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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 2015 by gezelter, Wed Aug 13 20:42:43 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/TetrahedralityParamXYZ.hpp"
81	+	#include "applications/staticProps/RNEMDStats.hpp"
82	+	#include "applications/staticProps/NitrileFrequencyMap.hpp"
83	+	#include "applications/staticProps/MultipoleSum.hpp"
84
85	<	using namespace oopse;
85	>	using namespace OpenMD;
86
87		int main(int argc, char* argv[]){
88
89	<	//register force fields
73	<	registerForceFields();
74	<
89	>
90		gengetopt_args_info args_info;
91	<
91	>
92		//parse the command line option
93		if (cmdline_parser (argc, argv, &args_info) != 0) {
94		exit(1) ;
95		}
96	<
96	>
97		//get the dumpfile name
98		std::string dumpFileName = args_info.input_arg;
99		std::string sele1;
100		std::string sele2;
101	<	bool userSpecifiedSelect1;
87	<	bool userSpecifiedSelect2;
88	<
101	>
102		// check the first selection argument, or set it to the environment
103		// variable, or failing that, set it to "select all"
104	<
104	>
105		if (args_info.sele1_given) {
106		sele1 = args_info.sele1_arg;
107		} else {
108	<	char*  sele1Env= getenv("OOPSE_SELE1");
108	>	char*  sele1Env= getenv("SELECTION1");
109		if (sele1Env) {
110		sele1 = sele1Env;
111		} else {
112		sele1 = "select all";
113		}
114		}
115	<
115	>
116		// check the second selection argument, or set it to the environment
117	<	// variable, or failing that, set it to "select all"
117	>	// variable, or failing that, set it to the first selection
118
119		if (args_info.sele2_given) {
120		sele2 = args_info.sele2_arg;
121		} else {
122	<	char* sele2Env = getenv("OOPSE_SELE2");
122	>	char* sele2Env = getenv("SELECTION2");
123		if (sele2Env) {
124		sele2 = sele2Env;
125		} else {
126	<	sele2 = "select all";
126	>	//If sele2 is not specified, then the default behavior
127	>	//should be what is already intended for sele1
128	>	sele2 = sele1;
129		}
130		}
131
117	–
118	–	// Problems if sele1 wasn't specified, but
119	–	// if (!args_info.scd_given) {
120	–	//       sprintf( painCave.errMsg,
121	–	//                "neither --sele1 option nor $OOPSE_SELE1 is set");
122	–	//       painCave.severity = OOPSE_ERROR;
123	–	//       painCave.isFatal = 1;
124	–	//       simError();
125	–	//     }
126	–	//   }
127	–
128	–	// Problems if sele1 wasn't specified
129	–
130	–	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
131	–	//       sprintf( painCave.errMsg,
132	–	//                "neither --sele2 option nor $OOPSE_SELE2 is set");
133	–	//       painCave.severity = OOPSE_ERROR;
134	–	//       painCave.isFatal = 1;
135	–	//       simError();
136	–	//     }
137	–	//   }
138	–
132		bool batchMode;
133		if (args_info.scd_given){
134	<	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
134	>	if (args_info.sele1_given &&
135	>	args_info.sele2_given && args_info.sele3_given) {
136		batchMode = false;
137	<	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
138	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
137	>	} else if (args_info.molname_given &&
138	>	args_info.begin_given && args_info.end_given) {
139	>	if (args_info.begin_arg < 0 ||
140	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
141		sprintf( painCave.errMsg,
142		"below conditions are not satisfied:\n"
143		"0 <= begin && 0<= end && begin <= end-2\n");
144	<	painCave.severity = OOPSE_ERROR;
144	>	painCave.severity = OPENMD_ERROR;
145		painCave.isFatal = 1;
146		simError();
147		}
#	Line 154 | Line 150 | int main(int argc, char* argv[]){
150		sprintf( painCave.errMsg,
151		"either --sele1, --sele2, --sele3 are specified,"
152		" or --molname, --begin, --end are specified\n");
153	<	painCave.severity = OOPSE_ERROR;
153	>	painCave.severity = OPENMD_ERROR;
154		painCave.isFatal = 1;
155	<	simError();
160	<
155	>	simError();
156		}
157		}
158	<
158	>
159		//parse md file and set up the system
160		SimCreator creator;
161		SimInfo* info = creator.createSim(dumpFileName);
162
163		RealType maxLen;
164	+	RealType zmaxLen;
165		if (args_info.length_given) {
166		maxLen = args_info.length_arg;
167	+	if (args_info.zlength_given){
168	+	zmaxLen = args_info.zlength_arg;
169	+	}
170		} else {
171		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
172	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
172	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
173	>	zmaxLen = hmat(2,2);
174		}
175	<
175	>
176		StaticAnalyser* analyser;
177		if (args_info.gofr_given){
178	<	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
178	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
179	>	args_info.nbins_arg);
180	>	} else if (args_info.gofz_given) {
181	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
182	>	args_info.nbins_arg);
183	>	} else if (args_info.r_z_given) {
184	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
185	>	args_info.nbins_arg, args_info.nbins_z_arg);
186		} else if (args_info.r_theta_given) {
187	<	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
187	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
188	>	args_info.nbins_arg, args_info.nanglebins_arg);
189		} else if (args_info.r_omega_given) {
190	<	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
190	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
191	>	args_info.nbins_arg, args_info.nanglebins_arg);
192		} else if (args_info.theta_omega_given) {
193	<	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
193	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
194	>	args_info.nanglebins_arg);
195		} else if (args_info.gxyz_given) {
196		if (args_info.refsele_given) {
197	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
197	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
198	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
199		} else {
200		sprintf( painCave.errMsg,
201	<	"--refsele must set when --gxyz is used");
202	<	painCave.severity = OOPSE_ERROR;
201	>	"--refsele must set when --gxyz is used");
202	>	painCave.severity = OPENMD_ERROR;
203		painCave.isFatal = 1;
204		simError();
205		}
206	+	} else if (args_info.twodgofr_given){
207	+	if (args_info.dz_given) {
208	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
209	+	args_info.dz_arg, args_info.nbins_arg);
210	+	} else {
211	+	sprintf( painCave.errMsg,
212	+	"A slab width (dz) must be specified when calculating TwoDGofR");
213	+	painCave.severity = OPENMD_ERROR;
214	+	painCave.isFatal = 1;
215	+	simError();
216	+	}
217		} else if (args_info.p2_given) {
218	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
218	>	if (args_info.sele1_given) {
219	>	if (args_info.sele2_given)
220	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
221	>	else
222	>	if (args_info.seleoffset_given)
223	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
224	>	args_info.seleoffset_arg);
225	>	else
226	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
227	>	} else {
228	>	sprintf( painCave.errMsg,
229	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
230	>	painCave.severity = OPENMD_ERROR;
231	>	painCave.isFatal = 1;
232	>	simError();
233	>	}
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 && args_info.LegendreL_given) {
237	>	if (args_info.rcut_given) {
238		analyser = new BondOrderParameter(info, dumpFileName, sele1,
239	<	args_info.rcut_arg,
240	<	args_info.LegendreL_arg);
239	>	args_info.rcut_arg,
240	>	args_info.nbins_arg);
241		} else {
242		sprintf( painCave.errMsg,
243	<	"Both the cutoff radius (rcut) and LegendreL must be specified when calculating Bond Order Parameters");
244	<	painCave.severity = OOPSE_ERROR;
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.multipole_given){
249	+	analyser = new MultipoleSum(info, dumpFileName, sele1,
250	+	maxLen, args_info.nbins_arg);
251	+	} else if (args_info.tet_param_given) {
252	+	if (args_info.rcut_given) {
253	+	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
254	+	args_info.rcut_arg,
255	+	args_info.nbins_arg);
256	+	} else {
257	+	sprintf( painCave.errMsg,
258	+	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
259	+	painCave.severity = OPENMD_ERROR;
260	+	painCave.isFatal = 1;
261	+	simError();
262	+	}
263	+	} else if (args_info.tet_param_z_given) {
264	+	if (args_info.rcut_given) {
265	+	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
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	+	} else if (args_info.tet_param_xyz_given) {
276	+	if (!args_info.rcut_given) {
277	+	sprintf( painCave.errMsg,
278	+	"A cutoff radius (rcut) must be specified when calculating"
279	+	" Tetrahedrality Parameters");
280	+	painCave.severity = OPENMD_ERROR;
281	+	painCave.isFatal = 1;
282	+	simError();
283	+	}
284	+	if (!args_info.voxelSize_given) {
285	+	sprintf( painCave.errMsg,
286	+	"A voxel size must be specified when calculating"
287	+	" volume-resolved Tetrahedrality Parameters");
288	+	painCave.severity = OPENMD_ERROR;
289	+	painCave.isFatal = 1;
290	+	simError();
291	+	}
292	+	if (!args_info.gaussWidth_given) {
293	+	sprintf( painCave.errMsg,
294	+	"A gaussian width must be specified when calculating"
295	+	" volume-resolved Tetrahedrality Parameters");
296	+	painCave.severity = OPENMD_ERROR;
297	+	painCave.isFatal = 1;
298	+	simError();
299	+	}
300	+	analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
301	+	args_info.rcut_arg,
302	+	args_info.voxelSize_arg,
303	+	args_info.gaussWidth_arg);
304	+	} else if (args_info.ior_given){
305	+	if (args_info.rcut_given) {
306	+	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
307	+	args_info.rcut_arg,
308	+	args_info.nbins_arg, maxLen);
309	+	} else {
310	+	sprintf( painCave.errMsg,
311	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
312	+	painCave.severity = OPENMD_ERROR;
313	+	painCave.isFatal = 1;
314	+	simError();
315	+	}
316	+	} else if (args_info.for_given){
317	+	if (args_info.rcut_given) {
318	+	analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
319	+	args_info.nbins_arg, maxLen);
320	+	} else {
321	+	sprintf( painCave.errMsg,
322	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
323	+	painCave.severity = OPENMD_ERROR;
324	+	painCave.isFatal = 1;
325	+	simError();
326	+	}
327	+	} else if (args_info.bad_given){
328	+	if (args_info.rcut_given) {
329	+	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
330	+	args_info.rcut_arg,
331	+	args_info.nbins_arg);
332	+	} else {
333	+	sprintf( painCave.errMsg,
334	+	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
335	+	painCave.severity = OPENMD_ERROR;
336	+	painCave.isFatal = 1;
337	+	simError();
338	+	}
339		} else if (args_info.scd_given) {
340		if (batchMode) {
341	<	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
342	<	args_info.begin_arg, args_info.end_arg);
341	>	analyser  = new SCDOrderParameter(info, dumpFileName,
342	>	args_info.molname_arg,
343	>	args_info.begin_arg, args_info.end_arg);
344		} else{
345		std::string sele3 = args_info.sele3_arg;
346	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
346	>	analyser  = new SCDOrderParameter(info, dumpFileName,
347	>	sele1, sele2, sele3);
348		}
349		}else if (args_info.density_given) {
350	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
350	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
351	>	args_info.nbins_arg);
352	>	} else if (args_info.count_given) {
353	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
354		} else if (args_info.slab_density_given) {
355	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
356	<	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg);
355	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
356	>	} else if (args_info.rnemdz_given) {
357	>	analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
358	>	} else if (args_info.rnemdr_given) {
359	>	analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
360	>	} else if (args_info.rnemdrt_given) {
361	>	analyser = new RNEMDRTheta(info, dumpFileName, sele1,
362	>	args_info.nbins_arg, args_info.nanglebins_arg);
363	>	} else if (args_info.nitrile_given) {
364	>	analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
365	>	args_info.nbins_arg);
366	>	} else if (args_info.p_angle_given) {
367	>	if (args_info.sele1_given) {
368	>	if (args_info.sele2_given)
369	>	analyser  = new pAngle(info, dumpFileName, sele1, sele2,
370	>	args_info.nbins_arg);
371	>	else
372	>	if (args_info.seleoffset_given) {
373	>	if (args_info.seleoffset2_given) {
374	>	analyser  = new pAngle(info, dumpFileName, sele1,
375	>	args_info.seleoffset_arg,
376	>	args_info.seleoffset2_arg,
377	>	args_info.nbins_arg);
378	>	} else {
379	>	analyser  = new pAngle(info, dumpFileName, sele1,
380	>	args_info.seleoffset_arg,
381	>	args_info.nbins_arg);
382	>	}
383	>	} else
384	>	analyser  = new pAngle(info, dumpFileName, sele1,
385	>	args_info.nbins_arg);
386	>	} else {
387	>	sprintf( painCave.errMsg,
388	>	"At least one selection script (--sele1) must be specified when "
389	>	"calculating P(angle) distributions");
390	>	painCave.severity = OPENMD_ERROR;
391	>	painCave.isFatal = 1;
392	>	simError();
393	>	}
394		#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
395		}else if (args_info.hxy_given) {
396	<	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
396	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
397	>	args_info.nbins_y_arg, args_info.nbins_arg);
398		#endif
399	+	}else if (args_info.rho_r_given) {
400	+	if (args_info.radius_given){
401	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
402	+	}else{
403	+	sprintf( painCave.errMsg,
404	+	"A particle radius (radius) must be specified when calculating Rho(r)");
405	+	painCave.severity = OPENMD_ERROR;
406	+	painCave.isFatal = 1;
407	+	simError();
408	+	}
409	+	} else if (args_info.hullvol_given) {
410	+	analyser = new NanoVolume(info, dumpFileName, sele1);
411	+	} else if (args_info.rodlength_given) {
412	+	analyser = new NanoLength(info, dumpFileName, sele1);
413	+	} else if (args_info.angle_r_given) {
414	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
415		}
416
417		if (args_info.output_given) {
#	Line 233 | Line 420 | int main(int argc, char* argv[]){
420		if (args_info.step_given) {
421		analyser->setStep(args_info.step_arg);
422		}
423	<
423	>
424		analyser->process();
425	<
425	>
426		delete analyser;
427		delete info;
428	<
428	>
429		return 0;
430		}
244	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 2015 by gezelter, Wed Aug 13 20:42:43 2014 UTC

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

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