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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 558 by tim, Mon Jun 13 18:25:30 2005 UTC vs.
Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 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.density_given) {
121	<	sele2 = "select all";
122	<	} else if(!args_info.scd_given && !args_info.density_given)  {
123	<	sprintf( painCave.errMsg,
124	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
112	<	painCave.severity = OOPSE_ERROR;
113	<	painCave.isFatal = 1;
114	<	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	>	//sele2 = "select all";
125		}
126		}
127	<
127	>
128	>
129	>	// Problems if sele1 wasn't specified, but
130	>	// if (!args_info.scd_given) {
131	>	//       sprintf( painCave.errMsg,
132	>	//                "neither --sele1 option nor $SELECTION1 is set");
133	>	//       painCave.severity = OPENMD_ERROR;
134	>	//       painCave.isFatal = 1;
135	>	//       simError();
136	>	//     }
137	>	//   }
138	>
139	>	// Problems if sele1 wasn't specified
140	>
141	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
142	>	//       sprintf( painCave.errMsg,
143	>	//                "neither --sele2 option nor $SELECTION1 is set");
144	>	//       painCave.severity = OPENMD_ERROR;
145	>	//       painCave.isFatal = 1;
146	>	//       simError();
147	>	//     }
148	>	//   }
149	>
150		bool batchMode;
151		if (args_info.scd_given){
152		if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
153	<	batchMode = false;
153	>	batchMode = false;
154		} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
155	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
124	<	sprintf( painCave.errMsg,
125	<	"below conditions are not satisfied:\n"
126	<	"0 <= begin && 0<= end && begin <= end-2\n");
127	<	painCave.severity = OOPSE_ERROR;
128	<	painCave.isFatal = 1;
129	<	simError();
130	<	}
131	<	batchMode = true;
132	<	} else{
155	>	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
156		sprintf( painCave.errMsg,
157	<	"either --sele1, --sele2, --sele3 are specified,"
158	<	" or --molname, --begin, --end are specified\n");
159	<	painCave.severity = OOPSE_ERROR;
157	>	"below conditions are not satisfied:\n"
158	>	"0 <= begin && 0<= end && begin <= end-2\n");
159	>	painCave.severity = OPENMD_ERROR;
160		painCave.isFatal = 1;
161	<	simError();
162	<
161	>	simError();
162	>	}
163	>	batchMode = true;
164	>	} else{
165	>	sprintf( painCave.errMsg,
166	>	"either --sele1, --sele2, --sele3 are specified,"
167	>	" or --molname, --begin, --end are specified\n");
168	>	painCave.severity = OPENMD_ERROR;
169	>	painCave.isFatal = 1;
170	>	simError();
171	>
172		}
173		}
174	<
174	>
175		//parse md file and set up the system
176		SimCreator creator;
177	<	SimInfo* info = creator.createSim(mdFileName);
177	>	std::cout << "dumpFile = " << dumpFileName << "\n";
178	>	SimInfo* info = creator.createSim(dumpFileName);
179
180	<	double maxLen;
180	>	RealType maxLen;
181	>	RealType zmaxLen;
182		if (args_info.length_given) {
183		maxLen = args_info.length_arg;
184	+	if (args_info.zlength_given){
185	+	zmaxLen = args_info.zlength_arg;
186	+	}
187		} else {
188		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
189	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
189	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
190	>	zmaxLen = hmat(2,2);
191		}
192	<
192	>
193		StaticAnalyser* analyser;
194		if (args_info.gofr_given){
195	<	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
195	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
196	>	args_info.nbins_arg);
197	>	} else if (args_info.gofz_given) {
198	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
199	>	args_info.nbins_arg);
200	>	} else if (args_info.r_z_given) {
201	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
202	>	args_info.nbins_arg, args_info.nbins_z_arg);
203		} else if (args_info.r_theta_given) {
204	<	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
204	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
205	>	args_info.nbins_arg, args_info.nanglebins_arg);
206		} else if (args_info.r_omega_given) {
207	<	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
207	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
208	>	args_info.nbins_arg, args_info.nanglebins_arg);
209		} else if (args_info.theta_omega_given) {
210	<	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
210	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
211	>	args_info.nanglebins_arg);
212		} else if (args_info.gxyz_given) {
213		if (args_info.refsele_given) {
214	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
214	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
215	>	maxLen, args_info.nbins_arg);
216		} else {
217		sprintf( painCave.errMsg,
218	<	"--refsele must set when --gxyz is used");
219	<	painCave.severity = OOPSE_ERROR;
218	>	"--refsele must set when --gxyz is used");
219	>	painCave.severity = OPENMD_ERROR;
220		painCave.isFatal = 1;
221		simError();
222		}
223	+	} else if (args_info.twodgofr_given){
224	+	if (args_info.dz_given) {
225	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
226	+	args_info.dz_arg, args_info.nbins_arg);
227	+	} else {
228	+	sprintf( painCave.errMsg,
229	+	"A slab width (dz) must be specified when calculating TwoDGofR");
230	+	painCave.severity = OPENMD_ERROR;
231	+	painCave.isFatal = 1;
232	+	simError();
233	+	}
234		} else if (args_info.p2_given) {
235	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
236	<	} else if (args_info.scd_given) {
237	<	if (batchMode) {
238	<	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
239	<	args_info.begin_arg, args_info.end_arg);
240	<	} else{
241	<	std::string sele3 = args_info.sele3_arg;
242	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
235	>	if (args_info.sele1_given) {
236	>	if (args_info.sele2_given)
237	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
238	>	else
239	>	if (args_info.seleoffset_given)
240	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
241	>	args_info.seleoffset_arg);
242	>	else
243	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
244	>	} else {
245	>	sprintf( painCave.errMsg,
246	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
247	>	painCave.severity = OPENMD_ERROR;
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	} else if (args_info.rp2_given){
252	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
253	>	} else if (args_info.bo_given){
254	>	if (args_info.rcut_given) {
255	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
256	>	args_info.rcut_arg,
257	>	args_info.nbins_arg);
258	>	} else {
259	>	sprintf( painCave.errMsg,
260	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
261	>	painCave.severity = OPENMD_ERROR;
262	>	painCave.isFatal = 1;
263	>	simError();
264	>	}
265	>
266	>	} else if (args_info.tet_param_given) {
267	>	if (args_info.rcut_given) {
268	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
269	>	args_info.rcut_arg,
270	>	args_info.nbins_arg);
271	>	} else {
272	>	sprintf( painCave.errMsg,
273	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
274	>	painCave.severity = OPENMD_ERROR;
275	>	painCave.isFatal = 1;
276	>	simError();
277	>	}
278	>	} else if (args_info.tet_param_z_given) {
279	>	if (args_info.rcut_given) {
280	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
281	>	args_info.rcut_arg,
282	>	args_info.nbins_arg);
283	>	} else {
284	>	sprintf( painCave.errMsg,
285	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
286	>	painCave.severity = OPENMD_ERROR;
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290	>	} else if (args_info.bor_given){
291	>	if (args_info.rcut_given) {
292	>	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
293	>	args_info.nbins_arg, maxLen);
294	>	} else {
295	>	sprintf( painCave.errMsg,
296	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
297	>	painCave.severity = OPENMD_ERROR;
298	>	painCave.isFatal = 1;
299	>	simError();
300	>	}
301	>	} else if (args_info.bad_given){
302	>	if (args_info.rcut_given) {
303	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
304	>	args_info.nbins_arg);
305	>	} else {
306	>	sprintf( painCave.errMsg,
307	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
308	>	painCave.severity = OPENMD_ERROR;
309	>	painCave.isFatal = 1;
310	>	simError();
311		}
312	+	} else if (args_info.scd_given) {
313	+	if (batchMode) {
314	+	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
315	+	args_info.begin_arg, args_info.end_arg);
316	+	} else{
317	+	std::string sele3 = args_info.sele3_arg;
318	+	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
319	+	}
320		}else if (args_info.density_given) {
321	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
321	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
322	>	args_info.nbins_arg);
323	>	} else if (args_info.count_given) {
324	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
325	>	} else if (args_info.slab_density_given) {
326	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
327	>	} else if (args_info.p_angle_given) {
328	>	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
329	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
330	>	}else if (args_info.hxy_given) {
331	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
332	>	args_info.nbins_y_arg, args_info.nbins_arg);
333	>	#endif
334	>	}else if (args_info.rho_r_given) {
335	>	if (args_info.radius_given){
336	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
337	>	}else{
338	>	sprintf( painCave.errMsg,
339	>	"A particle radius (radius) must be specified when calculating Rho(r)");
340	>	painCave.severity = OPENMD_ERROR;
341	>	painCave.isFatal = 1;
342	>	simError();
343	>	}
344	>	} else if (args_info.hullvol_given) {
345	>	analyser = new NanoVolume(info, dumpFileName, sele1);
346	>	} else if (args_info.rodlength_given) {
347	>	analyser = new NanoLength(info, dumpFileName, sele1);
348	>	} else if (args_info.angle_r_given) {
349	>	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
350		}
351
352		if (args_info.output_given) {
#	Line 191 | Line 355 | int main(int argc, char* argv[]){
355		if (args_info.step_given) {
356		analyser->setStep(args_info.step_arg);
357		}
358	<
358	>
359		analyser->process();
360	<
360	>
361		delete analyser;
362		delete info;
363

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 558 by tim, Mon Jun 13 18:25:30 2005 UTC vs.
Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

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

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+	Added lines
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