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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 955 by xsun, Fri May 12 21:34:43 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
69	<	registerForceFields();
70	<
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	<
95	<
79	<	//get the dumpfile name and meta-data file name
94	>
95	>	//get the dumpfile name
96		std::string dumpFileName = args_info.input_arg;
81	–
82	–	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
83	–
84	–
97		std::string sele1;
98		std::string sele2;
99	<
99	>
100	>	// check the first selection argument, or set it to the environment
101	>	// variable, or failing that, set it to "select all"
102	>
103		if (args_info.sele1_given) {
104		sele1 = args_info.sele1_arg;
105	<	}else {
106	<	char*  sele1Env= getenv("OOPSE_SELE1");
105	>	} else {
106	>	char*  sele1Env= getenv("SELECTION1");
107		if (sele1Env) {
108		sele1 = sele1Env;
109	<	}else if (!args_info.scd_given) {
110	<	sprintf( painCave.errMsg,
96	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
97	<	painCave.severity = OOPSE_ERROR;
98	<	painCave.isFatal = 1;
99	<	simError();
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 the first selection
116	>
117		if (args_info.sele2_given) {
118		sele2 = args_info.sele2_arg;
119	<	}else {
120	<	char* sele2Env = getenv("OOPSE_SELE2");
119	>	} else {
120	>	char* sele2Env = getenv("SELECTION2");
121		if (sele2Env) {
122		sele2 = sele2Env;
123	<	} else if (args_info.density_given) {
124	<	sele2 = "select all";
125	<	} else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
126	<	sprintf( painCave.errMsg,
113	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
114	<	painCave.severity = OOPSE_ERROR;
115	<	painCave.isFatal = 1;
116	<	simError();
123	>	} else {
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
130		bool batchMode;
131		if (args_info.scd_given){
132	<	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
133	<	batchMode = false;
134	<	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
135	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
136	<	sprintf( painCave.errMsg,
137	<	"below conditions are not satisfied:\n"
138	<	"0 <= begin && 0<= end && begin <= end-2\n");
129	<	painCave.severity = OOPSE_ERROR;
130	<	painCave.isFatal = 1;
131	<	simError();
132	<	}
133	<	batchMode = true;
134	<	} else{
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 &&
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	<	"either --sele1, --sele2, --sele3 are specified,"
141	<	" or --molname, --begin, --end are specified\n");
142	<	painCave.severity = OOPSE_ERROR;
140	>	"below conditions are not satisfied:\n"
141	>	"0 <= begin && 0<= end && begin <= end-2\n");
142	>	painCave.severity = OPENMD_ERROR;
143		painCave.isFatal = 1;
144	<	simError();
145	<
144	>	simError();
145	>	}
146	>	batchMode = true;
147	>	} else{
148	>	sprintf( painCave.errMsg,
149	>	"either --sele1, --sele2, --sele3 are specified,"
150	>	" or --molname, --begin, --end are specified\n");
151	>	painCave.severity = OPENMD_ERROR;
152	>	painCave.isFatal = 1;
153	>	simError();
154		}
155		}
156	<
156	>
157		//parse md file and set up the system
158		SimCreator creator;
159	<	SimInfo* info = creator.createSim(mdFileName);
159	>	SimInfo* info = creator.createSim(dumpFileName);
160
161	<	double maxLen;
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, args_info.nrbins_arg);
176	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
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, args_info.nrbins_arg, args_info.nanglebins_arg);
185	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
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, args_info.nrbins_arg, args_info.nanglebins_arg);
188	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
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, args_info.nanglebins_arg);
191	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
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, maxLen, args_info.nrbins_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);
239	>	} else {
240	>	sprintf( painCave.errMsg,
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);
310	<	} else{
311	<	std::string sele3 = args_info.sele3_arg;
312	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
313	<	}
307	>	if (batchMode) {
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,
314	>	sele1, sele2, sele3);
315	>	}
316		}else if (args_info.density_given) {
317	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_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.nrbins_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, args_info.nbins_y_arg, args_info.nrbins_arg);
363	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_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 = 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	<
383	>
384		if (args_info.output_given) {
385		analyser->setOutputName(args_info.output_arg);
386		}
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		}
209	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 955 by xsun, Fri May 12 21:34:43 2006 UTC vs.
Revision 1994 by gezelter, Wed Apr 30 18:50:45 2014 UTC

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