From 61ebf6265a89d86106f5701f193f8f1f775ffb27 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 12 Jan 2018 12:50:02 -0500
Subject: [PATCH] address some formatting/markup issues reported by Nandor
Tamaskovics
---
doc/src/compute_orientorder_atom.txt | 2 +-
doc/src/compute_sna_atom.txt | 2 +-
doc/src/fix_controller.txt | 6 +++---
doc/src/fix_shake.txt | 2 +-
doc/src/fix_smd_integrate_tlsph.txt | 7 ++-----
doc/src/fix_smd_integrate_ulsph.txt | 9 ++++-----
doc/src/pair_smd_hertz.txt | 2 +-
doc/src/pair_smd_triangulated_surface.txt | 2 +-
doc/src/pair_smd_ulsph.txt | 4 ++--
9 files changed, 16 insertions(+), 20 deletions(-)
diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt
index 70c7ef68f7..adf11dcfcf 100644
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@@ -67,7 +67,7 @@ parameters. This is followed by that number of integers giving the
degree of each order parameter. Because {Q}2 and all odd-degree order
parameters are zero for atoms in cubic crystals (see
"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
-{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn}=12, {Q}4
+{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn} =12, {Q}4
= sqrt(7/3)/8 = 0.19094.... The numerical values of all order
parameters up to {Q}12 for a range of commonly encountered
high-symmetry structures are given in Table I of "Mickel et
diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index defd98d520..1c3787e696 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -224,7 +224,7 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
notation. Each of these sub-blocks contains one column for each
bispectrum component, the same as for compute {sna/atom}
-For example, if {K}=30 and ntypes=1, the number of columns in the per-atom
+For example, if {K} =30 and ntypes=1, the number of columns in the per-atom
arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
are 30, 90, and 180, respectively. With {quadratic} value=1,
the numbers of columns are 930, 2790, and 5580, respectively.
diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt
index cd4d6adfdf..cfb26138fd 100644
--- a/doc/src/fix_controller.txt
+++ b/doc/src/fix_controller.txt
@@ -83,7 +83,7 @@ the following dynamic equation:
:c,image(Eqs/fix_controller1.jpg)
where {c} is the continuous time analog of the control variable,
-{e}={pvar}-{setpoint} is the error in the process variable, and
+{e} ={pvar}-{setpoint} is the error in the process variable, and
{alpha}, {Kp}, {Ki}, and {Kd} are constants set by the corresponding
keywords described above. The discretized version of this equation is:
@@ -106,10 +106,10 @@ the value of {alpha} to reflect this, while leaving {Kp}, {Ki}, and
When choosing the values of the four constants, it is best to first
pick a value and sign for {alpha} that is consistent with the
magnitudes and signs of {pvar} and {cvar}. The magnitude of {Kp}
-should then be tested over a large positive range keeping {Ki}={Kd}=0.
+should then be tested over a large positive range keeping {Ki} = {Kd} =0.
A good value for {Kp} will produce a fast response in {pvar}, without
overshooting the {setpoint}. For many applications, proportional
-feedback is sufficient, and so {Ki}={Kd}=0 can be used. In cases where
+feedback is sufficient, and so {Ki} = {Kd} =0 can be used. In cases where
there is a substantial lag time in the response of {pvar} to a change
in {cvar}, this can be counteracted by increasing {Kd}. In situations
where {pvar} plateaus without reaching {setpoint}, this can be
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index 9f82fc0fb6..46452a1f7e 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -58,7 +58,7 @@ required in order to eliminate velocity components along the bonds
In order to formulate individual constraints for SHAKE and RATTLE,
focus on a single molecule whose bonds are constrained. Let Ri and Vi
be the position and velocity of atom {i} at time {n}, for
-{i}=1,...,{N}, where {N} is the number of sites of our reference
+{i} =1,...,{N}, where {N} is the number of sites of our reference
molecule. The distance vector between sites {i} and {j} is given by
:c,image(Eqs/fix_rattle_rij.jpg)
diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt
index 24d319bdb9..17c9c0f400 100644
--- a/doc/src/fix_smd_integrate_tlsph.txt
+++ b/doc/src/fix_smd_integrate_tlsph.txt
@@ -14,15 +14,12 @@ fix ID group-ID smd/integrate_tlsph keyword values :pre
ID, group-ID are documented in "fix"_fix.html command
smd/integrate_tlsph = style name of this fix command
-zero or more keyword/value pairs may be appended :ul
-
-keyword = {limit_velocity} :l
+zero or more keyword/value pairs may be appended
+keyword = {limit_velocity} :ul
{limit_velocity} value = max_vel
max_vel = maximum allowed velocity :pre
-:ule
-
[Examples:]
fix 1 all smd/integrate_tlsph
diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt
index 0dfb9451de..28e38c7f97 100644
--- a/doc/src/fix_smd_integrate_ulsph.txt
+++ b/doc/src/fix_smd_integrate_ulsph.txt
@@ -14,9 +14,8 @@ fix ID group-ID smd/integrate_ulsph keyword :pre
ID, group-ID are documented in "fix"_fix.html command
smd/integrate_ulsph = style name of this fix command
-zero or more keyword/value pairs may be appended :ul
-
-keyword = adjust_radius or limit_velocity
+zero or more keyword/value pairs may be appended
+keyword = adjust_radius or limit_velocity :ul
adjust_radius values = adjust_radius_factor min_nn max_nn
adjust_radius_factor = factor which scale the smooth/kernel radius
@@ -28,7 +27,7 @@ limit_velocity values = max_velocity
[Examples:]
-fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 :pre
+fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre
[Description:]
@@ -38,7 +37,7 @@ See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics
The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are
-{adjust_radius_factor}=1.02, {min_nn}=15, and {max_nn}=20.
+{adjust_radius_factor} =1.02, {min_nn} =15, and {max_nn} =20.
The {limit_velocity} keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.
diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt
index 2a70c598ce..eeaa3387a4 100644
--- a/doc/src/pair_smd_hertz.txt
+++ b/doc/src/pair_smd_hertz.txt
@@ -28,7 +28,7 @@ The parameter <contact_stiffness> has units of pressure and should equal roughly
of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.
The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach each other. Usually, {scale_factor}=1.0.
+particles can approach each other. Usually, {scale_factor} =1.0.
:line
diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt
index 76d3891a3c..c32bf3a22e 100644
--- a/doc/src/pair_smd_triangulated_surface.txt
+++ b/doc/src/pair_smd_triangulated_surface.txt
@@ -29,7 +29,7 @@ The parameter <contact_stiffness> has units of pressure and should equal roughly
of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle
The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach the triangulated surface. Usually, {scale_factor}=1.0.
+particles can approach the triangulated surface. Usually, {scale_factor} =1.0.
:line
diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt
index 393bbc0665..268fe78d02 100644
--- a/doc/src/pair_smd_ulsph.txt
+++ b/doc/src/pair_smd_ulsph.txt
@@ -12,8 +12,8 @@ pair_style smd/ulsph command :h3
pair_style smd/ulsph args :pre
-these keywords must be given :l
-keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT} or {*NO_VELOCITY_GRADIENT} and {*GRADIENT_CORRECTION} or {*NO_GRADIENT_CORRECTION}
+these keywords must be given :ul
+keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT} or {*NO_VELOCITY_GRADIENT} and {*GRADIENT_CORRECTION} or {*NO_GRADIENT_CORRECTION} :pre
[Examples:]
--
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