Merge branch 'develop' into add_set_time

doc/src/Commands_pair.rst

@@ -34,7 +34,7 @@ OPT.
    *
    *
    *
-   * :doc:`adp (o) <pair_adp>`
+   * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`

doc/src/compute_reduce.rst

@@ -23,7 +23,7 @@ Syntax
        *reduce/region* arg = region-ID
          region-ID = ID of region to use for choosing atoms
 
-* mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq*
+* mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq* or *sumabs* or *aveabs*
 * one or more inputs can be listed
 * input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
 
@@ -77,7 +77,10 @@ option sums the square of the values in the vector into a global
 total.  The *avesq* setting does the same as *sumsq*, then divides the
 sum of squares by the number of values.  The last two options can be
 useful for calculating the variance of some quantity, e.g. variance =
-sumsq - ave\^2.
+sumsq - ave\^2.  The *sumabs* option sums the absolute values in the
+vector into a global total.  The *aveabs* setting does the same as
+*sumabs*, then divides the sum of absolute values by the number of
+values.
 
 Each listed input is operated on independently.  For per-atom inputs,
 the group specified with this command means only atoms within the
@@ -189,7 +192,7 @@ value.  If multiple inputs are specified, this compute produces a
 global vector of values, the length of which is equal to the number of
 inputs specified.
 
-As discussed below, for the *sum* and *sumsq* modes, the value(s)
+As discussed below, for the *sum*, *sumabs* and *sumsq* modes, the value(s)
 produced by this compute are all "extensive", meaning their value
 scales linearly with the number of atoms involved.  If normalized
 values are desired, this compute can be accessed by the :doc:`thermo_style custom <thermo_style>` command with :doc:`thermo_modify norm yes <thermo_modify>` set as an option.  Or it can be accessed by a
@@ -208,7 +211,7 @@ compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
 All the scalar or vector values calculated by this compute are
-"intensive", except when the *sum* or *sumsq* modes are used on
+"intensive", except when the *sum*, *sumabs* or *sumsq* modes are used on
 per-atom or local vectors, in which case the calculated values are
 "extensive".
 

doc/src/delete_atoms.rst

@@ -10,7 +10,7 @@ Syntax
 
    delete_atoms style args keyword value ...
 
-* style = *group* or *region* or *overlap* or *porosity*
+* style = *group* or *region* or *overlap* or *porosity* or *variable*
 
   .. parsed-literal::
 
@@ -26,6 +26,7 @@ Syntax
                      or NULL to only impose the group criterion
          fraction = delete this fraction of atoms
          seed = random number seed (positive integer)
+       *variable* args = variable-name
 
 * zero or more keyword/value pairs may be appended
 * keyword = *compress* or *bond* or *mol*
@@ -47,6 +48,7 @@ Examples
    delete_atoms overlap 0.5 solvent colloid
    delete_atoms porosity all cube 0.1 482793 bond yes
    delete_atoms porosity polymer cube 0.1 482793 bond yes
+   detele_atoms variable checkers
 
 Description
 """""""""""
@@ -91,6 +93,13 @@ guarantee that the exact fraction of atoms will be deleted, or that
 the same atoms will be deleted when running on different numbers of
 processors.
 
+For style *variable*, all atoms for which the atom-style variable with
+the given name evaluates to non-zero will be deleted. Additional atoms
+can be deleted if they are in a molecule for which one or more atoms
+were deleted within the region; see the *mol* keyword discussion below.
+This option allows complex selections of atoms not covered by the
+other options listed above.
+
 If the *compress* keyword is set to *yes*, then after atoms are
 deleted, then atom IDs are re-assigned so that they run from 1 to the
 number of atoms in the system.  Note that this is not done for

doc/src/pair_adp.rst

@@ -1,10 +1,11 @@
 .. index:: pair_style adp
+.. index:: pair_style adp/kk
 .. index:: pair_style adp/omp
 
 pair_style adp command
 ======================
 
-Accelerator Variants: *adp/omp*
+Accelerator Variants: *adp/kk*, *adp/omp*
 
 Syntax
 """"""