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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1267 by gpuliti, Mon Jun 30 17:53:42 2008 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 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 53 | Line 53
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
73	–	using namespace oopse;
74	–
82		int main(int argc, char* argv[]){
83
84	<	//register force fields
78	<	registerForceFields();
79	<
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	<
91	>
92		//get the dumpfile name
93		std::string dumpFileName = args_info.input_arg;
94		std::string sele1;
95		std::string sele2;
96	<	bool userSpecifiedSelect1;
92	<	bool userSpecifiedSelect2;
93	<
96	>
97		// check the first selection argument, or set it to the environment
98		// variable, or failing that, set it to "select all"
99	<
99	>
100		if (args_info.sele1_given) {
101		sele1 = args_info.sele1_arg;
102		} else {
103	<	char*  sele1Env= getenv("OOPSE_SELE1");
103	>	char*  sele1Env= getenv("SELECTION1");
104		if (sele1Env) {
105		sele1 = sele1Env;
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");
117	>	char* sele2Env = getenv("SELECTION1");
118		if (sele2Env) {
119		sele2 = sele2Env;
120		} else {
121	<	sele2 = "select all";
121	>	//It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior
122	>	//should not be 'select all' but rather what is already intended for sele1
123	>	//JRM 8/22/12
124	>	sele2 = sele1;
125	>	//sele2 = "select all";
126		}
127		}
128	<
129	<
128	>
129	>
130		// Problems if sele1 wasn't specified, but
131	<	// if (!args_info.scd_given) {
132	<	//       sprintf( painCave.errMsg,
133	<	//                "neither --sele1 option nor $OOPSE_SELE1 is set");
134	<	//       painCave.severity = OOPSE_ERROR;
135	<	//       painCave.isFatal = 1;
136	<	//       simError();
137	<	//     }
138	<	//   }
139	<
131	>	// if (!args_info.scd_given) {
132	>	//       sprintf( painCave.errMsg,
133	>	//                "neither --sele1 option nor $SELECTION1 is set");
134	>	//       painCave.severity = OPENMD_ERROR;
135	>	//       painCave.isFatal = 1;
136	>	//       simError();
137	>	//     }
138	>	//   }
139	>
140		// Problems if sele1 wasn't specified
141	<
142	<	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "neither --sele2 option nor $OOPSE_SELE2 is set");
145	<	//       painCave.severity = OOPSE_ERROR;
146	<	//       painCave.isFatal = 1;
147	<	//       simError();
148	<	//     }
149	<	//   }
150	<
141	>
142	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
143	>	//       sprintf( painCave.errMsg,
144	>	//                "neither --sele2 option nor $SELECTION1 is set");
145	>	//       painCave.severity = OPENMD_ERROR;
146	>	//       painCave.isFatal = 1;
147	>	//       simError();
148	>	//     }
149	>	//   }
150	>
151		bool batchMode;
152		if (args_info.scd_given){
153		if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
#	Line 150 | Line 157 | int main(int argc, char* argv[]){
157		sprintf( painCave.errMsg,
158		"below conditions are not satisfied:\n"
159		"0 <= begin && 0<= end && begin <= end-2\n");
160	<	painCave.severity = OOPSE_ERROR;
160	>	painCave.severity = OPENMD_ERROR;
161		painCave.isFatal = 1;
162		simError();
163		}
#	Line 159 | Line 166 | int main(int argc, char* argv[]){
166		sprintf( painCave.errMsg,
167		"either --sele1, --sele2, --sele3 are specified,"
168		" or --molname, --begin, --end are specified\n");
169	<	painCave.severity = OOPSE_ERROR;
169	>	painCave.severity = OPENMD_ERROR;
170		painCave.isFatal = 1;
171		simError();
172	<
172	>
173		}
174		}
175	<
175	>
176		//parse md file and set up the system
177		SimCreator creator;
178		std::cout << "dumpFile = " << dumpFileName << "\n";
179		SimInfo* info = creator.createSim(dumpFileName);
180
181		RealType maxLen;
182	+	RealType zmaxLen;
183		if (args_info.length_given) {
184		maxLen = args_info.length_arg;
185	+	if (args_info.zlength_given){
186	+	zmaxLen = args_info.zlength_arg;
187	+	}
188		} else {
189		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
190	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
190	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
191	>	zmaxLen = hmat(2,2);
192		}
193	<
193	>
194		StaticAnalyser* analyser;
195		if (args_info.gofr_given){
196		analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
197	<	args_info.nbins_arg);
197	>	args_info.nbins_arg);
198		} else if (args_info.gofz_given) {
199		analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
200	<	args_info.nbins_arg);
200	>	args_info.nbins_arg);
201	>	} else if (args_info.r_z_given) {
202	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
203	>	args_info.nbins_arg, args_info.nbins_z_arg);
204		} else if (args_info.r_theta_given) {
205		analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
206	<	args_info.nbins_arg, args_info.nanglebins_arg);
206	>	args_info.nbins_arg, args_info.nanglebins_arg);
207		} else if (args_info.r_omega_given) {
208		analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
209	<	args_info.nbins_arg, args_info.nanglebins_arg);
209	>	args_info.nbins_arg, args_info.nanglebins_arg);
210		} else if (args_info.theta_omega_given) {
211		analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
212	<	args_info.nanglebins_arg);
212	>	args_info.nanglebins_arg);
213		} else if (args_info.gxyz_given) {
214		if (args_info.refsele_given) {
215		analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
216	<	maxLen, args_info.nbins_arg);
216	>	maxLen, args_info.nbins_arg);
217		} else {
218		sprintf( painCave.errMsg,
219	<	"--refsele must set when --gxyz is used");
220	<	painCave.severity = OOPSE_ERROR;
219	>	"--refsele must set when --gxyz is used");
220	>	painCave.severity = OPENMD_ERROR;
221		painCave.isFatal = 1;
222		simError();
223		}
224	+	} else if (args_info.twodgofr_given){
225	+	if (args_info.dz_given) {
226	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
227	+	args_info.dz_arg, args_info.nbins_arg);
228	+	} else {
229	+	sprintf( painCave.errMsg,
230	+	"A slab width (dz) must be specified when calculating TwoDGofR");
231	+	painCave.severity = OPENMD_ERROR;
232	+	painCave.isFatal = 1;
233	+	simError();
234	+	}
235		} else if (args_info.p2_given) {
236	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
236	>	if (args_info.sele1_given) {
237	>	if (args_info.sele2_given)
238	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
239	>	else
240	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
241	>	} else {
242	>	sprintf( painCave.errMsg,
243	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
244	>	painCave.severity = OPENMD_ERROR;
245	>	painCave.isFatal = 1;
246	>	simError();
247	>	}
248		} else if (args_info.rp2_given){
249		analyser = new RippleOP(info, dumpFileName, sele1, sele2);
250		} else if (args_info.bo_given){
251		if (args_info.rcut_given) {
252		analyser = new BondOrderParameter(info, dumpFileName, sele1,
253	<	args_info.rcut_arg,
254	<	args_info.nbins_arg);
253	>	args_info.rcut_arg,
254	>	args_info.nbins_arg);
255		} else {
256		sprintf( painCave.errMsg,
257	<	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
258	<	painCave.severity = OOPSE_ERROR;
257	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
258	>	painCave.severity = OPENMD_ERROR;
259		painCave.isFatal = 1;
260		simError();
261		}
262	+
263	+	} else if (args_info.tet_param_given) {
264	+	if (args_info.rcut_given) {
265	+	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
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_z_given) {
276	+	if (args_info.rcut_given) {
277	+	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
278	+	args_info.rcut_arg,
279	+	args_info.nbins_arg);
280	+	} else {
281	+	sprintf( painCave.errMsg,
282	+	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
283	+	painCave.severity = OPENMD_ERROR;
284	+	painCave.isFatal = 1;
285	+	simError();
286	+	}
287		} else if (args_info.bor_given){
288		if (args_info.rcut_given) {
289		analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
290		args_info.nbins_arg, maxLen);
291		} else {
292		sprintf( painCave.errMsg,
293	<	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
294	<	painCave.severity = OOPSE_ERROR;
293	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
294	>	painCave.severity = OPENMD_ERROR;
295		painCave.isFatal = 1;
296		simError();
297		}
298		} else if (args_info.bad_given){
299		if (args_info.rcut_given) {
300		analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
301	<	args_info.nbins_arg);
301	>	args_info.nbins_arg);
302		} else {
303		sprintf( painCave.errMsg,
304	<	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
305	<	painCave.severity = OOPSE_ERROR;
304	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
305	>	painCave.severity = OPENMD_ERROR;
306		painCave.isFatal = 1;
307		simError();
308	<	}
308	>	}
309		} else if (args_info.scd_given) {
310		if (batchMode) {
311		analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
312	<	args_info.begin_arg, args_info.end_arg);
312	>	args_info.begin_arg, args_info.end_arg);
313		} else{
314		std::string sele3 = args_info.sele3_arg;
315		analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
316		}
317		}else if (args_info.density_given) {
318		analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
319	<	args_info.nbins_arg);
319	>	args_info.nbins_arg);
320	>	} else if (args_info.count_given) {
321	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
322		} else if (args_info.slab_density_given) {
323		analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
324	+	} else if (args_info.p_angle_given) {
325	+	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
326		#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
327		}else if (args_info.hxy_given) {
328		analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
329	<	args_info.nbins_y_arg, args_info.nbins_arg);
329	>	args_info.nbins_y_arg, args_info.nbins_arg);
330		#endif
331		}else if (args_info.rho_r_given) {
332		if (args_info.radius_given){
333		analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
334		}else{
335		sprintf( painCave.errMsg,
336	<	"A particle radius (radius) must be specified when calculating Rho(r)");
337	<	painCave.severity = OOPSE_ERROR;
336	>	"A particle radius (radius) must be specified when calculating Rho(r)");
337	>	painCave.severity = OPENMD_ERROR;
338		painCave.isFatal = 1;
339		simError();
340		}
341	<	}else if (args_info.hullvol_given) {
341	>	} else if (args_info.hullvol_given) {
342		analyser = new NanoVolume(info, dumpFileName, sele1);
343	+	} else if (args_info.rodlength_given) {
344	+	analyser = new NanoLength(info, dumpFileName, sele1);
345	+	} else if (args_info.angle_r_given) {
346	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
347		}
348	<
348	>
349		if (args_info.output_given) {
350		analyser->setOutputName(args_info.output_arg);
351		}
352		if (args_info.step_given) {
353		analyser->setStep(args_info.step_arg);
354		}
355	<
355	>
356		analyser->process();
357	<
357	>
358		delete analyser;
359		delete info;
360

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 1267 by gpuliti, Mon Jun 30 17:53:42 2008 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

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

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