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Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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 70 | Line 70
70   #endif
71   #include "applications/staticProps/RhoR.hpp"
72  
73 < using namespace oopse;
73 > using namespace OpenMD;
74  
75   int main(int argc, char* argv[]){
76    
# Line 97 | Line 97 | int main(int argc, char* argv[]){
97    if (args_info.sele1_given) {
98      sele1 = args_info.sele1_arg;
99    } else {
100 <    char*  sele1Env= getenv("OOPSE_SELE1");
100 >    char*  sele1Env= getenv("SELECTION1");
101      if (sele1Env) {
102        sele1 = sele1Env;
103      } else {
# Line 111 | Line 111 | int main(int argc, char* argv[]){
111    if (args_info.sele2_given) {
112      sele2 = args_info.sele2_arg;
113    } else {
114 <    char* sele2Env = getenv("OOPSE_SELE2");
114 >    char* sele2Env = getenv("SELECTION1");
115      if (sele2Env) {
116        sele2 = sele2Env;            
117      } else {
# Line 123 | Line 123 | int main(int argc, char* argv[]){
123    // Problems if sele1 wasn't specified, but
124   // if (!args_info.scd_given) {
125   //       sprintf( painCave.errMsg,
126 < //                "neither --sele1 option nor $OOPSE_SELE1 is set");
127 < //       painCave.severity = OOPSE_ERROR;
126 > //                "neither --sele1 option nor $SELECTION1 is set");
127 > //       painCave.severity = OPENMD_ERROR;
128   //       painCave.isFatal = 1;
129   //       simError();
130   //     }
# Line 134 | Line 134 | int main(int argc, char* argv[]){
134  
135   //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
136   //       sprintf( painCave.errMsg,
137 < //                "neither --sele2 option nor $OOPSE_SELE2 is set");
138 < //       painCave.severity = OOPSE_ERROR;
137 > //                "neither --sele2 option nor $SELECTION1 is set");
138 > //       painCave.severity = OPENMD_ERROR;
139   //       painCave.isFatal = 1;
140   //       simError();        
141   //     }
# Line 150 | Line 150 | int main(int argc, char* argv[]){
150          sprintf( painCave.errMsg,
151                   "below conditions are not satisfied:\n"
152                   "0 <= begin && 0<= end && begin <= end-2\n");
153 <        painCave.severity = OOPSE_ERROR;
153 >        painCave.severity = OPENMD_ERROR;
154          painCave.isFatal = 1;
155          simError();                    
156        }
# Line 159 | Line 159 | int main(int argc, char* argv[]){
159        sprintf( painCave.errMsg,
160                 "either --sele1, --sele2, --sele3 are specified,"
161                 " or --molname, --begin, --end are specified\n");
162 <      painCave.severity = OOPSE_ERROR;
162 >      painCave.severity = OPENMD_ERROR;
163        painCave.isFatal = 1;
164        simError();        
165      
# Line 184 | Line 184 | int main(int argc, char* argv[]){
184      analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
185                         args_info.nbins_arg);        
186    } else if (args_info.gofz_given) {
187 <    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
188 <                       args_info.nbins_arg);        
187 >    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
188 >                       args_info.nbins_arg);
189    } else if (args_info.r_theta_given) {
190      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
191                                args_info.nbins_arg, args_info.nanglebins_arg);
# Line 202 | Line 202 | int main(int argc, char* argv[]){
202      } else {
203        sprintf( painCave.errMsg,
204                 "--refsele must set when --gxyz is used");
205 <      painCave.severity = OOPSE_ERROR;
205 >      painCave.severity = OPENMD_ERROR;
206        painCave.isFatal = 1;
207        simError();  
208      }
# Line 218 | Line 218 | int main(int argc, char* argv[]){
218      } else {
219        sprintf( painCave.errMsg,
220                 "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
221 <      painCave.severity = OOPSE_ERROR;
221 >      painCave.severity = OPENMD_ERROR;
222        painCave.isFatal = 1;
223        simError();
224      }
# Line 229 | Line 229 | int main(int argc, char* argv[]){
229      } else {
230        sprintf( painCave.errMsg,
231                 "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
232 <      painCave.severity = OOPSE_ERROR;
232 >      painCave.severity = OPENMD_ERROR;
233        painCave.isFatal = 1;
234        simError();
235      }
# Line 240 | Line 240 | int main(int argc, char* argv[]){
240      } else {
241        sprintf( painCave.errMsg,
242                 "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
243 <      painCave.severity = OOPSE_ERROR;
243 >      painCave.severity = OPENMD_ERROR;
244        painCave.isFatal = 1;
245        simError();
246      }
# Line 253 | Line 253 | int main(int argc, char* argv[]){
253        analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
254      }
255    }else if (args_info.density_given) {
256 <    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
256 >    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
257                                args_info.nbins_arg);  
258    } else if (args_info.slab_density_given) {
259 <    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
260 <    analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
259 >    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
260   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
261    }else if (args_info.hxy_given) {
262      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
# Line 269 | Line 268 | int main(int argc, char* argv[]){
268      }else{
269        sprintf( painCave.errMsg,
270                 "A particle radius (radius) must be specified when calculating Rho(r)");
271 <      painCave.severity = OOPSE_ERROR;
271 >      painCave.severity = OPENMD_ERROR;
272        painCave.isFatal = 1;
273        simError();
274      }

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