Merge branch 'develop' into collected-small-changes

doc/src/Howto_chunk.rst

@@ -1,7 +1,7 @@
 Use chunks to calculate system properties
 =========================================
 
-In LAMMS, "chunks" are collections of atoms, as defined by the
+In LAMMPS, "chunks" are collections of atoms, as defined by the
 :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns
 each atom to a chunk ID (or to no chunk at all).  The number of chunks
 and the assignment of chunk IDs to atoms can be static or change over
@@ -148,14 +148,14 @@ Example calculations with chunks
 Here are examples using chunk commands to calculate various
 properties:
 
-(1) Average velocity in each of 1000 2d spatial bins:
+1. Average velocity in each of 1000 2d spatial bins:
 
 .. code-block:: LAMMPS
 
    compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
    fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
 
-(2) Temperature in each spatial bin, after subtracting a flow
+2. Temperature in each spatial bin, after subtracting a flow
 velocity:
 
 .. code-block:: LAMMPS
@@ -164,7 +164,7 @@ velocity:
    compute vbias all temp/profile 1 0 0 y 10
    fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
 
-(3) Center of mass of each molecule:
+3. Center of mass of each molecule:
 
 .. code-block:: LAMMPS
 
@@ -172,7 +172,7 @@ velocity:
    compute myChunk all com/chunk cc1
    fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
 
-(4) Total force on each molecule and ave/max across all molecules:
+4. Total force on each molecule and ave/max across all molecules:
 
 .. code-block:: LAMMPS
 
@@ -183,7 +183,7 @@ velocity:
    thermo 1000
    thermo_style custom step temp v_xave v_xmax
 
-(5) Histogram of cluster sizes:
+5. Histogram of cluster sizes:
 
 .. code-block:: LAMMPS
 
@@ -192,16 +192,16 @@ velocity:
    compute size all property/chunk cc1 count
    fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
 
-(6) An example for using a per-chunk value to apply per-atom forces to
+6. An example for using a per-chunk value to apply per-atom forces to
 compress individual polymer chains (molecules) in a mixture, is
 explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
 
-(7) An example for using one set of per-chunk values for molecule
+7. An example for using one set of per-chunk values for molecule
 chunks, to create a second set of micelle-scale chunks (clustered
 molecules, due to hydrophobicity), is explained on the
 :doc:`compute reduce/chunk <compute_reduce_chunk>` command doc page.
 
-(8) An example for using one set of per-chunk values (dipole moment
+8. An example for using one set of per-chunk values (dipole moment
 vectors) for molecule chunks, spreading the values to each atom in
 each chunk, then defining a second set of chunks as spatial bins, and
 using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an

doc/src/fix_electrode.rst

@@ -38,7 +38,7 @@ Syntax
        *electrode/thermo* args = potential eta *temp* values
             potential = electrode potential
             charge = electrode charge
-            eta = reciprocal width of electrode charge smearing
+            eta = reciprocal width of electrode charge smearing (can be NULL if eta keyword is used)
             *temp* values = T_v tau_v rng_v
                 T_v = temperature of thermo-potentiostat
                 tau_v = time constant of thermo-potentiostat
@@ -110,7 +110,7 @@ electrostatic configurations:
   :ref:`(Deissenbeck)<Deissenbeck>` between two electrodes
 
   * (resulting in changing charges and potentials with appropriate
-     average potential difference and thermal variance)
+    average potential difference and thermal variance)
 
 The first group-ID provided to each fix specifies the first electrode
 group, and more group(s) are added using the *couple* keyword for each
@@ -287,8 +287,18 @@ The *fix_modify tf* option enables the Thomas-Fermi metallicity model
    fix_modify ID tf type length voronoi
 
 
-If this option is used parameters must be set for all atom types of the
-electrode.
+If this option is used, these two parameters must be set for
+all atom types of the electrode:
+
+* `tf` is the Thomas-Fermi length :math:`l_{TF}`
+* `voronoi` is the Voronoi volume per atom in units of length cubed
+
+Different types may have different `tf` and `voronoi` values.
+The following self-energy term is then added for all electrode atoms:
+
+.. math::
+
+  A_{ii} += \frac{1}{4 \pi \epsilon_0} \times \frac{4 \pi l_{TF}^2}{\mathrm{Voronoi volume}}
 
 The *fix_modify timer* option turns on (off) additional timer outputs in the log
 file, for code developers to track optimization.
@@ -321,9 +331,11 @@ The global array has *N* rows and *2N+1* columns, where the fix manages
 array, the elements are:
 
 * array[I][1] = total charge that group *I* would have had *if it were
-  at 0 V applied potential* * array[I][2 to *N* + 1] = the *N* entries
+  at 0 V applied potential*
+* array[I][2 to *N* + 1] = the *N* entries
   of the *I*-th row of the electrode capacitance matrix (definition
-  follows) * array[I][*N* + 2 to *2N* + 1] = the *N* entries of the
+  follows)
+* array[I][*N* + 2 to *2N* + 1] = the *N* entries of the
   *I*-th row of the electrode elastance matrix (the inverse of the
   electrode capacitance matrix)
 

doc/src/read_data.rst

@@ -12,7 +12,7 @@ Syntax
 
 * file = name of data file to read in
 * zero or more keyword/arg pairs may be appended
-* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *group* or *nocoeff* or *fix*
+* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom* or *group* or *nocoeff* or *fix*
 
   .. parsed-literal::
 

doc/src/reset_atoms.rst

@@ -32,7 +32,7 @@ Syntax
 
   .. code-block:: LAMMPS
 
-     reset atoms mol group-ID keyword value ...
+     reset_atoms mol group-ID keyword value ...
 
   * group-ID = ID of group of atoms whose molecule IDs will be reset
   * zero or more keyword/value pairs can be appended
@@ -66,16 +66,16 @@ Description
 .. versionadded:: 22Dec2022
 
 The *reset_atoms* command resets the values of a specified atom
-property.  In contrast to the set command, it does this in a
+property.  In contrast to the *set* command, it does this in a
 collective manner which resets the values for many atoms in a
-self-consistent way.  This is often useful when the simulated system
-has undergone significant modifications like adding or removing atoms
-or molecules, joining data files, changing bonds, or large-scale
+self-consistent way.  This command is often useful when the simulated
+system has undergone significant modifications like adding or removing
+atoms or molecules, joining data files, changing bonds, or large-scale
 diffusion.
 
 The new values can be thought of as a *reset*, similar to values atoms
 would have if a new data file were being read or a new simulation
-performed.  Note that the set command also resets atom properties to
+performed.  Note that the *set* command also resets atom properties to
 new values, but it treats each atom independently.
 
 The *property* setting can be *id* or *image* or *mol*.  For *id*, the
@@ -90,7 +90,7 @@ keyword/value settings are given below.
 
 ----------
 
-*Property id*
+Property: *id*
 
 Reset atom IDs for the entire system, including all the global IDs
 stored for bond, angle, dihedral, improper topology data.  This will
@@ -146,7 +146,7 @@ processor have consecutive IDs, as the :doc:`create_atoms
 
 ----------
 
-*Property image*
+Property: *image*
 
 Reset the image flags of atoms so that at least one atom in each
 molecule has an image flag of 0.  Molecular topology is respected so
@@ -191,7 +191,7 @@ flags.
 
 ----------
 
-*Property mol*
+Property: *mol*
 
 Reset molecule IDs for a specified group of atoms based on current
 bond connectivity.  This will typically create a new set of molecule
@@ -203,7 +203,7 @@ For purposes of this operation, molecules are identified by the current
 bond connectivity in the system, which may or may not be consistent with
 the current molecule IDs.  A molecule in this context is a set of atoms
 connected to each other with explicit bonds.  The specific algorithm
-used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`
+used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`.
 Once the molecules are identified and a new molecule ID computed for
 each, this command will update the current molecule ID for all atoms in
 the group with the new molecule ID.  Note that if the group excludes
@@ -266,7 +266,7 @@ The *image* property can only be used when the atom style supports bonds.
 Related commands
 """"""""""""""""
 
-:doc:`compute fragment/atom <compute_cluster_atom>`
+:doc:`compute fragment/atom <compute_cluster_atom>`,
 :doc:`fix bond/react <fix_bond_react>`,
 :doc:`fix bond/create <fix_bond_create>`,
 :doc:`fix bond/break <fix_bond_break>`,