diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst
index 0926e3a72c..d74d5f7f35 100644
--- a/doc/src/Errors_common.rst
+++ b/doc/src/Errors_common.rst
@@ -71,7 +71,7 @@ Some commands allow for using variable references in place of numeric
 constants so that the value can be evaluated and may change over the
 course of a run.  This is typically done with the syntax *v\_name* for a
 parameter, where name is the name of the variable. On the other hand,
-immediate variable expansion with the syntax $\ *name* is performed while
+immediate variable expansion with the syntax ${name} is performed while
 reading the input and before parsing commands,
 
 .. note::
diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst
index 956e03cb87..1cad9cbeb8 100644
--- a/doc/src/Speed_intel.rst
+++ b/doc/src/Speed_intel.rst
@@ -192,7 +192,7 @@ will report every hardware thread as a separate core allowing one to
 determine the number of hardware threads available. On Linux systems,
 this information can normally be obtained with:
 
-.. parsed-literal::
+.. code-block:: bash
 
    cat /proc/cpuinfo
 
@@ -219,7 +219,7 @@ Phi x200 processors making it easier to cross-compile. For users with
 recent installations of Intel Parallel Studio, the process can be as
 simple as:
 
-.. parsed-literal::
+.. code-block:: bash
 
    make yes-user-intel
    source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
@@ -334,7 +334,7 @@ desired.
 Examples (see documentation for your MPI/Machine for differences in
 launching MPI applications):
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script                                 # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
    mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double   # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision
@@ -346,14 +346,14 @@ can be edited to enable the USER-INTEL package. This requires adding
 the :doc:`package intel <package>` command to the top of the input
 script. For the second example above, this would be:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    package intel 0 omp 2 mode double
 
 To enable the USER-INTEL package only for individual styles, you can
 add an "intel" suffix to the individual style, e.g.:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    pair_style lj/cut/intel 2.5
 
diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst
index 44ac153e60..46b4be571c 100644
--- a/doc/src/Speed_kokkos.rst
+++ b/doc/src/Speed_kokkos.rst
@@ -71,7 +71,7 @@ Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
 Here is a quick overview of how to use the KOKKOS package
 for CPU acceleration, assuming one or more 16-core nodes.
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj        # 1 node, 16 MPI tasks/node, no multi-threading
    mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj  # 2 nodes, 1 MPI task/node, 16 threads/task
@@ -119,7 +119,7 @@ below.
    page for details and default settings. Experimenting with its options
    can provide a speed-up for specific calculations. For example:
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm
 
@@ -180,9 +180,9 @@ tasks.
 
 Examples of mpirun commands that follow these rules are shown below.
 
-.. parsed-literal::
+.. code-block:: bash
 
-   Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):
+   # Running on an Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):
    mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 64 MPI tasks/node, 4 threads/task
    mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 66 MPI tasks/node, 4 threads/task
    mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj      # 1 node, 32 MPI tasks/node, 8 threads/task
@@ -205,7 +205,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
    details and default settings. Experimenting with its options can provide
    a speed-up for specific calculations. For example:
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax      #  Newton on, half neighbor list, threaded comm
    mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj      # Newton off, full neighbor list, non-threaded comm
@@ -246,7 +246,7 @@ then the number of MPI tasks/node should not exceed N.
 Here are examples of how to use the KOKKOS package for GPUs, assuming
 one or more nodes, each with two GPUs:
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
    mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total)
@@ -266,7 +266,7 @@ one or more nodes, each with two GPUs:
    default settings. Experimenting with its options can provide a speed-up
    for specific calculations. For example:
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
 
@@ -308,7 +308,7 @@ hardware options appropriate to your system, as documented above.
 You can use the :doc:`suffix kk <suffix>` command, or you can explicitly add a
 "kk" suffix to individual styles in your input script, e.g.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    pair_style lj/cut/kk 2.5
 
@@ -323,7 +323,7 @@ used together in a few special cases. In the Makefile, the
 KOKKOS\_DEVICES variable must include both "Cuda" and "OpenMP", as is
 the case for /src/MAKE/OPTIONS/Makefile.kokkos\_cuda\_mpi
 
-.. parsed-literal::
+.. code-block:: bash
 
    KOKKOS_DEVICES=Cuda,OpenMP
 
@@ -340,7 +340,7 @@ as "t Nt" and the number of GPUs as "g Ng"
 
 For example, the command to run with 1 GPU and 8 OpenMP threads is then:
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk
 
diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst
index 6abac88965..d1a683db87 100644
--- a/doc/src/compute_dpd_atom.rst
+++ b/doc/src/compute_dpd_atom.rst
@@ -16,7 +16,9 @@ Syntax
 Examples
 """"""""
 
-compute 1 all dpd/atom
+.. code-block:: LAMMPS
+
+   compute 1 all dpd/atom
 
 Description
 """""""""""
diff --git a/doc/src/dump.rst b/doc/src/dump.rst
index 3d243f71a4..2f1c58158f 100644
--- a/doc/src/dump.rst
+++ b/doc/src/dump.rst
@@ -125,18 +125,18 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump myDump all atom 100 dump.atom
    dump myDump all atom/mpiio 100 dump.atom.mpiio
    dump myDump all atom/gz 100 dump.atom.gz
    dump 2 subgroup atom 50 dump.run.bin
    dump 2 subgroup atom 50 dump.run.mpiio.bin
-   dump 4a all custom 100 dump.myforce.\* id type x y vx fx
+   dump 4a all custom 100 dump.myforce.* id type x y vx fx
    dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
    dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke
-   dump 2 inner cfg 10 dump.snap.\*.cfg mass type xs ys zs vx vy vz
-   dump snap all cfg 100 dump.config.\*.cfg mass type xs ys zs id type c_Stress[2]
+   dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
+   dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
    dump 1 all xtc 1000 file.xtc
 
 Description
@@ -425,7 +425,7 @@ library, which is part of the MPI standard for versions 2.0 and above.
 Using MPI-IO requires two steps.  First, build LAMMPS with its MPIIO
 package installed, e.g.
 
-.. parsed-literal::
+.. code-block:: bash
 
    make yes-mpiio    # installs the MPIIO package
    make mpi          # build LAMMPS for your platform
@@ -481,10 +481,10 @@ had been listed one by one.  E.g. these 2 dump commands are
 equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
 command creates a per-atom array with 6 columns:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute myPress all stress/atom NULL
-   dump 2 all custom 100 tmp.dump id myPress[\*]
+   dump 2 all custom 100 tmp.dump id myPress[*]
    dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
                                      myPress[4] myPress[5] myPress[6]
 
@@ -537,7 +537,7 @@ values.
 Here is an example of how to dump bond info for a system, including
 the distance and energy of each bond:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute 1 all property/local batom1 batom2 btype
    compute 2 all bond/local dist eng
diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst
index 099ac25ef5..69bd8aa8c2 100644
--- a/doc/src/dump_molfile.rst
+++ b/doc/src/dump_molfile.rst
@@ -21,10 +21,10 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump mf1 all molfile 10 melt1.xml hoomd
-   dump mf2 all molfile 10 melt2-\*.pdb pdb .
+   dump mf2 all molfile 10 melt2-*.pdb pdb .
    dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile
 
 Description
diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst
index 3dd8a7c5c5..5627060452 100644
--- a/doc/src/dump_netcdf.rst
+++ b/doc/src/dump_netcdf.rst
@@ -24,12 +24,12 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump 1 all netcdf 100 traj.nc type x y z vx vy vz
    dump_modify 1 append yes at -1 thermo yes
    dump 1 all netcdf/mpiio 1000 traj.nc id type x y z
-   dump 1 all netcdf 1000 traj.\*.nc id type x y z
+   dump 1 all netcdf 1000 traj.*.nc id type x y z
 
 Description
 """""""""""
diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst
index 8b5843a86b..e5264b783c 100644
--- a/doc/src/dump_vtk.rst
+++ b/doc/src/dump_vtk.rst
@@ -20,10 +20,10 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   dump dmpvtk all vtk 100 dump\*.myforce.vtk id type vx fx
-   dump dmpvtp flow vtk 100 dump\*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
+   dump dmpvtk all vtk 100 dump*.myforce.vtk id type vx fx
+   dump dmpvtp flow vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
 
 Description
 """""""""""
diff --git a/doc/src/echo.rst b/doc/src/echo.rst
index d91571ed0c..6fc00aa1e6 100644
--- a/doc/src/echo.rst
+++ b/doc/src/echo.rst
@@ -15,7 +15,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    echo both
    echo log
@@ -40,6 +40,6 @@ Restrictions
 Default
 """""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    echo log
diff --git a/doc/src/fix.rst b/doc/src/fix.rst
index 42fb071a43..b6088376bc 100644
--- a/doc/src/fix.rst
+++ b/doc/src/fix.rst
@@ -18,7 +18,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 1 all nve
    fix 3 all nvt temp 300.0 300.0 0.01
diff --git a/doc/src/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst
index 3ed7c3bbab..7113f1459c 100644
--- a/doc/src/fix_langevin_spin.rst
+++ b/doc/src/fix_langevin_spin.rst
@@ -19,7 +19,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 2 all langevin/spin 300.0 0.01 21
 
@@ -53,7 +53,7 @@ Note: due to the form of the sLLG equation, this fix has to be defined just
 before the nve/spin fix (and after all other magnetic fixes).
 As an example:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
    fix 2 all langevin/spin 300.0 0.01 21
diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst
index 1368a80139..d0adefee00 100644
--- a/doc/src/fix_saed_vtk.rst
+++ b/doc/src/fix_saed_vtk.rst
@@ -33,7 +33,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
    compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
@@ -65,7 +65,7 @@ which store their own "group" definitions.
 Fix saed/vtk is designed to work only with :doc:`compute saed <compute_saed>`
 values, e.g.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute 3 top saed 0.0251 Al O
    fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst
index 27ddc5bf0d..1b53bfe200 100644
--- a/doc/src/fix_setforce.rst
+++ b/doc/src/fix_setforce.rst
@@ -31,7 +31,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix freeze indenter setforce 0.0 0.0 0.0
    fix 2 edge setforce NULL 0.0 0.0
diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst
index 2df89918bc..d687920e97 100644
--- a/doc/src/fix_shake.rst
+++ b/doc/src/fix_shake.rst
@@ -39,7 +39,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
    fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst
index 8fd26c8471..a5ce32c89a 100644
--- a/doc/src/fix_shardlow.rst
+++ b/doc/src/fix_shardlow.rst
@@ -19,7 +19,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 1 all shardlow
 
diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst
index 9c269891c1..ddd6a15505 100644
--- a/doc/src/fix_smd.rst
+++ b/doc/src/fix_smd.rst
@@ -37,7 +37,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix  pull    cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
    fix  pull    cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst
index bd14ca1765..bdf97354f5 100644
--- a/doc/src/fix_smd_setvel.rst
+++ b/doc/src/fix_smd_setvel.rst
@@ -25,9 +25,9 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   fix top_velocity top_group setvel 1.0 0.0 0.0
+   fix top_velocity top_group smd/setvel 1.0 0.0 0.0
 
 Description
 """""""""""
diff --git a/doc/src/group.rst b/doc/src/group.rst
index 87c76f8ee4..42e1d29a85 100644
--- a/doc/src/group.rst
+++ b/doc/src/group.rst
@@ -48,7 +48,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    group edge region regstrip
    group water type 3 4
@@ -155,7 +155,7 @@ For example, these lines define a variable "eatom" that calculates the
 potential energy of each atom and includes it in the group if its
 potential energy is above the threshold value -3.0.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute         1 all pe/atom
    compute         2 all reduce sum c_1
@@ -167,7 +167,7 @@ potential energy is above the threshold value -3.0.
 
 Note that these lines
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute         2 all reduce sum c_1
    thermo_style    custom step temp pe c_2
@@ -266,7 +266,7 @@ used to model a quench of the system, freezing atoms outside the
 shrinking sphere, then converting the remaining atoms to a static
 group and running further.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable        nsteps equal 5000
    variable        rad equal 18-(step/v_nsteps)\*(18-5)
diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst
index b8b04ff19c..84e7b6df32 100644
--- a/doc/src/group2ndx.rst
+++ b/doc/src/group2ndx.rst
@@ -20,7 +20,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    group2ndx allindex.ndx
    group2ndx someindex.ndx upper lower mobile
diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst
index 60e5020ad4..d17af1d407 100644
--- a/doc/src/hyper.rst
+++ b/doc/src/hyper.rst
@@ -32,7 +32,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute event all event/displace 1.0
    fix HG mobile hyper/global 3.0 0.3 0.4 800.0
diff --git a/doc/src/if.rst b/doc/src/if.rst
index 4b7a4dbcbf..fff561bd77 100644
--- a/doc/src/if.rst
+++ b/doc/src/if.rst
@@ -21,7 +21,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    if "${steps} > 1000" then quit
    if "${myString} == a10" then quit
@@ -75,7 +75,7 @@ above.
 Note that by using the line continuation character "&", the if command
 can be spread across many lines, though it is still a single command:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    if "$a < $b" then &
      "print 'Minimum value = $a'" &
@@ -99,7 +99,7 @@ checked, so long as it is current on the timestep when the run
 completes.  As explained on the :doc:`variable <variable>` doc page,
 this can be insured by including the variable in thermodynamic output.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable myTemp equal temp
    label loop
@@ -115,19 +115,19 @@ Here is an example of a double loop which uses the if and
 :doc:`jump <jump>` commands to break out of the inner loop when a
 condition is met, then continues iterating through the outer loop.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    label       loopa
    variable    a loop 5
      label     loopb
      variable  b loop 5
-     print     "A,B = $a,$b"
-     run       10000
-     if        "$b > 2" then "jump SELF break"
+       print     "A,B = $a,$b"
+       run       10000
+       if        "$b > 2" then "jump SELF break"
      next      b
      jump      in.script loopb
-   label       break
-   variable    b delete
+     label       break
+     variable    b delete
    next        a
    jump        SELF loopa
 
diff --git a/doc/src/include.rst b/doc/src/include.rst
index 3721eabff2..e98ffa05e4 100644
--- a/doc/src/include.rst
+++ b/doc/src/include.rst
@@ -15,7 +15,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    include newfile
    include in.run2
diff --git a/doc/src/info.rst b/doc/src/info.rst
index f83813e637..77d430ea66 100644
--- a/doc/src/info.rst
+++ b/doc/src/info.rst
@@ -17,7 +17,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    info system
    info groups computes variables
diff --git a/doc/src/jump.rst b/doc/src/jump.rst
index d067b53832..d597b336d3 100644
--- a/doc/src/jump.rst
+++ b/doc/src/jump.rst
@@ -16,7 +16,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    jump newfile
    jump in.run2 runloop
@@ -39,7 +39,7 @@ script is re-opened and read again.
    The SELF option is not guaranteed to work when the current input
    script is being read through stdin (standard input), e.g.
 
-.. parsed-literal::
+.. code-block:: bash
 
    lmp_g++ < in.script
 
@@ -47,7 +47,7 @@ since the SELF option invokes the C-library rewind() call, which may
 not be supported for stdin on some systems or by some MPI
 implementations.  This can be worked around by using the :doc:`-in command-line switch <Run_options>`, e.g.
 
-.. parsed-literal::
+.. code-block:: bash
 
    lmp_g++ -in in.script
 
@@ -56,7 +56,7 @@ the script name as a variable to the input script.  In the latter
 case, a :doc:`variable <variable>` called "fname" could be used in place
 of SELF, e.g.
 
-.. parsed-literal::
+.. code-block:: bash
 
    lmp_g++ -var fname in.script < in.script
 
@@ -70,7 +70,7 @@ etc.  The :doc:`next <next>` command is used to exit the loop after 10
 iterations.  When the "a" variable has been incremented for the tenth
 time, it will cause the next jump command to be skipped.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable a loop 10
    label loop
@@ -87,7 +87,7 @@ partitions of 10 procs each.  An in.file containing the example
 variable and jump command will cause each partition to run a different
 simulation.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
 
@@ -101,7 +101,7 @@ checked, so long as it is current on the timestep when the run
 completes.  As explained on the :doc:`variable <variable>` doc page,
 this can be insured by including the variable in thermodynamic output.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable myTemp equal temp
    label loop
@@ -117,19 +117,19 @@ Here is an example of a double loop which uses the if and
 :doc:`jump <jump>` commands to break out of the inner loop when a
 condition is met, then continues iterating through the outer loop.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    label       loopa
    variable    a loop 5
      label     loopb
      variable  b loop 5
-     print     "A,B = $a,$b"
-     run       10000
-     if        "$b > 2" then "jump SELF break"
+       print     "A,B = $a,$b"
+       run       10000
+       if        "$b > 2" then "jump SELF break"
      next      b
      jump      in.script loopb
-   label       break
-   variable    b delete
+     label       break
+     variable    b delete
    next        a
    jump        SELF loopa
 
diff --git a/doc/src/label.rst b/doc/src/label.rst
index 75c5d2cccc..0b1273008f 100644
--- a/doc/src/label.rst
+++ b/doc/src/label.rst
@@ -15,7 +15,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    label xyz
    label loop
diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst
index 97d20ca181..693d0cd84a 100644
--- a/doc/src/lattice.rst
+++ b/doc/src/lattice.rst
@@ -38,7 +38,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    lattice fcc 3.52
    lattice hex 0.85
@@ -254,11 +254,11 @@ in commands that use the spacings should be decipherable.
 Example commands for generating a Wurtzite crystal (courtesy
 of Aidan Thompson), with its 8 atom unit cell.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable a equal  4.340330
-   variable b equal  $a\*sqrt(3.0)
-   variable c equal  $a\*sqrt(8.0/3.0)
+   variable b equal  $a*sqrt(3.0)
+   variable c equal  $a*sqrt(8.0/3.0)
 
    variable 1_3 equal 1.0/3.0
    variable 2_3 equal 2.0/3.0
@@ -304,7 +304,7 @@ Related commands
 Default
 """""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    lattice none 1.0
 
diff --git a/doc/src/log.rst b/doc/src/log.rst
index ab8f1b73d1..5c412d4d9f 100644
--- a/doc/src/log.rst
+++ b/doc/src/log.rst
@@ -16,7 +16,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    log log.equil
    log log.equil append
diff --git a/doc/src/mass.rst b/doc/src/mass.rst
index 4185cfbd7d..55ba9c61bf 100644
--- a/doc/src/mass.rst
+++ b/doc/src/mass.rst
@@ -16,11 +16,11 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    mass 1 1.0
-   mass \* 62.5
-   mass 2\* 62.5
+   mass * 62.5
+   mass 2* 62.5
 
 Description
 """""""""""
diff --git a/doc/src/message.rst b/doc/src/message.rst
index d1c6423e3d..f4ca5735e0 100644
--- a/doc/src/message.rst
+++ b/doc/src/message.rst
@@ -28,7 +28,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    message client md file tmp.couple
    message server md file tmp.couple
@@ -95,7 +95,7 @@ code's machine.  Support for socket messaging is provided by the
 open-source `ZeroMQ library <http://zeromq.org>`_, which must be
 installed on your system.  The client specifies an IP address (IPv4
 format) or the DNS name of the machine the server code is running on,
-followed by a 4-digit port ID for the socket, separated by a colon.
+followed by a 4 or 5 digit port ID for the socket, separated by a colon.
 E.g.
 
 .. parsed-literal::
@@ -110,7 +110,20 @@ what the client specifies.
 
 .. note::
 
-   What are allowed port IDs?
+   On Linux or Unix machines port IDs below 1024 are reserved to the
+   superuser and thus not available.  Other ports may already be in
+   use and cannot be opened by a second process.  On a Linux machine
+   the commands "netstat -t4an" or "ss -t4an" will list all locally
+   used port IDs for IPv4 addresses.
+
+.. note::
+
+   On many machines (and sometimes on local networks) also ports IDs
+   may be blocked by default through firewalls.  In that case either
+   access to the required port (or a desired range of ports) has to
+   be selectively enabled to the firewall disabled (the latter is
+   usually not a good idea unless you are on a (small) local network
+   that is already protected from outside access.
 
 .. note::
 
@@ -120,7 +133,7 @@ what the client specifies.
 For mode *mpi/one*\ , the 2 codes communicate via MPI and are launched
 by the same mpirun command, e.g. with this syntax for OpenMPI:
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args  # LAMMPS is client
    mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server  # LAMMPS is server
diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst
index 07fef5ca95..dde5284b7a 100644
--- a/doc/src/minimize.rst
+++ b/doc/src/minimize.rst
@@ -21,7 +21,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    minimize 1.0e-4 1.0e-6 100 1000
    minimize 0.0 1.0e-8 1000 100000
diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst
index e25684d6f4..f6839c57df 100644
--- a/doc/src/molecule.rst
+++ b/doc/src/molecule.rst
@@ -39,7 +39,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    molecule 1 mymol.txt
    molecule 1 co2.txt h2o.txt
diff --git a/doc/src/neb.rst b/doc/src/neb.rst
index c7641ed7c2..bd08ae3d1d 100644
--- a/doc/src/neb.rst
+++ b/doc/src/neb.rst
@@ -34,7 +34,7 @@ keyword = *verbose*
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    neb 0.1 0.0 1000 500 50 final coords.final
    neb 0.0 0.001 1000 500 50 each coords.initial.$i
@@ -147,7 +147,7 @@ For a *file-style* setting of *each*\ , a filename is specified which is
 assumed to be unique to each replica.  This can be done by using a
 variable in the filename, e.g.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable i equal part
    neb 0.0 0.001 1000 500 50 each coords.initial.$i
diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst
index 9e9431671a..cbeca25327 100644
--- a/doc/src/neb_spin.rst
+++ b/doc/src/neb_spin.rst
@@ -38,7 +38,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    neb/spin 0.1 0.0 1000 500 50 final coords.final
    neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i
diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst
index aa05146805..1bb591587c 100644
--- a/doc/src/neighbor.rst
+++ b/doc/src/neighbor.rst
@@ -16,7 +16,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    neighbor 0.3 bin
    neighbor 2.0 nsq
diff --git a/doc/src/newton.rst b/doc/src/newton.rst
index ca981e917a..df1298a9e4 100644
--- a/doc/src/newton.rst
+++ b/doc/src/newton.rst
@@ -18,7 +18,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    newton off
    newton on off
@@ -64,6 +64,6 @@ Related commands
 Default
 """""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    newton on
diff --git a/doc/src/next.rst b/doc/src/next.rst
index 828d6bd0f5..fd62e29ffe 100644
--- a/doc/src/next.rst
+++ b/doc/src/next.rst
@@ -15,7 +15,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    next x
    next a t x myTemp
@@ -82,7 +82,7 @@ command with an *index*\ -style variable.  If this input script is named
 in.polymer, 8 simulations would be run using data files from
 directories run1 through run8.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable d index run1 run2 run3 run4 run5 run6 run7 run8
    shell cd $d
@@ -103,7 +103,7 @@ finished.
 Jump and next commands can also be nested to enable multi-level loops.
 For example, this script will run 15 simulations in a double loop.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable i loop 3
      variable j loop 5
@@ -121,7 +121,7 @@ Here is an example of a double loop which uses the :doc:`if <if>` and
 :doc:`jump <jump>` commands to break out of the inner loop when a
 condition is met, then continues iterating through the outer loop.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    label       loopa
    variable    a loop 5
diff --git a/doc/src/package.rst b/doc/src/package.rst
index a4a70ccb59..059dfba957 100644
--- a/doc/src/package.rst
+++ b/doc/src/package.rst
@@ -102,7 +102,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    package gpu 1
    package gpu 1 split 0.75
@@ -230,7 +230,7 @@ As an example, if you have two GPUs per node and 8 CPU cores per node,
 and would like to run on 4 nodes (32 cores) with dynamic balancing of
 force calculation across CPU and GPU cores, you could specify
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpirun -np 32 -sf gpu -in in.script    # launch command
    package gpu 2 split -1                 # input script command
@@ -566,7 +566,7 @@ performance.
 Here are examples of how to set the environment variable when
 launching LAMMPS:
 
-.. parsed-literal::
+.. code-block:: bash
 
    env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
    env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
diff --git a/doc/src/partition.rst b/doc/src/partition.rst
index 7edddb6f92..be333ba581 100644
--- a/doc/src/partition.rst
+++ b/doc/src/partition.rst
@@ -17,12 +17,12 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    partition yes 1 processors 4 10 6
    partition no 5 print "Active partition"
-   partition yes \*5 fix all nve
-   partition yes 6\* fix all nvt temp 1.0 1.0 0.1
+   partition yes *5 fix all nve
+   partition yes 6* fix all nvt temp 1.0 1.0 0.1
 
 Description
 """""""""""
diff --git a/doc/src/prd.rst b/doc/src/prd.rst
index d3a9dcf339..d849c8f5a8 100644
--- a/doc/src/prd.rst
+++ b/doc/src/prd.rst
@@ -39,7 +39,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    prd 5000 100 10 10 100 1 54982
    prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200
diff --git a/doc/src/print.rst b/doc/src/print.rst
index b1a4a681d0..b9ed8555fa 100644
--- a/doc/src/print.rst
+++ b/doc/src/print.rst
@@ -24,7 +24,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    print "Done with equilibration" file info.dat
    print Vol=$v append info.dat screen no
diff --git a/doc/src/processors.rst b/doc/src/processors.rst
index 7c5db5563b..8fe13f69eb 100644
--- a/doc/src/processors.rst
+++ b/doc/src/processors.rst
@@ -41,15 +41,15 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   processors \* \* 5
+   processors * * 5
    processors 2 4 4
-   processors \* \* 8 map xyz
-   processors \* \* \* grid numa
-   processors \* \* \* grid twolevel 4 \* \* 1
+   processors * * 8 map xyz
+   processors * * * grid numa
+   processors * * * grid twolevel 4 * * 1
    processors 4 8 16 grid custom myfile
-   processors \* \* \* part 1 2 multiple
+   processors * * * part 1 2 multiple
 
 Description
 """""""""""
@@ -93,7 +93,7 @@ Px,Py,Pz values for different partitions.
 You can use the :doc:`partition <partition>` command to specify
 different processor grids for different partitions, e.g.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    partition yes 1 processors 4 4 4
    partition yes 2 processors 2 3 2
diff --git a/doc/src/quit.rst b/doc/src/quit.rst
index 08b96e28ce..8059232c6a 100644
--- a/doc/src/quit.rst
+++ b/doc/src/quit.rst
@@ -15,7 +15,7 @@ status = numerical exit status (optional)
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    quit
    if "$n > 10000" then "quit 1"
diff --git a/doc/src/region.rst b/doc/src/region.rst
index d791ab8642..f080992311 100644
--- a/doc/src/region.rst
+++ b/doc/src/region.rst
@@ -72,7 +72,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    region 1 block -3.0 5.0 INF 10.0 INF INF
    region 2 sphere 0.0 0.0 0.0 5 side out
@@ -289,7 +289,7 @@ For example, these commands would displace a region from its initial
 position, in the positive x direction, effectively at a constant
 velocity:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable dx equal ramp(0,10)
    region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
@@ -299,10 +299,10 @@ Note that the initial displacement is 0.0, though that is not required.
 Either of these variables would "wiggle" the region back and forth in
 the y direction:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable dy equal swiggle(0,5,100)
-   variable dysame equal 5\*sin(2\*PI\*elaplong\*dt/100)
+   variable dysame equal 5*sin(2*PI*elaplong*dt/100)
    region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL
 
 The *rotate* keyword rotates the region around a rotation axis *R* =
diff --git a/doc/src/replicate.rst b/doc/src/replicate.rst
index 8aef4086aa..18038ae2dd 100644
--- a/doc/src/replicate.rst
+++ b/doc/src/replicate.rst
@@ -21,7 +21,7 @@ nx,ny,nz = replication factors in each dimension
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    replicate 2 3 2
 
diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst
index f604ca51e1..c92947ac6d 100644
--- a/doc/src/rerun.rst
+++ b/doc/src/rerun.rst
@@ -33,7 +33,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    rerun dump.file dump x y z vx vy vz
    rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z
diff --git a/doc/src/restart.rst b/doc/src/restart.rst
index e11fe00971..fbbcdd27b4 100644
--- a/doc/src/restart.rst
+++ b/doc/src/restart.rst
@@ -29,7 +29,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    restart 0
    restart 1000 poly.restart
@@ -85,7 +85,7 @@ file via the MPI-IO library, which is part of the MPI standard for
 versions 2.0 and above.  Using MPI-IO requires two steps.  First,
 build LAMMPS with its MPIIO package installed, e.g.
 
-.. parsed-literal::
+.. code-block:: bash
 
    make yes-mpiio    # installs the MPIIO package
    make mpi          # build LAMMPS for your platform
@@ -117,7 +117,7 @@ For example, the following commands will write restart files
 every step from 1100 to 1200, and could be useful for debugging
 a simulation where something goes wrong at step 1163:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable       s equal stride(1100,1200,1)
    restart        v_s tmp.restart
@@ -180,6 +180,6 @@ Related commands
 Default
 """""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    restart 0
diff --git a/doc/src/run.rst b/doc/src/run.rst
index 15c2b3c030..f36fb73187 100644
--- a/doc/src/run.rst
+++ b/doc/src/run.rst
@@ -31,7 +31,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    run 10000
    run 1000000 upto
@@ -70,7 +70,7 @@ keywords.
 
 For example, consider this fix followed by 10 run commands:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix         1 all nvt 200.0 300.0 1.0
    run         1000 start 0 stop 10000
@@ -144,14 +144,14 @@ of M steps each.  After each M-length run, the specified commands are
 invoked.  If only a single command is specified as NULL, then no
 command is invoked.  Thus these lines:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable q equal x[100]
    run 6000 every 2000 "print 'Coord = $q'"
 
 are the equivalent of:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable q equal x[100]
    run 2000
@@ -169,7 +169,7 @@ Note that by using the line continuation character "&", the run every
 command can be spread across many lines, though it is still a single
 command:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    run 100000 every 1000 &
      "print 'Minimum value = $a'" &
@@ -187,7 +187,7 @@ skipped for intermediate runs.
    You might wish to specify a command that exits the run by
    jumping out of the loop, e.g.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable t equal temp
    run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'"
diff --git a/doc/src/server.rst b/doc/src/server.rst
index ce83c4c12a..a25d97ba40 100644
--- a/doc/src/server.rst
+++ b/doc/src/server.rst
@@ -15,7 +15,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    server md
 
diff --git a/doc/src/server_mc.rst b/doc/src/server_mc.rst
index c1ff976ea7..bf02da8e95 100644
--- a/doc/src/server_mc.rst
+++ b/doc/src/server_mc.rst
@@ -15,7 +15,7 @@ mc = the protocol argument to the :doc:`server <server>` command
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    server mc
 
diff --git a/doc/src/server_md.rst b/doc/src/server_md.rst
index 0782c64258..11b0db6554 100644
--- a/doc/src/server_md.rst
+++ b/doc/src/server_md.rst
@@ -15,7 +15,7 @@ md = the protocol argument to the :doc:`server <server>` command
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    server md
 
diff --git a/doc/src/set.rst b/doc/src/set.rst
index 790ed5040c..6d81eb1936 100644
--- a/doc/src/set.rst
+++ b/doc/src/set.rst
@@ -120,16 +120,16 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    set group solvent type 2
    set group solvent type/fraction 2 0.5 12393
    set group edge bond 4
    set region half charge 0.5
    set type 3 charge 0.5
-   set type 1\*3 charge 0.5
-   set atom \* charge v_atomfile
-   set atom 100\*200 x 0.5 y 1.0
+   set type 1*3 charge 0.5
+   set atom * charge v_atomfile
+   set atom 100*200 x 0.5 y 1.0
    set atom 100 vx 0.0 vy 0.0 vz -1.0
    set atom 1492 type 3
 
diff --git a/doc/src/shell.rst b/doc/src/shell.rst
index 9374a32c9a..08c6a8b635 100644
--- a/doc/src/shell.rst
+++ b/doc/src/shell.rst
@@ -32,7 +32,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    shell cd sub1
    shell cd ..
@@ -89,7 +89,7 @@ Any other cmd is passed as-is to the shell along with its arguments as
 one string, invoked by the C-library system() call.  For example,
 these lines in your input script:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable n equal 10
    variable foo string file2
@@ -97,7 +97,7 @@ these lines in your input script:
 
 would be the same as invoking
 
-.. parsed-literal::
+.. code-block:: bash
 
    % my_setup file1 10 file2
 
diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst
index f9dd9a32f7..68cbf5d25a 100644
--- a/doc/src/suffix.rst
+++ b/doc/src/suffix.rst
@@ -16,7 +16,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    suffix off
    suffix on
diff --git a/doc/src/tad.rst b/doc/src/tad.rst
index 2a036218a5..b8de42a7eb 100644
--- a/doc/src/tad.rst
+++ b/doc/src/tad.rst
@@ -41,7 +41,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    tad 2000 50 1800 2300 0.01 0.01 event
    tad 2000 50 1800 2300 0.01 0.01 event &
diff --git a/doc/src/temper.rst b/doc/src/temper.rst
index fe0976d28b..3ac6481ff1 100644
--- a/doc/src/temper.rst
+++ b/doc/src/temper.rst
@@ -21,7 +21,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    temper 100000 100 $t tempfix 0 58728
    temper 40000 100 $t tempfix 0 32285 $w
@@ -50,7 +50,7 @@ variable previously set in the input script, so that each partition is
 assigned a different temperature.  See the :doc:`variable <variable>`
 command for more details.  For example:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable t world 300.0 310.0 320.0 330.0
    fix myfix all nvt temp $t $t 100.0
@@ -102,10 +102,10 @@ screen.N files as time proceeds.
 You can have each replica create its own dump file in the following
 manner:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable rep world 0 1 2 3 4 5 6 7
-   dump 1 all atom 1000 dump.temper.$\ *rep*
+   dump 1 all atom 1000 dump.temper.${rep}
 
 .. note::
 
@@ -143,7 +143,7 @@ log file listed the following for a simulation with 5 replicas:
 
 then a setting of
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable w world 2 4 0 1 3
 
diff --git a/doc/src/temper_grem.rst b/doc/src/temper_grem.rst
index e5103ed39b..c492adfa69 100644
--- a/doc/src/temper_grem.rst
+++ b/doc/src/temper_grem.rst
@@ -22,10 +22,10 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   temper/grem 100000 1000 $\ *lambda* fxgREM fxnvt 0 58728
-   temper/grem 40000 100 $\ *lambda* fxgREM fxnpt 0 32285 $\ *walkers*
+   temper/grem 100000 1000 ${lambda} fxgREM fxnvt 0 58728
+   temper/grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 ${walkers}
 
 Description
 """""""""""
@@ -47,17 +47,18 @@ has the same dependencies, restraints, and input variables which are
 discussed there in greater detail.
 
 Instead of temperature, this command performs replica exchanges in
-lambda as per the generalized ensemble enforced by :doc:`fix grem <fix_grem>`.  The desired lambda is specified by *lambda*\ ,
-which is typically a variable previously set in the input script, so
-that each partition is assigned a different temperature.  See the
-:doc:`variable <variable>` command for more details.  For example:
+lambda as per the generalized ensemble enforced by :doc:`fix grem
+<fix_grem>`.  The desired lambda is specified by *lambda*\ , which is
+typically a variable previously set in the input script, so that each
+partition is assigned a different temperature.  See the :doc:`variable
+<variable>` command for more details.  For example:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable lambda world 400 420 440 460
    fix fxnvt all nvt temp 300.0 300.0 100.0
-   fix fxgREM all grem $\ *lambda* -0.05 -50000 fxnvt
-   temper 100000 100 $\ *lambda* fxgREM fxnvt 3847 58382
+   fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt
+   temper/grem 100000 100 ${lambda} fxgREM fxnvt 3847 58382
 
 would define 4 lambdas with constant kinetic temperature but unique
 generalized temperature, and assign one of them to :doc:`fix grem <fix_grem>` used by each replica, and to the grem command.
@@ -87,12 +88,12 @@ a simulation with 5 replicas:
 
 then a setting of
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable walkers world 2 4 0 1 3
 
 would be used to restart the run with a grem command like the example
-above with $\ *walkers* as the last argument. This functionality is
+above with ${walkers} as the last argument. This functionality is
 identical to :doc:`temper <temper>`.
 
 ----------
diff --git a/doc/src/temper_npt.rst b/doc/src/temper_npt.rst
index 98ae977696..e0897886f4 100644
--- a/doc/src/temper_npt.rst
+++ b/doc/src/temper_npt.rst
@@ -22,7 +22,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    temper/npt 100000 100 $t nptfix 0 58728 1
    temper/npt 2500000 1000 300 nptfix  0 32285 $p
diff --git a/doc/src/thermo.rst b/doc/src/thermo.rst
index 5419ca1860..3ab789457e 100644
--- a/doc/src/thermo.rst
+++ b/doc/src/thermo.rst
@@ -16,7 +16,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    thermo 100
 
@@ -45,7 +45,7 @@ options for :doc:`equal-style variables <variable>`.
 For example, the following commands will output thermodynamic info at
 timesteps 0,10,20,30,100,200,300,1000,2000,etc:
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable        s equal logfreq(10,3,10)
    thermo          v_s
@@ -62,6 +62,6 @@ Related commands
 Default
 """""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    thermo 0
diff --git a/doc/src/timer.rst b/doc/src/timer.rst
index 7aa9184622..eac86656af 100644
--- a/doc/src/timer.rst
+++ b/doc/src/timer.rst
@@ -26,7 +26,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    timer full sync
    timer timeout 2:00:00 every 100
@@ -125,7 +125,7 @@ Related commands
 Default
 """""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    timer normal nosync
    timer timeout off
diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst
index a1f0cea7a9..7ee090740a 100644
--- a/doc/src/timestep.rst
+++ b/doc/src/timestep.rst
@@ -15,7 +15,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    timestep 2.0
    timestep 0.003
diff --git a/doc/src/uncompute.rst b/doc/src/uncompute.rst
index 3721bbf614..16efdb86bf 100644
--- a/doc/src/uncompute.rst
+++ b/doc/src/uncompute.rst
@@ -15,7 +15,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    uncompute 2
    uncompute lower-boundary
diff --git a/doc/src/undump.rst b/doc/src/undump.rst
index 79f0859663..b45e10082b 100644
--- a/doc/src/undump.rst
+++ b/doc/src/undump.rst
@@ -15,7 +15,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    undump mine
    undump 2
diff --git a/doc/src/unfix.rst b/doc/src/unfix.rst
index 5b74cb7dcb..e5696a1d7d 100644
--- a/doc/src/unfix.rst
+++ b/doc/src/unfix.rst
@@ -15,7 +15,7 @@ Syntax
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    unfix 2
    unfix lower-boundary
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 7c498d9215..264c3fab50 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -1929,6 +1929,7 @@ Nelement
 Nelements
 nemd
 netcdf
+netstat
 Nettleton
 Neumann
 Nevent