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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 956 by gezelter, Tue May 16 02:06:37 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 < #ifndef WITHOUT_FFTW  
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 77 | Line 86 | int main(int argc, char* argv[]){
86      exit(1) ;
87    }
88  
89 <
81 <  //get the dumpfile name and meta-data file name
89 >  //get the dumpfile name
90    std::string dumpFileName = args_info.input_arg;
83 –
84 –  std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
85 –
86 –    
91    std::string sele1;
92    std::string sele2;
93 +  bool userSpecifiedSelect1;
94 +  bool userSpecifiedSelect2;
95  
96 +  // check the first selection argument, or set it to the environment
97 +  // variable, or failing that, set it to "select all"
98 +
99    if (args_info.sele1_given) {
100      sele1 = args_info.sele1_arg;
101 <  }else {
102 <    char*  sele1Env= getenv("OOPSE_SELE1");
101 >  } else {
102 >    char*  sele1Env= getenv("SELECTION1");
103      if (sele1Env) {
104        sele1 = sele1Env;
105 <    }else if (!args_info.scd_given) {
106 <      sprintf( painCave.errMsg,
98 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
99 <      painCave.severity = OOPSE_ERROR;
100 <      painCave.isFatal = 1;
101 <      simError();
105 >    } else {
106 >      sele1 = "select all";
107      }
108    }
109 <    
109 >
110 >  // check the second selection argument, or set it to the environment
111 >  // variable, or failing that, set it to "select all"
112 >  
113    if (args_info.sele2_given) {
114      sele2 = args_info.sele2_arg;
115 <  }else {
116 <    char* sele2Env = getenv("OOPSE_SELE2");
115 >  } else {
116 >    char* sele2Env = getenv("SELECTION1");
117      if (sele2Env) {
118        sele2 = sele2Env;            
119 <    } else if (args_info.density_given) {
119 >    } else {
120        sele2 = "select all";
113 –    } else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
114 –      sprintf( painCave.errMsg,
115 –               "neither --sele2 option nor $OOPSE_SELE2 is set");
116 –      painCave.severity = OOPSE_ERROR;
117 –      painCave.isFatal = 1;
118 –      simError();        
121      }
122    }
123  
124 +
125 +  // Problems if sele1 wasn't specified, but
126 + // if (!args_info.scd_given) {
127 + //       sprintf( painCave.errMsg,
128 + //                "neither --sele1 option nor $SELECTION1 is set");
129 + //       painCave.severity = OPENMD_ERROR;
130 + //       painCave.isFatal = 1;
131 + //       simError();
132 + //     }
133 + //   }
134 +
135 +  // Problems if sele1 wasn't specified
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 $SELECTION1 is set");
140 + //       painCave.severity = OPENMD_ERROR;
141 + //       painCave.isFatal = 1;
142 + //       simError();        
143 + //     }
144 + //   }
145 +
146    bool batchMode;
147    if (args_info.scd_given){
148      if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
149 <        batchMode = false;
149 >      batchMode = false;
150      } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
151 <        if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
128 <            sprintf( painCave.errMsg,
129 <                     "below conditions are not satisfied:\n"
130 <                     "0 <= begin && 0<= end && begin <= end-2\n");
131 <            painCave.severity = OOPSE_ERROR;
132 <            painCave.isFatal = 1;
133 <            simError();                    
134 <        }
135 <        batchMode = true;        
136 <    } else{
151 >      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
152          sprintf( painCave.errMsg,
153 <                 "either --sele1, --sele2, --sele3 are specified,"
154 <                 " or --molname, --begin, --end are specified\n");
155 <        painCave.severity = OOPSE_ERROR;
153 >                 "below conditions are not satisfied:\n"
154 >                 "0 <= begin && 0<= end && begin <= end-2\n");
155 >        painCave.severity = OPENMD_ERROR;
156          painCave.isFatal = 1;
157 <        simError();        
157 >        simError();                    
158 >      }
159 >      batchMode = true;        
160 >    } else{
161 >      sprintf( painCave.errMsg,
162 >               "either --sele1, --sele2, --sele3 are specified,"
163 >               " or --molname, --begin, --end are specified\n");
164 >      painCave.severity = OPENMD_ERROR;
165 >      painCave.isFatal = 1;
166 >      simError();        
167      
168      }
169    }
170  
171    //parse md file and set up the system
172    SimCreator creator;
173 <  SimInfo* info = creator.createSim(mdFileName);
173 >  std::cout << "dumpFile = " << dumpFileName << "\n";
174 >  SimInfo* info = creator.createSim(dumpFileName);
175  
176 <  double maxLen;
176 >  RealType maxLen;
177    if (args_info.length_given) {
178      maxLen = args_info.length_arg;
179    } else {
# Line 158 | Line 183 | int main(int argc, char* argv[]){
183  
184    StaticAnalyser* analyser;
185    if (args_info.gofr_given){
186 <    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);        
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, args_info.nrbins_arg, args_info.nanglebins_arg);
195 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
196 >                              args_info.nbins_arg, args_info.nanglebins_arg);
197    } else if (args_info.r_omega_given) {
198 <    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
198 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
199 >                              args_info.nbins_arg, args_info.nanglebins_arg);
200    } else if (args_info.theta_omega_given) {
201 <    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
201 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
202 >                              args_info.nanglebins_arg);
203    } else if (args_info.gxyz_given) {
204      if (args_info.refsele_given) {
205 <      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);        
205 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
206 >                           maxLen, args_info.nbins_arg);        
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      }
214    } else if (args_info.p2_given) {
215 <      analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
215 >    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
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) {
220 >      analyser = new BondOrderParameter(info, dumpFileName, sele1,
221 >                                        args_info.rcut_arg,
222 >                                        args_info.nbins_arg);
223 >    } else {
224 >      sprintf( painCave.errMsg,
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,
255 <            args_info.begin_arg, args_info.end_arg);
256 <      } else{
257 <          std::string sele3 = args_info.sele3_arg;
258 <          analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
259 <      }
253 >    if (batchMode) {
254 >      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
255 >                                        args_info.begin_arg, args_info.end_arg);
256 >    } else{
257 >      std::string sele3 = args_info.sele3_arg;
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, args_info.nrbins_arg);  
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.nrbins_arg);
266 < #ifndef WITHOUT_FFTW  
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, args_info.nbins_y_arg, args_info.nrbins_arg);
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 <    
285 >  
286    if (args_info.output_given) {
287      analyser->setOutputName(args_info.output_arg);
288    }

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