diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index 6cd6fa2f56..48f5b33a74 100644 --- a/doc/src/fix_atom_swap.rst +++ b/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 `. The vector values are the following global cumulative quantities: -* 1 = swap attempts -* 2 = swap accepts + #. swap attempts + #. swap accepts The vector values calculated by this fix are "intensive". diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index ac3b77086e..0fa4b02e58 100644 --- a/doc/src/fix_ave_histo.rst +++ b/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 -* 2 = values that were not histogrammed (see *beyond* keyword) -* 3 = min value of all input values, including ones not histogrammed -* 4 = max value of all input values, including ones not histogrammed + #. total counts in the histogram + #. values that were not histogrammed (see *beyond* keyword) + #. min 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 diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 3065707dc7..2447967e44 100644 --- a/doc/src/fix_balance.rst +++ b/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 -* 2 = total # iterations performed in last re-balance -* 3 = imbalance factor right before the last re-balance was performed + #. max # of particles per processor + #. total # iterations performed in last re-balance + #. 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 diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index fe77deb91e..020288ff9a 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/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 -* 2 = cumulative MC successes -* 3 = current # of neutral acid atoms -* 4 = current # of -1 charged acid atoms -* 5 = current # of neutral base atoms -* 6 = current # of +1 charged base atoms -* 7 = current # of free cations -* 8 = current # of free anions + #. cumulative MC attempts + #. cumulative MC successes + #. current # of neutral acid atoms + #. current # of -1 charged acid atoms + #. current # of neutral base atoms + #. current # of +1 charged base atoms + #. current # of free cations + #. current # of free anions Restrictions diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index aee8bdc90b..e6037af586 100644 --- a/doc/src/fix_gcmc.rst +++ b/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 `. The vector values are the following global cumulative quantities: -* 1 = translation attempts -* 2 = translation successes -* 3 = insertion attempts -* 4 = insertion successes -* 5 = deletion attempts -* 6 = deletion successes -* 7 = rotation attempts -* 8 = rotation successes + #. translation attempts + #. translation successes + #. insertion attempts + #. insertion successes + #. deletion attempts + #. deletion successes + #. rotation attempts + #. rotation successes The vector values calculated by this fix are "intensive". diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index 2ac1e5e4f3..3ab1c8c995 100644 --- a/doc/src/fix_hyper_global.rst +++ b/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) -* 2 = max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless) -* 3 = ID of first atom in the max-strain bond -* 4 = ID of second atom in the max-strain bond -* 5 = average # of bonds/atom on this step + #. boost factor on this step (unitless) + #. max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless) + #. ID of first atom in the max-strain bond + #. ID of second atom in the max-strain bond + #. average # of bonds/atom on this step -* 6 = 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 -* 8 = max drift distance of any atom during this run (distance units) -* 9 = max bond length during this run (distance units) + #. fraction of timesteps where the biased bond has bias = 0.0 during this run + #. fraction of timesteps where the biased bond has negative strain during this run + #. max drift distance of any atom during this run (distance units) + #. max bond length during this run (distance units) -* 10 = cumulative hyper time since fix was defined (time units) -* 11 = cumulative count of event timesteps since fix was defined -* 12 = cumulative count of atoms in events since fix was defined + #. cumulative hyper time since fix was defined (time units) + #. cumulative count of event timesteps 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 diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 54a4516fd1..26f8979ef1 100644 --- a/doc/src/fix_hyper_local.rst +++ b/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) -* 2 = # of biased bonds on this step -* 3 = 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) -* 5 = average bias coeff for all bonds on this step (unitless) -* 6 = min bias coeff for all bonds on this step (unitless) -* 7 = max bias coeff for all bonds on this step (unitless) -* 8 = average # of bonds/atom on this step -* 9 = average neighbor bonds/bond on this step within *Dcut* + #. average boost for all bonds on this step (unitless) + #. # of biased bonds on this step + #. max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless) + #. value of :math:`V^{max}` on this step (energy units) + #. average bias coeff for all bonds on this step (unitless) + #. min bias coeff for all bonds on this step (unitless) + #. max bias coeff for all bonds on this step (unitless) + #. average # of bonds/atom on this step + #. average neighbor bonds/bond on this step within *Dcut* -* 10 = average boost for all bonds during this run (unitless) -* 11 = average # of biased bonds/step during this run -* 12 = fraction of biased bonds with no bias during this run -* 13 = fraction of biased bonds with negative strain during this run -* 14 = max bond length during this run (distance units) -* 15 = average bias coeff for all bonds during this run (unitless) -* 16 = min bias coeff for any bond during this run (unitless) -* 17 = max bias coeff for any bond during this run (unitless) + #. average boost for all bonds during this run (unitless) + #. average # of biased bonds/step during this run + #. fraction of biased bonds with no bias during this run + #. fraction of biased bonds with negative strain during this run + #. max bond length during this run (distance units) + #. average bias coeff for all bonds during this run (unitless) + #. min 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) -* 19 = 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) -* 21 = 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 + #. max drift distance of any bond atom during this run (distance units) + #. max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units) + #. max distance outside my box of any ghost atom with any maxstrain during this run (distance units) + #. count of ghost atoms that could not be found on reneighbor steps during this run + #. count of bias overlaps (< *Dcut*) found during this run -* 23 = cumulative hyper time since fix created (time units) -* 24 = cumulative count of event timesteps since fix created -* 25 = cumulative count of atoms in events since fix created -* 26 = cumulative # of new bonds formed since fix created + #. cumulative hyper time since fix created (time units) + #. cumulative count of event timesteps since fix created + #. cumulative count of atoms in events since fix created + #. cumulative # of new bonds formed since fix created -27 = average boost for biased bonds on this step (unitless) -28 = # of bonds with absolute strain >= q on this step + #. average boost for biased bonds on this step (unitless) + #. # of bonds with absolute strain >= q on this step -The first quantities 1-9 are for the current timestep. Quantities -10-22 are for the current hyper run. They are reset each time a new +Quantities 1-9 are for the current timestep. Quantities 10-22 +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). diff --git a/doc/src/fix_mol_swap.rst b/doc/src/fix_mol_swap.rst index d437a6c2fe..2bd3756893 100644 --- a/doc/src/fix_mol_swap.rst +++ b/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 `. The vector values are the following global cumulative quantities: -* 1 = swap attempts -* 2 = swap accepts + #. swap attempts + #. swap accepts The vector values calculated by this fix are "intensive". diff --git a/doc/src/fix_reaxff_species.rst b/doc/src/fix_reaxff_species.rst index fba7fcaa93..107695f0f6 100644 --- a/doc/src/fix_reaxff_species.rst +++ b/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 -* 2 = total number of distinct species + #. total number of molecules + #. 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. diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index b9bdbfd849..3b124dd010 100644 --- a/doc/src/fix_restrain.rst +++ b/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 -* 2 = angle energy -* 3 = dihedral energy + #. bond energy + #. angle energy + #. dihedral energy The scalar and vector values calculated by this fix are "extensive". diff --git a/doc/src/fix_sgcmc.rst b/doc/src/fix_sgcmc.rst index 51ec572a47..b9d933cec3 100644 --- a/doc/src/fix_sgcmc.rst +++ b/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". diff --git a/doc/src/fix_widom.rst b/doc/src/fix_widom.rst index e9cffcba88..41ef133354 100644 --- a/doc/src/fix_widom.rst +++ b/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 `. The vector values are the following global cumulative quantities: -* 1 = average excess chemical potential on each timestep -* 2 = average difference in potential energy on each timestep -* 3 = volume of the insertion region + #. average excess chemical potential on each timestep + #. average difference in potential energy on each timestep + #. volume of the insertion region The vector values calculated by this fix are "intensive".