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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 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
68	–	using namespace oopse;
69	–
82		int main(int argc, char* argv[]){
83
84	<	//register force fields
73	<	registerForceFields();
74	<
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;
87	<	bool userSpecifiedSelect2;
88	<
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";
122		}
123		}
124	<
125	<
124	>
125	>
126		// Problems if sele1 wasn't specified, but
127	<	// if (!args_info.scd_given) {
128	<	//       sprintf( painCave.errMsg,
129	<	//                "neither --sele1 option nor $OOPSE_SELE1 is set");
130	<	//       painCave.severity = OOPSE_ERROR;
131	<	//       painCave.isFatal = 1;
132	<	//       simError();
133	<	//     }
134	<	//   }
135	<
127	>	// if (!args_info.scd_given) {
128	>	//       sprintf( painCave.errMsg,
129	>	//                "neither --sele1 option nor $SELECTION1 is set");
130	>	//       painCave.severity = OPENMD_ERROR;
131	>	//       painCave.isFatal = 1;
132	>	//       simError();
133	>	//     }
134	>	//   }
135	>
136		// Problems if sele1 wasn't specified
137	<
138	<	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
139	<	//       sprintf( painCave.errMsg,
140	<	//                "neither --sele2 option nor $OOPSE_SELE2 is set");
141	<	//       painCave.severity = OOPSE_ERROR;
142	<	//       painCave.isFatal = 1;
143	<	//       simError();
144	<	//     }
145	<	//   }
146	<
137	>
138	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
139	>	//       sprintf( painCave.errMsg,
140	>	//                "neither --sele2 option nor $SELECTION1 is set");
141	>	//       painCave.severity = OPENMD_ERROR;
142	>	//       painCave.isFatal = 1;
143	>	//       simError();
144	>	//     }
145	>	//   }
146	>
147		bool batchMode;
148		if (args_info.scd_given){
149		if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
#	Line 145 | Line 153 | int main(int argc, char* argv[]){
153		sprintf( painCave.errMsg,
154		"below conditions are not satisfied:\n"
155		"0 <= begin && 0<= end && begin <= end-2\n");
156	<	painCave.severity = OOPSE_ERROR;
156	>	painCave.severity = OPENMD_ERROR;
157		painCave.isFatal = 1;
158		simError();
159		}
#	Line 154 | Line 162 | int main(int argc, char* argv[]){
162		sprintf( painCave.errMsg,
163		"either --sele1, --sele2, --sele3 are specified,"
164		" or --molname, --begin, --end are specified\n");
165	<	painCave.severity = OOPSE_ERROR;
165	>	painCave.severity = OPENMD_ERROR;
166		painCave.isFatal = 1;
167		simError();
168	<
168	>
169		}
170		}
171	<
171	>
172		//parse md file and set up the system
173		SimCreator creator;
174	+	std::cout << "dumpFile = " << dumpFileName << "\n";
175		SimInfo* info = creator.createSim(dumpFileName);
176
177		RealType maxLen;
178	+	RealType zmaxLen;
179		if (args_info.length_given) {
180		maxLen = args_info.length_arg;
181	+	if (args_info.zlength_given){
182	+	zmaxLen = args_info.zlength_arg;
183	+	}
184		} else {
185		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
186	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
186	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
187	>	zmaxLen = hmat(2,2);
188		}
189	<
189	>
190		StaticAnalyser* analyser;
191		if (args_info.gofr_given){
192	<	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
192	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
193	>	args_info.nbins_arg);
194	>	} else if (args_info.gofz_given) {
195	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
196	>	args_info.nbins_arg);
197	>	} else if (args_info.r_z_given) {
198	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
199	>	args_info.nbins_arg, args_info.nbins_z_arg);
200		} else if (args_info.r_theta_given) {
201	<	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
201	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
202	>	args_info.nbins_arg, args_info.nanglebins_arg);
203		} else if (args_info.r_omega_given) {
204	<	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
204	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
205	>	args_info.nbins_arg, args_info.nanglebins_arg);
206		} else if (args_info.theta_omega_given) {
207	<	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
207	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
208	>	args_info.nanglebins_arg);
209		} else if (args_info.gxyz_given) {
210		if (args_info.refsele_given) {
211	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
211	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
212	>	maxLen, args_info.nbins_arg);
213		} else {
214		sprintf( painCave.errMsg,
215	<	"--refsele must set when --gxyz is used");
216	<	painCave.severity = OOPSE_ERROR;
215	>	"--refsele must set when --gxyz is used");
216	>	painCave.severity = OPENMD_ERROR;
217		painCave.isFatal = 1;
218		simError();
219		}
220	+	} else if (args_info.twodgofr_given){
221	+	if (args_info.dz_given) {
222	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
223	+	args_info.dz_arg, args_info.nbins_arg);
224	+	} else {
225	+	sprintf( painCave.errMsg,
226	+	"A slab width (dz) must be specified when calculating TwoDGofR");
227	+	painCave.severity = OPENMD_ERROR;
228	+	painCave.isFatal = 1;
229	+	simError();
230	+	}
231		} else if (args_info.p2_given) {
232	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
232	>	if (args_info.sele1_given) {
233	>	if (args_info.sele2_given)
234	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
235	>	else
236	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
237	>	} else {
238	>	sprintf( painCave.errMsg,
239	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
240	>	painCave.severity = OPENMD_ERROR;
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244		} else if (args_info.rp2_given){
245		analyser = new RippleOP(info, dumpFileName, sele1, sele2);
246		} else if (args_info.bo_given){
247	<	if (args_info.rcut_given && args_info.LegendreL_given) {
247	>	if (args_info.rcut_given) {
248		analyser = new BondOrderParameter(info, dumpFileName, sele1,
249	<	args_info.rcut_arg,
250	<	args_info.LegendreL_arg);
249	>	args_info.rcut_arg,
250	>	args_info.nbins_arg);
251		} else {
252		sprintf( painCave.errMsg,
253	<	"Both the cutoff radius (rcut) and LegendreL must be specified when calculating Bond Order Parameters");
254	<	painCave.severity = OOPSE_ERROR;
253	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
254	>	painCave.severity = OPENMD_ERROR;
255		painCave.isFatal = 1;
256		simError();
257		}
258	+
259	+	} else if (args_info.tet_param_given) {
260	+	if (args_info.rcut_given) {
261	+	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
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.tet_param_z_given) {
272	+	if (args_info.rcut_given) {
273	+	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
274	+	args_info.rcut_arg,
275	+	args_info.nbins_arg);
276	+	} else {
277	+	sprintf( painCave.errMsg,
278	+	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
279	+	painCave.severity = OPENMD_ERROR;
280	+	painCave.isFatal = 1;
281	+	simError();
282	+	}
283	+	} else if (args_info.bor_given){
284	+	if (args_info.rcut_given) {
285	+	analyser = new BOPofR(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, 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, args_info.molname_arg,
308	<	args_info.begin_arg, args_info.end_arg);
308	>	args_info.begin_arg, args_info.end_arg);
309		} else{
310		std::string sele3 = args_info.sele3_arg;
311		analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
312		}
313		}else if (args_info.density_given) {
314	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
314	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
315	>	args_info.nbins_arg);
316	>	} else if (args_info.count_given) {
317	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
318		} else if (args_info.slab_density_given) {
319	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
320	<	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg);
319	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
320	>	} else if (args_info.p_angle_given) {
321	>	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
322		#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
323		}else if (args_info.hxy_given) {
324	<	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
324	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
325	>	args_info.nbins_y_arg, args_info.nbins_arg);
326		#endif
327	+	}else if (args_info.rho_r_given) {
328	+	if (args_info.radius_given){
329	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
330	+	}else{
331	+	sprintf( painCave.errMsg,
332	+	"A particle radius (radius) must be specified when calculating Rho(r)");
333	+	painCave.severity = OPENMD_ERROR;
334	+	painCave.isFatal = 1;
335	+	simError();
336	+	}
337	+	} else if (args_info.hullvol_given) {
338	+	analyser = new NanoVolume(info, dumpFileName, sele1);
339	+	} else if (args_info.rodlength_given) {
340	+	analyser = new NanoLength(info, dumpFileName, sele1);
341	+	} else if (args_info.angle_r_given) {
342	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
343		}
344	<
344	>
345		if (args_info.output_given) {
346		analyser->setOutputName(args_info.output_arg);
347		}
348		if (args_info.step_given) {
349		analyser->setStep(args_info.step_arg);
350		}
351	<
351	>
352		analyser->process();
353	<
353	>
354		delete analyser;
355		delete info;
356

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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

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+	Added lines
<	Changed lines
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