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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 1846 by gezelter, Thu Jan 31 15:55:47 2013 UTC

#	Line 36 | Line 36
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).
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	<
77	>	#include "applications/staticProps/AngleR.hpp"
78	>	#include "applications/staticProps/TetrahedralityParam.hpp"
79	>	#include "applications/staticProps/TetrahedralityParamZ.hpp"
80		using namespace OpenMD;
81
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 {
#	Line 104 | Line 107 | int main(int argc, char* argv[]){
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
#	Line 115 | Line 118 | int main(int argc, char* argv[]){
118		if (sele2Env) {
119		sele2 = sele2Env;
120		} else {
121	<	sele2 = "select all";
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
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	–
127		bool batchMode;
128		if (args_info.scd_given){
129	<	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
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 && args_info.begin_given && args_info.end_given) {
133	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
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		"below conditions are not satisfied:\n"
138		"0 <= begin && 0<= end && begin <= end-2\n");
#	Line 161 | Line 147 | int main(int argc, char* argv[]){
147		" or --molname, --begin, --end are specified\n");
148		painCave.severity = OPENMD_ERROR;
149		painCave.isFatal = 1;
150	<	simError();
165	<
150	>	simError();
151		}
152		}
153	<
153	>
154		//parse md file and set up the system
155		SimCreator creator;
171	–	std::cout << "dumpFile = " << dumpFileName << "\n";
156		SimInfo* info = creator.createSim(dumpFileName);
157
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,
174	<	args_info.nbins_arg);
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);
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,
183	<	args_info.nbins_arg, args_info.nanglebins_arg);
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,
186	<	args_info.nbins_arg, args_info.nanglebins_arg);
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,
189	<	args_info.nanglebins_arg);
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,
193	<	maxLen, args_info.nbins_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");
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);
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");
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");
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, args_info.rcut_arg,
282	<	args_info.nbins_arg);
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");
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);
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, sele1, sele2, sele3);
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, sele2, maxLen,
303	<	args_info.nbins_arg);
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);
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)");
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) {
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
333		if (args_info.output_given) {
#	Line 282 | Line 336 | int main(int argc, char* argv[]){
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		}
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 1846 by gezelter, Thu Jan 31 15:55:47 2013 UTC

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

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+	Added lines
<	Changed lines
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