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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 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 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 50 | Line 50
50   #include "utils/simError.h"
51  
52   #include "applications/staticProps/StaticPropsCmd.h"
53 + #include "applications/staticProps/StaticAnalyser.hpp"
54   #include "applications/staticProps/GofR.hpp"
55   #include "applications/staticProps/GofRAngle.hpp"
56   #include "applications/staticProps/GofAngle2.hpp"
57   #include "applications/staticProps/GofXyz.hpp"
58 + #include "applications/staticProps/P2OrderParameter.hpp"
59 + #include "applications/staticProps/BondOrderParameter.hpp"
60 + #include "applications/staticProps/RippleOP.hpp"
61 + #include "applications/staticProps/SCDOrderParameter.hpp"
62 + #include "applications/staticProps/DensityPlot.hpp"
63 + #include "applications/staticProps/RhoZ.hpp"
64 + #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
65 + #include "applications/staticProps/Hxy.hpp"
66 + #endif
67  
68   using namespace oopse;
69  
70   int main(int argc, char* argv[]){
71    
72 <    //register force fields
73 <    registerForceFields();
72 >  //register force fields
73 >  registerForceFields();
74  
75 <    gengetopt_args_info args_info;
75 >  gengetopt_args_info args_info;
76  
77 <    //parse the command line option
78 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
79 <        exit(1) ;
80 <    }
77 >  //parse the command line option
78 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
79 >    exit(1) ;
80 >  }
81  
82 +  //get the dumpfile name
83 +  std::string dumpFileName = args_info.input_arg;
84 +  std::string sele1;
85 +  std::string sele2;
86 +  bool userSpecifiedSelect1;
87 +  bool userSpecifiedSelect2;
88  
89 <    //get the dumpfile name and meta-data file name
90 <    std::string dumpFileName = args_info.input_arg;
89 >  // check the first selection argument, or set it to the environment
90 >  // variable, or failing that, set it to "select all"
91  
92 <    std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
93 <
94 <    
95 <    std::string sele1;
96 <    std::string sele2;
97 <
82 <    if (args_info.sele1_given) {
83 <        sele1 = args_info.sele1_arg;
84 <    }else {
85 <        char*  sele1Env= getenv("OOPSE_SELE1");
86 <        if (sele1Env) {
87 <            sele1 = sele1Env;
88 <        }else {
89 <            sprintf( painCave.errMsg,
90 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
91 <            painCave.severity = OOPSE_ERROR;
92 <            painCave.isFatal = 1;
93 <            simError();
94 <        }
95 <    }
96 <    
97 <    if (args_info.sele2_given) {
98 <        sele2 = args_info.sele2_arg;
99 <    }else {
100 <        char* sele2Env = getenv("OOPSE_SELE2");
101 <        if (sele2Env) {
102 <            sele2 = sele2Env;            
103 <        } else {
104 <            sprintf( painCave.errMsg,
105 <               "neither --sele2 option nor $OOPSE_SELE2 is set");
106 <            painCave.severity = OOPSE_ERROR;
107 <            painCave.isFatal = 1;
108 <            simError();        
109 <        }
110 <    }
111 <
112 <    //parse md file and set up the system
113 <    SimCreator creator;
114 <    SimInfo* info = creator.createSim(mdFileName, false);
115 <
116 <    double maxLen;
117 <    if (args_info.length_given) {
118 <        maxLen = args_info.length_arg;
92 >  if (args_info.sele1_given) {
93 >    sele1 = args_info.sele1_arg;
94 >  } else {
95 >    char*  sele1Env= getenv("OOPSE_SELE1");
96 >    if (sele1Env) {
97 >      sele1 = sele1Env;
98      } else {
99 <        double rcut;
121 <        double rsw;
122 <        info->getCutoff(rcut, rsw);
123 <        maxLen = rcut + rsw;        
99 >      sele1 = "select all";
100      }
101 <    
101 >  }
102  
103 <    RadialDistrFunc* rdf;
104 <    if (args_info.gofr_given){
105 <        GofR* r = new GofR(info, dumpFileName, sele1, sele2);
106 <        
107 <        r->setNRBins(args_info.nrbins_arg);            
108 <        r->setLength(maxLen);
109 <        
110 <        rdf = r;
111 <    } else if (args_info.r_theta_given) {
112 <        GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2);
113 <          
138 <        rTheta->setNRBins(args_info.nrbins_arg);            
139 <        rTheta->setLength(maxLen);      
140 <        rTheta->setNAngleBins(args_info.nanglebins_arg);
141 <
142 <        
143 <        rdf = rTheta;
103 >  // check the second selection argument, or set it to the environment
104 >  // variable, or failing that, set it to "select all"
105 >  
106 >  if (args_info.sele2_given) {
107 >    sele2 = args_info.sele2_arg;
108 >  } else {
109 >    char* sele2Env = getenv("OOPSE_SELE2");
110 >    if (sele2Env) {
111 >      sele2 = sele2Env;            
112 >    } else {
113 >      sele2 = "select all";
114      }
115 <    else if (args_info.r_omega_given) {
146 <        GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2);
115 >  }
116  
148 –      
149 –        rOmega->setNRBins(args_info.nrbins_arg);            
150 –        rOmega->setLength(maxLen);
151 –        rOmega->setNAngleBins(args_info.nanglebins_arg);
117  
118 <        rdf = rOmega;    
119 <    } else if (args_info.theta_omega_given) {
120 <        GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2);
121 <        rAngle2->setNAngleBins(args_info.nanglebins_arg);
118 >  // Problems if sele1 wasn't specified, but
119 > // if (!args_info.scd_given) {
120 > //       sprintf( painCave.errMsg,
121 > //                "neither --sele1 option nor $OOPSE_SELE1 is set");
122 > //       painCave.severity = OOPSE_ERROR;
123 > //       painCave.isFatal = 1;
124 > //       simError();
125 > //     }
126 > //   }
127  
128 <        rdf = rAngle2;  
159 <    } else if (args_info.xyz_given) {
128 >  // Problems if sele1 wasn't specified
129  
130 <        GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2);
131 <          
132 <        xyz->setNRBins(args_info.nrbins_arg);            
133 <        xyz->setLength(maxLen);
130 > //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
131 > //       sprintf( painCave.errMsg,
132 > //                "neither --sele2 option nor $OOPSE_SELE2 is set");
133 > //       painCave.severity = OOPSE_ERROR;
134 > //       painCave.isFatal = 1;
135 > //       simError();        
136 > //     }
137 > //   }
138  
139 <        
140 <        rdf = xyz;
141 <    }
139 >  bool batchMode;
140 >  if (args_info.scd_given){
141 >    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
142 >      batchMode = false;
143 >    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
144 >      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
145 >        sprintf( painCave.errMsg,
146 >                 "below conditions are not satisfied:\n"
147 >                 "0 <= begin && 0<= end && begin <= end-2\n");
148 >        painCave.severity = OOPSE_ERROR;
149 >        painCave.isFatal = 1;
150 >        simError();                    
151 >      }
152 >      batchMode = true;        
153 >    } else{
154 >      sprintf( painCave.errMsg,
155 >               "either --sele1, --sele2, --sele3 are specified,"
156 >               " or --molname, --begin, --end are specified\n");
157 >      painCave.severity = OOPSE_ERROR;
158 >      painCave.isFatal = 1;
159 >      simError();        
160      
170 –
171 –    if (args_info.output_given) {
172 –        rdf->setOutputName(args_info.output_arg);
161      }
162 +  }
163  
164 <    if (args_info.step_given) {
165 <        rdf->setStep(args_info.step_arg);
164 >  //parse md file and set up the system
165 >  SimCreator creator;
166 >  SimInfo* info = creator.createSim(dumpFileName);
167 >
168 >  RealType maxLen;
169 >  if (args_info.length_given) {
170 >    maxLen = args_info.length_arg;
171 >  } else {
172 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
173 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
174 >  }    
175 >
176 >  StaticAnalyser* analyser;
177 >  if (args_info.gofr_given){
178 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);        
179 >  } else if (args_info.r_theta_given) {
180 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
181 >  } else if (args_info.r_omega_given) {
182 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
183 >  } else if (args_info.theta_omega_given) {
184 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
185 >  } else if (args_info.gxyz_given) {
186 >    if (args_info.refsele_given) {
187 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);        
188 >    } else {
189 >      sprintf( painCave.errMsg,
190 >               "--refsele must set when --gxyz is used");
191 >      painCave.severity = OOPSE_ERROR;
192 >      painCave.isFatal = 1;
193 >      simError();  
194      }
195 +  } else if (args_info.p2_given) {
196 +    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
197 +  } else if (args_info.rp2_given){
198 +    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
199 +  } else if (args_info.bo_given){
200 +    if (args_info.rcut_given && args_info.LegendreL_given) {
201 +      analyser = new BondOrderParameter(info, dumpFileName, sele1,
202 +                                        args_info.rcut_arg,
203 +                                        args_info.LegendreL_arg);
204 +    } else {
205 +      sprintf( painCave.errMsg,
206 +               "Both the cutoff radius (rcut) and LegendreL must be specified when calculating Bond Order Parameters");
207 +      painCave.severity = OOPSE_ERROR;
208 +      painCave.isFatal = 1;
209 +      simError();
210 +    }
211 +  } else if (args_info.scd_given) {
212 +    if (batchMode) {
213 +      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
214 +                                        args_info.begin_arg, args_info.end_arg);
215 +    } else{
216 +      std::string sele3 = args_info.sele3_arg;
217 +      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
218 +    }
219 +  }else if (args_info.density_given) {
220 +    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);  
221 +  } else if (args_info.slab_density_given) {
222 +    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
223 +    analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg);
224 + #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
225 +  }else if (args_info.hxy_given) {
226 +    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
227 + #endif
228 +  }
229 +  
230 +  if (args_info.output_given) {
231 +    analyser->setOutputName(args_info.output_arg);
232 +  }
233 +  if (args_info.step_given) {
234 +    analyser->setStep(args_info.step_arg);
235 +  }
236  
237 <    rdf->process();
237 >  analyser->process();
238  
239 <    delete rdf;    
240 <    delete info;
239 >  delete analyser;    
240 >  delete info;
241  
242 <    return 0;  
242 >  return 0;  
243   }
244  

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