Some more code-blocks instead of parsed-literal

doc/src/Build_link.rst

@@ -11,7 +11,7 @@ The :doc:`Build basics <Build_basics>` doc page explains how to build
 LAMMPS as either a shared or static library.  This results in one of
 these 2 files:
 
-.. parsed-literal::
+.. code-block:: bash
 
    liblammps.so      # shared library
    liblammps.a       # static library

doc/src/Build_make.rst

@@ -73,7 +73,7 @@ in the LAMMPS distribution.  Typing "make machine" uses
 use Makefile.serial and Makefile.mpi, respectively.  Other makefiles
 are in these directories:
 
-.. parsed-literal::
+.. code-block:: bash
 
    OPTIONS      # Makefiles which enable specific options
    MACHINES     # Makefiles for specific machines

doc/src/Examples.rst

@@ -155,7 +155,7 @@ Lowercase directories
 
 Here is how you can run and visualize one of the sample problems:
 
-.. parsed-literal::
+.. code-block:: bash
 
    cd indent
    cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
@@ -177,9 +177,9 @@ like ImageMagick or QuickTime or various Windows-based tools.  See the
 Imagemagick command would create a GIF file suitable for viewing in a
 browser.
 
-.. parsed-literal::
+.. code-block:: bash
 
-   % convert -loop 1 \*.jpg foo.gif
+   % convert -loop 1 *.jpg foo.gif
 
 ----------
 

doc/src/Howto_drude2.rst

@@ -83,7 +83,7 @@ You can use the *polarizer* tool (Python script distributed with the
 USER-DRUDE package) to convert a non-polarizable data file (here
 *data.102494.lmp*\ ) to a polarizable data file (\ *data-p.lmp*\ )
 
-.. parsed-literal::
+.. code-block:: bash
 
    polarizer -q -f phenol.dff data.102494.lmp data-p.lmp
 

doc/src/Manual_build.rst

@@ -5,7 +5,7 @@ Depending on how you obtained LAMMPS, the doc directory has up
 to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
 plus 2 e-book format files:
 
-.. parsed-literal::
+.. code-block:: bash
 
    src             # content files for LAMMPS documentation
    html            # HTML version of the LAMMPS manual (see html/Manual.html)

doc/src/Python_call.rst

@@ -59,7 +59,7 @@ new potential.
 To use any of these commands, you only need to build LAMMPS with the
 PYTHON package installed:
 
-.. parsed-literal::
+.. code-block:: bash
 
    make yes-python
    make machine

doc/src/Python_install.rst

@@ -31,7 +31,7 @@ If you set the paths to these files as environment variables, you only
 have to do it once.  For the csh or tcsh shells, add something like
 this to your ~/.cshrc file, one line for each of the two files:
 
-.. parsed-literal::
+.. code-block:: csh
 
    setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
    setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src

doc/src/Python_mpi.rst

@@ -18,7 +18,7 @@ LAMMPS instances on subsets of the total MPI ranks.
 To install mpi4py (version mpi4py-3.0.3 as of Nov 2019), unpack it
 and from its main directory, type
 
-.. parsed-literal::
+.. code-block:: bash
 
    python setup.py build
    sudo python setup.py install
@@ -27,27 +27,27 @@ Again, the "sudo" is only needed if required to copy mpi4py files into
 your Python distribution's site-packages directory. To install with
 user privilege into the user local directory type
 
-.. parsed-literal::
+.. code-block:: bash
 
    python setup.py install --user
 
 If you have successfully installed mpi4py, you should be able to run
 Python and type
 
-.. parsed-literal::
+.. code-block:: python
 
    from mpi4py import MPI
 
 without error.  You should also be able to run python in parallel
 on a simple test script
 
-.. parsed-literal::
+.. code-block:: bash
 
    % mpirun -np 4 python test.py
 
 where test.py contains the lines
 
-.. parsed-literal::
+.. code-block:: python
 
    from mpi4py import MPI
    comm = MPI.COMM_WORLD

doc/src/Python_shlib.rst

@@ -12,7 +12,7 @@ wrap LAMMPS.  On Linux this is a library file that ends in ".so", not
 
 From the src directory, type
 
-.. parsed-literal::
+.. code-block:: bash
 
    make foo mode=shlib
 
@@ -37,7 +37,7 @@ Build LAMMPS as a shared library using CMake
 When using CMake the following two options are necessary to generate the LAMMPS
 shared library:
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D BUILD_LIB=on            # enable building LAMMPS as a library
    -D BUILD_SHARED_LIBS=on    # enable building of LAMMPS shared library (both options are needed!)
@@ -50,7 +50,7 @@ library path (e.g. /usr/lib64/) or in the LD_LIBRARY_PATH.
 If you want to use the shared library with Python the recommended way is to create a virtualenv and use it as
 CMAKE_INSTALL_PREFIX.
 
-.. parsed-literal::
+.. code-block:: bash
 
    # create virtualenv
    virtualenv --python=$(which python3) myenv3
@@ -69,7 +69,7 @@ This will also install the Python module into your virtualenv. Since virtualenv
 doesn't change your LD_LIBRARY_PATH, you still need to add its lib64 folder to
 it, which contains the installed liblammps.so.
 
-.. parsed-literal::
+.. code-block:: bash
 
    export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib64:$LD_LIBRARY_PATH
 

doc/src/Python_test.rst

@@ -49,7 +49,7 @@ interactively from the bench directory:
 
 Or put the same lines in the file test.py and run it as
 
-.. parsed-literal::
+.. code-block:: bash
 
    % python test.py
 
@@ -68,7 +68,7 @@ To run LAMMPS in parallel, assuming you have installed the
 `PyPar <https://github.com/daleroberts/pypar>`_ package as discussed
 above, create a test.py file containing these lines:
 
-.. parsed-literal::
+.. code-block:: python
 
    import pypar
    from lammps import lammps
@@ -81,7 +81,7 @@ To run LAMMPS in parallel, assuming you have installed the
 `mpi4py <https://bitbucket.org/mpi4py/mpi4py>`_ package as discussed
 above, create a test.py file containing these lines:
 
-.. parsed-literal::
+.. code-block:: python
 
    from mpi4py import MPI
    from lammps import lammps
@@ -94,13 +94,13 @@ above, create a test.py file containing these lines:
 
 You can either script in parallel as:
 
-.. parsed-literal::
+.. code-block:: bash
 
    % mpirun -np 4 python test.py
 
 and you should see the same output as if you had typed
 
-.. parsed-literal::
+.. code-block:: bash
 
    % mpirun -np 4 lmp_g++ -in in.lj
 
@@ -124,7 +124,7 @@ Running Python scripts:
 Note that any Python script (not just for LAMMPS) can be invoked in
 one of several ways:
 
-.. parsed-literal::
+.. code-block:: bash
 
    % python foo.script
    % python -i foo.script
@@ -133,7 +133,7 @@ one of several ways:
 The last command requires that the first line of the script be
 something like this:
 
-.. parsed-literal::
+.. code-block:: bash
 
    #!/usr/local/bin/python
    #!/usr/local/bin/python -i
@@ -141,7 +141,7 @@ something like this:
 where the path points to where you have Python installed, and that you
 have made the script file executable:
 
-.. parsed-literal::
+.. code-block:: bash
 
    % chmod +x foo.script
 

doc/src/Run_windows.rst

@@ -14,7 +14,7 @@ Note that the serial executable includes support for multi-threading
 parallelization from the styles in the USER-OMP packages.  To run with
 4 threads, you can type this:
 
-.. parsed-literal::
+.. code-block:: bash
 
    lmp_serial -in in.lj -pk omp 4 -sf omp
 
@@ -43,7 +43,7 @@ into the MPICH2 installation directory, then into the sub-directory
 
 Then type something like this:
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpiexec -localonly 4 lmp_mpi -in in.file
    mpiexec -np 4 lmp_mpi -in in.file
@@ -58,13 +58,13 @@ patient before the output shows up.
 The parallel executable can also run on a single processor by typing
 something like this:
 
-.. parsed-literal::
+.. code-block:: bash
 
    lmp_mpi -in in.lj
 
 Note that the parallel executable also includes OpenMP
 multi-threading, which can be combined with MPI using something like:
 
-.. parsed-literal::
+.. code-block:: bash
 
    mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp

doc/src/Speed_gpu.rst

@@ -76,7 +76,7 @@ automatically append "gpu" to styles that support it.  Use the "-pk
 gpu Ng" :doc:`command-line switch <Run_options>` to set Ng = # of
 GPUs/node to use.
 
-.. parsed-literal::
+.. code-block:: bash
 
    lmp_machine -sf gpu -pk gpu 1 -in in.script                         # 1 MPI task uses 1 GPU
    mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script           # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
@@ -106,7 +106,7 @@ and use of multiple MPI tasks/GPU is the same.
 Use the :doc:`suffix gpu <suffix>` command, or you can explicitly add an
 "gpu" suffix to individual styles in your input script, e.g.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    pair_style lj/cut/gpu 2.5
 

doc/src/Speed_intel.rst

@@ -205,7 +205,7 @@ For building with make, several example Makefiles for building with
 the Intel compiler are included with LAMMPS in the src/MAKE/OPTIONS/
 directory:
 
-.. parsed-literal::
+.. code-block:: bash
 
    Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
    Makefile.knl                # Intel Compiler, Intel MPI, No Offload

doc/src/Speed_omp.rst

@@ -23,7 +23,7 @@ instructions.
 
 These examples assume one or more 16-core nodes.
 
-.. parsed-literal::
+.. code-block:: bash
 
    env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script           # 1 MPI task, 16 threads according to OMP_NUM_THREADS
    lmp_mpi -sf omp -in in.script                                  # 1 MPI task, no threads, optimized kernels
@@ -60,7 +60,7 @@ and threads/MPI task is the same.
 Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
 "omp" suffix to individual styles in your input script, e.g.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    pair_style lj/cut/omp 2.5
 

doc/src/Speed_opt.rst

@@ -17,7 +17,7 @@ See the :ref:`Build extras <opt>` doc page for instructions.
 
 **Run with the OPT package from the command line:**
 
-.. parsed-literal::
+.. code-block:: bash
 
    lmp_mpi -sf opt -in in.script                # run in serial
    mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel
@@ -30,7 +30,7 @@ automatically append "opt" to styles that support it.
 Use the :doc:`suffix opt <suffix>` command, or you can explicitly add an
 "opt" suffix to individual styles in your input script, e.g.
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    pair_style lj/cut/opt 2.5
 

doc/src/Speed_packages.rst

@@ -132,7 +132,7 @@ packages.  As an example, here is a command that builds with all the
 GPU related packages installed (GPU, KOKKOS with Cuda), including
 settings to build the needed auxiliary GPU libraries for Kepler GPUs:
 
-.. parsed-literal::
+.. code-block:: bash
 
    Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi   -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
 

doc/src/Tools.rst

@@ -99,7 +99,7 @@ binary2txt tool
 The file binary2txt.cpp converts one or more binary LAMMPS dump file
 into ASCII text files.  The syntax for running the tool is
 
-.. parsed-literal::
+.. code-block:: bash
 
    binary2txt file1 file2 ...
 
@@ -149,7 +149,7 @@ chains and solvent atoms can strongly overlap, so LAMMPS needs to run
 the system initially with a "soft" pair potential to un-overlap it.
 The syntax for running the tool is
 
-.. parsed-literal::
+.. code-block:: bash
 
    chain < def.chain > data.file
 
@@ -178,11 +178,11 @@ Version 20110511
 
 .. parsed-literal::
 
-   Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0\|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
+   ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0\|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
 
 The LAMMPS interface to the colvars collective variable library, as
 well as these tools, were created by Axel Kohlmeyer (akohlmey at
-gmail.com) at ICTP, Italy.
+gmail.com) while at ICTP, Italy.
 
 ----------
 
@@ -427,7 +427,7 @@ atoms can strongly overlap, so LAMMPS needs to run the system
 initially with a "soft" pair potential to un-overlap it.  The syntax
 for running the tool is
 
-.. parsed-literal::
+.. code-block:: bash
 
    micelle2d < def.micelle2d > data.file