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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1513 by gezelter, Tue Oct 19 18:40:54 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <iostream>
#	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		#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
73		#include "applications/staticProps/Hxy.hpp"
74		#endif
75	+	#include "applications/staticProps/RhoR.hpp"
76
77	<	using namespace oopse;
77	>	using namespace OpenMD;
78
79		int main(int argc, char* argv[]){
80
81		//register force fields
82		registerForceFields();
83	<
83	>
84		gengetopt_args_info args_info;
85	<
85	>
86		//parse the command line option
87		if (cmdline_parser (argc, argv, &args_info) != 0) {
88		exit(1) ;
89		}
90	<
90	>
91		//get the dumpfile name
92		std::string dumpFileName = args_info.input_arg;
93		std::string sele1;
94		std::string sele2;
95		bool userSpecifiedSelect1;
96		bool userSpecifiedSelect2;
97	<
97	>
98		// check the first selection argument, or set it to the environment
99		// variable, or failing that, set it to "select all"
100	<
100	>
101		if (args_info.sele1_given) {
102		sele1 = args_info.sele1_arg;
103		} else {
104	<	char*  sele1Env= getenv("OOPSE_SELE1");
104	>	char*  sele1Env= getenv("SELECTION1");
105		if (sele1Env) {
106		sele1 = sele1Env;
107		} else {
108		sele1 = "select all";
109		}
110		}
111	<
111	>
112		// check the second selection argument, or set it to the environment
113		// variable, or failing that, set it to "select all"
114
115		if (args_info.sele2_given) {
116		sele2 = args_info.sele2_arg;
117		} else {
118	<	char* sele2Env = getenv("OOPSE_SELE2");
118	>	char* sele2Env = getenv("SELECTION1");
119		if (sele2Env) {
120		sele2 = sele2Env;
121		} else {
122		sele2 = "select all";
123		}
124		}
125	<
126	<
125	>
126	>
127		// Problems if sele1 wasn't specified, but
128	<	// if (!args_info.scd_given) {
129	<	//       sprintf( painCave.errMsg,
130	<	//                "neither --sele1 option nor $OOPSE_SELE1 is set");
131	<	//       painCave.severity = OOPSE_ERROR;
132	<	//       painCave.isFatal = 1;
133	<	//       simError();
134	<	//     }
135	<	//   }
136	<
128	>	// if (!args_info.scd_given) {
129	>	//       sprintf( painCave.errMsg,
130	>	//                "neither --sele1 option nor $SELECTION1 is set");
131	>	//       painCave.severity = OPENMD_ERROR;
132	>	//       painCave.isFatal = 1;
133	>	//       simError();
134	>	//     }
135	>	//   }
136	>
137		// Problems if sele1 wasn't specified
138	<
139	<	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
140	<	//       sprintf( painCave.errMsg,
141	<	//                "neither --sele2 option nor $OOPSE_SELE2 is set");
142	<	//       painCave.severity = OOPSE_ERROR;
143	<	//       painCave.isFatal = 1;
144	<	//       simError();
145	<	//     }
146	<	//   }
147	<
138	>
139	>	//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
140	>	//       sprintf( painCave.errMsg,
141	>	//                "neither --sele2 option nor $SELECTION1 is set");
142	>	//       painCave.severity = OPENMD_ERROR;
143	>	//       painCave.isFatal = 1;
144	>	//       simError();
145	>	//     }
146	>	//   }
147	>
148		bool batchMode;
149		if (args_info.scd_given){
150		if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
#	Line 145 | Line 154 | int main(int argc, char* argv[]){
154		sprintf( painCave.errMsg,
155		"below conditions are not satisfied:\n"
156		"0 <= begin && 0<= end && begin <= end-2\n");
157	<	painCave.severity = OOPSE_ERROR;
157	>	painCave.severity = OPENMD_ERROR;
158		painCave.isFatal = 1;
159		simError();
160		}
#	Line 154 | Line 163 | int main(int argc, char* argv[]){
163		sprintf( painCave.errMsg,
164		"either --sele1, --sele2, --sele3 are specified,"
165		" or --molname, --begin, --end are specified\n");
166	<	painCave.severity = OOPSE_ERROR;
166	>	painCave.severity = OPENMD_ERROR;
167		painCave.isFatal = 1;
168		simError();
169	<
169	>
170		}
171		}
172	<
172	>
173		//parse md file and set up the system
174		SimCreator creator;
175	+	std::cout << "dumpFile = " << dumpFileName << "\n";
176		SimInfo* info = creator.createSim(dumpFileName);
177
178		RealType maxLen;
179	+	RealType zmaxLen;
180		if (args_info.length_given) {
181		maxLen = args_info.length_arg;
182	+	if (args_info.zlength_given){
183	+	zmaxLen = args_info.zlength_arg;
184	+	}
185		} else {
186		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
187	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
187	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
188	>	zmaxLen = hmat(2,2);
189		}
190
191		StaticAnalyser* analyser;
192		if (args_info.gofr_given){
193	<	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
193	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
194	>	args_info.nbins_arg);
195	>	} else if (args_info.gofz_given) {
196	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
197	>	args_info.nbins_arg);
198	>	} else if (args_info.r_z_given) {
199	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
200	>	args_info.nbins_arg, args_info.nbins_z_arg);
201		} else if (args_info.r_theta_given) {
202	<	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
202	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
203	>	args_info.nbins_arg, args_info.nanglebins_arg);
204		} else if (args_info.r_omega_given) {
205	<	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
205	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
206	>	args_info.nbins_arg, args_info.nanglebins_arg);
207		} else if (args_info.theta_omega_given) {
208	<	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
208	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
209	>	args_info.nanglebins_arg);
210		} else if (args_info.gxyz_given) {
211		if (args_info.refsele_given) {
212	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
212	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
213	>	maxLen, args_info.nbins_arg);
214		} else {
215		sprintf( painCave.errMsg,
216		"--refsele must set when --gxyz is used");
217	<	painCave.severity = OOPSE_ERROR;
217	>	painCave.severity = OPENMD_ERROR;
218		painCave.isFatal = 1;
219		simError();
220		}
221	+	} else if (args_info.twodgofr_given){
222	+	if (args_info.dz_given) {
223	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
224	+	args_info.dz_arg, args_info.nbins_arg);
225	+	} else {
226	+	sprintf( painCave.errMsg,
227	+	"A slab width (dz) must be specified when calculating TwoDGofR");
228	+	painCave.severity = OPENMD_ERROR;
229	+	painCave.isFatal = 1;
230	+	simError();
231	+	}
232		} else if (args_info.p2_given) {
233		analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
234		} else if (args_info.rp2_given){
235		analyser = new RippleOP(info, dumpFileName, sele1, sele2);
236		} else if (args_info.bo_given){
237	<	if (args_info.rcut_given && args_info.LegendreL_given) {
237	>	if (args_info.rcut_given) {
238		analyser = new BondOrderParameter(info, dumpFileName, sele1,
239		args_info.rcut_arg,
240	<	args_info.LegendreL_arg);
240	>	args_info.nbins_arg);
241		} else {
242		sprintf( painCave.errMsg,
243	<	"Both the cutoff radius (rcut) and LegendreL must be specified when calculating Bond Order Parameters");
244	<	painCave.severity = OOPSE_ERROR;
243	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
244	>	painCave.severity = OPENMD_ERROR;
245		painCave.isFatal = 1;
246		simError();
247		}
248	+	} else if (args_info.bor_given){
249	+	if (args_info.rcut_given) {
250	+	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
251	+	args_info.nbins_arg, maxLen);
252	+	} else {
253	+	sprintf( painCave.errMsg,
254	+	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
255	+	painCave.severity = OPENMD_ERROR;
256	+	painCave.isFatal = 1;
257	+	simError();
258	+	}
259	+	} else if (args_info.bad_given){
260	+	if (args_info.rcut_given) {
261	+	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
262	+	args_info.nbins_arg);
263	+	} else {
264	+	sprintf( painCave.errMsg,
265	+	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
266	+	painCave.severity = OPENMD_ERROR;
267	+	painCave.isFatal = 1;
268	+	simError();
269	+	}
270		} else if (args_info.scd_given) {
271		if (batchMode) {
272		analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
#	Line 217 | Line 276 | int main(int argc, char* argv[]){
276		analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
277		}
278		}else if (args_info.density_given) {
279	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
279	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
280	>	args_info.nbins_arg);
281	>	} else if (args_info.count_given) {
282	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
283		} else if (args_info.slab_density_given) {
284	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
285	<	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg);
284	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
285	>	} else if (args_info.p_angle_given) {
286	>	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
287		#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
288		}else if (args_info.hxy_given) {
289	<	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
289	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
290	>	args_info.nbins_y_arg, args_info.nbins_arg);
291		#endif
292	+	}else if (args_info.rho_r_given) {
293	+	if (args_info.radius_given){
294	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
295	+	}else{
296	+	sprintf( painCave.errMsg,
297	+	"A particle radius (radius) must be specified when calculating Rho(r)");
298	+	painCave.severity = OPENMD_ERROR;
299	+	painCave.isFatal = 1;
300	+	simError();
301	+	}
302	+	}else if (args_info.hullvol_given) {
303	+	analyser = new NanoVolume(info, dumpFileName, sele1);
304		}
305
306		if (args_info.output_given) {

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1513 by gezelter, Tue Oct 19 18:40:54 2010 UTC

#	Line 0 | Line 1
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