Moving temp/heat keywords out of dump to compute prop/atom

doc/src/Howto_granular.rst

@@ -45,10 +45,15 @@ atoms, and should be used for granular system instead of the fix style
 
 To model heat conduction, one must add the temperature and heatflow
 atom variables with:
+
 * :doc:`fix property/atom <fix_property_atom>`
+
 a temperature integration fix
+
 * :doc:`fix heat/flow <fix_heat_flow>`
+
 and a heat conduction option defined in both
+
 * :doc:`pair_style granular <pair_granular>`
 * :doc:`fix wall/gran <fix_wall_gran>`
 

doc/src/compute_property_atom.rst

@@ -23,8 +23,9 @@ Syntax
                              spx, spy, spz, sp, fmx, fmy, fmz,
                              nbonds,
                              radius, diameter, omegax, omegay, omegaz,
+                             temperature, heatflow,
                              angmomx, angmomy, angmomz,
-                             shapex,shapey, shapez,
+                             shapex, shapey, shapez,
                              quatw, quati, quatj, quatk, tqx, tqy, tqz,
                              end1x, end1y, end1z, end2x, end2y, end2z,
                              corner1x, corner1y, corner1z,
@@ -56,6 +57,8 @@ Syntax
            *nbonds* = number of bonds assigned to an atom
            *radius,diameter* = radius,diameter of spherical particle
            *omegax,omegay,omegaz* = angular velocity of spherical particle
+           *temperature* = internal temperature of spherical particle
+           *heatflow* = internal heat flow of spherical particle
            *angmomx,angmomy,angmomz* = angular momentum of aspherical particle
            *shapex,shapey,shapez* = 3 diameters of aspherical particle
            *quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles

doc/src/dump.rst

@@ -104,7 +104,6 @@ Syntax
                                q, mux, muy, muz, mu,
                                radius, diameter, omegax, omegay, omegaz,
                                angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                               heatflow, temperature,
                                c_ID, c_ID[I], f_ID, f_ID[I], v_name,
                                i_name, d_name, i2_name[I], d2_name[I]
 
@@ -131,8 +130,6 @@ Syntax
            omegax,omegay,omegaz = angular velocity of spherical particle
            angmomx,angmomy,angmomz = angular momentum of aspherical particle
            tqx,tqy,tqz = torque on finite-size particles
-           heatflow = rate of heat flow into particle
-           temperature = temperature of particle
            c_ID = per-atom vector calculated by a compute with ID
            c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
            f_ID = per-atom vector calculated by a fix with ID

doc/src/fix_property_atom.rst

@@ -22,6 +22,8 @@ Syntax
        *mol* = molecule IDs
        *q* = charge
        *rmass* = per-atom mass
+       *temperature* = internal temperature of atom
+       *heatflow* = internal heat flow of atom
        i_name = new integer vector referenced by name
        d_name = new floating-point vector referenced by name
        i2_name = new integer array referenced by name
@@ -59,14 +61,18 @@ these properties for each atom in the system when a data file is read.
 This fix augments the set of per-atom properties with new custom
 ones. This can be useful in several scenarios.
 
-If the atom style does not define molecule IDs, per-atom charge, or
-per-atom mass, they can be added using the *mol*\ , *q* or *rmass*
+If the atom style does not define molecule IDs, per-atom charge,
+per-atom mass, internal temperature, or internal heat flow, they can
+be added using the *mol*\ , *q*, *rmass*, *temperature*, or *heatflow*
 keywords.  This could be useful to define "molecules" to use as rigid
 bodies with the :doc:`fix rigid <fix_rigid>` command, or to carry
 around an extra flag with atoms (stored as a molecule ID) that can be
 used by various commands like :doc:`compute chunk/atom
 <compute_chunk_atom>` to group atoms without having to use the group
 command (which is limited to a total of 32 groups including *all*\ ).
+For finite-size particles, an internal temperature and heat flow can
+be used to model heat conduction as in the
+:doc:`GRANULAR package <Howto_granular>`.
 
 Another application is to use the *rmass* flag in order to have
 per-atom masses instead of per-type masses.  This could be used to
@@ -85,9 +91,10 @@ properties that are not needed such as bond lists, which incurs some
 overhead when there are no bonds.
 
 In the future, we may add additional existing per-atom properties to
-fix property/atom, similar to *mol*\ , *q* or *rmass*\ , which
-"turn-on" specific properties defined by some atom styles, so they can
-be easily used by atom styles that do not define them.
+fix property/atom, similar to *mol*\ , *q*, *rmass*\ , *temperature*\ ,
+or *heatflow* which "turn-on" specific properties defined by some atom
+styles, so they can be easily used by atom styles that do not define
+them.
 
 More generally, the *i_name* and *d_name* options allow one or more
 new custom per-atom vectors to be defined.  Likewise the *i2_name* and