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Axel Kohlmeyer
2023-01-06 00:00:14 -05:00
parent 8dc7a37ba0
commit 289d319a6c
8 changed files with 40 additions and 40 deletions
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10
doc/src/Howto_amoeba.rst
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@ -261,11 +261,11 @@ all the options available to use with the tinker2lmp.py script:
.. code-block:: bash .. 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 -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_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 -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 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 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. Switches and their arguments may be specified in any order.

26
doc/src/Howto_mdi.rst
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@ -134,18 +134,18 @@ used in stand-alone mode:
.. code-block:: bash .. code-block:: bash
% git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
% build the executable pw.x, following the `QE build guide <https://gitlab.com/QEF/q-e/-/wikis/Developers/CMake-build-system>`_ build the executable pw.x, following the `QE build guide <https://gitlab.com/QEF/q-e/-/wikis/Developers/CMake-build-system>`_
Here is how to build QE as a shared library which can be used in plugin mode, 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 <base_path>/q-e/MDI/src: which results in a libqemdi.so file in <base_path>/q-e/MDI/src:
.. code-block:: bash .. code-block:: bash
% git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
% cd <base_path>/q-e cd <base_path>/q-e
% ./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" foxflags="-fPIC" try_foxflags="-fPIC" ./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" foxflags="-fPIC" try_foxflags="-fPIC"
% make -j 4 mdi make -j 4 mdi
INQ cannot be built as a stand-alone code; it is by design a library. 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 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 .. code-block:: bash
% git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git <base_path>/inq git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git <base_path>/inq
% cd <base_path>/inq cd <base_path>/inq
% mkdir -p build mkdir -p build
% cd build cd build
% ../configure --prefix=<install_path>/install ../configure --prefix=<install_path>/install
% make -j 4 make -j 4
% make install make install

12
doc/src/Install_conda.rst
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@ -1,7 +1,7 @@
Download an executable for Linux or Mac via Conda 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 <conda_>`_ package management system. `Conda <conda_>`_ package management system.
First, one must setup the Conda package manager on your system. Follow the First, one must setup the Conda package manager on your system. Follow the
@ -11,15 +11,15 @@ install:
.. code-block:: bash .. code-block:: bash
% conda config --add channels conda-forge conda config --add channels conda-forge
% conda create -n my-lammps-env conda create -n my-lammps-env
Then, you can install LAMMPS on your system with the following command: Then, you can install LAMMPS on your system with the following command:
.. code-block:: bash .. code-block:: bash
% conda activate my-lammps-env conda activate my-lammps-env
% conda install lammps conda install lammps
The LAMMPS binary is built with the :ref:`KIM package <kim>` which The LAMMPS binary is built with the :ref:`KIM package <kim>` which
results in Conda also installing the `kim-api` binaries when LAMMPS is results in Conda also installing the `kim-api` binaries when LAMMPS is
@ -28,7 +28,7 @@ install the `openkim-models` package
.. code-block:: bash .. code-block:: bash
% conda install openkim-models conda install openkim-models
If you have problems with the installation you can post issues to If you have problems with the installation you can post issues to
`this link <conda_forge_lammps_>`_. `this link <conda_forge_lammps_>`_.

4
doc/src/Install_linux.rst
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@ -197,7 +197,7 @@ typing:
.. code-block:: bash .. code-block:: bash
% emerge --ask lammps emerge --ask lammps
Note that in Gentoo the LAMMPS source is downloaded and the package is Note that in Gentoo the LAMMPS source is downloaded and the package is
built on the your machine. built on the your machine.
@ -206,7 +206,7 @@ Certain LAMMPS packages can be enable via USE flags, type
.. code-block:: bash .. code-block:: bash
% equery uses lammps equery uses lammps
for details. for details.

6
doc/src/Install_mac.rst
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@ -12,7 +12,7 @@ the following commands:
.. code-block:: bash .. code-block:: bash
% brew install lammps brew install lammps
This will install the executables "lammps_serial" and "lammps_mpi", as well as This will install the executables "lammps_serial" and "lammps_mpi", as well as
the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories. the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
@ -22,7 +22,7 @@ Lennard-Jones benchmark file:
.. code-block:: bash .. code-block:: bash
% brew test lammps -v brew test lammps -v
The LAMMPS binary is built with the :ref:`KIM package <kim>` which The LAMMPS binary is built with the :ref:`KIM package <kim>` which
results in Homebrew also installing the `kim-api` binaries when LAMMPS is results in Homebrew also installing the `kim-api` binaries when LAMMPS is
@ -31,7 +31,7 @@ install the `openkim-models` package
.. code-block:: bash .. code-block:: bash
% brew install openkim-models brew install openkim-models
If you have problems with the installation you can post issues to If you have problems with the installation you can post issues to
`this link <https://github.com/Homebrew/homebrew-core/issues>`_. `this link <https://github.com/Homebrew/homebrew-core/issues>`_.

8
doc/src/dump_image.rst
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@ -621,8 +621,8 @@ MPEG or other movie file you can use:
.. code-block:: bash .. code-block:: bash
% convert *.jpg foo.gif convert *.jpg foo.gif
% convert -loop 1 *.ppm foo.mpg convert -loop 1 *.ppm foo.mpg
Animated GIF files from ImageMagick are not optimized. You can use Animated GIF files from ImageMagick are not optimized. You can use
a program like gifsicle to optimize and thus massively shrink them. a program like gifsicle to optimize and thus massively shrink them.
@ -668,8 +668,8 @@ Play the movie:
.. code-block:: bash .. code-block:: bash
% mplayer foo.mpg mplayer foo.mpg
% ffplay bar.avi ffplay bar.avi
* c) Use the `Pizza.py <https://lammps.github.io/pizza>`_ * c) Use the `Pizza.py <https://lammps.github.io/pizza>`_
`animate tool <https://lammps.github.io/pizza/doc/animate.html>`_, `animate tool <https://lammps.github.io/pizza/doc/animate.html>`_,

12
doc/src/pair_coeff.rst
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@ -131,21 +131,21 @@ for
csh, tcsh: csh, tcsh:
.. parsed-literal:: .. code-block:: tcsh
% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
bash: bash:
.. parsed-literal:: .. code-block:: bash
% export LAMMPS_POTENTIALS=/path/to/lammps/potentials export LAMMPS_POTENTIALS=/path/to/lammps/potentials
Windows: 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 The ``LAMMPS_POTENTIALS`` environment variable may contain paths
to multiple folders, if they are separated by ";" on Windows and to multiple folders, if they are separated by ";" on Windows and

2
doc/src/shell.rst
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@ -105,7 +105,7 @@ would be the same as invoking
.. code-block:: bash .. 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 from a command-line prompt. The executable program "my_setup" is run
with 3 arguments: file1 10 file2. with 3 arguments: file1 10 file2.