The displacement of an atom is from its original position at the time -the compute command was issued. To store the original coordinates, -the compute creates its own fix of style "store/state", as if this -command had been issued: +the compute command was issued. The value of the displacement will be +0.0 for atoms not in the specified compute group.
-fix compute-ID_store_state group-ID store/state xu yu zu --
See the fix store/state command for details. -Note that the ID of the new fix is the compute-ID + underscore + -"store/state", and the group for the new fix is the same as the -compute group. -
-The value of the displacement will be 0.0 for atoms not in the -specified compute group. -
-IMPORTANT NOTE: Fix store/state 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 this compute by using the set -image command. +
IMPORTANT NOTE: Initial coordinates are stored 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 this compute by +using the set image command.
IMPORTANT NOTE: If an atom is part of a rigid body (see the fix rigid command), it's periodic image flags are altered, diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt index 5b7363db93..70c2244ac0 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -31,28 +31,16 @@ The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy + dz*dz). The displacement of an atom is from its original position at the time -the compute command was issued. To store the original coordinates, -the compute creates its own fix of style "store/state", as if this -command had been issued: +the compute command was issued. The value of the displacement will be +0.0 for atoms not in the specified compute group. -fix compute-ID_store_state group-ID store/state xu yu zu :pre - -See the "fix store/state"_fix_store_state.html command for details. -Note that the ID of the new fix is the compute-ID + underscore + -"store/state", and the group for the new fix is the same as the -compute group. - -The value of the displacement will be 0.0 for atoms not in the -specified compute group. - -IMPORTANT NOTE: Fix store/state 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 this compute by using the "set -image"_set.html command. +IMPORTANT NOTE: Initial coordinates are stored 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 this compute by +using the "set image"_set.html command. IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix rigid"_fix_rigid.html command), it's periodic image flags are altered, diff --git a/doc/compute_msd.html b/doc/compute_msd.html index 7814701ffd..df60e2d3bd 100644 --- a/doc/compute_msd.html +++ b/doc/compute_msd.html @@ -36,7 +36,9 @@ compute 1 upper msd com yes
Define a computation that calculates the mean-squared displacement (MSD) of the group of atoms, including all effects due to atoms -passing thru periodic boundaries. +passing thru periodic boundaries. For computation of the non-Gaussian +parameter of mean-squared displacement, see the compute +msd/nongauss command.
A vector of four quantites is calculated by this compute. The first 3 elements of the vector are the squared dx,dy,dz displacements, summed @@ -48,30 +50,20 @@ averaged over atoms in the group. proportional to the diffusion coefficient of the diffusing atoms.
The displacement of an atom is from its original position at the time -the compute command was issued. To store the original coordinates, -the compute creates its own fix of style "store/state", as if this -command had been issued: -
-fix compute-ID_store_state group-ID store/state xu yu zu --
See the fix store/state command for details. -Note that the ID of the new fix is the compute-ID + underscore + -"store_state", and the group for the new fix is the same as the -compute group. +the compute command was issued. The value of the displacement will be +0.0 for atoms not in the specified compute group.
If the com option is set to yes then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calcluated. The com option is also -passed to the created fix store/state. +displacment of each atom is calcluated.
-IMPORTANT NOTE: Fix store/state 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 this compute by using the set -image command. +
IMPORTANT NOTE: Initial coordinates are stored 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 this compute by +using the set image command.
IMPORTANT NOTE: If an atom is part of a rigid body (see the fix rigid command), it's periodic image flags are altered, @@ -103,7 +95,8 @@ distance^2 units.
Related commands:
-compute displace_atom, fix
+ compute msd/nongauss, compute
+displace_atom, fix
store/state, compute
msd/molecule