new SCDOrderParameter(info, dumpFileName,
309	>	args_info.molname_arg,
310	>	args_info.begin_arg, args_info.end_arg);
311		} else{
312		std::string sele3 = args_info.sele3_arg;
313	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
313	>	analyser  = new SCDOrderParameter(info, dumpFileName,
314	>	sele1, sele2, sele3);
315		}
316		}else if (args_info.density_given) {
317	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
318	<	args_info.nbins_arg);
317	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
318	>	args_info.nbins_arg);
319	>	} else if (args_info.count_given) {
320	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
321		} else if (args_info.slab_density_given) {
322	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
323	<	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
322	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
323	>	} else if (args_info.rnemdz_given) {
324	>	analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
325	>	} else if (args_info.rnemdr_given) {
326	>	analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
327	>	} else if (args_info.rnemdrt_given) {
328	>	analyser = new RNEMDRTheta(info, dumpFileName, sele1,
329	>	args_info.nbins_arg, args_info.nanglebins_arg);
330	>	} else if (args_info.nitrile_given) {
331	>	analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
332	>	args_info.nbins_arg);
333	>	} else if (args_info.p_angle_given) {
334	>	if (args_info.sele1_given) {
335	>	if (args_info.sele2_given)
336	>	analyser  = new pAngle(info, dumpFileName, sele1, sele2,
337	>	args_info.nbins_arg);
338	>	else
339	>	if (args_info.seleoffset_given) {
340	>	if (args_info.seleoffset2_given) {
341	>	analyser  = new pAngle(info, dumpFileName, sele1,
342	>	args_info.seleoffset_arg,
343	>	args_info.seleoffset2_arg,
344	>	args_info.nbins_arg);
345	>	} else {
346	>	analyser  = new pAngle(info, dumpFileName, sele1,
347	>	args_info.seleoffset_arg,
348	>	args_info.nbins_arg);
349	>	}
350	>	} else
351	>	analyser  = new pAngle(info, dumpFileName, sele1,
352	>	args_info.nbins_arg);
353	>	} else {
354	>	sprintf( painCave.errMsg,
355	>	"At least one selection script (--sele1) must be specified when "
356	>	"calculating P(angle) distributions");
357	>	painCave.severity = OPENMD_ERROR;
358	>	painCave.isFatal = 1;
359	>	simError();
360	>	}
361		#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
362		}else if (args_info.hxy_given) {
363		analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
364	<	args_info.nbins_y_arg, args_info.nbins_arg);
364	>	args_info.nbins_y_arg, args_info.nbins_arg);
365		#endif
366		}else if (args_info.rho_r_given) {
367		if (args_info.radius_given){
368		analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
369		}else{
370		sprintf( painCave.errMsg,
371	<	"A particle radius (radius) must be specified when calculating Rho(r)");
372	<	painCave.severity = OOPSE_ERROR;
371	>	"A particle radius (radius) must be specified when calculating Rho(r)");
372	>	painCave.severity = OPENMD_ERROR;
373		painCave.isFatal = 1;
374		simError();
375		}
376	+	} else if (args_info.hullvol_given) {
377	+	analyser = new NanoVolume(info, dumpFileName, sele1);
378	+	} else if (args_info.rodlength_given) {
379	+	analyser = new NanoLength(info, dumpFileName, sele1);
380	+	} else if (args_info.angle_r_given) {
381	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
382		}
383
384		if (args_info.output_given) {
#	Line 252 | Line 387 | int main(int argc, char* argv[]){
387		if (args_info.step_given) {
388		analyser->setStep(args_info.step_arg);
389		}
390	<
390	>
391		analyser->process();
392	<
392	>
393		delete analyser;
394		delete info;
395	<
395	>
396		return 0;
397		}
263	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 1091 by chuckv, Fri Nov 10 18:45:29 2006 UTC vs.
Revision 1994 by gezelter, Wed Apr 30 18:50:45 2014 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines