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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 369 by tim, Fri Feb 18 23:07:32 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 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>
#	Line 50 | Line 50
50		#include "utils/simError.h"
51
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/P2OrderParameter.hpp"
61	+	#include "applications/staticProps/BondOrderParameter.hpp"
62	+	#include "applications/staticProps/BOPofR.hpp"
63	+	#include "applications/staticProps/RippleOP.hpp"
64	+	#include "applications/staticProps/SCDOrderParameter.hpp"
65	+	#include "applications/staticProps/DensityPlot.hpp"
66	+	#include "applications/staticProps/RhoZ.hpp"
67	+	#include "applications/staticProps/pAngle.hpp"
68	+	#include "applications/staticProps/BondAngleDistribution.hpp"
69	+	#include "applications/staticProps/NanoVolume.hpp"
70	+	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
71	+	#include "applications/staticProps/Hxy.hpp"
72	+	#endif
73	+	#include "applications/staticProps/RhoR.hpp"
74
75	<	using namespace oopse;
75	>	using namespace OpenMD;
76
77		int main(int argc, char* argv[]){
78
79	<	//register force fields
80	<	registerForceFields();
79	>	//register force fields
80	>	registerForceFields();
81
82	<	gengetopt_args_info args_info;
82	>	gengetopt_args_info args_info;
83
84	<	//parse the command line option
85	<	if (cmdline_parser (argc, argv, &args_info) != 0) {
86	<	exit(1) ;
84	>	//parse the command line option
85	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
86	>	exit(1) ;
87	>	}
88	>
89	>	//get the dumpfile name
90	>	std::string dumpFileName = args_info.input_arg;
91	>	std::string sele1;
92	>	std::string sele2;
93	>	bool userSpecifiedSelect1;
94	>	bool userSpecifiedSelect2;
95	>
96	>	// check the first selection argument, or set it to the environment
97	>	// variable, or failing that, set it to "select all"
98	>
99	>	if (args_info.sele1_given) {
100	>	sele1 = args_info.sele1_arg;
101	>	} else {
102	>	char*  sele1Env= getenv("SELECTION1");
103	>	if (sele1Env) {
104	>	sele1 = sele1Env;
105	>	} else {
106	>	sele1 = "select all";
107		}
108	+	}
109
110	+	// check the second selection argument, or set it to the environment
111	+	// variable, or failing that, set it to "select all"
112	+
113	+	if (args_info.sele2_given) {
114	+	sele2 = args_info.sele2_arg;
115	+	} else {
116	+	char* sele2Env = getenv("SELECTION1");
117	+	if (sele2Env) {
118	+	sele2 = sele2Env;
119	+	} else {
120	+	sele2 = "select all";
121	+	}
122	+	}
123
73	–	//get the dumpfile name and meta-data file name
74	–	std::string dumpFileName = args_info.input_arg;
124
125	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
125	>	// Problems if sele1 wasn't specified, but
126	>	// if (!args_info.scd_given) {
127	>	//       sprintf( painCave.errMsg,
128	>	//                "neither --sele1 option nor $SELECTION1 is set");
129	>	//       painCave.severity = OPENMD_ERROR;
130	>	//       painCave.isFatal = 1;
131	>	//       simError();
132	>	//     }
133	>	//   }
134
135	<
79	<	std::string sele1;
80	<	std::string sele2;
135	>	// Problems if sele1 wasn't specified
136
137	<	if (args_info.sele1_given) {
138	<	sele1 = args_info.sele1_arg;
139	<	}else {
140	<	char*  sele1Env= getenv("OOPSE_SELE1");
141	<	if (sele1Env) {
142	<	sele1 = sele1Env;
143	<	}else {
144	<	sprintf( painCave.errMsg,
145	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
146	<	painCave.severity = OOPSE_ERROR;
147	<	painCave.isFatal = 1;
148	<	simError();
149	<	}
150	<	}
137	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
138	>	//       sprintf( painCave.errMsg,
139	>	//                "neither --sele2 option nor $SELECTION1 is set");
140	>	//       painCave.severity = OPENMD_ERROR;
141	>	//       painCave.isFatal = 1;
142	>	//       simError();
143	>	//     }
144	>	//   }
145	>
146	>	bool batchMode;
147	>	if (args_info.scd_given){
148	>	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
149	>	batchMode = false;
150	>	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
151	>	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
152	>	sprintf( painCave.errMsg,
153	>	"below conditions are not satisfied:\n"
154	>	"0 <= begin && 0<= end && begin <= end-2\n");
155	>	painCave.severity = OPENMD_ERROR;
156	>	painCave.isFatal = 1;
157	>	simError();
158	>	}
159	>	batchMode = true;
160	>	} else{
161	>	sprintf( painCave.errMsg,
162	>	"either --sele1, --sele2, --sele3 are specified,"
163	>	" or --molname, --begin, --end are specified\n");
164	>	painCave.severity = OPENMD_ERROR;
165	>	painCave.isFatal = 1;
166	>	simError();
167
97	–	if (args_info.sele2_given) {
98	–	sele2 = args_info.sele2_arg;
99	–	}else {
100	–	char* sele2Env = getenv("OOPSE_SELE2");
101	–	if (sele2Env) {
102	–	sele2 = sele2Env;
103	–	} else {
104	–	sprintf( painCave.errMsg,
105	–	"neither --sele2 option nor $OOPSE_SELE2 is set");
106	–	painCave.severity = OOPSE_ERROR;
107	–	painCave.isFatal = 1;
108	–	simError();
109	–	}
168		}
169	+	}
170
171	<	//parse md file and set up the system
172	<	SimCreator creator;
173	<	SimInfo* info = creator.createSim(mdFileName);
171	>	//parse md file and set up the system
172	>	SimCreator creator;
173	>	std::cout << "dumpFile = " << dumpFileName << "\n";
174	>	SimInfo* info = creator.createSim(dumpFileName);
175
176	<	double maxLen;
177	<	if (args_info.length_given) {
178	<	maxLen = args_info.length_arg;
179	<	} else {
180	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
181	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
182	<	}
176	>	RealType maxLen;
177	>	if (args_info.length_given) {
178	>	maxLen = args_info.length_arg;
179	>	} else {
180	>	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
181	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
182	>	}
183
184	<	RadialDistrFunc* rdf;
185	<	if (args_info.gofr_given){
186	<	rdf= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
187	<	} else if (args_info.r_theta_given) {
188	<	rdf  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
189	<	} else if (args_info.r_omega_given) {
190	<	rdf  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
191	<	} else if (args_info.theta_omega_given) {
192	<	rdf  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
193	<	} else if (args_info.gxyz_given) {
194	<	if (args_info.refsele_given) {
195	<	rdf= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
196	<	} else {
197	<	sprintf( painCave.errMsg,
184	>	StaticAnalyser* analyser;
185	>	if (args_info.gofr_given){
186	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
187	>	args_info.nbins_arg);
188	>	} else if (args_info.gofz_given) {
189	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
190	>	args_info.nbins_arg);
191	>	} else if (args_info.r_z_given) {
192	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen,
193	>	args_info.nbins_arg, args_info.nbins_z_arg);
194	>	} else if (args_info.r_theta_given) {
195	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
196	>	args_info.nbins_arg, args_info.nanglebins_arg);
197	>	} else if (args_info.r_omega_given) {
198	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
199	>	args_info.nbins_arg, args_info.nanglebins_arg);
200	>	} else if (args_info.theta_omega_given) {
201	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
202	>	args_info.nanglebins_arg);
203	>	} else if (args_info.gxyz_given) {
204	>	if (args_info.refsele_given) {
205	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
206	>	maxLen, args_info.nbins_arg);
207	>	} else {
208	>	sprintf( painCave.errMsg,
209		"--refsele must set when --gxyz is used");
210	<	painCave.severity = OOPSE_ERROR;
211	<	painCave.isFatal = 1;
212	<	simError();
142	<	}
210	>	painCave.severity = OPENMD_ERROR;
211	>	painCave.isFatal = 1;
212	>	simError();
213		}
214	<
215	<	if (args_info.output_given) {
216	<	rdf->setOutputName(args_info.output_arg);
214	>	} else if (args_info.p2_given) {
215	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
216	>	} else if (args_info.rp2_given){
217	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
218	>	} else if (args_info.bo_given){
219	>	if (args_info.rcut_given) {
220	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
221	>	args_info.rcut_arg,
222	>	args_info.nbins_arg);
223	>	} else {
224	>	sprintf( painCave.errMsg,
225	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
226	>	painCave.severity = OPENMD_ERROR;
227	>	painCave.isFatal = 1;
228	>	simError();
229		}
230	<	if (args_info.step_given) {
231	<	rdf->setStep(args_info.step_arg);
230	>	} else if (args_info.bor_given){
231	>	if (args_info.rcut_given) {
232	>	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
233	>	args_info.nbins_arg, maxLen);
234	>	} else {
235	>	sprintf( painCave.errMsg,
236	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
237	>	painCave.severity = OPENMD_ERROR;
238	>	painCave.isFatal = 1;
239	>	simError();
240		}
241	+	} else if (args_info.bad_given){
242	+	if (args_info.rcut_given) {
243	+	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
244	+	args_info.nbins_arg);
245	+	} else {
246	+	sprintf( painCave.errMsg,
247	+	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
248	+	painCave.severity = OPENMD_ERROR;
249	+	painCave.isFatal = 1;
250	+	simError();
251	+	}
252	+	} else if (args_info.scd_given) {
253	+	if (batchMode) {
254	+	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
255	+	args_info.begin_arg, args_info.end_arg);
256	+	} else{
257	+	std::string sele3 = args_info.sele3_arg;
258	+	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
259	+	}
260	+	}else if (args_info.density_given) {
261	+	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
262	+	args_info.nbins_arg);
263	+	} else if (args_info.slab_density_given) {
264	+	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
265	+	} else if (args_info.p_angle_given) {
266	+	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
267	+	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
268	+	}else if (args_info.hxy_given) {
269	+	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
270	+	args_info.nbins_y_arg, args_info.nbins_arg);
271	+	#endif
272	+	}else if (args_info.rho_r_given) {
273	+	if (args_info.radius_given){
274	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
275	+	}else{
276	+	sprintf( painCave.errMsg,
277	+	"A particle radius (radius) must be specified when calculating Rho(r)");
278	+	painCave.severity = OPENMD_ERROR;
279	+	painCave.isFatal = 1;
280	+	simError();
281	+	}
282	+	}else if (args_info.hullvol_given) {
283	+	analyser = new NanoVolume(info, dumpFileName, sele1);
284	+	}
285	+
286	+	if (args_info.output_given) {
287	+	analyser->setOutputName(args_info.output_arg);
288	+	}
289	+	if (args_info.step_given) {
290	+	analyser->setStep(args_info.step_arg);
291	+	}
292
293	<	rdf->process();
293	>	analyser->process();
294
295	<	delete rdf;
296	<	delete info;
295	>	delete analyser;
296	>	delete info;
297
298	<	return 0;
298	>	return 0;
299		}
300

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 369 by tim, Fri Feb 18 23:07:32 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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

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