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Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1041 by gezelter, Wed Sep 20 20:13:40 2006 UTC vs.
Revision 1440 by gezelter, Thu Apr 29 14:41:48 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    
# Line 92 | 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 106 | 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 118 | 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 129 | 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 145 | 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 154 | 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 163 | Line 170 | int main(int argc, char* argv[]){
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;
# Line 177 | Line 185 | int main(int argc, char* argv[]){
185    if (args_info.gofr_given){
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);
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 193 | 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 202 | Line 216 | int main(int argc, char* argv[]){
216    } else if (args_info.rp2_given){
217      analyser = new RippleOP(info, dumpFileName, sele1, sele2);
218    } else if (args_info.bo_given){
219 <    if (args_info.rcut_given && args_info.LegendreL_given) {
219 >    if (args_info.rcut_given) {
220        analyser = new BondOrderParameter(info, dumpFileName, sele1,
221                                          args_info.rcut_arg,
208 –                                        args_info.LegendreL_arg,
222                                          args_info.nbins_arg);
223      } else {
224        sprintf( painCave.errMsg,
225 <               "Both the cutoff radius (rcut) and LegendreL must be specified when calculating Bond Order Parameters");
226 <      painCave.severity = OOPSE_ERROR;
225 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
226 >      painCave.severity = OPENMD_ERROR;
227        painCave.isFatal = 1;
228        simError();
229      }
230 +  } else if (args_info.bor_given){
231 +    if (args_info.rcut_given) {
232 +      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
233 +                            args_info.nbins_arg, maxLen);
234 +    } else {
235 +      sprintf( painCave.errMsg,
236 +               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
237 +      painCave.severity = OPENMD_ERROR;
238 +      painCave.isFatal = 1;
239 +      simError();
240 +    }
241 +  } else if (args_info.bad_given){
242 +    if (args_info.rcut_given) {
243 +      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
244 +                            args_info.nbins_arg);
245 +    } else {
246 +      sprintf( painCave.errMsg,
247 +               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
248 +      painCave.severity = OPENMD_ERROR;
249 +      painCave.isFatal = 1;
250 +      simError();
251 +    }
252    } else if (args_info.scd_given) {
253      if (batchMode) {
254        analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
# Line 223 | 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,
270                         args_info.nbins_y_arg, args_info.nbins_arg);
271   #endif
272 +  }else if (args_info.rho_r_given) {
273 +    if (args_info.radius_given){
274 +      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
275 +    }else{
276 +      sprintf( painCave.errMsg,
277 +               "A particle radius (radius) must be specified when calculating Rho(r)");
278 +      painCave.severity = OPENMD_ERROR;
279 +      painCave.isFatal = 1;
280 +      simError();
281 +    }
282 +        }else if (args_info.hullvol_given) {
283 +    analyser = new NanoVolume(info, dumpFileName, sele1);
284    }
285    
286    if (args_info.output_given) {

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