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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 956 by gezelter, Tue May 16 02:06:37 2006 UTC vs.
Revision 1999 by gezelter, Sat May 31 21:00:46 2014 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, 234107 (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	<	#ifndef WITHOUT_FFTW
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	+	#include "applications/staticProps/TetrahedralityParamZ.hpp"
80	+	#include "applications/staticProps/RNEMDStats.hpp"
81	+	#include "applications/staticProps/NitrileFrequencyMap.hpp"
82	+	#include "applications/staticProps/MultipoleSum.hpp"
83
84	<	using namespace oopse;
84	>	using namespace OpenMD;
85
86		int main(int argc, char* argv[]){
87
88	<	//register force fields
71	<	registerForceFields();
72	<
88	>
89		gengetopt_args_info args_info;
90	<
90	>
91		//parse the command line option
92		if (cmdline_parser (argc, argv, &args_info) != 0) {
93		exit(1) ;
94		}
95	<
96	<
81	<	//get the dumpfile name and meta-data file name
95	>
96	>	//get the dumpfile name
97		std::string dumpFileName = args_info.input_arg;
83	–
84	–	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
85	–
86	–
98		std::string sele1;
99		std::string sele2;
100	<
100	>
101	>	// check the first selection argument, or set it to the environment
102	>	// variable, or failing that, set it to "select all"
103	>
104		if (args_info.sele1_given) {
105		sele1 = args_info.sele1_arg;
106	<	}else {
107	<	char*  sele1Env= getenv("OOPSE_SELE1");
106	>	} else {
107	>	char*  sele1Env= getenv("SELECTION1");
108		if (sele1Env) {
109		sele1 = sele1Env;
110	<	}else if (!args_info.scd_given) {
111	<	sprintf( painCave.errMsg,
98	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
99	<	painCave.severity = OOPSE_ERROR;
100	<	painCave.isFatal = 1;
101	<	simError();
110	>	} else {
111	>	sele1 = "select all";
112		}
113		}
114	<
114	>
115	>	// check the second selection argument, or set it to the environment
116	>	// variable, or failing that, set it to the first selection
117	>
118		if (args_info.sele2_given) {
119		sele2 = args_info.sele2_arg;
120	<	}else {
121	<	char* sele2Env = getenv("OOPSE_SELE2");
120	>	} else {
121	>	char* sele2Env = getenv("SELECTION2");
122		if (sele2Env) {
123		sele2 = sele2Env;
124	<	} else if (args_info.density_given) {
125	<	sele2 = "select all";
126	<	} else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
127	<	sprintf( painCave.errMsg,
115	<	"neither --sele2 option nor $OOPSE_SELE2 is set");
116	<	painCave.severity = OOPSE_ERROR;
117	<	painCave.isFatal = 1;
118	<	simError();
124	>	} else {
125	>	//If sele2 is not specified, then the default behavior
126	>	//should be what is already intended for sele1
127	>	sele2 = sele1;
128		}
129		}
130
131		bool batchMode;
132		if (args_info.scd_given){
133	<	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
134	<	batchMode = false;
135	<	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
136	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
137	<	sprintf( painCave.errMsg,
138	<	"below conditions are not satisfied:\n"
139	<	"0 <= begin && 0<= end && begin <= end-2\n");
131	<	painCave.severity = OOPSE_ERROR;
132	<	painCave.isFatal = 1;
133	<	simError();
134	<	}
135	<	batchMode = true;
136	<	} else{
133	>	if (args_info.sele1_given &&
134	>	args_info.sele2_given && args_info.sele3_given) {
135	>	batchMode = false;
136	>	} else if (args_info.molname_given &&
137	>	args_info.begin_given && args_info.end_given) {
138	>	if (args_info.begin_arg < 0 ||
139	>	args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
140		sprintf( painCave.errMsg,
141	<	"either --sele1, --sele2, --sele3 are specified,"
142	<	" or --molname, --begin, --end are specified\n");
143	<	painCave.severity = OOPSE_ERROR;
141	>	"below conditions are not satisfied:\n"
142	>	"0 <= begin && 0<= end && begin <= end-2\n");
143	>	painCave.severity = OPENMD_ERROR;
144		painCave.isFatal = 1;
145	<	simError();
146	<
145	>	simError();
146	>	}
147	>	batchMode = true;
148	>	} else{
149	>	sprintf( painCave.errMsg,
150	>	"either --sele1, --sele2, --sele3 are specified,"
151	>	" or --molname, --begin, --end are specified\n");
152	>	painCave.severity = OPENMD_ERROR;
153	>	painCave.isFatal = 1;
154	>	simError();
155		}
156		}
157	<
157	>
158		//parse md file and set up the system
159		SimCreator creator;
160	<	SimInfo* info = creator.createSim(mdFileName);
160	>	SimInfo* info = creator.createSim(dumpFileName);
161
162	<	double maxLen;
162	>	RealType maxLen;
163	>	RealType zmaxLen;
164		if (args_info.length_given) {
165		maxLen = args_info.length_arg;
166	+	if (args_info.zlength_given){
167	+	zmaxLen = args_info.zlength_arg;
168	+	}
169		} else {
170		Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
171	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
171	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
172	>	zmaxLen = hmat(2,2);
173		}
174	<
174	>
175		StaticAnalyser* analyser;
176		if (args_info.gofr_given){
177	<	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
177	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
178	>	args_info.nbins_arg);
179	>	} else if (args_info.gofz_given) {
180	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
181	>	args_info.nbins_arg);
182	>	} else if (args_info.r_z_given) {
183	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
184	>	args_info.nbins_arg, args_info.nbins_z_arg);
185		} else if (args_info.r_theta_given) {
186	<	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
186	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
187	>	args_info.nbins_arg, args_info.nanglebins_arg);
188		} else if (args_info.r_omega_given) {
189	<	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
189	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
190	>	args_info.nbins_arg, args_info.nanglebins_arg);
191		} else if (args_info.theta_omega_given) {
192	<	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
192	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
193	>	args_info.nanglebins_arg);
194		} else if (args_info.gxyz_given) {
195		if (args_info.refsele_given) {
196	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
196	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
197	>	args_info.refsele_arg, maxLen, args_info.nbins_arg);
198		} else {
199		sprintf( painCave.errMsg,
200	<	"--refsele must set when --gxyz is used");
201	<	painCave.severity = OOPSE_ERROR;
200	>	"--refsele must set when --gxyz is used");
201	>	painCave.severity = OPENMD_ERROR;
202		painCave.isFatal = 1;
203		simError();
204		}
205	+	} else if (args_info.twodgofr_given){
206	+	if (args_info.dz_given) {
207	+	analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
208	+	args_info.dz_arg, args_info.nbins_arg);
209	+	} else {
210	+	sprintf( painCave.errMsg,
211	+	"A slab width (dz) must be specified when calculating TwoDGofR");
212	+	painCave.severity = OPENMD_ERROR;
213	+	painCave.isFatal = 1;
214	+	simError();
215	+	}
216		} else if (args_info.p2_given) {
217	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
217	>	if (args_info.sele1_given) {
218	>	if (args_info.sele2_given)
219	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
220	>	else
221	>	if (args_info.seleoffset_given)
222	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1,
223	>	args_info.seleoffset_arg);
224	>	else
225	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1);
226	>	} else {
227	>	sprintf( painCave.errMsg,
228	>	"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
229	>	painCave.severity = OPENMD_ERROR;
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
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.multipole_given){
248	>	analyser = new MultipoleSum(info, dumpFileName, sele1,
249	>	maxLen, args_info.nbins_arg);
250	>	} else if (args_info.tet_param_given) {
251	>	if (args_info.rcut_given) {
252	>	analyser = new TetrahedralityParam(info, dumpFileName, sele1,
253	>	args_info.rcut_arg,
254	>	args_info.nbins_arg);
255	>	} else {
256	>	sprintf( painCave.errMsg,
257	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
258	>	painCave.severity = OPENMD_ERROR;
259	>	painCave.isFatal = 1;
260	>	simError();
261	>	}
262	>	} else if (args_info.tet_param_z_given) {
263	>	if (args_info.rcut_given) {
264	>	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
265	>	args_info.rcut_arg,
266	>	args_info.nbins_arg);
267	>	} else {
268	>	sprintf( painCave.errMsg,
269	>	"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
270	>	painCave.severity = OPENMD_ERROR;
271	>	painCave.isFatal = 1;
272	>	simError();
273	>	}
274	>	} else if (args_info.ior_given){
275	>	if (args_info.rcut_given) {
276	>	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
277	>	args_info.rcut_arg,
278	>	args_info.nbins_arg, maxLen);
279	>	} else {
280	>	sprintf( painCave.errMsg,
281	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
282	>	painCave.severity = OPENMD_ERROR;
283	>	painCave.isFatal = 1;
284	>	simError();
285	>	}
286	>	} else if (args_info.for_given){
287	>	if (args_info.rcut_given) {
288	>	analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
289	>	args_info.nbins_arg, maxLen);
290	>	} else {
291	>	sprintf( painCave.errMsg,
292	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
293	>	painCave.severity = OPENMD_ERROR;
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	} else if (args_info.bad_given){
298	>	if (args_info.rcut_given) {
299	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
300	>	args_info.rcut_arg,
301	>	args_info.nbins_arg);
302	>	} else {
303	>	sprintf( painCave.errMsg,
304	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
305	>	painCave.severity = OPENMD_ERROR;
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309		} else if (args_info.scd_given) {
310	<	if (batchMode) {
311	<	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
312	<	args_info.begin_arg, args_info.end_arg);
313	<	} else{
314	<	std::string sele3 = args_info.sele3_arg;
315	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
316	<	}
310	>	if (batchMode) {
311	>	analyser  = new SCDOrderParameter(info, dumpFileName,
312	>	args_info.molname_arg,
313	>	args_info.begin_arg, args_info.end_arg);
314	>	} else{
315	>	std::string sele3 = args_info.sele3_arg;
316	>	analyser  = new SCDOrderParameter(info, dumpFileName,
317	>	sele1, sele2, sele3);
318	>	}
319		}else if (args_info.density_given) {
320	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
320	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
321	>	args_info.nbins_arg);
322	>	} else if (args_info.count_given) {
323	>	analyser = new ObjectCount(info, dumpFileName, sele1 );
324		} else if (args_info.slab_density_given) {
325	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
326	<	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg);
327	<	#ifndef WITHOUT_FFTW
325	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
326	>	} else if (args_info.rnemdz_given) {
327	>	analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
328	>	} else if (args_info.rnemdr_given) {
329	>	analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
330	>	} else if (args_info.rnemdrt_given) {
331	>	analyser = new RNEMDRTheta(info, dumpFileName, sele1,
332	>	args_info.nbins_arg, args_info.nanglebins_arg);
333	>	} else if (args_info.nitrile_given) {
334	>	analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
335	>	args_info.nbins_arg);
336	>	} else if (args_info.p_angle_given) {
337	>	if (args_info.sele1_given) {
338	>	if (args_info.sele2_given)
339	>	analyser  = new pAngle(info, dumpFileName, sele1, sele2,
340	>	args_info.nbins_arg);
341	>	else
342	>	if (args_info.seleoffset_given) {
343	>	if (args_info.seleoffset2_given) {
344	>	analyser  = new pAngle(info, dumpFileName, sele1,
345	>	args_info.seleoffset_arg,
346	>	args_info.seleoffset2_arg,
347	>	args_info.nbins_arg);
348	>	} else {
349	>	analyser  = new pAngle(info, dumpFileName, sele1,
350	>	args_info.seleoffset_arg,
351	>	args_info.nbins_arg);
352	>	}
353	>	} else
354	>	analyser  = new pAngle(info, dumpFileName, sele1,
355	>	args_info.nbins_arg);
356	>	} else {
357	>	sprintf( painCave.errMsg,
358	>	"At least one selection script (--sele1) must be specified when "
359	>	"calculating P(angle) distributions");
360	>	painCave.severity = OPENMD_ERROR;
361	>	painCave.isFatal = 1;
362	>	simError();
363	>	}
364	>	#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
365		}else if (args_info.hxy_given) {
366	<	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
366	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
367	>	args_info.nbins_y_arg, args_info.nbins_arg);
368		#endif
369	+	}else if (args_info.rho_r_given) {
370	+	if (args_info.radius_given){
371	+	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
372	+	}else{
373	+	sprintf( painCave.errMsg,
374	+	"A particle radius (radius) must be specified when calculating Rho(r)");
375	+	painCave.severity = OPENMD_ERROR;
376	+	painCave.isFatal = 1;
377	+	simError();
378	+	}
379	+	} else if (args_info.hullvol_given) {
380	+	analyser = new NanoVolume(info, dumpFileName, sele1);
381	+	} else if (args_info.rodlength_given) {
382	+	analyser = new NanoLength(info, dumpFileName, sele1);
383	+	} else if (args_info.angle_r_given) {
384	+	analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
385		}
386	<
386	>
387		if (args_info.output_given) {
388		analyser->setOutputName(args_info.output_arg);
389		}
390		if (args_info.step_given) {
391		analyser->setStep(args_info.step_arg);
392		}
393	<
393	>
394		analyser->process();
395	<
395	>
396		delete analyser;
397		delete info;
398	<
398	>
399		return 0;
400		}
213	–

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 956 by gezelter, Tue May 16 02:06:37 2006 UTC vs.
Revision 1999 by gezelter, Sat May 31 21:00:46 2014 UTC

#	Line 0 | Line 1
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