From e01ef140253b9d58ba4f19347e07390ca3dc0234 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Sun, 12 Jun 2022 10:06:16 -0600 Subject: [PATCH] Adding documentation and integration fix --- doc/src/atom_style.rst | 14 ++++--- doc/src/fix_temp_integrate.rst | 75 ++++++++++++++++++++++++++++++++++ doc/src/set.rst | 9 +++- 3 files changed, 91 insertions(+), 7 deletions(-) create mode 100644 doc/src/fix_temp_integrate.rst diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index bd0c193962..5b93c56887 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -121,6 +121,8 @@ quantities. +--------------+-----------------------------------------------------+--------------------------------------+ | *sphere* | diameter, mass, angular velocity | granular models | +--------------+-----------------------------------------------------+--------------------------------------+ +| *sphere/temp*| diameter, mass, angular velocity, temperature | thermal granular models | ++--------------+-----------------------------------------------------+--------------------------------------+ | *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)| +--------------+-----------------------------------------------------+--------------------------------------+ | *spin* | magnetic moment | system with magnetic particles | @@ -144,7 +146,7 @@ quantities. output the custom values. All of the above styles define point particles, except the *sphere*, -*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*, +*sphere/temp*, *bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*, *tri*, and *body* styles, which define finite-size particles. See the :doc:`Howto spherical ` page for an overview of using finite-size particle models with LAMMPS. @@ -154,15 +156,15 @@ per-type basis, using the :doc:`mass ` command, The finite-size particle styles assign mass to individual particles on a per-particle basis. -For the *sphere* and *bpm/sphere* styles, the particles are spheres and each stores a -per-particle diameter and mass. If the diameter > 0.0, the particle -is a finite-size sphere. If the diameter = 0.0, it is a point -particle. Note that by use of the *disc* keyword with the :doc:`fix +For the *sphere*, *sphere/temp*, and *bpm/sphere* styles, the particles +are spheres and each stores a per-particle diameter and mass. If the +diameter > 0.0, the particle is a finite-size sphere. If the diameter = 0.0, +it is a point particle. Note that by use of the *disc* keyword with the :doc:`fix nve/sphere `, :doc:`fix nvt/sphere `, :doc:`fix nph/sphere `, :doc:`fix npt/sphere ` commands for the *sphere* style, spheres can be effectively treated as 2d discs for a 2d simulation if desired. See also the :doc:`set -density/disc ` command. The *sphere* and *bpm/sphere* styles take an optional 0 +density/disc ` command. These styles take an optional 0 or 1 argument. A value of 0 means the radius of each sphere is constant for the duration of the simulation. A value of 1 means the radii may vary dynamically during the simulation, e.g. due to use of diff --git a/doc/src/fix_temp_integrate.rst b/doc/src/fix_temp_integrate.rst new file mode 100644 index 0000000000..c2f1257075 --- /dev/null +++ b/doc/src/fix_temp_integrate.rst @@ -0,0 +1,75 @@ +.. index:: fix temp/integrate + +fix temp/integrate command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID temp/integrate style values ... + +* ID, group-ID are documented in :doc:`fix ` command +* temp/integrate = style name of this fix command +* one style with corresponding value(s) needs to be listed + + .. parsed-literal:: + + style = *constant* or *type* + *constant* = cp + cp = value of specifc heat (energy/(mass * temperature) units) + *type* = cp1 ... cpN + cpN = value of specifc heat for type N (energy/(mass * temperature) units) + +* + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all temp/integrate constant 1.0 + fix 1 all temp/integrate type 1.0 0.5 + +Description +""""""""""" + +Perform plain time integration to update temperature for atoms in the +group each timestep. The specific heat of atoms can be defined using either +the *constant* or *type* keywords. For style *constant*, the specific heat +is a constant value *cp* for all atoms. For style *type*, *N* different values +of the specific heat are defined, one for each of the *N* types of atoms. + + + +---------- + +.. include:: accel_styles.rst + +---------- + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :doc:`output commands `. +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + +This fix requires that atoms store temperature and a heat flux +as defined by the :doc:`atom_style sphere/temp ` command. + +Related commands +"""""""""""""""" + +:doc:`pair granular ` + +Default +""""""" + +none diff --git a/doc/src/set.rst b/doc/src/set.rst index cc1d2766e3..d11d3fc229 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -18,7 +18,7 @@ Syntax *dipole/random* or *quat* or *spin* or *spin/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or - *omega* or *mass* or *density* or *density/disc* or + *omega* or *mass* or *density* or *density/disc* or *temperature* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *sph/e* or *sph/cv* or *sph/rho* or *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or @@ -95,6 +95,8 @@ Syntax value can be an atom-style variable (see below) *density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units) value can be an atom-style variable (see below) + *temperature* value = particle temperature for a finite-size particle particle (temperature units)s + value can be an atom-style variable (see below) *volume* value = particle volume for Peridynamic particle (distance\^3 units) value can be an atom-style variable (see below) *image* nx ny nz @@ -410,6 +412,11 @@ assumed to be in mass/distance\^2 units). If none of these cases are valid, then the mass is set to the density value directly (the input density is assumed to be in mass units). +Keyword *temperature* sets the temperature of a finite-size particle +as defined by the GRANULAR package. Currently, only +:doc:`atom_style sphere/temperature ` defines particles +with this attribute. The values for the temperature must be positive. + Keyword *volume* sets the volume of all selected particles. Currently, only the :doc:`atom_style peri ` command defines particles with a volume attribute. Note that this command does not adjust the