convert lists with global values from fixes to use automatic numbering

doc/src/fix_atom_swap.rst

@@ -165,8 +165,8 @@ This fix computes a global vector of length 2, which can be accessed
 by various :doc:`output commands <Howto_output>`.  The vector values are
 the following global cumulative quantities:
 
-* 1 = swap attempts
+  #. swap attempts
-* 2 = swap accepts
+  #. swap accepts
 
 The vector values calculated by this fix are "intensive".
 

doc/src/fix_ave_histo.rst

@@ -376,10 +376,10 @@ can only be accessed on timesteps that are multiples of :math:`N_\text{freq}`
 since that is when a histogram is generated.  The global vector has four
 values:
 
-* 1 = total counts in the histogram
+  #. total counts in the histogram
-* 2 = values that were not histogrammed (see *beyond* keyword)
+  #. values that were not histogrammed (see *beyond* keyword)
-* 3 = min value of all input values, including ones not histogrammed
+  #. min value of all input values, including ones not histogrammed
-* 4 = max value of all input values, including ones not histogrammed
+  #. max value of all input values, including ones not histogrammed
 
 The global array has :math:`N_\text{bins}` rows and three columns.  The
 first column has the bin coordinate, the second column has the count of

doc/src/fix_balance.rst

@@ -393,9 +393,9 @@ after the most recent re-balance and a global vector of length 3 with
 additional information about the most recent re-balancing.  The three
 values in the vector are as follows:
 
-* 1 = max # of particles per processor
+  #. max # of particles per processor
-* 2 = total # iterations performed in last re-balance
+  #. total # iterations performed in last re-balance
-* 3 = imbalance factor right before the last re-balance was performed
+  #. imbalance factor right before the last re-balance was performed
 
 As explained above, the imbalance factor is the ratio of the maximum
 number of particles (or total weight) on any processor to the average

doc/src/fix_charge_regulation.rst

@@ -238,14 +238,14 @@ This fix computes a global vector of length 8, which can be accessed by
 various output commands. The vector values are the following global
 quantities:
 
-* 1 = cumulative MC attempts
+  #. cumulative MC attempts
-* 2 = cumulative MC successes
+  #. cumulative MC successes
-* 3 = current # of neutral acid atoms
+  #. current # of neutral acid atoms
-* 4 = current # of -1 charged acid atoms
+  #. current # of -1 charged acid atoms
-* 5 = current # of neutral base atoms
+  #. current # of neutral base atoms
-* 6 = current # of +1 charged base atoms
+  #. current # of +1 charged base atoms
-* 7 = current # of free cations
+  #. current # of free cations
-* 8 = current # of free anions
+  #. current # of free anions
 
 
 Restrictions

doc/src/fix_gcmc.rst

@@ -413,14 +413,14 @@ This fix computes a global vector of length 8, which can be accessed
 by various :doc:`output commands <Howto_output>`.  The vector values are
 the following global cumulative quantities:
 
-* 1 = translation attempts
+  #. translation attempts
-* 2 = translation successes
+  #. translation successes
-* 3 = insertion attempts
+  #. insertion attempts
-* 4 = insertion successes
+  #. insertion successes
-* 5 = deletion attempts
+  #. deletion attempts
-* 6 = deletion successes
+  #. deletion successes
-* 7 = rotation attempts
+  #. rotation attempts
-* 8 = rotation successes
+  #. rotation successes
 
 The vector values calculated by this fix are "intensive".
 

doc/src/fix_hyper_global.rst

@@ -215,20 +215,20 @@ which can be accessed by various :doc:`output commands
 (energy units) applied on the current timestep.  The vector stores the
 following quantities:
 
-* 1 = boost factor on this step (unitless)
+  #. boost factor on this step (unitless)
-* 2 = max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless)
+  #. max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless)
-* 3 = ID of first atom in the max-strain bond
+  #. ID of first atom in the max-strain bond
-* 4 = ID of second atom in the max-strain bond
+  #. ID of second atom in the max-strain bond
-* 5 = average # of bonds/atom on this step
+  #. average # of bonds/atom on this step
 
-* 6 = fraction of timesteps where the biased bond has bias = 0.0 during this run
+  #. fraction of timesteps where the biased bond has bias = 0.0 during this run
-* 7 = fraction of timesteps where the biased bond has negative strain during this run
+  #. fraction of timesteps where the biased bond has negative strain during this run
-* 8 = max drift distance of any atom during this run (distance units)
+  #. max drift distance of any atom during this run (distance units)
-* 9 = max bond length during this run (distance units)
+  #. max bond length during this run (distance units)
 
-* 10 = cumulative hyper time since fix was defined (time units)
+  #. cumulative hyper time since fix was defined (time units)
-* 11 = cumulative count of event timesteps since fix was defined
+  #. cumulative count of event timesteps since fix was defined
-* 12 = cumulative count of atoms in events since fix was defined
+  #. cumulative count of atoms in events since fix was defined
 
 The first 5 quantities are for the current timestep.  Quantities 6-9
 are for the current hyper run.  They are reset each time a new hyper

doc/src/fix_hyper_local.rst

@@ -382,41 +382,41 @@ which can be accessed by various :doc:`output commands
 (energy units) applied on the current timestep, summed over all biased
 bonds.  The vector stores the following quantities:
 
-* 1 = average boost for all bonds on this step (unitless)
+  #. average boost for all bonds on this step (unitless)
-* 2 = # of biased bonds on this step
+  #. # of biased bonds on this step
-* 3 = max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless)
+  #. max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless)
-* 4 = value of :math:`V^{max}` on this step (energy units)
+  #. value of :math:`V^{max}` on this step (energy units)
-* 5 = average bias coeff for all bonds on this step (unitless)
+  #. average bias coeff for all bonds on this step (unitless)
-* 6 = min bias coeff for all bonds on this step (unitless)
+  #. min bias coeff for all bonds on this step (unitless)
-* 7 = max bias coeff for all bonds on this step (unitless)
+  #. max bias coeff for all bonds on this step (unitless)
-* 8 = average # of bonds/atom on this step
+  #. average # of bonds/atom on this step
-* 9 = average neighbor bonds/bond on this step within *Dcut*
+  #. average neighbor bonds/bond on this step within *Dcut*
 
-* 10 = average boost for all bonds during this run (unitless)
+  #. average boost for all bonds during this run (unitless)
-* 11 = average # of biased bonds/step during this run
+  #. average # of biased bonds/step during this run
-* 12 = fraction of biased bonds with no bias during this run
+  #. fraction of biased bonds with no bias during this run
-* 13 = fraction of biased bonds with negative strain during this run
+  #. fraction of biased bonds with negative strain during this run
-* 14 = max bond length during this run (distance units)
+  #. max bond length during this run (distance units)
-* 15 = average bias coeff for all bonds during this run (unitless)
+  #. average bias coeff for all bonds during this run (unitless)
-* 16 = min bias coeff for any bond during this run (unitless)
+  #. min bias coeff for any bond during this run (unitless)
-* 17 = max bias coeff for any bond during this run (unitless)
+  #. max bias coeff for any bond during this run (unitless)
 
-* 18 = max drift distance of any bond atom during this run (distance units)
+  #. max drift distance of any bond atom during this run (distance units)
-* 19 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
+  #. max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
-* 20 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
+  #. max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
-* 21 = count of ghost atoms that could not be found on reneighbor steps during this run
+  #. count of ghost atoms that could not be found on reneighbor steps during this run
-* 22 = count of bias overlaps (< Dcut) found during this run
+  #. count of bias overlaps (< *Dcut*) found during this run
 
-* 23 = cumulative hyper time since fix created (time units)
+  #. cumulative hyper time since fix created (time units)
-* 24 = cumulative count of event timesteps since fix created
+  #. cumulative count of event timesteps since fix created
-* 25 = cumulative count of atoms in events since fix created
+  #. cumulative count of atoms in events since fix created
-* 26 = cumulative # of new bonds formed since fix created
+  #. cumulative # of new bonds formed since fix created
 
-27 = average boost for biased bonds on this step (unitless)
+  #. average boost for biased bonds on this step (unitless)
-28 = # of bonds with absolute strain >= q on this step
+  #. # of bonds with absolute strain >= q on this step
 
-The first quantities 1-9 are for the current timestep.  Quantities
+Quantities 1-9 are for the current timestep.  Quantities 10-22
-10-22 are for the current hyper run.  They are reset each time a new
+are for the current hyper run.  They are reset each time a new
 hyper run is performed.  Quantities 23-26 are cumulative across
 multiple runs (since the point in the input script the fix was
 defined).

doc/src/fix_mol_swap.rst

@@ -146,8 +146,8 @@ This fix computes a global vector of length 2, which can be accessed
 by various :doc:`output commands <Howto_output>`.  The vector values are
 the following global cumulative quantities:
 
-* 1 = swap attempts
+  #. swap attempts
-* 2 = swap accepts
+  #. swap accepts
 
 The vector values calculated by this fix are "intensive".
 

doc/src/fix_reaxff_species.rst

@@ -194,8 +194,8 @@ The values in the global vector are "intensive".
 
 The 2 values in the global vector are as follows:
 
-* 1 = total number of molecules
+  #. total number of molecules
-* 2 = total number of distinct species
+  #. total number of distinct species
 
 The per-atom vector stores the molecule ID for each atom as identified
 by the fix.  If an atom is not in a molecule, its ID will be 0.

doc/src/fix_restrain.rst

@@ -246,9 +246,9 @@ The scalar is the total potential energy for *all* the restraints as
 discussed above. The vector values are the sum of contributions to the
 following individual categories:
 
-* 1 = bond energy
+  #. bond energy
-* 2 = angle energy
+  #. angle energy
-* 3 = dihedral energy
+  #. dihedral energy
 
 The scalar and vector values calculated by this fix are "extensive".
 

doc/src/fix_sgcmc.rst

@@ -145,7 +145,7 @@ components of the vector represent the following quantities:
 * 3 = Current global concentration `c_1` (= number of atoms of type 1 / total number of atoms)
 * 4 = Current global concentration `c_2` (= number of atoms of type 2 / total number of atoms)
 * ...
-* N+2: Current global concentration `c_N` (= number of atoms of type *N* / total number of atoms)
+* N+2 = Current global concentration `c_N` (= number of atoms of type *N* / total number of atoms)
 
 The vector values calculated by this fix are "intensive".
 

doc/src/fix_widom.rst

@@ -178,9 +178,9 @@ This fix computes a global vector of length 3, which can be accessed by
 various :doc:`output commands <Howto_output>`.  The vector values are
 the following global cumulative quantities:
 
-* 1 = average excess chemical potential on each timestep
+  #. average excess chemical potential on each timestep
-* 2 = average difference in potential energy on each timestep
+  #. average difference in potential energy on each timestep
-* 3 = volume of the insertion region
+  #. volume of the insertion region
 
 The vector values calculated by this fix are "intensive".