ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 35 | Line 35
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]  Vardeman & Gezelter, in progress (2009).
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 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	+	#include "applications/staticProps/RNEMDStats.hpp"
81
82		using namespace OpenMD;
83
84		int main(int argc, char* argv[]){
85
86	<	//register force fields
78	<	registerForceFields();
79	<
86	>
87		gengetopt_args_info args_info;
88	<
88	>
89		//parse the command line option
90		if (cmdline_parser (argc, argv, &args_info) != 0) {
91		exit(1) ;
92		}
93	<
93	>
94		//get the dumpfile name
95		std::string dumpFileName = args_info.input_arg;
96		std::string sele1;
97		std::string sele2;
98	<	bool userSpecifiedSelect1;
92	<	bool userSpecifiedSelect2;
93	<
98	>
99		// check the first selection argument, or set it to the environment
100		// variable, or failing that, set it to "select all"
101	<
101	>
102		if (args_info.sele1_given) {
103		sele1 = args_info.sele1_arg;
104		} else {
#	Line 104 | Line 109 | int main(int argc, char* argv[]){
109		sele1 = "select all";
110		}
111		}
112	<
112	>
113		// check the second selection argument, or set it to the environment
114		// variable, or failing that, set it to "select all"
115
#	Line 115 | Line 120 | int main(int argc, char* argv[]){
120		if (sele2Env) {
121		sele2 = sele2Env;
122		} else {
123	<	sele2 = "select all";
123	>	//If sele2 is not specified, then the default behavior
124	>	//should be what is already intended for sele1
125	>	sele2 = sele1;
126		}
127		}
128
122	–
123	–	// Problems if sele1 wasn't specified, but
124	–	// if (!args_info.scd_given) {
125	–	//       sprintf( painCave.errMsg,
126	–	//                "neither --sele1 option nor $SELECTION1 is set");
127	–	//       painCave.severity = OPENMD_ERROR;
128	–	//       painCave.isFatal = 1;
129	–	//       simError();
130	–	//     }
131	–	//   }
132	–
133	–	// Problems if sele1 wasn't specified
134	–
135	–	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
136	–	//       sprintf( painCave.errMsg,
137	–	//                "neither --sele2 option nor $SELECTION1 is set");
138	–	//       painCave.severity = OPENMD_ERROR;
139	–	//       painCave.isFatal = 1;
140	–	//       simError();
141	–	//     }
142	–	//   }
143	–
129		bool batchMode;
130		if (args_info.scd_given){
131	<	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
131	>	if (args_info.sele1_given &&
132	>	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) {
134	>	} else if (args_info.molname_given &&
135	>	args_info.begin_given && args_info.end_given) {
136	>	if (args_info.begin_arg < 0 ||
137	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
138		sprintf( painCave.errMsg,
139		"below conditions are not satisfied:\n"
140		"0 <= begin && 0<= end && begin <= end-2\n");
#	Line 161 | Line 149 | int main(int argc, char* argv[]){
149		" or --molname, --begin, --end are specified\n");
150		painCave.severity = OPENMD_ERROR;
151		painCave.isFatal = 1;
152	<	simError();
165	<
152	>	simError();
153		}
154		}
155	<
155	>
156		//parse md file and set up the system
157		SimCreator creator;
171	–	std::cout << "dumpFile = " << dumpFileName << "\n";
158		SimInfo* info = creator.createSim(dumpFileName);
159
160		RealType maxLen;
161	+	RealType zmaxLen;
162		if (args_info.length_given) {
163		maxLen = args_info.length_arg;
164	+	if (args_info.zlength_given){
165	+	zmaxLen = args_info.zlength_arg;
166	+	}
167		} else {
168		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
169	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
169	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
170	>	zmaxLen = hmat(2,2);
171		}
172	<
172	>
173		StaticAnalyser* analyser;
174		if (args_info.gofr_given){
175		analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
176	<	args_info.nbins_arg);
176	>	args_info.nbins_arg);
177		} else if (args_info.gofz_given) {
178		analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
179	<	args_info.nbins_arg);
179	>	args_info.nbins_arg);
180	>	} else if (args_info.r_z_given) {
181	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
182	>	args_info.nbins_arg, args_info.nbins_z_arg);
183		} else if (args_info.r_theta_given) {
184		analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
185	<	args_info.nbins_arg, args_info.nanglebins_arg);
185	>	args_info.nbins_arg, args_info.nanglebins_arg);
186		} else if (args_info.r_omega_given) {
187		analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
188	<	args_info.nbins_arg, args_info.nanglebins_arg);
188	>	args_info.nbins_arg, args_info.nanglebins_arg);
189		} else if (args_info.theta_omega_given) {
190		analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
191	<	args_info.nanglebins_arg);
191	>	args_info.nanglebins_arg);
192		} else if (args_info.gxyz_given) {
193		if (args_info.refsele_given) {
194	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
195	<	maxLen, args_info.nbins_arg);
194	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
195	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
196		} else {
197		sprintf( painCave.errMsg,
198	<	"--refsele must set when --gxyz is used");
198	>	"--refsele must set when --gxyz is used");
199		painCave.severity = OPENMD_ERROR;
200		painCave.isFatal = 1;
201		simError();
202		}
203	+	} else if (args_info.twodgofr_given){
204	+	if (args_info.dz_given) {
205	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
206	+	args_info.dz_arg, args_info.nbins_arg);
207	+	} else {
208	+	sprintf( painCave.errMsg,
209	+	"A slab width (dz) must be specified when calculating TwoDGofR");
210	+	painCave.severity = OPENMD_ERROR;
211	+	painCave.isFatal = 1;
212	+	simError();
213	+	}
214		} else if (args_info.p2_given) {
215	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
215	>	if (args_info.sele1_given) {
216	>	if (args_info.sele2_given)
217	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
218	>	else
219	>	if (args_info.seleoffset_given)
220	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
221	>	args_info.seleoffset_arg);
222	>	else
223	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
224	>	} else {
225	>	sprintf( painCave.errMsg,
226	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
227	>	painCave.severity = OPENMD_ERROR;
228	>	painCave.isFatal = 1;
229	>	simError();
230	>	}
231		} else if (args_info.rp2_given){
232		analyser = new RippleOP(info, dumpFileName, sele1, sele2);
233		} else if (args_info.bo_given){
234		if (args_info.rcut_given) {
235		analyser = new BondOrderParameter(info, dumpFileName, sele1,
236	<	args_info.rcut_arg,
237	<	args_info.nbins_arg);
236	>	args_info.rcut_arg,
237	>	args_info.nbins_arg);
238		} else {
239		sprintf( painCave.errMsg,
240	<	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
240	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
241		painCave.severity = OPENMD_ERROR;
242		painCave.isFatal = 1;
243		simError();
244		}
245	+
246	+	} else if (args_info.tet_param_given) {
247	+	if (args_info.rcut_given) {
248	+	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
249	+	args_info.rcut_arg,
250	+	args_info.nbins_arg);
251	+	} else {
252	+	sprintf( painCave.errMsg,
253	+	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
254	+	painCave.severity = OPENMD_ERROR;
255	+	painCave.isFatal = 1;
256	+	simError();
257	+	}
258	+	} else if (args_info.tet_param_z_given) {
259	+	if (args_info.rcut_given) {
260	+	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
261	+	args_info.rcut_arg,
262	+	args_info.nbins_arg);
263	+	} else {
264	+	sprintf( painCave.errMsg,
265	+	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
266	+	painCave.severity = OPENMD_ERROR;
267	+	painCave.isFatal = 1;
268	+	simError();
269	+	}
270		} else if (args_info.bor_given){
271		if (args_info.rcut_given) {
272		analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
273		args_info.nbins_arg, maxLen);
274		} else {
275		sprintf( painCave.errMsg,
276	<	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
276	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
277		painCave.severity = OPENMD_ERROR;
278		painCave.isFatal = 1;
279		simError();
280		}
281		} else if (args_info.bad_given){
282		if (args_info.rcut_given) {
283	<	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
284	<	args_info.nbins_arg);
283	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
284	>	args_info.rcut_arg,
285	>	args_info.nbins_arg);
286		} else {
287		sprintf( painCave.errMsg,
288	<	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
288	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
289		painCave.severity = OPENMD_ERROR;
290		painCave.isFatal = 1;
291		simError();
292		}
293		} else if (args_info.scd_given) {
294		if (batchMode) {
295	<	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
296	<	args_info.begin_arg, args_info.end_arg);
295	>	analyser  = new SCDOrderParameter(info, dumpFileName,
296	>	args_info.molname_arg,
297	>	args_info.begin_arg, args_info.end_arg);
298		} else{
299		std::string sele3 = args_info.sele3_arg;
300	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
300	>	analyser  = new SCDOrderParameter(info, dumpFileName,
301	>	sele1, sele2, sele3);
302		}
303		}else if (args_info.density_given) {
304		analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
305	<	args_info.nbins_arg);
305	>	args_info.nbins_arg);
306	>	} else if (args_info.count_given) {
307	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
308		} else if (args_info.slab_density_given) {
309		analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
310	+	} else if (args_info.rnemdz_given) {
311	+	analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
312	+	} else if (args_info.rnemdr_given) {
313	+	analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
314	+	} else if (args_info.p_angle_given) {
315	+	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
316		#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
317		}else if (args_info.hxy_given) {
318		analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
319	<	args_info.nbins_y_arg, args_info.nbins_arg);
319	>	args_info.nbins_y_arg, args_info.nbins_arg);
320		#endif
321		}else if (args_info.rho_r_given) {
322		if (args_info.radius_given){
323		analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
324		}else{
325		sprintf( painCave.errMsg,
326	<	"A particle radius (radius) must be specified when calculating Rho(r)");
326	>	"A particle radius (radius) must be specified when calculating Rho(r)");
327		painCave.severity = OPENMD_ERROR;
328		painCave.isFatal = 1;
329		simError();
330		}
331	<	}else if (args_info.hullvol_given) {
331	>	} else if (args_info.hullvol_given) {
332		analyser = new NanoVolume(info, dumpFileName, sele1);
333	+	} else if (args_info.rodlength_given) {
334	+	analyser = new NanoLength(info, dumpFileName, sele1);
335	+	} else if (args_info.angle_r_given) {
336	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
337		}
338
339		if (args_info.output_given) {
#	Line 282 | Line 342 | int main(int argc, char* argv[]){
342		if (args_info.step_given) {
343		analyser->setStep(args_info.step_arg);
344		}
345	<
345	>
346		analyser->process();
347	<
347	>
348		delete analyser;
349		delete info;
350	<
350	>
351		return 0;
352		}
293	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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

Diff Legend

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