These are compute styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index c1a3ca0de9..06f29cbd6f 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -464,6 +464,7 @@ each style or click on the style itself for a full description: "centro/atom"_compute_centro_atom.html, "cna/atom"_compute_cna_atom.html, +"com"_compute_com.html, "coord/atom"_compute_coord_atom.html, "damage/atom"_compute_damage_atom.html, "displace/atom"_compute_displace_atom.html, diff --git a/doc/compute.html b/doc/compute.html index d332d67077..0a54ec677a 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -111,6 +111,7 @@ available in LAMMPS:
Syntax: +
+compute ID group-ID com ++
Examples: +
+compute 1 all com ++
Description: +
+Define a computation that calculates the center-of-mass of the group +of atoms, including all effects due to atoms passing thru periodic +boundaries. +
+A vector of three quantites is calculated by this compute, which +are the x,y,z coordinates of the center of mass. +
+IMPORTANT NOTE: The coordinates of an atom contribute to the +center-of-mass 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, +and its contribution to the center-of-mass may not reflect its true +contribution. See the fix rigid command for details. +Thus, to compute the center-of-mass of rigid bodies as they cross +periodic boundaries, you will need to post-process a dump +file containing coordinates of the atoms in the bodies. +
+Output info: +
+This compute calculates a global vector of length 3, which can be +accessed by indices 1-3 by any command that uses global vector values +from a compute as input. See this section +for an overview of LAMMPS output options. +
+The vector values are "intensive", meaning they are independent of the +number of atoms in the simulation. +
+Restrictions: none +
+Related commands: none +
+Default: none +
+ diff --git a/doc/compute_com.txt b/doc/compute_com.txt new file mode 100644 index 0000000000..57737f443b --- /dev/null +++ b/doc/compute_com.txt @@ -0,0 +1,62 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute com command :h3 + +[Syntax:] + +compute ID group-ID com :pre + +ID, group-ID are documented in "compute"_compute.html command +com = style name of this compute command :ul + +[Examples:] + +compute 1 all com :pre + +[Description:] + +Define a computation that calculates the center-of-mass of the group +of atoms, including all effects due to atoms passing thru periodic +boundaries. + +A vector of three quantites is calculated by this compute, which +are the x,y,z coordinates of the center of mass. + +IMPORTANT NOTE: The coordinates of an atom contribute to the +center-of-mass 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, +and its contribution to the center-of-mass may not reflect its true +contribution. See the "fix rigid"_fix_rigid.html command for details. +Thus, to compute the center-of-mass of rigid bodies as they cross +periodic boundaries, you will need to post-process a "dump +file"_dump.html containing coordinates of the atoms in the bodies. + +[Output info:] + +This compute calculates a global vector of length 3, which can be +accessed by indices 1-3 by any command that uses global vector values +from a compute as input. See "this section"_Section_howto.html#4_15 +for an overview of LAMMPS output options. + +The vector values are "intensive", meaning they are independent of the +number of atoms in the simulation. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html index 0b76b05331..c5db4ae1bf 100644 --- a/doc/compute_displace_atom.html +++ b/doc/compute_displace_atom.html @@ -59,7 +59,7 @@ 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, -and the computed displacement will not reflect its true displacement. +and the computed displacement may not reflect its true displacement. See the fix rigid command for details. Thus, to compute the displacement of rigid bodies as they cross periodic boundaries, you will need to post-process a dump file diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt index acf9dcd73b..94df70a5c3 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -56,7 +56,7 @@ 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, -and the computed displacement will not reflect its true displacement. +and the computed displacement may not reflect its true displacement. See the "fix rigid"_fix_rigid.html command for details. Thus, to compute the displacement of rigid bodies as they cross periodic boundaries, you will need to post-process a "dump file"_dump.html diff --git a/doc/compute_msd.html b/doc/compute_msd.html index 436a16b514..4af1d6a1d2 100644 --- a/doc/compute_msd.html +++ b/doc/compute_msd.html @@ -29,8 +29,8 @@
Examples:
-fix 1 all compute -fix 1 upper compute com yes +compute 1 all msd +compute 1 upper msd com yesDescription:
@@ -44,8 +44,8 @@ and averaged over atoms in the group. The 4th component is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the group. -The slope of the mean-squared displacement versus time is proportional -to the diffusion coefficient of the diffusing atoms. +
The slope of the mean-squared displacement (MSD) versus time is +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, @@ -75,11 +75,11 @@ 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, -and the computed MSD will not reflect its true displacement. See the -fix rigid command for details. Thus, to compute the -MSD of rigid bodies as they cross periodic boundaries, you will need -to post-process a dump file containing coordinates of the -atoms in the bodies. +and its contribution to the MSD may not reflect its true contribution. +See the fix rigid command for details. Thus, to +compute the MSD of rigid bodies as they cross periodic boundaries, you +will need to post-process a dump file containing +coordinates of the atoms in the bodies.
IMPORTANT NOTE: If you want the quantities calculated by this compute to be continuous when running from a restart file, diff --git a/doc/compute_msd.txt b/doc/compute_msd.txt index 953f2720ee..523b224801 100644 --- a/doc/compute_msd.txt +++ b/doc/compute_msd.txt @@ -21,8 +21,8 @@ keyword = {com} :l [Examples:] -fix 1 all compute -fix 1 upper compute com yes :pre +compute 1 all msd +compute 1 upper msd com yes :pre [Description:] @@ -36,8 +36,8 @@ and averaged over atoms in the group. The 4th component is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the group. -The slope of the mean-squared displacement versus time is proportional -to the diffusion coefficient of the diffusing atoms. +The slope of the mean-squared displacement (MSD) versus time is +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, @@ -67,11 +67,11 @@ 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, -and the computed MSD will not reflect its true displacement. See the -"fix rigid"_fix_rigid.html command for details. Thus, to compute the -MSD of rigid bodies as they cross periodic boundaries, you will need -to post-process a "dump file"_dump.html containing coordinates of the -atoms in the bodies. +and its contribution to the MSD may not reflect its true contribution. +See the "fix rigid"_fix_rigid.html command for details. Thus, to +compute the MSD of rigid bodies as they cross periodic boundaries, you +will need to post-process a "dump file"_dump.html containing +coordinates of the atoms in the bodies. IMPORTANT NOTE: If you want the quantities calculated by this compute to be continuous when running from a "restart file"_read_restart.html,