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Merge branch 'master' into write-bonus-data

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Axel Kohlmeyer
2020-07-11 18:31:44 -04:00
parent 64dad33c12 284b1618f9
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32
doc/src/Install_linux.rst
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@ -21,8 +21,14 @@ Pre-built Ubuntu Linux executables
A pre-built LAMMPS executable suitable for running on the latest
Ubuntu Linux versions, can be downloaded as a Debian package. This
allows you to install LAMMPS with a single command, and stay
up-to-date with the current version of LAMMPS by simply updating your
operating system.
up-to-date with the current stable version of LAMMPS by simply updating
your operating system. Please note, that the repository below offers
two LAMMPS packages, ``lammps-daily`` and ``lammps-stable``. The
LAMMPS developers recommend to use the ``lammps-stable`` package for
any production simulations. The ``lammps-daily`` package is built
from the LAMMPS development sources, and those versions may have known
issues and bugs when new features are added and the software has not
undergone full release testing.
To install the appropriate personal-package archives (PPAs), do the
following once:
@ -37,16 +43,16 @@ To install LAMMPS do the following once:
.. code-block:: bash
$ sudo apt-get install lammps-daily
$ sudo apt-get install lammps-stable
This downloads an executable named ``lmp_daily`` to your box, which
This downloads an executable named ``lmp_stable`` to your box, which
can then be used in the usual way to run input scripts:
.. code-block:: bash
$ lmp_daily -in in.lj
$ lmp_stable -in in.lj
To update LAMMPS to the most current version, do the following:
To update LAMMPS to the most current stable version, do the following:
.. code-block:: bash
@ -58,25 +64,25 @@ To get a copy of the current documentation and examples:
.. code-block:: bash
$ sudo apt-get install lammps-daily-doc
$ sudo apt-get install lammps-stable-doc
which will download the doc files in
``/usr/share/doc/lammps-daily-doc/doc`` and example problems in
``/usr/share/doc/lammps-stable-doc/doc`` and example problems in
``/usr/share/doc/lammps-doc/examples``.
To get a copy of the current potentials files:
.. code-block:: bash
$ sudo apt-get install lammps-daily-data
$ sudo apt-get install lammps-stable-data
which will download the potentials files to
``/usr/share/lammps-daily/potentials``. The ``lmp_daily`` binary is
``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is
hard-coded to look for potential files in this directory (it does not
use the `LAMMPS_POTENTIALS` environment variable, as described
in :doc:`pair_coeff <pair_coeff>` command).
The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which
The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which
results in the above command also installing the `kim-api` binaries when LAMMPS
is installed. In order to use potentials from `openkim.org <openkim_>`_, you
can install the `openkim-models` package
@ -89,9 +95,9 @@ To un-install LAMMPS, do the following:
.. code-block:: bash
$ sudo apt-get remove lammps-daily
$ sudo apt-get remove lammps-stable
Please use ``lmp_daily -help`` to see which compilation options, packages,
Please use ``lmp_stable -help`` to see which compilation options, packages,
and styles are included in the binary.
Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this

7
doc/src/angle_charmm.rst
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@ -49,13 +49,14 @@ The following coefficients must be defined for each angle type via the
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
* :math:`K_{ub}` (energy/distance\^2)
* :math:`r_{ub}` (distance)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
----------

42
doc/src/angle_class2.rst
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@ -41,27 +41,29 @@ The *class2* angle style uses the potential
E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\
E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a
bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are
the equilibrium bond lengths.
where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond
term, and :math:`E_{ba}` is a bond-angle term. :math:`\theta_0` is
the equilibrium angle and :math:`r_1` and :math:`r_2` are the
equilibrium bond lengths.
See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field.
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for
each angle type via the :doc:`angle_coeff <angle_coeff>` command as in
the example above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands.
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}`
formulas must be defined for each angle type via the :doc:`angle_coeff
<angle_coeff>` command as in the example above, or in the data file or
restart files read by the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands.
These are the 4 coefficients for the :math:`E_a` formula:
* :math:`\theta_0` (degrees)
* :math:`K_2` (energy/radian\^2)
* :math:`K_3` (energy/radian\^3)
* :math:`K_4` (energy/radian\^4)
* :math:`K_2` (energy)
* :math:`K_3` (energy)
* :math:`K_4` (energy)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of the various :math:`K` are in per-radian.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the various :math:`K` are effectively energy
per radian\^2 or radian\^3 or radian\^4.
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
command in the input script lists 4 coefficients, the first of which
@ -122,11 +124,15 @@ The *class2/p6* angle style uses the *class2* potential expanded to sixth order:
In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
* :math:`\theta_0` (degrees)
* :math:`K_2` (energy/radian\^2)
* :math:`K_3` (energy/radian\^3)
* :math:`K_4` (energy/radian\^4)
* :math:`K_5` (energy/radian\^5)
* :math:`K_6` (energy/radian\^6)
* :math:`K_2` (energy)
* :math:`K_3` (energy)
* :math:`K_4` (energy)
* :math:`K_5` (energy)
* :math:`K_6` (energy)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the various :math:`K` are effectively energy
per radian\^2 or radian\^3 or radian\^4 or radian\^5 or radian\^6.
The bond-bond and bond-angle terms remain unchanged.

9
doc/src/angle_cross.rst
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@ -40,14 +40,15 @@ the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K_{SS}` (energy/distance\^2)
* :math:`K_{BS0}` (energy/distance/rad)
* :math:`K_{BS1}` (energy/distance/rad)
* :math:`K_{BS0}` (energy/distance)
* :math:`K_{BS1}` (energy/distance)
* :math:`r_{12,0}` (distance)
* :math:`r_{32,0}` (distance)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the :math:`K_{BS0}` and :math:`K_{BS1}` are
effectively energy/distance per radian.
Restrictions
""""""""""""

15
doc/src/angle_harmonic.rst
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@ -44,11 +44,12 @@ The following coefficients must be defined for each angle type via the
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
----------
@ -61,11 +62,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with those packages. See the :doc:`Build package
<Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
by including their suffix, or you can use the :doc:`-suffix
command-line switch <Run_options>` when you invoke LAMMPS, or you can
use the :doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.

14
doc/src/angle_mm3.rst
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@ -28,20 +28,22 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>`
E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example
:math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ...
where :math:`\theta_0` is the equilibrium value of the angle, and
:math:`K` is a prefactor. The anharmonic prefactors have units
:math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6
\cdot 10^{-5} \deg^{-2}`, ...
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
Restrictions
""""""""""""

11
doc/src/angle_quartic.rst
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@ -39,12 +39,13 @@ the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`\theta_0` (degrees)
* :math:`K_2` (energy/radian\^2)
* :math:`K_3` (energy/radian\^3)
* :math:`K_4` (energy/radian\^4)
* :math:`K_2` (energy)
* :math:`K_3` (energy)
* :math:`K_4` (energy)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the various :math:`K` are effectively energy
per radian\^2 or radian\^3 or radian\^4.
----------

15
doc/src/angle_sdk.rst
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@ -44,13 +44,15 @@ is included in :math:`K`.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
The also required *lj/sdk* parameters will be extracted automatically
from the pair_style.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
The required *lj/sdk* parameters are extracted automatically from the
pair_style.
----------
@ -63,7 +65,8 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with those packages. See the :doc:`Build package
<Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the

38
doc/src/dihedral_class2.rst
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@ -111,34 +111,34 @@ be listed under a *AngleTorsion Coeffs* heading and you must leave out
the *at*, i.e. only list 8 coefficients after the dihedral type.
* *at*
* :math:`D_1` (energy/radian)
* :math:`D_2` (energy/radian)
* :math:`D_3` (energy/radian)
* :math:`E_1` (energy/radian)
* :math:`E_2` (energy/radian)
* :math:`E_3` (energy/radian)
* :math:`D_1` (energy)
* :math:`D_2` (energy)
* :math:`D_3` (energy)
* :math:`E_1` (energy)
* :math:`E_2` (energy)
* :math:`E_3` (energy)
* :math:`\theta_1` (degrees)
* :math:`\theta_2` (degrees)
:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but LAMMPS converts
them to radians internally; hence the units of :math:`D` and :math:`E` are in
energy/radian.
:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but
LAMMPS converts them to radians internally; hence the various
:math:`D` and :math:`E` are effectively energy per radian.
For the :math:`E_{aat}` formula, each line in a
:doc:`dihedral_coeff <dihedral_coeff>` command in the input script lists
4 coefficients, the first of which is *aat* to indicate they are
AngleAngleTorsion coefficients. In a data file, these coefficients
should be listed under a *AngleAngleTorsion Coeffs* heading and you
must leave out the *aat*, i.e. only list 3 coefficients after the
dihedral type.
For the :math:`E_{aat}` formula, each line in a :doc:`dihedral_coeff
<dihedral_coeff>` command in the input script lists 4 coefficients,
the first of which is *aat* to indicate they are AngleAngleTorsion
coefficients. In a data file, these coefficients should be listed
under a *AngleAngleTorsion Coeffs* heading and you must leave out the
*aat*, i.e. only list 3 coefficients after the dihedral type.
* *aat*
* :math:`M` (energy/radian\^2)
* :math:`M` (energy)
* :math:`\theta_1` (degrees)
* :math:`\theta_2` (degrees)
:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but LAMMPS converts
them to radians internally; hence the units of M are in energy/radian\^2.
:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but
LAMMPS converts them to radians internally; hence :math:`M` is
effectively energy per radian\^2.
For the :math:`E_{bb13}` formula, each line in a
:doc:`dihedral_coeff <dihedral_coeff>` command in the input script lists

6
doc/src/dihedral_quadratic.rst
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@ -39,9 +39,13 @@ above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\phi_0` (degrees)
:math:`\phi_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are

8
doc/src/fix_restrain.rst
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@ -183,11 +183,13 @@ the restraint is
with the following coefficients:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
:math:`K` and :math:`\theta_0` are specified with the fix. Note that the usual 1/2
factor is included in :math:`K`.
:math:`K` and :math:`\theta_0` are specified with the fix.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2. Note that the usual 1/2 factor is included in :math:`K`.
----------

33
doc/src/improper_class2.rst
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@ -74,29 +74,31 @@ commands.
These are the 2 coefficients for the :math:`E_i` formula:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\chi_0` (degrees)
:math:`\chi_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian\^2.
:math:`\chi_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
For the :math:`E_{aa}` formula, each line in a
:doc:`improper_coeff <improper_coeff>` command in the input script lists
7 coefficients, the first of which is *aa* to indicate they are
AngleAngle coefficients. In a data file, these coefficients should be
listed under a *AngleAngle Coeffs* heading and you must leave out the
*aa*, i.e. only list 6 coefficients after the improper type.
For the :math:`E_{aa}` formula, each line in a :doc:`improper_coeff
<improper_coeff>` command in the input script lists 7 coefficients,
the first of which is *aa* to indicate they are AngleAngle
coefficients. In a data file, these coefficients should be listed
under a *AngleAngle Coeffs* heading and you must leave out the *aa*,
i.e. only list 6 coefficients after the improper type.
* *aa*
* :math:`M_1` (energy/distance)
* :math:`M_2` (energy/distance)
* :math:`M_3` (energy/distance)
* :math:`M_1` (energy)
* :math:`M_2` (energy)
* :math:`M_3` (energy)
* :math:`\theta_1` (degrees)
* :math:`\theta_2` (degrees)
* :math:`\theta_3` (degrees)
The theta values are specified in degrees, but LAMMPS converts them to
radians internally; hence the units of M are in energy/radian\^2.
The :math:`\theta` values are specified in degrees, but LAMMPS
converts them to radians internally; hence the hence the various
:math:`M` are effectively energy per radian\^2.
----------
@ -109,7 +111,8 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with those packages. See the :doc:`Build package
<Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the

15
doc/src/improper_harmonic.rst
View File

@ -59,11 +59,12 @@ above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\chi_0` (degrees)
:math:`\chi_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian\^2.
:math:`\chi_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
----------
@ -76,11 +77,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with those packages. See the :doc:`Build package
<Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
by including their suffix, or you can use the :doc:`-suffix
command-line switch <Run_options>` when you invoke LAMMPS, or you can
use the :doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.