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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 980 by xsun, Thu Jun 1 18:06:33 2006 UTC vs.
Revision 1445 by chuckv, Tue Jun 8 20:26:50 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/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) ;
87	<	}
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	<	//get the dumpfile name and meta-data file name
97	<	std::string dumpFileName = args_info.input_arg;
96	>	// check the first selection argument, or set it to the environment
97	>	// variable, or failing that, set it to "select all"
98
99	<	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
100	<
101	<
102	<	std::string sele1;
103	<	std::string sele2;
104	<
105	<	if (args_info.sele1_given) {
106	<	sele1 = args_info.sele1_arg;
107	<	}else {
94	<	char*  sele1Env= getenv("OOPSE_SELE1");
95	<	if (sele1Env) {
96	<	sele1 = sele1Env;
97	<	}else if (!args_info.scd_given) {
98	<	sprintf( painCave.errMsg,
99	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
100	<	painCave.severity = OOPSE_ERROR;
101	<	painCave.isFatal = 1;
102	<	simError();
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		}
104	–	}
105	–
106	–	if (args_info.sele2_given) {
107	–	sele2 = args_info.sele2_arg;
108	–	}else {
109	–	char* sele2Env = getenv("OOPSE_SELE2");
110	–	if (sele2Env) {
111	–	sele2 = sele2Env;
112	–	} else if (args_info.density_given) {
113	–	sele2 = "select all";
114	–	} else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
115	–	sprintf( painCave.errMsg,
116	–	"neither --sele2 option nor $OOPSE_SELE2 is set");
117	–	painCave.severity = OOPSE_ERROR;
118	–	painCave.isFatal = 1;
119	–	simError();
120	–	}
121	–	}
109
110	<	bool batchMode;
111	<	if (args_info.scd_given){
112	<	if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
113	<	batchMode = false;
114	<	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
115	<	if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
116	<	sprintf( painCave.errMsg,
117	<	"below conditions are not satisfied:\n"
118	<	"0 <= begin && 0<= end && begin <= end-2\n");
119	<	painCave.severity = OOPSE_ERROR;
120	<	painCave.isFatal = 1;
121	<	simError();
135	<	}
136	<	batchMode = true;
137	<	} else{
138	<	sprintf( painCave.errMsg,
139	<	"either --sele1, --sele2, --sele3 are specified,"
140	<	" or --molname, --begin, --end are specified\n");
141	<	painCave.severity = OOPSE_ERROR;
142	<	painCave.isFatal = 1;
143	<	simError();
144	<
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		}
146	–	}
123
148	–	//parse md file and set up the system
149	–	SimCreator creator;
150	–	SimInfo* info = creator.createSim(mdFileName);
124
125	<	RealType maxLen;
126	<	if (args_info.length_given) {
127	<	maxLen = args_info.length_arg;
128	<	} else {
129	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
130	<	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
131	<	}
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	<	StaticAnalyser* analyser;
136	<	if (args_info.gofr_given){
137	<	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
138	<	} else if (args_info.r_theta_given) {
139	<	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
140	<	} else if (args_info.r_omega_given) {
141	<	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
142	<	} else if (args_info.theta_omega_given) {
143	<	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
144	<	} else if (args_info.gxyz_given) {
145	<	if (args_info.refsele_given) {
146	<	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
147	<	} else {
148	<	sprintf( painCave.errMsg,
149	<	"--refsele must set when --gxyz is used");
150	<	painCave.severity = OOPSE_ERROR;
151	<	painCave.isFatal = 1;
152	<	simError();
135	>	// Problems if sele1 wasn't specified
136	>
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	>
168	>	}
169		}
170	<	} else if (args_info.p2_given) {
171	<	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
172	<	}    else if (args_info.rp2_given){
173	<	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
174	<	}else if (args_info.scd_given) {
175	<	if (batchMode) {
176	<	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
177	<	args_info.begin_arg, args_info.end_arg);
178	<	} else{
179	<	std::string sele3 = args_info.sele3_arg;
180	<	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
181	<	}
182	<	}else if (args_info.density_given) {
183	<	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
184	<	} else if (args_info.slab_density_given) {
185	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
186	<	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg);
170	>
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	>	RealType maxLen;
177	>	RealType zmaxLen;
178	>	if (args_info.length_given) {
179	>	maxLen = args_info.length_arg;
180	>	if (args_info.zlength_given){
181	>	zmaxLen = args_info.zlength_arg;
182	>	}
183	>	} else {
184	>	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
185	>	maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
186	>	zmaxLen = hmat(2,2);
187	>	}
188	>
189	>	StaticAnalyser* analyser;
190	>	if (args_info.gofr_given){
191	>	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
192	>	args_info.nbins_arg);
193	>	} else if (args_info.gofz_given) {
194	>	analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
195	>	args_info.nbins_arg);
196	>	} else if (args_info.r_z_given) {
197	>	analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
198	>	args_info.nbins_arg, args_info.nbins_z_arg);
199	>	} else if (args_info.r_theta_given) {
200	>	analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
201	>	args_info.nbins_arg, args_info.nanglebins_arg);
202	>	} else if (args_info.r_omega_given) {
203	>	analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
204	>	args_info.nbins_arg, args_info.nanglebins_arg);
205	>	} else if (args_info.theta_omega_given) {
206	>	analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
207	>	args_info.nanglebins_arg);
208	>	} else if (args_info.gxyz_given) {
209	>	if (args_info.refsele_given) {
210	>	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
211	>	maxLen, args_info.nbins_arg);
212	>	} else {
213	>	sprintf( painCave.errMsg,
214	>	"--refsele must set when --gxyz is used");
215	>	painCave.severity = OPENMD_ERROR;
216	>	painCave.isFatal = 1;
217	>	simError();
218	>	}
219	>	} else if (args_info.p2_given) {
220	>	analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
221	>	} else if (args_info.rp2_given){
222	>	analyser = new RippleOP(info, dumpFileName, sele1, sele2);
223	>	} else if (args_info.bo_given){
224	>	if (args_info.rcut_given) {
225	>	analyser = new BondOrderParameter(info, dumpFileName, sele1,
226	>	args_info.rcut_arg,
227	>	args_info.nbins_arg);
228	>	} else {
229	>	sprintf( painCave.errMsg,
230	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
231	>	painCave.severity = OPENMD_ERROR;
232	>	painCave.isFatal = 1;
233	>	simError();
234	>	}
235	>	} else if (args_info.bor_given){
236	>	if (args_info.rcut_given) {
237	>	analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
238	>	args_info.nbins_arg, maxLen);
239	>	} else {
240	>	sprintf( painCave.errMsg,
241	>	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
242	>	painCave.severity = OPENMD_ERROR;
243	>	painCave.isFatal = 1;
244	>	simError();
245	>	}
246	>	} else if (args_info.bad_given){
247	>	if (args_info.rcut_given) {
248	>	analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
249	>	args_info.nbins_arg);
250	>	} else {
251	>	sprintf( painCave.errMsg,
252	>	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
253	>	painCave.severity = OPENMD_ERROR;
254	>	painCave.isFatal = 1;
255	>	simError();
256	>	}
257	>	} else if (args_info.scd_given) {
258	>	if (batchMode) {
259	>	analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
260	>	args_info.begin_arg, args_info.end_arg);
261	>	} else{
262	>	std::string sele3 = args_info.sele3_arg;
263	>	analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
264	>	}
265	>	}else if (args_info.density_given) {
266	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
267	>	args_info.nbins_arg);
268	>	} else if (args_info.slab_density_given) {
269	>	analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
270	>	} else if (args_info.p_angle_given) {
271	>	analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
272		#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
273	<	}else if (args_info.hxy_given) {
274	<	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
273	>	}else if (args_info.hxy_given) {
274	>	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
275	>	args_info.nbins_y_arg, args_info.nbins_arg);
276		#endif
277	<	}
278	<
279	<	if (args_info.output_given) {
280	<	analyser->setOutputName(args_info.output_arg);
281	<	}
282	<	if (args_info.step_given) {
283	<	analyser->setStep(args_info.step_arg);
284	<	}
277	>	}else if (args_info.rho_r_given) {
278	>	if (args_info.radius_given){
279	>	analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
280	>	}else{
281	>	sprintf( painCave.errMsg,
282	>	"A particle radius (radius) must be specified when calculating Rho(r)");
283	>	painCave.severity = OPENMD_ERROR;
284	>	painCave.isFatal = 1;
285	>	simError();
286	>	}
287	>	}else if (args_info.hullvol_given) {
288	>	analyser = new NanoVolume(info, dumpFileName, sele1);
289	>	}
290	>
291	>	if (args_info.output_given) {
292	>	analyser->setOutputName(args_info.output_arg);
293	>	}
294	>	if (args_info.step_given) {
295	>	analyser->setStep(args_info.step_arg);
296	>	}
297
298	<	analyser->process();
298	>	analyser->process();
299
300	<	delete analyser;
301	<	delete info;
300	>	delete analyser;
301	>	delete info;
302
303	<	return 0;
303	>	return 0;
304		}
305

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 980 by xsun, Thu Jun 1 18:06:33 2006 UTC vs.
Revision 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC

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

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+	Added lines
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