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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 1819 by gezelter, Thu Dec 13 16:57:39 2012 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	>	//sele2 = "select all";
125		}
126		}
127	<
128	<
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	<
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	<
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) {
#	Line 162 | Line 168 | int main(int argc, char* argv[]){
168		painCave.severity = OPENMD_ERROR;
169		painCave.isFatal = 1;
170		simError();
171	<
171	>
172		}
173		}
174	<
174	>
175		//parse md file and set up the system
176		SimCreator creator;
177		std::cout << "dumpFile = " << dumpFileName << "\n";
178		SimInfo* info = creator.createSim(dumpFileName);
179
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,
196	<	args_info.nbins_arg);
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);
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,
205	<	args_info.nbins_arg, args_info.nanglebins_arg);
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,
208	<	args_info.nbins_arg, args_info.nanglebins_arg);
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,
211	<	args_info.nanglebins_arg);
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,
215	<	maxLen, args_info.nbins_arg);
215	>	maxLen, args_info.nbins_arg);
216		} else {
217		sprintf( painCave.errMsg,
218	<	"--refsele must set when --gxyz is used");
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);
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);
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");
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");
296	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
297		painCave.severity = OPENMD_ERROR;
298		painCave.isFatal = 1;
299		simError();
#	Line 236 | Line 301 | int main(int argc, char* argv[]){
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);
304	>	args_info.nbins_arg);
305		} else {
306		sprintf( painCave.errMsg,
307	<	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
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	<	}
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);
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,
322	<	args_info.nbins_arg);
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);
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)");
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) {
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	<
351	>
352		if (args_info.output_given) {
353		analyser->setOutputName(args_info.output_arg);
354		}
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 1390 by gezelter, Wed Nov 25 20:02:06 2009 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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