# | Line 1 | Line 1 | |
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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 43 | Line 43 | |
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 | + | #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/BOPofR.hpp" |
61 | + | #include "applications/staticProps/RippleOP.hpp" |
62 | + | #include "applications/staticProps/SCDOrderParameter.hpp" |
63 | + | #include "applications/staticProps/DensityPlot.hpp" |
64 | + | #include "applications/staticProps/RhoZ.hpp" |
65 | + | #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
66 | + | #include "applications/staticProps/Hxy.hpp" |
67 | + | #endif |
68 | + | #include "applications/staticProps/RhoR.hpp" |
69 | + | |
70 | using namespace oopse; | |
71 | ||
72 | int main(int argc, char* argv[]){ | |
73 | ||
74 | < | //register force fields |
75 | < | registerForceFields(); |
74 | > | //register force fields |
75 | > | registerForceFields(); |
76 | ||
77 | < | gengetopt_args_info args_info; |
77 | > | gengetopt_args_info args_info; |
78 | ||
79 | < | //parse the command line option |
80 | < | if (cmdline_parser (argc, argv, &args_info) != 0) { |
81 | < | exit(1) ; |
82 | < | } |
79 | > | //parse the command line option |
80 | > | if (cmdline_parser (argc, argv, &args_info) != 0) { |
81 | > | exit(1) ; |
82 | > | } |
83 | ||
84 | + | //get the dumpfile name |
85 | + | std::string dumpFileName = args_info.input_arg; |
86 | + | std::string sele1; |
87 | + | std::string sele2; |
88 | + | bool userSpecifiedSelect1; |
89 | + | bool userSpecifiedSelect2; |
90 | ||
91 | < | //get the dumpfile name and meta-data file name |
92 | < | std::string dumpFileName = args_info.input_arg; |
91 | > | // check the first selection argument, or set it to the environment |
92 | > | // variable, or failing that, set it to "select all" |
93 | ||
94 | < | std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md"; |
94 | > | if (args_info.sele1_given) { |
95 | > | sele1 = args_info.sele1_arg; |
96 | > | } else { |
97 | > | char* sele1Env= getenv("OOPSE_SELE1"); |
98 | > | if (sele1Env) { |
99 | > | sele1 = sele1Env; |
100 | > | } else { |
101 | > | sele1 = "select all"; |
102 | > | } |
103 | > | } |
104 | ||
105 | < | |
106 | < | //parse md file and set up the system |
107 | < | SimCreator creator; |
108 | < | SimInfo* info = creator.createSim(mdFileName, false); |
105 | > | // check the second selection argument, or set it to the environment |
106 | > | // variable, or failing that, set it to "select all" |
107 | > | |
108 | > | if (args_info.sele2_given) { |
109 | > | sele2 = args_info.sele2_arg; |
110 | > | } else { |
111 | > | char* sele2Env = getenv("OOPSE_SELE2"); |
112 | > | if (sele2Env) { |
113 | > | sele2 = sele2Env; |
114 | > | } else { |
115 | > | sele2 = "select all"; |
116 | > | } |
117 | > | } |
118 | ||
119 | ||
120 | < | std::string sele1; |
121 | < | std::string sele2; |
120 | > | // Problems if sele1 wasn't specified, but |
121 | > | // if (!args_info.scd_given) { |
122 | > | // sprintf( painCave.errMsg, |
123 | > | // "neither --sele1 option nor $OOPSE_SELE1 is set"); |
124 | > | // painCave.severity = OOPSE_ERROR; |
125 | > | // painCave.isFatal = 1; |
126 | > | // simError(); |
127 | > | // } |
128 | > | // } |
129 | ||
130 | < | if (args_info.sele1_given) { |
83 | < | sele1 = args_info.sele1_arg; |
84 | < | }else { |
130 | > | // Problems if sele1 wasn't specified |
131 | ||
132 | < | } |
133 | < | if (args_info.sele1_given) { |
134 | < | sele1 = args_info.sele1_arg; |
135 | < | }else { |
132 | > | // if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) { |
133 | > | // sprintf( painCave.errMsg, |
134 | > | // "neither --sele2 option nor $OOPSE_SELE2 is set"); |
135 | > | // painCave.severity = OOPSE_ERROR; |
136 | > | // painCave.isFatal = 1; |
137 | > | // simError(); |
138 | > | // } |
139 | > | // } |
140 | ||
141 | < | } |
141 | > | bool batchMode; |
142 | > | if (args_info.scd_given){ |
143 | > | if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) { |
144 | > | batchMode = false; |
145 | > | } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) { |
146 | > | if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) { |
147 | > | sprintf( painCave.errMsg, |
148 | > | "below conditions are not satisfied:\n" |
149 | > | "0 <= begin && 0<= end && begin <= end-2\n"); |
150 | > | painCave.severity = OOPSE_ERROR; |
151 | > | painCave.isFatal = 1; |
152 | > | simError(); |
153 | > | } |
154 | > | batchMode = true; |
155 | > | } else{ |
156 | > | sprintf( painCave.errMsg, |
157 | > | "either --sele1, --sele2, --sele3 are specified," |
158 | > | " or --molname, --begin, --end are specified\n"); |
159 | > | painCave.severity = OOPSE_ERROR; |
160 | > | painCave.isFatal = 1; |
161 | > | simError(); |
162 | ||
163 | < | GofR rdf(info, dumpFileName, sele1, sele2, args_info.length_arg); |
163 | > | } |
164 | > | } |
165 | ||
166 | < | if (args_info.nbins_given) { |
167 | < | rdf.setNBins(args_info.nbins_arg); |
166 | > | //parse md file and set up the system |
167 | > | SimCreator creator; |
168 | > | std::cout << "dumpFile = " << dumpFileName << "\n"; |
169 | > | SimInfo* info = creator.createSim(dumpFileName); |
170 | > | |
171 | > | RealType maxLen; |
172 | > | if (args_info.length_given) { |
173 | > | maxLen = args_info.length_arg; |
174 | > | } else { |
175 | > | Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
176 | > | maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; |
177 | > | } |
178 | > | |
179 | > | StaticAnalyser* analyser; |
180 | > | if (args_info.gofr_given){ |
181 | > | analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, |
182 | > | args_info.nbins_arg); |
183 | > | } else if (args_info.r_theta_given) { |
184 | > | analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, |
185 | > | args_info.nbins_arg, args_info.nanglebins_arg); |
186 | > | } else if (args_info.r_omega_given) { |
187 | > | analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, |
188 | > | args_info.nbins_arg, args_info.nanglebins_arg); |
189 | > | } else if (args_info.theta_omega_given) { |
190 | > | analyser = new GofAngle2(info, dumpFileName, sele1, sele2, |
191 | > | args_info.nanglebins_arg); |
192 | > | } else if (args_info.gxyz_given) { |
193 | > | if (args_info.refsele_given) { |
194 | > | analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, |
195 | > | maxLen, args_info.nbins_arg); |
196 | > | } else { |
197 | > | sprintf( painCave.errMsg, |
198 | > | "--refsele must set when --gxyz is used"); |
199 | > | painCave.severity = OOPSE_ERROR; |
200 | > | painCave.isFatal = 1; |
201 | > | simError(); |
202 | } | |
203 | + | } else if (args_info.p2_given) { |
204 | + | analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
205 | + | } else if (args_info.rp2_given){ |
206 | + | analyser = new RippleOP(info, dumpFileName, sele1, sele2); |
207 | + | } else if (args_info.bo_given){ |
208 | + | if (args_info.rcut_given) { |
209 | + | analyser = new BondOrderParameter(info, dumpFileName, sele1, |
210 | + | args_info.rcut_arg, |
211 | + | args_info.nbins_arg); |
212 | + | } else { |
213 | + | sprintf( painCave.errMsg, |
214 | + | "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
215 | + | painCave.severity = OOPSE_ERROR; |
216 | + | painCave.isFatal = 1; |
217 | + | simError(); |
218 | + | } |
219 | + | } else if (args_info.bor_given){ |
220 | + | if (args_info.rcut_given) { |
221 | + | analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg, |
222 | + | args_info.nbins_arg, maxLen); |
223 | + | } else { |
224 | + | sprintf( painCave.errMsg, |
225 | + | "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
226 | + | painCave.severity = OOPSE_ERROR; |
227 | + | painCave.isFatal = 1; |
228 | + | simError(); |
229 | + | } |
230 | + | } else if (args_info.scd_given) { |
231 | + | if (batchMode) { |
232 | + | analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg, |
233 | + | args_info.begin_arg, args_info.end_arg); |
234 | + | } else{ |
235 | + | std::string sele3 = args_info.sele3_arg; |
236 | + | analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3); |
237 | + | } |
238 | + | }else if (args_info.density_given) { |
239 | + | analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, |
240 | + | args_info.nbins_arg); |
241 | + | } else if (args_info.slab_density_given) { |
242 | + | Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
243 | + | analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg); |
244 | + | #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
245 | + | }else if (args_info.hxy_given) { |
246 | + | analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, |
247 | + | args_info.nbins_y_arg, args_info.nbins_arg); |
248 | + | #endif |
249 | + | }else if (args_info.rho_r_given) { |
250 | + | if (args_info.radius_given){ |
251 | + | analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg); |
252 | + | }else{ |
253 | + | sprintf( painCave.errMsg, |
254 | + | "A particle radius (radius) must be specified when calculating Rho(r)"); |
255 | + | painCave.severity = OOPSE_ERROR; |
256 | + | painCave.isFatal = 1; |
257 | + | simError(); |
258 | + | } |
259 | + | } |
260 | + | |
261 | + | if (args_info.output_given) { |
262 | + | analyser->setOutputName(args_info.output_arg); |
263 | + | } |
264 | + | if (args_info.step_given) { |
265 | + | analyser->setStep(args_info.step_arg); |
266 | + | } |
267 | ||
268 | < | rdf.process(); |
100 | < | |
101 | < | delete info; |
268 | > | analyser->process(); |
269 | ||
270 | < | return 0; |
270 | > | delete analyser; |
271 | > | delete info; |
272 | > | |
273 | > | return 0; |
274 | } | |
275 |
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