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Merge branch 'lammps:develop' into fortran-expansion

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hammondkd
2022-10-30 15:30:59 -05:00
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59
doc/src/Build_extras.rst
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@ -234,7 +234,7 @@ LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG``\ ,
Makefile you use.
You can also build the library in one step from the ``lammps/src`` dir,
using a command like these, which simply invoke the ``lib/gpu/Install.py``
using a command like these, which simply invokes the ``lib/gpu/Install.py``
script with the specified args:
.. code-block:: bash
@ -350,7 +350,7 @@ minutes to hours) to build. Of course you only need to do that once.)
You can download and build the KIM library manually if you prefer;
follow the instructions in ``lib/kim/README``. You can also do
this in one step from the lammps/src directory, using a command like
these, which simply invoke the ``lib/kim/Install.py`` script with
these, which simply invokes the ``lib/kim/Install.py`` script with
the specified args.
.. code-block:: bash
@ -954,7 +954,7 @@ more details.
You can download and build the MS-CG library manually if you
prefer; follow the instructions in ``lib/mscg/README``\ . You can
also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
command like these, which simply invokes the
``lib/mscg/Install.py`` script with the specified args:
.. code-block:: bash
@ -1011,7 +1011,7 @@ POEMS package
``lib/poems``\ . You can do this manually if you prefer; follow
the instructions in ``lib/poems/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/poems/Install.py`` script with the
which simply invokes the ``lib/poems/Install.py`` script with the
specified args:
.. code-block:: bash
@ -1100,7 +1100,7 @@ binary package provided by your operating system.
You can download and build the Voro++ library manually if you
prefer; follow the instructions in ``lib/voronoi/README``. You
can also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
command like these, which simply invokes the
``lib/voronoi/Install.py`` script with the specified args:
.. code-block:: bash
@ -1179,7 +1179,7 @@ The ATC package requires the MANYBODY package also be installed.
``lib/atc``. You can do this manually if you prefer; follow the
instructions in ``lib/atc/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/atc/Install.py`` script with the
which simply invokes the ``lib/atc/Install.py`` script with the
specified args:
.. code-block:: bash
@ -1230,7 +1230,7 @@ AWPMD package
``lib/awpmd``. You can do this manually if you prefer; follow the
instructions in ``lib/awpmd/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/awpmd/Install.py`` script with the
which simply invokes the ``lib/awpmd/Install.py`` script with the
specified args:
.. code-block:: bash
@ -1293,7 +1293,7 @@ be built for the most part with all major versions of the C++ language.
In general, it is safer to use build setting consistent with the
rest of LAMMPS. This is best carried out from the LAMMPS src
directory using a command like these, which simply invoke the
directory using a command like these, which simply invokes the
``lib/colvars/Install.py`` script with the specified args:
.. code-block:: bash
@ -1334,20 +1334,30 @@ This package depends on the KSPACE package.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_KSPACE=yes`` and ``-D
PKG_ELECTRODE=yes``.
No additional settings are needed besides ``-D PKG_KSPACE=yes`` and
``-D PKG_ELECTRODE=yes``.
.. tab:: Traditional make
The package is activated with ``make yes-KSPACE`` and ``make
yes-ELECTRODE``
Before building LAMMPS, you must configure the ELECTRODE support
libraries and settings in ``lib/electrode``. You can do this
manually, if you prefer, or do it in one step from the
``lammps/src`` dir, using a command like these, which simply
invokes the ``lib/electrode/Install.py`` script with the specified
args:
.. code-block:: bash
$ make lib-electrode # print help message
$ make lib-electrode args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-electrode args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
Note that the ``Makefile.lammps`` file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in ``lib/awpmd/README``
these can either exist on your system, or you can use the files provided
in ``lib/linalg``. In the latter case you also need to build the library
in ``lib/linalg`` with a command like these:
Note that the ``Makefile.lammps`` file has settings for the BLAS
and LAPACK linear algebra libraries. These can either exist on
your system, or you can use the files provided in ``lib/linalg``.
In the latter case you also need to build the library in
``lib/linalg`` with a command like these:
.. code-block:: bash
@ -1356,6 +1366,9 @@ This package depends on the KSPACE package.
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
The package itself is activated with ``make yes-KSPACE`` and
``make yes-ELECTRODE``
----------
.. _ml-pace:
@ -1555,7 +1568,7 @@ the HDF5 library.
``lib/h5md``. You can do this manually if you prefer; follow the
instructions in ``lib/h5md/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/h5md/Install.py`` script with the
which simply invokes the ``lib/h5md/Install.py`` script with the
specified args:
.. code-block:: bash
@ -1611,7 +1624,7 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
You can download and build the *n2p2* library manually if you prefer;
follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these, which
simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
simply invokes the ``lib/hdnnp/Install.py`` script with the specified args:
.. code-block:: bash
@ -1748,7 +1761,7 @@ they will be downloaded the first time this package is installed.
Before building LAMMPS, you must build the *mesont* library in
``lib/mesont``\ . You can also do it in one step from the
``lammps/src`` dir, using a command like these, which simply
invoke the ``lib/mesont/Install.py`` script with the specified
invokes the ``lib/mesont/Install.py`` script with the specified
args:
.. code-block:: bash
@ -1917,7 +1930,7 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
``lib/qmmm``. You can do this manually if you prefer; follow the
first two steps explained in ``lib/qmmm/README``. You can also do
it in one step from the ``lammps/src`` dir, using a command like
these, which simply invoke the ``lib/qmmm/Install.py`` script with
these, which simply invokes the ``lib/qmmm/Install.py`` script with
the specified args:
.. code-block:: bash
@ -2025,7 +2038,7 @@ To build with this package, you must download and build the
You can download and build the ScaFaCoS library manually if you
prefer; follow the instructions in ``lib/scafacos/README``. You
can also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
command like these, which simply invokes the
``lib/scafacos/Install.py`` script with the specified args:
.. code-block:: bash
@ -2069,7 +2082,7 @@ Eigen3 is a template library, so you do not need to build it.
You can download the Eigen3 library manually if you prefer; follow
the instructions in ``lib/smd/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/smd/Install.py`` script with the
which simply invokes the ``lib/smd/Install.py`` script with the
specified args:
.. code-block:: bash

37
doc/src/Howto_tip4p.rst
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@ -8,18 +8,28 @@ This site M is located at a fixed distance away from the oxygen along
the bisector of the HOH bond angle. A bond style of *harmonic* and an
angle style of *harmonic* or *charmm* should also be used.
A TIP4P model is run with LAMMPS using either this command
A TIP4P model is run with LAMMPS using either these commands
for a cutoff model:
* :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
or these two commands for a long-range model:
or these commands for a long-range model:
* :doc:`pair_style tip4p/long <pair_coul>`
* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
* :doc:`pair_style lj/long/tip4p/long <pair_lj_long>`
* :doc:`pair_style tip4p/long/soft <pair_fep_soft>`
* :doc:`pair_style lj/cut/tip4p/long/soft <pair_fep_soft>`
* :doc:`kspace_style pppm/tip4p <kspace_style>`
* :doc:`kspace_style pppm/disp/tip4p <kspace_style>`
For both models, the bond lengths and bond angles should be held fixed
using the :doc:`fix shake <fix_shake>` command.
The bond lengths and bond angles should be held fixed using the
:doc:`fix shake <fix_shake>` or :doc:`fix rattle <fix_shake>` command,
unless a parameterization for a flexible TIP4P model is used. The
parameter sets listed below are all for rigid TIP4P model variants and
thus the bond and angle force constants are not used and can be set to
any legal value; only equilibrium length and angle are used.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
@ -87,15 +97,16 @@ solver (e.g. Ewald or PPPM in LAMMPS):
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
Note that the when using the TIP4P pair style, the neighbor list
cutoff for Coulomb interactions is effectively extended by a distance
2 \* (OM distance), to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
typically best in an efficiency sense to use a LJ cutoff >= Coulomb
cutoff + 2\*(OM distance), to shrink the size of the neighbor list.
This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
Note that the when using the TIP4P pair style, the neighbor list cutoff
for Coulomb interactions is effectively extended by a distance 2 \* (OM
distance), to account for the offset distance of the fictitious charges
on O atoms in water molecules. Thus it is typically best in an
efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM
distance), to shrink the size of the neighbor list. This leads to
slightly larger cost for the long-range calculation, so you can test the
trade-off for your model. The OM distance and the LJ and Coulombic
cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
<pair_lj_cut_tip4p>` command.
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.