From ac48852b2d02005d1f92504a7d6474d4cdb808f7 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 10 Jun 2022 08:30:23 -0600 Subject: [PATCH] edits to 1st paragraph of description --- doc/src/compute_ave_sphere_atom.rst | 64 ++++++++++++++++------------- 1 file changed, 36 insertions(+), 28 deletions(-) diff --git a/doc/src/compute_ave_sphere_atom.rst b/doc/src/compute_ave_sphere_atom.rst index a6607356c9..48dbf377cb 100644 --- a/doc/src/compute_ave_sphere_atom.rst +++ b/doc/src/compute_ave_sphere_atom.rst @@ -35,18 +35,24 @@ Examples Description """"""""""" -Define a computation that calculates the local mass density and temperature -for each atom and neighbors inside a spherical cutoff. The center-of-mass -velocity of the atoms in the sphere is subtracted out before computing the -temperature, which leaves only the thermal velocity, similar to :doc:`compute temp/com `. +Define a computation that calculates the local mass density and +temperature for each atom based on its neighbors inside a spherical +cutoff. If an atom has M neighbors, then its local mass density is +calculated as the sum of its mass and its M neighbor masses, divided +by the volume of the cutoff sphere (or circle in 2d). The local +temperature of the atom is calculated as the temperature of the +collection of M+1 atoms, after subtracting the center-of-mass velocity +of the M+1 atoms from each of the M+1 atom's velocities. This is +effectively the thermal velocity of the neighborhood of the central +atom, similar to :doc:`compute temp/com `. -The optional keyword *cutoff* defines the distance cutoff -used when searching for neighbors. The default value is the cutoff -specified by the pair style. If no pair style is defined, then a cutoff -must be defined using this keyword. If the specified cutoff is larger than -that of the pair_style plus neighbor skin (or no pair style is defined), -the *comm_modify cutoff* option must also be set to match that of the -*cutoff* keyword. +The optional keyword *cutoff* defines the distance cutoff used when +searching for neighbors. The default value is the cutoff specified by +the pair style. If no pair style is defined, then a cutoff must be +defined using this keyword. If the specified cutoff is larger than +that of the pair_style plus neighbor skin (or no pair style is +defined), the *comm_modify cutoff* option must also be set to match +that of the *cutoff* keyword. The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms @@ -57,16 +63,16 @@ too frequently. If you have a bonded system, then the settings of :doc:`special_bonds ` command can remove pairwise - interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special_bonds ` - command, and means those pairwise interactions do not appear in the - neighbor list. Because this compute uses the neighbor list, it also means - those pairs will not be included in the order parameter. This - difficulty can be circumvented by writing a dump file, and using the - :doc:`rerun ` command to compute the order parameter for - snapshots in the dump file. The rerun script can use a - :doc:`special_bonds ` command that includes all pairs in - the neighbor list. + interactions between atoms in the same bond, angle, or dihedral. + This is the default setting for the :doc:`special_bonds + ` command, and means those pairwise interactions do + not appear in the neighbor list. Because this compute uses the + neighbor list, it also means those pairs will not be included in + the order parameter. This difficulty can be circumvented by + writing a dump file, and using the :doc:`rerun ` command to + compute the order parameter for snapshots in the dump file. The + rerun script can use a :doc:`special_bonds ` command + that includes all pairs in the neighbor list. ---------- @@ -79,18 +85,20 @@ too frequently. Output info """"""""""" -This compute calculates a per-atom array with two columns: mass density in density -:doc:`units ` and temperature in temperature :doc:`units `. +This compute calculates a per-atom array with two columns: mass +density in density :doc:`units ` and temperature in temperature +:doc:`units `. These values can be accessed by any command that uses per-atom values -from a compute as input. See the :doc:`Howto output ` doc -page for an overview of LAMMPS output options. +from a compute as input. See the :doc:`Howto output ` +doc page for an overview of LAMMPS output options. Restrictions """""""""""" -This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" @@ -100,5 +108,5 @@ Related commands Default """"""" -The option defaults are *cutoff* = pair style cutoff +The option defaults are *cutoff* = pair style cutoff.