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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1026 by gezelter, Wed Aug 30 21:04:04 2006 UTC vs.
Revision 1992 by gezelter, Thu Apr 24 17:30:00 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
82	<	using namespace oopse;
82	>	using namespace OpenMD;
83
84		int main(int argc, char* argv[]){
85
86	<	//register force fields
72	<	registerForceFields();
73	<
86	>
87		gengetopt_args_info args_info;
88	<
88	>
89		//parse the command line option
90		if (cmdline_parser (argc, argv, &args_info) != 0) {
91		exit(1) ;
92		}
93	<
94	<
82	<	//get the dumpfile name and meta-data file name
93	>
94	>	//get the dumpfile name
95		std::string dumpFileName = args_info.input_arg;
84	–
85	–
96		std::string sele1;
97		std::string sele2;
98	<
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("OOPSE_SELE1");
104	>	} else {
105	>	char*  sele1Env= getenv("SELECTION1");
106		if (sele1Env) {
107		sele1 = sele1Env;
108	<	}else if (!args_info.scd_given) {
109	<	sprintf( painCave.errMsg,
97	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
98	<	painCave.severity = OOPSE_ERROR;
99	<	painCave.isFatal = 1;
100	<	simError();
108	>	} else {
109	>	sele1 = "select all";
110		}
111		}
112	<
112	>
113	>	// check the second selection argument, or set it to the environment
114	>	// variable, or failing that, set it to the first selection
115	>
116		if (args_info.sele2_given) {
117		sele2 = args_info.sele2_arg;
118	<	}else {
119	<	char* sele2Env = getenv("OOPSE_SELE2");
118	>	} else {
119	>	char* sele2Env = getenv("SELECTION2");
120		if (sele2Env) {
121		sele2 = sele2Env;
122	<	} else if (args_info.density_given) {
123	<	sele2 = "select all";
124	<	} else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
125	<	sprintf( painCave.errMsg,
114	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
115	<	painCave.severity = OOPSE_ERROR;
116	<	painCave.isFatal = 1;
117	<	simError();
122	>	} else {
123	>	//If sele2 is not specified, then the default behavior
124	>	//should be what is already intended for sele1
125	>	sele2 = sele1;
126		}
127		}
128
129		bool batchMode;
130		if (args_info.scd_given){
131	<	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
132	<	batchMode = false;
133	<	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
134	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
135	<	sprintf( painCave.errMsg,
136	<	"below conditions are not satisfied:\n"
137	<	"0 <= begin && 0<= end && begin <= end-2\n");
130	<	painCave.severity = OOPSE_ERROR;
131	<	painCave.isFatal = 1;
132	<	simError();
133	<	}
134	<	batchMode = true;
135	<	} else{
131	>	if (args_info.sele1_given &&
132	>	args_info.sele2_given && args_info.sele3_given) {
133	>	batchMode = false;
134	>	} else if (args_info.molname_given &&
135	>	args_info.begin_given && args_info.end_given) {
136	>	if (args_info.begin_arg < 0 ||
137	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
138		sprintf( painCave.errMsg,
139	<	"either --sele1, --sele2, --sele3 are specified,"
140	<	" or --molname, --begin, --end are specified\n");
141	<	painCave.severity = OOPSE_ERROR;
139	>	"below conditions are not satisfied:\n"
140	>	"0 <= begin && 0<= end && begin <= end-2\n");
141	>	painCave.severity = OPENMD_ERROR;
142		painCave.isFatal = 1;
143	<	simError();
144	<
143	>	simError();
144	>	}
145	>	batchMode = true;
146	>	} else{
147	>	sprintf( painCave.errMsg,
148	>	"either --sele1, --sele2, --sele3 are specified,"
149	>	" or --molname, --begin, --end are specified\n");
150	>	painCave.severity = OPENMD_ERROR;
151	>	painCave.isFatal = 1;
152	>	simError();
153		}
154		}
155	<
155	>
156		//parse md file and set up the system
157		SimCreator creator;
158		SimInfo* info = creator.createSim(dumpFileName);
159
160		RealType maxLen;
161	+	RealType zmaxLen;
162		if (args_info.length_given) {
163		maxLen = args_info.length_arg;
164	+	if (args_info.zlength_given){
165	+	zmaxLen = args_info.zlength_arg;
166	+	}
167		} else {
168		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
169	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
169	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
170	>	zmaxLen = hmat(2,2);
171		}
172	<
172	>
173		StaticAnalyser* analyser;
174		if (args_info.gofr_given){
175	<	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
175	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
176	>	args_info.nbins_arg);
177	>	} else if (args_info.gofz_given) {
178	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
179	>	args_info.nbins_arg);
180	>	} else if (args_info.r_z_given) {
181	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
182	>	args_info.nbins_arg, args_info.nbins_z_arg);
183		} else if (args_info.r_theta_given) {
184	<	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
184	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
185	>	args_info.nbins_arg, args_info.nanglebins_arg);
186		} else if (args_info.r_omega_given) {
187	<	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
187	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
188	>	args_info.nbins_arg, args_info.nanglebins_arg);
189		} else if (args_info.theta_omega_given) {
190	<	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
190	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
191	>	args_info.nanglebins_arg);
192		} else if (args_info.gxyz_given) {
193		if (args_info.refsele_given) {
194	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
194	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
195	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
196		} else {
197		sprintf( painCave.errMsg,
198	<	"--refsele must set when --gxyz is used");
199	<	painCave.severity = OOPSE_ERROR;
198	>	"--refsele must set when --gxyz is used");
199	>	painCave.severity = OPENMD_ERROR;
200		painCave.isFatal = 1;
201		simError();
202		}
203	<	} else if (args_info.p2_given) {
204	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
205	<	}    else if (args_info.rp2_given){
206	<	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
207	<	}else if (args_info.scd_given) {
208	<	if (batchMode) {
209	<	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
210	<	args_info.begin_arg, args_info.end_arg);
211	<	} else{
212	<	std::string sele3 = args_info.sele3_arg;
213	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
214	<	}
215	<	}else if (args_info.density_given) {
216	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
203	>	} else if (args_info.twodgofr_given){
204	>	if (args_info.dz_given) {
205	>	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
206	>	args_info.dz_arg, args_info.nbins_arg);
207	>	} else {
208	>	sprintf( painCave.errMsg,
209	>	"A slab width (dz) must be specified when calculating TwoDGofR");
210	>	painCave.severity = OPENMD_ERROR;
211	>	painCave.isFatal = 1;
212	>	simError();
213	>	}
214	>	} else if (args_info.p2_given) {
215	>	if (args_info.sele1_given) {
216	>	if (args_info.sele2_given)
217	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
218	>	else
219	>	if (args_info.seleoffset_given)
220	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
221	>	args_info.seleoffset_arg);
222	>	else
223	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
224	>	} else {
225	>	sprintf( painCave.errMsg,
226	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
227	>	painCave.severity = OPENMD_ERROR;
228	>	painCave.isFatal = 1;
229	>	simError();
230	>	}
231	>	} else if (args_info.rp2_given){
232	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
233	>	} else if (args_info.bo_given){
234	>	if (args_info.rcut_given) {
235	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
236	>	args_info.rcut_arg,
237	>	args_info.nbins_arg);
238	>	} else {
239	>	sprintf( painCave.errMsg,
240	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
241	>	painCave.severity = OPENMD_ERROR;
242	>	painCave.isFatal = 1;
243	>	simError();
244	>	}
245	>
246	>	} else if (args_info.tet_param_given) {
247	>	if (args_info.rcut_given) {
248	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
249	>	args_info.rcut_arg,
250	>	args_info.nbins_arg);
251	>	} else {
252	>	sprintf( painCave.errMsg,
253	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
254	>	painCave.severity = OPENMD_ERROR;
255	>	painCave.isFatal = 1;
256	>	simError();
257	>	}
258	>	} else if (args_info.tet_param_z_given) {
259	>	if (args_info.rcut_given) {
260	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
261	>	args_info.rcut_arg,
262	>	args_info.nbins_arg);
263	>	} else {
264	>	sprintf( painCave.errMsg,
265	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
266	>	painCave.severity = OPENMD_ERROR;
267	>	painCave.isFatal = 1;
268	>	simError();
269	>	}
270	>	} else if (args_info.ior_given){
271	>	if (args_info.rcut_given) {
272	>	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
273	>	args_info.rcut_arg,
274	>	args_info.nbins_arg, maxLen);
275	>	} else {
276	>	sprintf( painCave.errMsg,
277	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
278	>	painCave.severity = OPENMD_ERROR;
279	>	painCave.isFatal = 1;
280	>	simError();
281	>	}
282	>	} else if (args_info.for_given){
283	>	if (args_info.rcut_given) {
284	>	analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
285	>	args_info.nbins_arg, maxLen);
286	>	} else {
287	>	sprintf( painCave.errMsg,
288	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
289	>	painCave.severity = OPENMD_ERROR;
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293	>	} else if (args_info.bad_given){
294	>	if (args_info.rcut_given) {
295	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
296	>	args_info.rcut_arg,
297	>	args_info.nbins_arg);
298	>	} else {
299	>	sprintf( painCave.errMsg,
300	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
301	>	painCave.severity = OPENMD_ERROR;
302	>	painCave.isFatal = 1;
303	>	simError();
304	>	}
305	>	} else if (args_info.scd_given) {
306	>	if (batchMode) {
307	>	analyser  = new SCDOrderParameter(info, dumpFileName,
308	>	args_info.molname_arg,
309	>	args_info.begin_arg, args_info.end_arg);
310	>	} else{
311	>	std::string sele3 = args_info.sele3_arg;
312	>	analyser  = new SCDOrderParameter(info, dumpFileName,
313	>	sele1, sele2, sele3);
314	>	}
315	>	}else if (args_info.density_given) {
316	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
317	>	args_info.nbins_arg);
318	>	} else if (args_info.count_given) {
319	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
320		} else if (args_info.slab_density_given) {
321	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
322	<	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg);
321	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
322	>	} else if (args_info.rnemdz_given) {
323	>	analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
324	>	} else if (args_info.rnemdr_given) {
325	>	analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
326	>	} else if (args_info.rnemdrt_given) {
327	>	analyser = new RNEMDRTheta(info, dumpFileName, sele1,
328	>	args_info.nbins_arg, args_info.nanglebins_arg);
329	>	} else if (args_info.p_angle_given) {
330	>	if (args_info.sele1_given) {
331	>	if (args_info.sele2_given)
332	>	analyser  = new pAngle(info, dumpFileName, sele1, sele2,
333	>	args_info.nbins_arg);
334	>	else
335	>	if (args_info.seleoffset_given) {
336	>	if (args_info.seleoffset2_given) {
337	>	analyser  = new pAngle(info, dumpFileName, sele1,
338	>	args_info.seleoffset_arg,
339	>	args_info.seleoffset2_arg,
340	>	args_info.nbins_arg);
341	>	} else {
342	>	analyser  = new pAngle(info, dumpFileName, sele1,
343	>	args_info.seleoffset_arg,
344	>	args_info.nbins_arg);
345	>	}
346	>	} else
347	>	analyser  = new pAngle(info, dumpFileName, sele1,
348	>	args_info.nbins_arg);
349	>	} else {
350	>	sprintf( painCave.errMsg,
351	>	"At least one selection script (--sele1) must be specified when "
352	>	"calculating P(angle) distributions");
353	>	painCave.severity = OPENMD_ERROR;
354	>	painCave.isFatal = 1;
355	>	simError();
356	>	}
357		#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
358		}else if (args_info.hxy_given) {
359	<	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
359	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
360	>	args_info.nbins_y_arg, args_info.nbins_arg);
361		#endif
362	+	}else if (args_info.rho_r_given) {
363	+	if (args_info.radius_given){
364	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
365	+	}else{
366	+	sprintf( painCave.errMsg,
367	+	"A particle radius (radius) must be specified when calculating Rho(r)");
368	+	painCave.severity = OPENMD_ERROR;
369	+	painCave.isFatal = 1;
370	+	simError();
371	+	}
372	+	} else if (args_info.hullvol_given) {
373	+	analyser = new NanoVolume(info, dumpFileName, sele1);
374	+	} else if (args_info.rodlength_given) {
375	+	analyser = new NanoLength(info, dumpFileName, sele1);
376	+	} else if (args_info.angle_r_given) {
377	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
378		}
379	<
379	>
380		if (args_info.output_given) {
381		analyser->setOutputName(args_info.output_arg);
382		}
383		if (args_info.step_given) {
384		analyser->setStep(args_info.step_arg);
385		}
386	<
386	>
387		analyser->process();
388	<
388	>
389		delete analyser;
390		delete info;
391	<
391	>
392		return 0;
393		}
214	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 1026 by gezelter, Wed Aug 30 21:04:04 2006 UTC vs.
Revision 1992 by gezelter, Thu Apr 24 17:30:00 2014 UTC

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