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

Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 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 53 | Line 53
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"
#	Line 63 | Line 64
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)
#	Line 70 | Line 72
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
#	Line 97 | Line 99 | int main(int argc, char* argv[]){
99		if (args_info.sele1_given) {
100		sele1 = args_info.sele1_arg;
101		} else {
102	<	char*  sele1Env= getenv("OOPSE_SELE1");
102	>	char*  sele1Env= getenv("SELECTION1");
103		if (sele1Env) {
104		sele1 = sele1Env;
105		} else {
#	Line 111 | Line 113 | int main(int argc, char* argv[]){
113		if (args_info.sele2_given) {
114		sele2 = args_info.sele2_arg;
115		} else {
116	<	char* sele2Env = getenv("OOPSE_SELE2");
116	>	char* sele2Env = getenv("SELECTION1");
117		if (sele2Env) {
118		sele2 = sele2Env;
119		} else {
#	Line 123 | Line 125 | int main(int argc, char* argv[]){
125		// Problems if sele1 wasn't specified, but
126		// if (!args_info.scd_given) {
127		//       sprintf( painCave.errMsg,
128	<	//                "neither --sele1 option nor $OOPSE_SELE1 is set");
129	<	//       painCave.severity = OOPSE_ERROR;
128	>	//                "neither --sele1 option nor $SELECTION1 is set");
129	>	//       painCave.severity = OPENMD_ERROR;
130		//       painCave.isFatal = 1;
131		//       simError();
132		//     }
#	Line 134 | Line 136 | int main(int argc, char* argv[]){
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 $OOPSE_SELE2 is set");
140	<	//       painCave.severity = OOPSE_ERROR;
139	>	//                "neither --sele2 option nor $SELECTION1 is set");
140	>	//       painCave.severity = OPENMD_ERROR;
141		//       painCave.isFatal = 1;
142		//       simError();
143		//     }
#	Line 150 | Line 152 | int main(int argc, char* argv[]){
152		sprintf( painCave.errMsg,
153		"below conditions are not satisfied:\n"
154		"0 <= begin && 0<= end && begin <= end-2\n");
155	<	painCave.severity = OOPSE_ERROR;
155	>	painCave.severity = OPENMD_ERROR;
156		painCave.isFatal = 1;
157		simError();
158		}
#	Line 159 | Line 161 | int main(int argc, char* argv[]){
161		sprintf( painCave.errMsg,
162		"either --sele1, --sele2, --sele3 are specified,"
163		" or --molname, --begin, --end are specified\n");
164	<	painCave.severity = OOPSE_ERROR;
164	>	painCave.severity = OPENMD_ERROR;
165		painCave.isFatal = 1;
166		simError();
167
#	Line 184 | Line 186 | int main(int argc, char* argv[]){
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);
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);
#	Line 202 | Line 207 | int main(int argc, char* argv[]){
207		} else {
208		sprintf( painCave.errMsg,
209		"--refsele must set when --gxyz is used");
210	<	painCave.severity = OOPSE_ERROR;
210	>	painCave.severity = OPENMD_ERROR;
211		painCave.isFatal = 1;
212		simError();
213		}
#	Line 218 | Line 223 | int main(int argc, char* argv[]){
223		} else {
224		sprintf( painCave.errMsg,
225		"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
226	<	painCave.severity = OOPSE_ERROR;
226	>	painCave.severity = OPENMD_ERROR;
227		painCave.isFatal = 1;
228		simError();
229		}
#	Line 229 | Line 234 | int main(int argc, char* argv[]){
234		} else {
235		sprintf( painCave.errMsg,
236		"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
237	<	painCave.severity = OOPSE_ERROR;
237	>	painCave.severity = OPENMD_ERROR;
238		painCave.isFatal = 1;
239		simError();
240		}
#	Line 240 | Line 245 | int main(int argc, char* argv[]){
245		} else {
246		sprintf( painCave.errMsg,
247		"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
248	<	painCave.severity = OOPSE_ERROR;
248	>	painCave.severity = OPENMD_ERROR;
249		painCave.isFatal = 1;
250		simError();
251		}
#	Line 253 | Line 258 | int main(int argc, char* argv[]){
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,
261	>	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
262		args_info.nbins_arg);
263		} else if (args_info.slab_density_given) {
264	<	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
265	<	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
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,
#	Line 269 | Line 275 | int main(int argc, char* argv[]){
275		}else{
276		sprintf( painCave.errMsg,
277		"A particle radius (radius) must be specified when calculating Rho(r)");
278	<	painCave.severity = OOPSE_ERROR;
278	>	painCave.severity = OPENMD_ERROR;
279		painCave.isFatal = 1;
280		simError();
281		}

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 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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