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root/OpenMD/trunk/src/applications/staticProps/StaticProps.cpp
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Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 310 by tim, Thu Feb 10 18:14:03 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# 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>
43   #include <fstream>
44   #include <string>
45  
46 – #include "applications/staticProps/StaticPropsCmd.h"
46   #include "brains/Register.hpp"
47   #include "brains/SimCreator.hpp"
48   #include "brains/SimInfo.hpp"
49   #include "io/DumpReader.hpp"
50   #include "utils/simError.h"
51  
52 < using namespace oopse;
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 OpenMD;
74 +
75   int main(int argc, char* argv[]){
76    
77 <    //register force fields
78 <    registerForceFields();
77 >  //register force fields
78 >  registerForceFields();
79  
80 <    gengetopt_args_info args_info;
80 >  gengetopt_args_info args_info;
81  
82 <    //parse the command line option
83 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
84 <        exit(1) ;
85 <    }
82 >  //parse the command line option
83 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
84 >    exit(1) ;
85 >  }
86  
87 +  //get the dumpfile name
88 +  std::string dumpFileName = args_info.input_arg;
89 +  std::string sele1;
90 +  std::string sele2;
91 +  bool userSpecifiedSelect1;
92 +  bool userSpecifiedSelect2;
93  
94 <    //get the dumpfile name and meta-data file name
95 <    std::string dumpFileName = args_info.input_arg;
94 >  // check the first selection argument, or set it to the environment
95 >  // variable, or failing that, set it to "select all"
96  
97 <    std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
97 >  if (args_info.sele1_given) {
98 >    sele1 = args_info.sele1_arg;
99 >  } else {
100 >    char*  sele1Env= getenv("SELECTION1");
101 >    if (sele1Env) {
102 >      sele1 = sele1Env;
103 >    } else {
104 >      sele1 = "select all";
105 >    }
106 >  }
107  
108 <    
109 <    //parse md file and set up the system
110 <    SimCreator creator;
111 <    SimInfo* info = creator.createSim(mdFileName, false);
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("SELECTION1");
115 >    if (sele2Env) {
116 >      sele2 = sele2Env;            
117 >    } else {
118 >      sele2 = "select all";
119 >    }
120 >  }
121  
122  
123 <    std::string sele1;
124 <    std::string sele2;
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 <    if (args_info.sele1_given) {
83 <        sele1 = args_info.sele1_arg;
84 <    }else {
133 >  // Problems if sele1 wasn't specified
134  
135 <    }
136 <    if (args_info.sele1_given) {
137 <        sele1 = args_info.sele1_arg;
138 <    }else {
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 <    }
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;
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) {
150 >        sprintf( painCave.errMsg,
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();                    
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 <    GofR rdf(info, dumpFileName, sele1, sele2, args_info.length_arg);
166 >    }
167 >  }
168  
169 <    if (args_info.nbins_given) {
170 <        rdf.setNBins(args_info.nbins_arg);
169 >  //parse md file and set up the system
170 >  SimCreator creator;
171 >  std::cout << "dumpFile = " << dumpFileName << "\n";
172 >  SimInfo* info = creator.createSim(dumpFileName);
173 >
174 >  RealType maxLen;
175 >  if (args_info.length_given) {
176 >    maxLen = args_info.length_arg;
177 >  } else {
178 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
179 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
180 >  }    
181 >
182 >  StaticAnalyser* analyser;
183 >  if (args_info.gofr_given){
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,
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,
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,
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,
201 >                           maxLen, args_info.nbins_arg);        
202 >    } else {
203 >      sprintf( painCave.errMsg,
204 >               "--refsele must set when --gxyz is used");
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.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,
257 +                              args_info.nbins_arg);  
258 +  } else if (args_info.slab_density_given) {
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,
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 +  
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 +  }
285  
286 <    rdf.process();
100 <    
101 <    delete info;
286 >  analyser->process();
287  
288 <    return 0;  
288 >  delete analyser;    
289 >  delete info;
290 >
291 >  return 0;  
292   }
293  

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