Syntax:
-compute ID group-ID displace/atom fix-ID +compute ID group-ID displace/atom
Examples:
-compute 1 all displace/atom myCoords +compute 1 all displace/atomDescription:
Define a computation that calculates the current displacement of each atom in the group from its original coordinates, including all effects -due to atoms passing thru periodic boundaries. The original -coordinates are stored by a fix -coord/original command, whose ID must be -specified with this compute. They are the coordinates at the time the -fix command was issued. +due to atoms passing thru periodic boundaries. Four quantites per +atom are computed: the x,y,z displacements and the total displacement. +See below for details.
-IMPORTANT NOTE: The fix coord/original command stores the initial -coordinates in "unwrapped" form, by using the image flags associated -with each atom. See the dump custom command for a -discussion of "unwrapped" coordinates. See the Atoms section of the +
To store the original coordinates at the time this compute is issued, +the compute creates its own fix of style "coord/original", as if this +command had been issued: +
+fix compute-ID_coord_original group-ID coord/original ++See the fix coord/original command for +details. Note that the ID of the new fix is the compute-ID + +underscore + "coord_original", and the group for the new fix is +the same as the compute group. +
+IMPORTANT NOTE: Fix coord/original stores the initial coordinates in +"unwrapped" form, by using the image flags associated with each atom. +See the dump custom command for a discussion of +"unwrapped" coordinates. See the Atoms section of the read_data command for a discussion of image flags and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking the fix and this compute by using the set +(e.g. to 0) before invoking this compute by using the set image command.
The displacements can be output directly via the dump custom command.
The value of the displacement will be 0.0 for atoms not in the -specified compute group. Note that the fix defines its own group and -stores (0.0,0.0,0.0) for the original coordinates of any atom not in -the fix group. +specified compute group.
Output info:
diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt index 8de18a560b..40d147528e 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -10,42 +10,48 @@ compute displace/atom command :h3 [Syntax:] -compute ID group-ID displace/atom fix-ID :pre +compute ID group-ID displace/atom :pre ID, group-ID are documented in "compute"_compute.html command -displace/atom = style name of this compute command -fix-ID = ID of a fix of style "coord/original"_fix_coord_original.html :ul +displace/atom = style name of this compute command :ul [Examples:] -compute 1 all displace/atom myCoords :pre +compute 1 all displace/atom :pre [Description:] Define a computation that calculates the current displacement of each atom in the group from its original coordinates, including all effects -due to atoms passing thru periodic boundaries. The original -coordinates are stored by a "fix -coord/original"_fix_coord_original.html command, whose ID must be -specified with this compute. They are the coordinates at the time the -fix command was issued. +due to atoms passing thru periodic boundaries. Four quantites per +atom are computed: the x,y,z displacements and the total displacement. +See below for details. -IMPORTANT NOTE: The fix coord/original command stores the initial -coordinates in "unwrapped" form, by using the image flags associated -with each atom. See the "dump custom"_dump.html command for a -discussion of "unwrapped" coordinates. See the Atoms section of the +To store the original coordinates at the time this compute is issued, +the compute creates its own fix of style "coord/original", as if this +command had been issued: + +fix compute-ID_coord_original group-ID coord/original :pre + +See the "fix coord/original"_fix_coord_original.html command for +details. Note that the ID of the new fix is the compute-ID + +underscore + "coord_original", and the group for the new fix is +the same as the compute group. + +IMPORTANT NOTE: Fix coord/original stores the initial coordinates in +"unwrapped" form, by using the image flags associated with each atom. +See the "dump custom"_dump.html command for a discussion of +"unwrapped" coordinates. See the Atoms section of the "read_data"_read_data.html command for a discussion of image flags and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking the fix and this compute by using the "set +(e.g. to 0) before invoking this compute by using the "set image"_set.html command. The displacements can be output directly via the "dump custom"_dump.html command. The value of the displacement will be 0.0 for atoms not in the -specified compute group. Note that the fix defines its own group and -stores (0.0,0.0,0.0) for the original coordinates of any atom not in -the fix group. +specified compute group. [Output info:]