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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
% 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.

26
doc/src/Howto_mdi.rst
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@ -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 <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>`_
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>`_
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:
.. code-block:: bash
% git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <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"
% make -j 4 mdi
git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <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"
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 <base_path>/inq
% cd <base_path>/inq
% mkdir -p build
% cd build
% ../configure --prefix=<install_path>/install
% make -j 4
% make install
git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git <base_path>/inq
cd <base_path>/inq
mkdir -p build
cd build
../configure --prefix=<install_path>/install
make -j 4
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
-------------------------------------------------
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.
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 <kim>` 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 <conda_forge_lammps_>`_.

4
doc/src/Install_linux.rst
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@ -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.

6
doc/src/Install_mac.rst
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@ -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 <kim>` 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 <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
% 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 <https://lammps.github.io/pizza>`_
`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:
.. 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

2
doc/src/shell.rst
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@ -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.