Adding documentation and integration fix

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 <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 <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 <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
 :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
 <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 <set>` command.  The *sphere* and *bpm/sphere* styles take an optional 0
+density/disc <set>` 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

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 <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 <restart>`.  None of the :doc:`fix_modify <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 <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+This fix requires that atoms store temperature and a heat flux
+as defined by the :doc:`atom_style sphere/temp <atom_style>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair granular <pair_granular>`
+
+Default
+"""""""
+
+none

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 <atom_style>` 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 <atom_style>` command defines particles
 with a volume attribute.  Note that this command does not adjust the