diff --git a/doc/src/Howto_amoeba.rst b/doc/src/Howto_amoeba.rst index 6b84fc9f00..c927c28a1f 100644 --- a/doc/src/Howto_amoeba.rst +++ b/doc/src/Howto_amoeba.rst @@ -261,11 +261,11 @@ all the options available to use with the tinker2lmp.py script: .. code-block:: bash - % python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba # AMOEBA non-periodic system - % python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo # HIPPO non-periodic system - % python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643 # AMOEBA periodic system - % python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643 # HIPPO periodic system - % python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new # system with bitorsions + python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba # AMOEBA non-periodic system + python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo # HIPPO non-periodic system + python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643 # AMOEBA periodic system + python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643 # HIPPO periodic system + python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new # system with bitorsions Switches and their arguments may be specified in any order. diff --git a/doc/src/Howto_mdi.rst b/doc/src/Howto_mdi.rst index 14bef1a546..9a26aa9243 100644 --- a/doc/src/Howto_mdi.rst +++ b/doc/src/Howto_mdi.rst @@ -134,18 +134,18 @@ used in stand-alone mode: .. code-block:: bash - % git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git /q-e - % build the executable pw.x, following the `QE build guide `_ + git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git /q-e + build the executable pw.x, following the `QE build guide `_ Here is how to build QE as a shared library which can be used in plugin mode, which results in a libqemdi.so file in /q-e/MDI/src: .. code-block:: bash - % git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git /q-e - % cd /q-e - % ./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" foxflags="-fPIC" try_foxflags="-fPIC" - % make -j 4 mdi + git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git /q-e + cd /q-e + ./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" foxflags="-fPIC" try_foxflags="-fPIC" + make -j 4 mdi INQ cannot be built as a stand-alone code; it is by design a library. Here is how to build INQ as a shared library which can be used in @@ -154,10 +154,10 @@ plugin mode, which results in a libinqmdi.so file in .. code-block:: bash - % git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git /inq - % cd /inq - % mkdir -p build - % cd build - % ../configure --prefix=/install - % make -j 4 - % make install + git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git /inq + cd /inq + mkdir -p build + cd build + ../configure --prefix=/install + make -j 4 + make install diff --git a/doc/src/Install_conda.rst b/doc/src/Install_conda.rst index df1d64e7da..8856da2600 100644 --- a/doc/src/Install_conda.rst +++ b/doc/src/Install_conda.rst @@ -1,7 +1,7 @@ Download an executable for Linux or Mac via Conda ------------------------------------------------- -Precompiled LAMMPS binaries are available for macOS or Linux via the +Pre-compiled LAMMPS binaries are available for macOS or Linux via the `Conda `_ package management system. First, one must setup the Conda package manager on your system. Follow the @@ -11,15 +11,15 @@ install: .. code-block:: bash - % conda config --add channels conda-forge - % conda create -n my-lammps-env + conda config --add channels conda-forge + conda create -n my-lammps-env Then, you can install LAMMPS on your system with the following command: .. code-block:: bash - % conda activate my-lammps-env - % conda install lammps + conda activate my-lammps-env + conda install lammps The LAMMPS binary is built with the :ref:`KIM package ` which results in Conda also installing the `kim-api` binaries when LAMMPS is @@ -28,7 +28,7 @@ install the `openkim-models` package .. code-block:: bash - % conda install openkim-models + conda install openkim-models If you have problems with the installation you can post issues to `this link `_. diff --git a/doc/src/Install_linux.rst b/doc/src/Install_linux.rst index 9d14b37f58..2d2035d68d 100644 --- a/doc/src/Install_linux.rst +++ b/doc/src/Install_linux.rst @@ -197,7 +197,7 @@ typing: .. code-block:: bash - % emerge --ask lammps + emerge --ask lammps Note that in Gentoo the LAMMPS source is downloaded and the package is built on the your machine. @@ -206,7 +206,7 @@ Certain LAMMPS packages can be enable via USE flags, type .. code-block:: bash - % equery uses lammps + equery uses lammps for details. diff --git a/doc/src/Install_mac.rst b/doc/src/Install_mac.rst index 4bc0dcb88b..3b7be3722c 100644 --- a/doc/src/Install_mac.rst +++ b/doc/src/Install_mac.rst @@ -12,7 +12,7 @@ the following commands: .. code-block:: bash - % brew install lammps + brew install lammps This will install the executables "lammps_serial" and "lammps_mpi", as well as the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories. @@ -22,7 +22,7 @@ Lennard-Jones benchmark file: .. code-block:: bash - % brew test lammps -v + brew test lammps -v The LAMMPS binary is built with the :ref:`KIM package ` which results in Homebrew also installing the `kim-api` binaries when LAMMPS is @@ -31,7 +31,7 @@ install the `openkim-models` package .. code-block:: bash - % brew install openkim-models + brew install openkim-models If you have problems with the installation you can post issues to `this link `_. diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 01cecf5e87..fe13e9e5a4 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -621,8 +621,8 @@ MPEG or other movie file you can use: .. code-block:: bash - % convert *.jpg foo.gif - % convert -loop 1 *.ppm foo.mpg + convert *.jpg foo.gif + convert -loop 1 *.ppm foo.mpg Animated GIF files from ImageMagick are not optimized. You can use a program like gifsicle to optimize and thus massively shrink them. @@ -668,8 +668,8 @@ Play the movie: .. code-block:: bash - % mplayer foo.mpg - % ffplay bar.avi + mplayer foo.mpg + ffplay bar.avi * c) Use the `Pizza.py `_ `animate tool `_, diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 83519a2051..da8b802fd4 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -131,21 +131,21 @@ for csh, tcsh: -.. parsed-literal:: +.. code-block:: tcsh - % setenv LAMMPS_POTENTIALS /path/to/lammps/potentials + setenv LAMMPS_POTENTIALS /path/to/lammps/potentials bash: -.. parsed-literal:: +.. code-block:: bash - % export LAMMPS_POTENTIALS=/path/to/lammps/potentials + export LAMMPS_POTENTIALS=/path/to/lammps/potentials Windows: -.. parsed-literal:: +.. code-block:: console - % set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials" + set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials" The ``LAMMPS_POTENTIALS`` environment variable may contain paths to multiple folders, if they are separated by ";" on Windows and diff --git a/doc/src/shell.rst b/doc/src/shell.rst index 6ebd9e2abf..50f148565c 100644 --- a/doc/src/shell.rst +++ b/doc/src/shell.rst @@ -105,7 +105,7 @@ would be the same as invoking .. code-block:: bash - % my_setup file1 10 file2 + my_setup file1 10 file2 from a command-line prompt. The executable program "my_setup" is run with 3 arguments: file1 10 file2.