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root/OpenMD/branches/development/src/applications/staticProps/StaticProps.cpp

Comparing:
trunk/src/applications/staticProps/StaticProps.cpp (file contents), Revision 955 by xsun, Fri May 12 21:34:43 2006 UTC vs.
branches/development/src/applications/staticProps/StaticProps.cpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 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
80	<	using namespace oopse;
80	>	using namespace OpenMD;
81
82		int main(int argc, char* argv[]){
83
84	<	//register force fields
69	<	registerForceFields();
70	<
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	<
92	<
79	<	//get the dumpfile name and meta-data file name
91	>
92	>	//get the dumpfile name
93		std::string dumpFileName = args_info.input_arg;
81	–
82	–	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
83	–
84	–
94		std::string sele1;
95		std::string sele2;
96	<
96	>	bool userSpecifiedSelect1;
97	>	bool userSpecifiedSelect2;
98	>
99	>	// check the first selection argument, or set it to the environment
100	>	// variable, or failing that, set it to "select all"
101	>
102		if (args_info.sele1_given) {
103		sele1 = args_info.sele1_arg;
104	<	}else {
105	<	char*  sele1Env= getenv("OOPSE_SELE1");
104	>	} else {
105	>	char*  sele1Env= getenv("SELECTION1");
106		if (sele1Env) {
107		sele1 = sele1Env;
108	<	}else if (!args_info.scd_given) {
109	<	sprintf( painCave.errMsg,
96	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
97	<	painCave.severity = OOPSE_ERROR;
98	<	painCave.isFatal = 1;
99	<	simError();
108	>	} else {
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	>
116		if (args_info.sele2_given) {
117		sele2 = args_info.sele2_arg;
118	<	}else {
119	<	char* sele2Env = getenv("OOPSE_SELE2");
118	>	} else {
119	>	char* sele2Env = getenv("SELECTION1");
120		if (sele2Env) {
121		sele2 = sele2Env;
122	<	} else if (args_info.density_given) {
122	>	} else {
123		sele2 = "select all";
111	–	} else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
112	–	sprintf( painCave.errMsg,
113	–	"neither --sele2 option nor $OOPSE_SELE2 is set");
114	–	painCave.severity = OOPSE_ERROR;
115	–	painCave.isFatal = 1;
116	–	simError();
124		}
125		}
126	<
126	>
127	>
128	>	// Problems if sele1 wasn't specified, but
129	>	// if (!args_info.scd_given) {
130	>	//       sprintf( painCave.errMsg,
131	>	//                "neither --sele1 option nor $SELECTION1 is set");
132	>	//       painCave.severity = OPENMD_ERROR;
133	>	//       painCave.isFatal = 1;
134	>	//       simError();
135	>	//     }
136	>	//   }
137	>
138	>	// Problems if sele1 wasn't specified
139	>
140	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
141	>	//       sprintf( painCave.errMsg,
142	>	//                "neither --sele2 option nor $SELECTION1 is set");
143	>	//       painCave.severity = OPENMD_ERROR;
144	>	//       painCave.isFatal = 1;
145	>	//       simError();
146	>	//     }
147	>	//   }
148	>
149		bool batchMode;
150		if (args_info.scd_given){
151		if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
152	<	batchMode = false;
152	>	batchMode = false;
153		} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
154	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
126	<	sprintf( painCave.errMsg,
127	<	"below conditions are not satisfied:\n"
128	<	"0 <= begin && 0<= end && begin <= end-2\n");
129	<	painCave.severity = OOPSE_ERROR;
130	<	painCave.isFatal = 1;
131	<	simError();
132	<	}
133	<	batchMode = true;
134	<	} else{
154	>	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
155		sprintf( painCave.errMsg,
156	<	"either --sele1, --sele2, --sele3 are specified,"
157	<	" or --molname, --begin, --end are specified\n");
158	<	painCave.severity = OOPSE_ERROR;
156	>	"below conditions are not satisfied:\n"
157	>	"0 <= begin && 0<= end && begin <= end-2\n");
158	>	painCave.severity = OPENMD_ERROR;
159		painCave.isFatal = 1;
160	<	simError();
161	<
160	>	simError();
161	>	}
162	>	batchMode = true;
163	>	} else{
164	>	sprintf( painCave.errMsg,
165	>	"either --sele1, --sele2, --sele3 are specified,"
166	>	" or --molname, --begin, --end are specified\n");
167	>	painCave.severity = OPENMD_ERROR;
168	>	painCave.isFatal = 1;
169	>	simError();
170	>
171		}
172		}
173	<
173	>
174		//parse md file and set up the system
175		SimCreator creator;
176	<	SimInfo* info = creator.createSim(mdFileName);
176	>	std::cout << "dumpFile = " << dumpFileName << "\n";
177	>	SimInfo* info = creator.createSim(dumpFileName);
178
179	<	double maxLen;
179	>	RealType maxLen;
180	>	RealType zmaxLen;
181		if (args_info.length_given) {
182		maxLen = args_info.length_arg;
183	+	if (args_info.zlength_given){
184	+	zmaxLen = args_info.zlength_arg;
185	+	}
186		} else {
187		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
188	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
188	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
189	>	zmaxLen = hmat(2,2);
190		}
191	<
191	>
192		StaticAnalyser* analyser;
193		if (args_info.gofr_given){
194	<	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
194	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
195	>	args_info.nbins_arg);
196	>	} else if (args_info.gofz_given) {
197	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
198	>	args_info.nbins_arg);
199	>	} else if (args_info.r_z_given) {
200	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
201	>	args_info.nbins_arg, args_info.nbins_z_arg);
202		} else if (args_info.r_theta_given) {
203	<	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
203	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
204	>	args_info.nbins_arg, args_info.nanglebins_arg);
205		} else if (args_info.r_omega_given) {
206	<	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
206	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
207	>	args_info.nbins_arg, args_info.nanglebins_arg);
208		} else if (args_info.theta_omega_given) {
209	<	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
209	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
210	>	args_info.nanglebins_arg);
211		} else if (args_info.gxyz_given) {
212		if (args_info.refsele_given) {
213	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
213	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
214	>	maxLen, args_info.nbins_arg);
215		} else {
216		sprintf( painCave.errMsg,
217	<	"--refsele must set when --gxyz is used");
218	<	painCave.severity = OOPSE_ERROR;
217	>	"--refsele must set when --gxyz is used");
218	>	painCave.severity = OPENMD_ERROR;
219		painCave.isFatal = 1;
220		simError();
221		}
222	+	} else if (args_info.twodgofr_given){
223	+	if (args_info.dz_given) {
224	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
225	+	args_info.dz_arg, args_info.nbins_arg);
226	+	} else {
227	+	sprintf( painCave.errMsg,
228	+	"A slab width (dz) must be specified when calculating TwoDGofR");
229	+	painCave.severity = OPENMD_ERROR;
230	+	painCave.isFatal = 1;
231	+	simError();
232	+	}
233		} else if (args_info.p2_given) {
234	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
235	<	} else if (args_info.scd_given) {
236	<	if (batchMode) {
237	<	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
238	<	args_info.begin_arg, args_info.end_arg);
239	<	} else{
240	<	std::string sele3 = args_info.sele3_arg;
241	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
234	>	if (args_info.sele1_given) {
235	>	if (args_info.sele2_given)
236	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
237	>	else
238	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
239	>	} else {
240	>	sprintf( painCave.errMsg,
241	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
242	>	painCave.severity = OPENMD_ERROR;
243	>	painCave.isFatal = 1;
244	>	simError();
245	>	}
246	>	} else if (args_info.rp2_given){
247	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
248	>	} else if (args_info.bo_given){
249	>	if (args_info.rcut_given) {
250	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
251	>	args_info.rcut_arg,
252	>	args_info.nbins_arg);
253	>	} else {
254	>	sprintf( painCave.errMsg,
255	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
256	>	painCave.severity = OPENMD_ERROR;
257	>	painCave.isFatal = 1;
258	>	simError();
259	>	}
260	>
261	>	} else if (args_info.tet_param_given) {
262	>	if (args_info.rcut_given) {
263	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
264	>	args_info.rcut_arg,
265	>	args_info.nbins_arg);
266	>	} else {
267	>	sprintf( painCave.errMsg,
268	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
269	>	painCave.severity = OPENMD_ERROR;
270	>	painCave.isFatal = 1;
271	>	simError();
272	>	}
273	>	} else if (args_info.bor_given){
274	>	if (args_info.rcut_given) {
275	>	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
276	>	args_info.nbins_arg, maxLen);
277	>	} else {
278	>	sprintf( painCave.errMsg,
279	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
280	>	painCave.severity = OPENMD_ERROR;
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	} else if (args_info.bad_given){
285	>	if (args_info.rcut_given) {
286	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
287	>	args_info.nbins_arg);
288	>	} else {
289	>	sprintf( painCave.errMsg,
290	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
291	>	painCave.severity = OPENMD_ERROR;
292	>	painCave.isFatal = 1;
293	>	simError();
294		}
295	+	} else if (args_info.scd_given) {
296	+	if (batchMode) {
297	+	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
298	+	args_info.begin_arg, args_info.end_arg);
299	+	} else{
300	+	std::string sele3 = args_info.sele3_arg;
301	+	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
302	+	}
303		}else if (args_info.density_given) {
304	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
304	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
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	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
310	<	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg);
309	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
310	>	} else if (args_info.p_angle_given) {
311	>	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
312	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
313		}else if (args_info.hxy_given) {
314	<	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
314	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
315	>	args_info.nbins_y_arg, args_info.nbins_arg);
316	>	#endif
317	>	}else if (args_info.rho_r_given) {
318	>	if (args_info.radius_given){
319	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
320	>	}else{
321	>	sprintf( painCave.errMsg,
322	>	"A particle radius (radius) must be specified when calculating Rho(r)");
323	>	painCave.severity = OPENMD_ERROR;
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>	} else if (args_info.hullvol_given) {
328	>	analyser = new NanoVolume(info, dumpFileName, sele1);
329	>	} else if (args_info.rodlength_given) {
330	>	analyser = new NanoLength(info, dumpFileName, sele1);
331	>	} else if (args_info.angle_r_given) {
332	>	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
333		}
334
335		if (args_info.output_given) {
#	Line 198 | Line 338 | int main(int argc, char* argv[]){
338		if (args_info.step_given) {
339		analyser->setStep(args_info.step_arg);
340		}
341	<
341	>
342		analyser->process();
343	<
343	>
344		delete analyser;
345		delete info;
346

Comparing:
trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords), Revision 955 by xsun, Fri May 12 21:34:43 2006 UTC vs.
branches/development/src/applications/staticProps/StaticProps.cpp (property svn:keywords), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

#	Line 0 | Line 1
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