| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 77 |
|
#include "applications/staticProps/AngleR.hpp" |
| 78 |
|
#include "applications/staticProps/TetrahedralityParam.hpp" |
| 79 |
|
#include "applications/staticProps/TetrahedralityParamZ.hpp" |
| 80 |
+ |
#include "applications/staticProps/RNEMDStats.hpp" |
| 81 |
+ |
|
| 82 |
|
using namespace OpenMD; |
| 83 |
|
|
| 84 |
|
int main(int argc, char* argv[]){ |
| 111 |
|
} |
| 112 |
|
|
| 113 |
|
// check the second selection argument, or set it to the environment |
| 114 |
< |
// variable, or failing that, set it to "select all" |
| 114 |
> |
// variable, or failing that, set it to the first selection |
| 115 |
|
|
| 116 |
|
if (args_info.sele2_given) { |
| 117 |
|
sele2 = args_info.sele2_arg; |
| 118 |
|
} else { |
| 119 |
< |
char* sele2Env = getenv("SELECTION1"); |
| 119 |
> |
char* sele2Env = getenv("SELECTION2"); |
| 120 |
|
if (sele2Env) { |
| 121 |
|
sele2 = sele2Env; |
| 122 |
|
} else { |
| 307 |
|
analyser = new ObjectCount(info, dumpFileName, sele1 ); |
| 308 |
|
} else if (args_info.slab_density_given) { |
| 309 |
|
analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg); |
| 310 |
+ |
} else if (args_info.rnemdz_given) { |
| 311 |
+ |
analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg); |
| 312 |
+ |
} else if (args_info.rnemdr_given) { |
| 313 |
+ |
analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg); |
| 314 |
+ |
} else if (args_info.rnemdrt_given) { |
| 315 |
+ |
analyser = new RNEMDRTheta(info, dumpFileName, sele1, |
| 316 |
+ |
args_info.nbins_arg, args_info.nanglebins_arg); |
| 317 |
|
} else if (args_info.p_angle_given) { |
| 318 |
< |
analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg); |
| 318 |
> |
if (args_info.sele1_given) { |
| 319 |
> |
if (args_info.sele2_given) |
| 320 |
> |
analyser = new pAngle(info, dumpFileName, sele1, sele2, |
| 321 |
> |
args_info.nbins_arg); |
| 322 |
> |
else |
| 323 |
> |
if (args_info.seleoffset_given) { |
| 324 |
> |
if (args_info.seleoffset2_given) { |
| 325 |
> |
analyser = new pAngle(info, dumpFileName, sele1, |
| 326 |
> |
args_info.seleoffset_arg, |
| 327 |
> |
args_info.seleoffset2_arg, |
| 328 |
> |
args_info.nbins_arg); |
| 329 |
> |
} else { |
| 330 |
> |
analyser = new pAngle(info, dumpFileName, sele1, |
| 331 |
> |
args_info.seleoffset_arg, |
| 332 |
> |
args_info.nbins_arg); |
| 333 |
> |
} |
| 334 |
> |
} else |
| 335 |
> |
analyser = new pAngle(info, dumpFileName, sele1, |
| 336 |
> |
args_info.nbins_arg); |
| 337 |
> |
} else { |
| 338 |
> |
sprintf( painCave.errMsg, |
| 339 |
> |
"At least one selection script (--sele1) must be specified when " |
| 340 |
> |
"calculating P(angle) distributions"); |
| 341 |
> |
painCave.severity = OPENMD_ERROR; |
| 342 |
> |
painCave.isFatal = 1; |
| 343 |
> |
simError(); |
| 344 |
> |
} |
| 345 |
|
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
| 346 |
|
}else if (args_info.hxy_given) { |
| 347 |
|
analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, |
