Loading doc/src/compute_ptm_atom.rst +5 −2 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ Syntax * ptm/atom = style name of this compute command * structures = structure types to search for * threshold = lattice distortion threshold (RMSD) * group2-ID determines which groups are used for neighbor selection (optional, default "all") * group2-ID determines which group is used for neighbor selection (optional, default "all") Examples """""""" Loading Loading @@ -83,7 +83,9 @@ The neighbor list needed to compute this quantity is constructed each time the calculation is performed (e.g. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each with a *ptm/atom* style. *ptm/atom* style. By default the compute processes **all** neighbors unless the optional *group2-ID* argument is given, then only members of that group are considered as neighbors. **Output info:** Loading @@ -107,6 +109,7 @@ The interatomic distance is computed from the scale factor in the RMSD equation. The (qw,qx,qy,qz) parameters represent the orientation of the local structure in quaternion form. The reference coordinates for each template (from which the orientation is determined) can be found in the *ptm\_constants.h* file in the PTM source directory. For atoms that are not within the compute group-ID, all values are set to zero. Restrictions """""""""""" Loading Loading
doc/src/compute_ptm_atom.rst +5 −2 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ Syntax * ptm/atom = style name of this compute command * structures = structure types to search for * threshold = lattice distortion threshold (RMSD) * group2-ID determines which groups are used for neighbor selection (optional, default "all") * group2-ID determines which group is used for neighbor selection (optional, default "all") Examples """""""" Loading Loading @@ -83,7 +83,9 @@ The neighbor list needed to compute this quantity is constructed each time the calculation is performed (e.g. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each with a *ptm/atom* style. *ptm/atom* style. By default the compute processes **all** neighbors unless the optional *group2-ID* argument is given, then only members of that group are considered as neighbors. **Output info:** Loading @@ -107,6 +109,7 @@ The interatomic distance is computed from the scale factor in the RMSD equation. The (qw,qx,qy,qz) parameters represent the orientation of the local structure in quaternion form. The reference coordinates for each template (from which the orientation is determined) can be found in the *ptm\_constants.h* file in the PTM source directory. For atoms that are not within the compute group-ID, all values are set to zero. Restrictions """""""""""" Loading
