| 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); |
| 156 |
< |
rAngle2->setNAngleBins(args_info.nanglebins_arg); |
| 157 |
< |
|
| 158 |
< |
rdf = rAngle2; |
| 132 |
> |
rdf = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg); |
| 133 |
|
} else if (args_info.xyz_given) { |
| 134 |
< |
|
| 161 |
< |
GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2); |
| 162 |
< |
|
| 163 |
< |
xyz->setNRBins(args_info.nrbins_arg); |
| 164 |
< |
xyz->setLength(maxLen); |
| 165 |
< |
|
| 166 |
< |
|
| 167 |
< |
rdf = xyz; |
| 134 |
> |
rdf= new GofXyz(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); |
| 135 |
|
} |
| 136 |
|
|
| 170 |
– |
|
| 137 |
|
if (args_info.output_given) { |
| 138 |
|
rdf->setOutputName(args_info.output_arg); |
| 139 |
|
} |
| 174 |
– |
|
| 140 |
|
if (args_info.step_given) { |
| 141 |
|
rdf->setStep(args_info.step_arg); |
| 142 |
|
} |
