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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 310 by tim, Thu Feb 10 18:14:03 2005 UTC vs.
Revision 1454 by gezelter, Wed Jun 23 19:25:02 2010 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <iostream>
43		#include <fstream>
44		#include <string>
45
46	–	#include "applications/staticProps/StaticPropsCmd.h"
46		#include "brains/Register.hpp"
47		#include "brains/SimCreator.hpp"
48		#include "brains/SimInfo.hpp"
49		#include "io/DumpReader.hpp"
50		#include "utils/simError.h"
51
52	<	using namespace oopse;
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/RhoZ.hpp"
68	>	#include "applications/staticProps/pAngle.hpp"
69	>	#include "applications/staticProps/BondAngleDistribution.hpp"
70	>	#include "applications/staticProps/NanoVolume.hpp"
71	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
72	>	#include "applications/staticProps/Hxy.hpp"
73	>	#endif
74	>	#include "applications/staticProps/RhoR.hpp"
75
76	+	using namespace OpenMD;
77	+
78		int main(int argc, char* argv[]){
79
80		//register force fields
#	Line 61 | Line 84 | int main(int argc, char* argv[]){
84
85		//parse the command line option
86		if (cmdline_parser (argc, argv, &args_info) != 0) {
87	<	exit(1) ;
87	>	exit(1) ;
88		}
89
90	<
68	<	//get the dumpfile name and meta-data file name
90	>	//get the dumpfile name
91		std::string dumpFileName = args_info.input_arg;
70	–
71	–	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
72	–
73	–
74	–	//parse md file and set up the system
75	–	SimCreator creator;
76	–	SimInfo* info = creator.createSim(mdFileName, false);
77	–
78	–
92		std::string sele1;
93		std::string sele2;
94	+	bool userSpecifiedSelect1;
95	+	bool userSpecifiedSelect2;
96
97	<	if (args_info.sele1_given) {
98	<	sele1 = args_info.sele1_arg;
84	<	}else {
97	>	// check the first selection argument, or set it to the environment
98	>	// variable, or failing that, set it to "select all"
99
86	–	}
100		if (args_info.sele1_given) {
101	<	sele1 = args_info.sele1_arg;
102	<	}else {
101	>	sele1 = args_info.sele1_arg;
102	>	} else {
103	>	char*  sele1Env= getenv("SELECTION1");
104	>	if (sele1Env) {
105	>	sele1 = sele1Env;
106	>	} else {
107	>	sele1 = "select all";
108	>	}
109	>	}
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("SELECTION1");
118	+	if (sele2Env) {
119	+	sele2 = sele2Env;
120	+	} else {
121	+	sele2 = "select all";
122	+	}
123		}
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 $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 $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) {
150	+	batchMode = false;
151	+	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
152	+	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
153	+	sprintf( painCave.errMsg,
154	+	"below conditions are not satisfied:\n"
155	+	"0 <= begin && 0<= end && begin <= end-2\n");
156	+	painCave.severity = OPENMD_ERROR;
157	+	painCave.isFatal = 1;
158	+	simError();
159	+	}
160	+	batchMode = true;
161	+	} else{
162	+	sprintf( painCave.errMsg,
163	+	"either --sele1, --sele2, --sele3 are specified,"
164	+	" or --molname, --begin, --end are specified\n");
165	+	painCave.severity = OPENMD_ERROR;
166	+	painCave.isFatal = 1;
167	+	simError();
168
169	<	GofR rdf(info, dumpFileName, sele1, sele2, args_info.length_arg);
169	>	}
170	>	}
171
172	<	if (args_info.nbins_given) {
173	<	rdf.setNBins(args_info.nbins_arg);
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;
187	>	zmaxLen = hmat(2,2);
188	>	}
189	>
190	>	StaticAnalyser* analyser;
191	>	if (args_info.gofr_given){
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,
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,
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,
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,
212	>	maxLen, args_info.nbins_arg);
213	>	} else {
214	>	sprintf( painCave.errMsg,
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);
233	>	} else if (args_info.rp2_given){
234	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
235	>	} else if (args_info.bo_given){
236	>	if (args_info.rcut_given) {
237	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
238	>	args_info.rcut_arg,
239	>	args_info.nbins_arg);
240	>	} else {
241	>	sprintf( painCave.errMsg,
242	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
243	>	painCave.severity = OPENMD_ERROR;
244	>	painCave.isFatal = 1;
245	>	simError();
246	>	}
247	>	} else if (args_info.bor_given){
248	>	if (args_info.rcut_given) {
249	>	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
250	>	args_info.nbins_arg, maxLen);
251	>	} else {
252	>	sprintf( painCave.errMsg,
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	>	} else if (args_info.bad_given){
259	>	if (args_info.rcut_given) {
260	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
261	>	args_info.nbins_arg);
262	>	} else {
263	>	sprintf( painCave.errMsg,
264	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
265	>	painCave.severity = OPENMD_ERROR;
266	>	painCave.isFatal = 1;
267	>	simError();
268	>	}
269	>	} else if (args_info.scd_given) {
270	>	if (batchMode) {
271	>	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
272	>	args_info.begin_arg, args_info.end_arg);
273	>	} else{
274	>	std::string sele3 = args_info.sele3_arg;
275	>	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
276	>	}
277	>	}else if (args_info.density_given) {
278	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
279	>	args_info.nbins_arg);
280	>	} else if (args_info.slab_density_given) {
281	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
282	>	} else if (args_info.p_angle_given) {
283	>	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
284	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
285	>	}else if (args_info.hxy_given) {
286	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
287	>	args_info.nbins_y_arg, args_info.nbins_arg);
288	>	#endif
289	>	}else if (args_info.rho_r_given) {
290	>	if (args_info.radius_given){
291	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
292	>	}else{
293	>	sprintf( painCave.errMsg,
294	>	"A particle radius (radius) must be specified when calculating Rho(r)");
295	>	painCave.severity = OPENMD_ERROR;
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299	>	}else if (args_info.hullvol_given) {
300	>	analyser = new NanoVolume(info, dumpFileName, sele1);
301		}
302	+
303	+	if (args_info.output_given) {
304	+	analyser->setOutputName(args_info.output_arg);
305	+	}
306	+	if (args_info.step_given) {
307	+	analyser->setStep(args_info.step_arg);
308	+	}
309
310	<	rdf.process();
311	<
310	>	analyser->process();
311	>
312	>	delete analyser;
313		delete info;
314
315		return 0;

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 310 by tim, Thu Feb 10 18:14:03 2005 UTC vs.
Revision 1454 by gezelter, Wed Jun 23 19:25:02 2010 UTC

#	Line 0 | Line 1
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