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 |
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/SCDOrderParameter.hpp" |
60 |
+ |
#include "applications/staticProps/DensityPlot.hpp" |
61 |
+ |
#include "applications/staticProps/RhoZ.hpp" |
62 |
+ |
|
63 |
|
using namespace oopse; |
64 |
|
|
65 |
|
int main(int argc, char* argv[]){ |
66 |
|
|
67 |
< |
//register force fields |
68 |
< |
registerForceFields(); |
67 |
> |
//register force fields |
68 |
> |
registerForceFields(); |
69 |
|
|
70 |
< |
gengetopt_args_info args_info; |
70 |
> |
gengetopt_args_info args_info; |
71 |
|
|
72 |
< |
//parse the command line option |
73 |
< |
if (cmdline_parser (argc, argv, &args_info) != 0) { |
74 |
< |
exit(1) ; |
75 |
< |
} |
72 |
> |
//parse the command line option |
73 |
> |
if (cmdline_parser (argc, argv, &args_info) != 0) { |
74 |
> |
exit(1) ; |
75 |
> |
} |
76 |
|
|
77 |
|
|
78 |
< |
//get the dumpfile name and meta-data file name |
79 |
< |
std::string dumpFileName = args_info.input_arg; |
78 |
> |
//get the dumpfile name and meta-data file name |
79 |
> |
std::string dumpFileName = args_info.input_arg; |
80 |
|
|
81 |
< |
std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md"; |
81 |
> |
std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md"; |
82 |
|
|
83 |
|
|
84 |
< |
//parse md file and set up the system |
85 |
< |
SimCreator creator; |
76 |
< |
SimInfo* info = creator.createSim(mdFileName, false); |
84 |
> |
std::string sele1; |
85 |
> |
std::string sele2; |
86 |
|
|
87 |
+ |
if (args_info.sele1_given) { |
88 |
+ |
sele1 = args_info.sele1_arg; |
89 |
+ |
}else { |
90 |
+ |
char* sele1Env= getenv("OOPSE_SELE1"); |
91 |
+ |
if (sele1Env) { |
92 |
+ |
sele1 = sele1Env; |
93 |
+ |
}else if (!args_info.scd_given) { |
94 |
+ |
sprintf( painCave.errMsg, |
95 |
+ |
"neither --sele1 option nor $OOPSE_SELE1 is set"); |
96 |
+ |
painCave.severity = OOPSE_ERROR; |
97 |
+ |
painCave.isFatal = 1; |
98 |
+ |
simError(); |
99 |
+ |
} |
100 |
+ |
} |
101 |
+ |
|
102 |
+ |
if (args_info.sele2_given) { |
103 |
+ |
sele2 = args_info.sele2_arg; |
104 |
+ |
}else { |
105 |
+ |
char* sele2Env = getenv("OOPSE_SELE2"); |
106 |
+ |
if (sele2Env) { |
107 |
+ |
sele2 = sele2Env; |
108 |
+ |
} else if (args_info.density_given) { |
109 |
+ |
sele2 = "select all"; |
110 |
+ |
} else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) { |
111 |
+ |
sprintf( painCave.errMsg, |
112 |
+ |
"neither --sele2 option nor $OOPSE_SELE2 is set"); |
113 |
+ |
painCave.severity = OOPSE_ERROR; |
114 |
+ |
painCave.isFatal = 1; |
115 |
+ |
simError(); |
116 |
+ |
} |
117 |
+ |
} |
118 |
|
|
119 |
< |
std::string sele1; |
120 |
< |
std::string sele2; |
119 |
> |
bool batchMode; |
120 |
> |
if (args_info.scd_given){ |
121 |
> |
if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) { |
122 |
> |
batchMode = false; |
123 |
> |
} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) { |
124 |
> |
if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) { |
125 |
> |
sprintf( painCave.errMsg, |
126 |
> |
"below conditions are not satisfied:\n" |
127 |
> |
"0 <= begin && 0<= end && begin <= end-2\n"); |
128 |
> |
painCave.severity = OOPSE_ERROR; |
129 |
> |
painCave.isFatal = 1; |
130 |
> |
simError(); |
131 |
> |
} |
132 |
> |
batchMode = true; |
133 |
> |
} else{ |
134 |
> |
sprintf( painCave.errMsg, |
135 |
> |
"either --sele1, --sele2, --sele3 are specified," |
136 |
> |
" or --molname, --begin, --end are specified\n"); |
137 |
> |
painCave.severity = OOPSE_ERROR; |
138 |
> |
painCave.isFatal = 1; |
139 |
> |
simError(); |
140 |
> |
|
141 |
> |
} |
142 |
> |
} |
143 |
|
|
144 |
< |
if (args_info.sele1_given) { |
145 |
< |
sele1 = args_info.sele1_arg; |
146 |
< |
}else { |
144 |
> |
//parse md file and set up the system |
145 |
> |
SimCreator creator; |
146 |
> |
SimInfo* info = creator.createSim(mdFileName); |
147 |
|
|
148 |
< |
} |
149 |
< |
if (args_info.sele1_given) { |
150 |
< |
sele1 = args_info.sele1_arg; |
151 |
< |
}else { |
148 |
> |
double maxLen; |
149 |
> |
if (args_info.length_given) { |
150 |
> |
maxLen = args_info.length_arg; |
151 |
> |
} else { |
152 |
> |
Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
153 |
> |
maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; |
154 |
> |
} |
155 |
|
|
156 |
+ |
StaticAnalyser* analyser; |
157 |
+ |
if (args_info.gofr_given){ |
158 |
+ |
analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); |
159 |
+ |
} else if (args_info.r_theta_given) { |
160 |
+ |
analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
161 |
+ |
} else if (args_info.r_omega_given) { |
162 |
+ |
analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
163 |
+ |
} else if (args_info.theta_omega_given) { |
164 |
+ |
analyser = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg); |
165 |
+ |
} else if (args_info.gxyz_given) { |
166 |
+ |
if (args_info.refsele_given) { |
167 |
+ |
analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg); |
168 |
+ |
} else { |
169 |
+ |
sprintf( painCave.errMsg, |
170 |
+ |
"--refsele must set when --gxyz is used"); |
171 |
+ |
painCave.severity = OOPSE_ERROR; |
172 |
+ |
painCave.isFatal = 1; |
173 |
+ |
simError(); |
174 |
|
} |
175 |
+ |
} else if (args_info.p2_given) { |
176 |
+ |
analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
177 |
+ |
} else if (args_info.scd_given) { |
178 |
+ |
if (batchMode) { |
179 |
+ |
analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg, |
180 |
+ |
args_info.begin_arg, args_info.end_arg); |
181 |
+ |
} else{ |
182 |
+ |
std::string sele3 = args_info.sele3_arg; |
183 |
+ |
analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3); |
184 |
+ |
} |
185 |
+ |
}else if (args_info.density_given) { |
186 |
+ |
analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); |
187 |
+ |
} else if (args_info.slab_density_given) { |
188 |
+ |
Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
189 |
+ |
analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg); |
190 |
+ |
} |
191 |
|
|
192 |
< |
GofR rdf(info, dumpFileName, sele1, sele2, args_info.length_arg); |
192 |
> |
if (args_info.output_given) { |
193 |
> |
analyser->setOutputName(args_info.output_arg); |
194 |
> |
} |
195 |
> |
if (args_info.step_given) { |
196 |
> |
analyser->setStep(args_info.step_arg); |
197 |
> |
} |
198 |
|
|
199 |
< |
if (args_info.nbins_given) { |
96 |
< |
rdf.setNBins(args_info.nbins_arg); |
97 |
< |
} |
199 |
> |
analyser->process(); |
200 |
|
|
201 |
< |
rdf.process(); |
202 |
< |
|
101 |
< |
delete info; |
201 |
> |
delete analyser; |
202 |
> |
delete info; |
203 |
|
|
204 |
< |
return 0; |
204 |
> |
return 0; |
205 |
|
} |
206 |
|
|