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Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 980 by xsun, Thu Jun 1 18:06:33 2006 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 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/GofRAngle.hpp"
57   #include "applications/staticProps/GofAngle2.hpp"
58   #include "applications/staticProps/GofXyz.hpp"
59   #include "applications/staticProps/P2OrderParameter.hpp"
60 + #include "applications/staticProps/BondOrderParameter.hpp"
61 + #include "applications/staticProps/BOPofR.hpp"
62   #include "applications/staticProps/RippleOP.hpp"
63   #include "applications/staticProps/SCDOrderParameter.hpp"
64   #include "applications/staticProps/DensityPlot.hpp"
65   #include "applications/staticProps/RhoZ.hpp"
66 + #include "applications/staticProps/BondAngleDistribution.hpp"
67 + #include "applications/staticProps/NanoVolume.hpp"
68   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
69   #include "applications/staticProps/Hxy.hpp"
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 78 | Line 84 | int main(int argc, char* argv[]){
84      exit(1) ;
85    }
86  
87 <
82 <  //get the dumpfile name and meta-data file name
87 >  //get the dumpfile name
88    std::string dumpFileName = args_info.input_arg;
84 –
85 –  std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
86 –
87 –    
89    std::string sele1;
90    std::string sele2;
91 +  bool userSpecifiedSelect1;
92 +  bool userSpecifiedSelect2;
93  
94 +  // check the first selection argument, or set it to the environment
95 +  // variable, or failing that, set it to "select all"
96 +
97    if (args_info.sele1_given) {
98      sele1 = args_info.sele1_arg;
99 <  }else {
100 <    char*  sele1Env= getenv("OOPSE_SELE1");
99 >  } else {
100 >    char*  sele1Env= getenv("SELECTION1");
101      if (sele1Env) {
102        sele1 = sele1Env;
103 <    }else if (!args_info.scd_given) {
104 <      sprintf( painCave.errMsg,
99 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
100 <      painCave.severity = OOPSE_ERROR;
101 <      painCave.isFatal = 1;
102 <      simError();
103 >    } else {
104 >      sele1 = "select all";
105      }
106    }
107 <    
107 >
108 >  // check the second selection argument, or set it to the environment
109 >  // variable, or failing that, set it to "select all"
110 >  
111    if (args_info.sele2_given) {
112      sele2 = args_info.sele2_arg;
113 <  }else {
114 <    char* sele2Env = getenv("OOPSE_SELE2");
113 >  } else {
114 >    char* sele2Env = getenv("SELECTION1");
115      if (sele2Env) {
116        sele2 = sele2Env;            
117 <    } else if (args_info.density_given) {
117 >    } else {
118        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();        
119      }
120    }
121  
122 +
123 +  // Problems if sele1 wasn't specified, but
124 + // if (!args_info.scd_given) {
125 + //       sprintf( painCave.errMsg,
126 + //                "neither --sele1 option nor $SELECTION1 is set");
127 + //       painCave.severity = OPENMD_ERROR;
128 + //       painCave.isFatal = 1;
129 + //       simError();
130 + //     }
131 + //   }
132 +
133 +  // Problems if sele1 wasn't specified
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 $SELECTION1 is set");
138 + //       painCave.severity = OPENMD_ERROR;
139 + //       painCave.isFatal = 1;
140 + //       simError();        
141 + //     }
142 + //   }
143 +
144    bool batchMode;
145    if (args_info.scd_given){
146      if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
147 <        batchMode = false;
147 >      batchMode = false;
148      } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
149 <        if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
129 <            sprintf( painCave.errMsg,
130 <                     "below conditions are not satisfied:\n"
131 <                     "0 <= begin && 0<= end && begin <= end-2\n");
132 <            painCave.severity = OOPSE_ERROR;
133 <            painCave.isFatal = 1;
134 <            simError();                    
135 <        }
136 <        batchMode = true;        
137 <    } else{
149 >      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
150          sprintf( painCave.errMsg,
151 <                 "either --sele1, --sele2, --sele3 are specified,"
152 <                 " or --molname, --begin, --end are specified\n");
153 <        painCave.severity = OOPSE_ERROR;
151 >                 "below conditions are not satisfied:\n"
152 >                 "0 <= begin && 0<= end && begin <= end-2\n");
153 >        painCave.severity = OPENMD_ERROR;
154          painCave.isFatal = 1;
155 <        simError();        
155 >        simError();                    
156 >      }
157 >      batchMode = true;        
158 >    } else{
159 >      sprintf( painCave.errMsg,
160 >               "either --sele1, --sele2, --sele3 are specified,"
161 >               " or --molname, --begin, --end are specified\n");
162 >      painCave.severity = OPENMD_ERROR;
163 >      painCave.isFatal = 1;
164 >      simError();        
165      
166      }
167    }
168  
169    //parse md file and set up the system
170    SimCreator creator;
171 <  SimInfo* info = creator.createSim(mdFileName);
171 >  std::cout << "dumpFile = " << dumpFileName << "\n";
172 >  SimInfo* info = creator.createSim(dumpFileName);
173  
174    RealType maxLen;
175    if (args_info.length_given) {
# Line 159 | Line 181 | int main(int argc, char* argv[]){
181  
182    StaticAnalyser* analyser;
183    if (args_info.gofr_given){
184 <    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);        
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);
189    } else if (args_info.r_theta_given) {
190 <    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
190 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
191 >                              args_info.nbins_arg, args_info.nanglebins_arg);
192    } else if (args_info.r_omega_given) {
193 <    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
193 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
194 >                              args_info.nbins_arg, args_info.nanglebins_arg);
195    } else if (args_info.theta_omega_given) {
196 <    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
196 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
197 >                              args_info.nanglebins_arg);
198    } else if (args_info.gxyz_given) {
199      if (args_info.refsele_given) {
200 <      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);        
200 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
201 >                           maxLen, args_info.nbins_arg);        
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      }
209    } else if (args_info.p2_given) {
210 <      analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
211 <  }    else if (args_info.rp2_given){
212 <      analyser = new RippleOP(info, dumpFileName, sele1, sele2);
213 < }else if (args_info.scd_given) {
214 <      if (batchMode) {
215 <          analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
216 <            args_info.begin_arg, args_info.end_arg);
217 <      } else{
218 <          std::string sele3 = args_info.sele3_arg;
219 <          analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
220 <      }
210 >    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
211 >  } else if (args_info.rp2_given){
212 >    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
213 >  } else if (args_info.bo_given){
214 >    if (args_info.rcut_given) {
215 >      analyser = new BondOrderParameter(info, dumpFileName, sele1,
216 >                                        args_info.rcut_arg,
217 >                                        args_info.nbins_arg);
218 >    } else {
219 >      sprintf( painCave.errMsg,
220 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
221 >      painCave.severity = OPENMD_ERROR;
222 >      painCave.isFatal = 1;
223 >      simError();
224 >    }
225 >  } else if (args_info.bor_given){
226 >    if (args_info.rcut_given) {
227 >      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
228 >                            args_info.nbins_arg, maxLen);
229 >    } else {
230 >      sprintf( painCave.errMsg,
231 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
232 >      painCave.severity = OPENMD_ERROR;
233 >      painCave.isFatal = 1;
234 >      simError();
235 >    }
236 >  } else if (args_info.bad_given){
237 >    if (args_info.rcut_given) {
238 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1, 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 Angle Distributions");
243 >      painCave.severity = OPENMD_ERROR;
244 >      painCave.isFatal = 1;
245 >      simError();
246 >    }
247 >  } else if (args_info.scd_given) {
248 >    if (batchMode) {
249 >      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
250 >                                        args_info.begin_arg, args_info.end_arg);
251 >    } else{
252 >      std::string sele3 = args_info.sele3_arg;
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, args_info.nrbins_arg);  
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();
195 <      analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_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, args_info.nbins_y_arg, args_info.nrbins_arg);
262 >    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
263 >                       args_info.nbins_y_arg, args_info.nbins_arg);
264   #endif
265 +  }else if (args_info.rho_r_given) {
266 +    if (args_info.radius_given){
267 +      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
268 +    }else{
269 +      sprintf( painCave.errMsg,
270 +               "A particle radius (radius) must be specified when calculating Rho(r)");
271 +      painCave.severity = OPENMD_ERROR;
272 +      painCave.isFatal = 1;
273 +      simError();
274 +    }
275 +        }else if (args_info.hullvol_given) {
276 +    analyser = new NanoVolume(info, dumpFileName, sele1);
277    }
278 <    
278 >  
279    if (args_info.output_given) {
280      analyser->setOutputName(args_info.output_arg);
281    }

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