111 |
|
|
112 |
|
//parse md file and set up the system |
113 |
|
SimCreator creator; |
114 |
< |
SimInfo* info = creator.createSim(mdFileName, false); |
114 |
> |
SimInfo* info = creator.createSim(mdFileName); |
115 |
|
|
116 |
|
double maxLen; |
117 |
|
if (args_info.length_given) { |
118 |
|
maxLen = args_info.length_arg; |
119 |
|
} else { |
120 |
< |
double rcut; |
121 |
< |
double rsw; |
122 |
< |
info->getCutoff(rcut, rsw); |
123 |
< |
maxLen = rcut + rsw; |
124 |
< |
} |
125 |
< |
|
120 |
> |
Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
121 |
> |
maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; |
122 |
> |
} |
123 |
|
|
124 |
|
RadialDistrFunc* rdf; |
125 |
|
if (args_info.gofr_given){ |
126 |
< |
GofR* r = new GofR(info, dumpFileName, sele1, sele2); |
130 |
< |
|
131 |
< |
r->setNRBins(args_info.nrbins_arg); |
132 |
< |
r->setLength(maxLen); |
133 |
< |
|
134 |
< |
rdf = r; |
126 |
> |
rdf= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); |
127 |
|
} else if (args_info.r_theta_given) { |
128 |
< |
GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2); |
129 |
< |
|
130 |
< |
rTheta->setNRBins(args_info.nrbins_arg); |
139 |
< |
rTheta->setLength(maxLen); |
140 |
< |
rTheta->setNAngleBins(args_info.nanglebins_arg); |
141 |
< |
|
142 |
< |
|
143 |
< |
rdf = rTheta; |
144 |
< |
} |
145 |
< |
else if (args_info.r_omega_given) { |
146 |
< |
GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2); |
147 |
< |
|
148 |
< |
|
149 |
< |
rOmega->setNRBins(args_info.nrbins_arg); |
150 |
< |
rOmega->setLength(maxLen); |
151 |
< |
rOmega->setNAngleBins(args_info.nanglebins_arg); |
152 |
< |
|
153 |
< |
rdf = rOmega; |
128 |
> |
rdf = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
129 |
> |
} else if (args_info.r_omega_given) { |
130 |
> |
rdf = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
131 |
|
} else if (args_info.theta_omega_given) { |
132 |
< |
GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2); |
133 |
< |
rAngle2->setNAngleBins(args_info.nanglebins_arg); |
134 |
< |
|
135 |
< |
rdf = rAngle2; |
136 |
< |
} else if (args_info.xyz_given) { |
137 |
< |
|
138 |
< |
GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2); |
139 |
< |
|
140 |
< |
xyz->setNRBins(args_info.nrbins_arg); |
141 |
< |
xyz->setLength(maxLen); |
142 |
< |
|
166 |
< |
|
167 |
< |
rdf = xyz; |
132 |
> |
rdf = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg); |
133 |
> |
} else if (args_info.gxyz_given) { |
134 |
> |
if (args_info.refsele_given) { |
135 |
> |
rdf= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg); |
136 |
> |
} else { |
137 |
> |
sprintf( painCave.errMsg, |
138 |
> |
"--refsele must set when --gxyz is used"); |
139 |
> |
painCave.severity = OOPSE_ERROR; |
140 |
> |
painCave.isFatal = 1; |
141 |
> |
simError(); |
142 |
> |
} |
143 |
|
} |
144 |
|
|
170 |
– |
|
145 |
|
if (args_info.output_given) { |
146 |
|
rdf->setOutputName(args_info.output_arg); |
147 |
|
} |
174 |
– |
|
148 |
|
if (args_info.step_given) { |
149 |
|
rdf->setStep(args_info.step_arg); |
150 |
|
} |