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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 545 by tim, Fri May 27 21:11:24 2005 UTC vs.
Revision 1846 by gezelter, Thu Jan 31 15:55:47 2013 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, 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"
#	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	+	using namespace OpenMD;
81
62	–	using namespace oopse;
63	–
82		int main(int argc, char* argv[]){
83
84	<	//register force fields
67	<	registerForceFields();
68	<
84	>
85		gengetopt_args_info args_info;
86	<
86	>
87		//parse the command line option
88		if (cmdline_parser (argc, argv, &args_info) != 0) {
89		exit(1) ;
90		}
91	<
92	<
77	<	//get the dumpfile name and meta-data file name
91	>
92	>	//get the dumpfile name
93		std::string dumpFileName = args_info.input_arg;
79	–
80	–	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
81	–
82	–
94		std::string sele1;
95		std::string sele2;
96	<
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("OOPSE_SELE1");
102	>	} else {
103	>	char*  sele1Env= getenv("SELECTION1");
104		if (sele1Env) {
105		sele1 = sele1Env;
106	<	}else if (!args_info.scd_given) {
107	<	sprintf( painCave.errMsg,
94	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
95	<	painCave.severity = OOPSE_ERROR;
96	<	painCave.isFatal = 1;
97	<	simError();
106	>	} else {
107	>	sele1 = "select all";
108		}
109		}
110	<
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("OOPSE_SELE2");
116	>	} else {
117	>	char* sele2Env = getenv("SELECTION1");
118		if (sele2Env) {
119		sele2 = sele2Env;
120	<	} else if(!args_info.scd_given && !args_info.density_given)  {
121	<	sprintf( painCave.errMsg,
122	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
123	<	painCave.severity = OOPSE_ERROR;
111	<	painCave.isFatal = 1;
112	<	simError();
120	>	} else {
121	>	//If sele2 is not specified, then the default behavior
122	>	//should be what is already intended for sele1
123	>	sele2 = sele1;
124		}
125		}
126
127		bool batchMode;
128		if (args_info.scd_given){
129	<	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
130	<	batchMode = false;
131	<	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
132	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
133	<	sprintf( painCave.errMsg,
134	<	"below conditions are not satisfied:\n"
135	<	"0 <= begin && 0<= end && begin <= end-2\n");
125	<	painCave.severity = OOPSE_ERROR;
126	<	painCave.isFatal = 1;
127	<	simError();
128	<	}
129	<	batchMode = true;
130	<	} else{
129	>	if (args_info.sele1_given &&
130	>	args_info.sele2_given && args_info.sele3_given) {
131	>	batchMode = false;
132	>	} else if (args_info.molname_given &&
133	>	args_info.begin_given && args_info.end_given) {
134	>	if (args_info.begin_arg < 0 ||
135	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
136		sprintf( painCave.errMsg,
137	<	"either --sele1, --sele2, --sele3 are specified,"
138	<	" or --molname, --begin, --end are specified\n");
139	<	painCave.severity = OOPSE_ERROR;
137	>	"below conditions are not satisfied:\n"
138	>	"0 <= begin && 0<= end && begin <= end-2\n");
139	>	painCave.severity = OPENMD_ERROR;
140		painCave.isFatal = 1;
141	<	simError();
142	<
141	>	simError();
142	>	}
143	>	batchMode = true;
144	>	} else{
145	>	sprintf( painCave.errMsg,
146	>	"either --sele1, --sele2, --sele3 are specified,"
147	>	" or --molname, --begin, --end are specified\n");
148	>	painCave.severity = OPENMD_ERROR;
149	>	painCave.isFatal = 1;
150	>	simError();
151		}
152		}
153	<
153	>
154		//parse md file and set up the system
155		SimCreator creator;
156	<	SimInfo* info = creator.createSim(mdFileName);
156	>	SimInfo* info = creator.createSim(dumpFileName);
157
158	<	double maxLen;
158	>	RealType maxLen;
159	>	RealType zmaxLen;
160		if (args_info.length_given) {
161		maxLen = args_info.length_arg;
162	+	if (args_info.zlength_given){
163	+	zmaxLen = args_info.zlength_arg;
164	+	}
165		} else {
166		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
167	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
167	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
168	>	zmaxLen = hmat(2,2);
169		}
170	<
170	>
171		StaticAnalyser* analyser;
172		if (args_info.gofr_given){
173	<	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
173	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
174	>	args_info.nbins_arg);
175	>	} else if (args_info.gofz_given) {
176	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
177	>	args_info.nbins_arg);
178	>	} else if (args_info.r_z_given) {
179	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
180	>	args_info.nbins_arg, args_info.nbins_z_arg);
181		} else if (args_info.r_theta_given) {
182	<	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
182	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
183	>	args_info.nbins_arg, args_info.nanglebins_arg);
184		} else if (args_info.r_omega_given) {
185	<	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
185	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
186	>	args_info.nbins_arg, args_info.nanglebins_arg);
187		} else if (args_info.theta_omega_given) {
188	<	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
188	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
189	>	args_info.nanglebins_arg);
190		} else if (args_info.gxyz_given) {
191		if (args_info.refsele_given) {
192	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
192	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
193	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
194		} else {
195		sprintf( painCave.errMsg,
196	<	"--refsele must set when --gxyz is used");
197	<	painCave.severity = OOPSE_ERROR;
196	>	"--refsele must set when --gxyz is used");
197	>	painCave.severity = OPENMD_ERROR;
198		painCave.isFatal = 1;
199		simError();
200		}
201	+	} else if (args_info.twodgofr_given){
202	+	if (args_info.dz_given) {
203	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
204	+	args_info.dz_arg, args_info.nbins_arg);
205	+	} else {
206	+	sprintf( painCave.errMsg,
207	+	"A slab width (dz) must be specified when calculating TwoDGofR");
208	+	painCave.severity = OPENMD_ERROR;
209	+	painCave.isFatal = 1;
210	+	simError();
211	+	}
212		} else if (args_info.p2_given) {
213	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
213	>	if (args_info.sele1_given) {
214	>	if (args_info.sele2_given)
215	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
216	>	else
217	>	if (args_info.seleoffset_given)
218	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
219	>	args_info.seleoffset_arg);
220	>	else
221	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
222	>	} else {
223	>	sprintf( painCave.errMsg,
224	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
225	>	painCave.severity = OPENMD_ERROR;
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	} else if (args_info.rp2_given){
230	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
231	>	} else if (args_info.bo_given){
232	>	if (args_info.rcut_given) {
233	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
234	>	args_info.rcut_arg,
235	>	args_info.nbins_arg);
236	>	} else {
237	>	sprintf( painCave.errMsg,
238	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
239	>	painCave.severity = OPENMD_ERROR;
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243	>
244	>	} else if (args_info.tet_param_given) {
245	>	if (args_info.rcut_given) {
246	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
247	>	args_info.rcut_arg,
248	>	args_info.nbins_arg);
249	>	} else {
250	>	sprintf( painCave.errMsg,
251	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
252	>	painCave.severity = OPENMD_ERROR;
253	>	painCave.isFatal = 1;
254	>	simError();
255	>	}
256	>	} else if (args_info.tet_param_z_given) {
257	>	if (args_info.rcut_given) {
258	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
259	>	args_info.rcut_arg,
260	>	args_info.nbins_arg);
261	>	} else {
262	>	sprintf( painCave.errMsg,
263	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
264	>	painCave.severity = OPENMD_ERROR;
265	>	painCave.isFatal = 1;
266	>	simError();
267	>	}
268	>	} else if (args_info.bor_given){
269	>	if (args_info.rcut_given) {
270	>	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
271	>	args_info.nbins_arg, maxLen);
272	>	} else {
273	>	sprintf( painCave.errMsg,
274	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
275	>	painCave.severity = OPENMD_ERROR;
276	>	painCave.isFatal = 1;
277	>	simError();
278	>	}
279	>	} else if (args_info.bad_given){
280	>	if (args_info.rcut_given) {
281	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
282	>	args_info.rcut_arg,
283	>	args_info.nbins_arg);
284	>	} else {
285	>	sprintf( painCave.errMsg,
286	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
287	>	painCave.severity = OPENMD_ERROR;
288	>	painCave.isFatal = 1;
289	>	simError();
290	>	}
291		} else if (args_info.scd_given) {
292	<	if (batchMode) {
293	<	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
294	<	args_info.begin_arg, args_info.end_arg);
295	<	} else{
296	<	std::string sele3 = args_info.sele3_arg;
297	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
298	<	}
292	>	if (batchMode) {
293	>	analyser  = new SCDOrderParameter(info, dumpFileName,
294	>	args_info.molname_arg,
295	>	args_info.begin_arg, args_info.end_arg);
296	>	} else{
297	>	std::string sele3 = args_info.sele3_arg;
298	>	analyser  = new SCDOrderParameter(info, dumpFileName,
299	>	sele1, sele2, sele3);
300	>	}
301		}else if (args_info.density_given) {
302	<	analyser= new DensityPlot(info, dumpFileName, sele1, maxLen, args_info.nrbins_arg);
302	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
303	>	args_info.nbins_arg);
304	>	} else if (args_info.count_given) {
305	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
306	>	} else if (args_info.slab_density_given) {
307	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
308	>	} else if (args_info.p_angle_given) {
309	>	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
310	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
311	>	}else if (args_info.hxy_given) {
312	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
313	>	args_info.nbins_y_arg, args_info.nbins_arg);
314	>	#endif
315	>	}else if (args_info.rho_r_given) {
316	>	if (args_info.radius_given){
317	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
318	>	}else{
319	>	sprintf( painCave.errMsg,
320	>	"A particle radius (radius) must be specified when calculating Rho(r)");
321	>	painCave.severity = OPENMD_ERROR;
322	>	painCave.isFatal = 1;
323	>	simError();
324	>	}
325	>	} else if (args_info.hullvol_given) {
326	>	analyser = new NanoVolume(info, dumpFileName, sele1);
327	>	} else if (args_info.rodlength_given) {
328	>	analyser = new NanoLength(info, dumpFileName, sele1);
329	>	} else if (args_info.angle_r_given) {
330	>	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
331		}
332	<
332	>
333		if (args_info.output_given) {
334		analyser->setOutputName(args_info.output_arg);
335		}
336		if (args_info.step_given) {
337		analyser->setStep(args_info.step_arg);
338		}
339	<
339	>
340		analyser->process();
341	<
341	>
342		delete analyser;
343		delete info;
344	<
344	>
345		return 0;
346		}
200	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 545 by tim, Fri May 27 21:11:24 2005 UTC vs.
Revision 1846 by gezelter, Thu Jan 31 15:55:47 2013 UTC

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

Diff Legend

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