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more description. address typos.

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Axel Kohlmeyer
2023-03-02 15:52:17 -05:00
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186
doc/src/Developer_write_pair.rst
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@ -1,10 +1,10 @@
Writing new pair styles
^^^^^^^^^^^^^^^^^^^^^^^
Pair styles are at the core of most simulations with LAMMPS since they
Pair styles are at the core of most simulations with LAMMPS, since they
are used to compute the forces (plus energy and virial contributions, if
needed) on atoms for pairs of atoms within a given cutoff. This is
often the dominant computation in LAMMPS and sometimes even the only
often the dominant computation in LAMMPS, and sometimes even the only
one. Pair styles can be grouped in multiple categories:
#. simple pairwise additive interactions of point particles
@ -17,31 +17,31 @@ one. Pair styles can be grouped in multiple categories:
#. complex interactions that include additional per-atom properties
(e.g. Discrete Element Models (DEM), Peridynamics, Ellipsoids)
In the text below we will discuss aspects of implementing pair styles in
LAMMPS by looking at representative case studies. The design of LAMMPS
allows to focus on the essentials, which is to compute the forces (and
energies or virial contributions), enter and manage the global settings
as well as the potential parameters, and the pair style specific parts
of reading and writing restart and data files. Most of the complex
tasks like management of the atom positions, domain decomposition and
boundaries, or neighbor list creation are handled transparently by other
parts of the LAMMPS code.
In the text below, we will discuss aspects of implementing pair styles
in LAMMPS by looking at representative case studies. The design of
LAMMPS allows developers to focus on the essentials, which is to compute
the forces (and energies or virial contributions), enter and manage the
global settings as well as the potential parameters, and the pair style
specific parts of reading and writing restart and data files. Most of
the complex tasks like management of the atom positions, domain
decomposition and boundaries, or neighbor list creation are handled
transparently by other parts of the LAMMPS code.
As shown on the page for :doc:`writing or extending pair styles
<Modify_pair>` for the implementation of a pair style a new class must
<Modify_pair>`, in order to implement a new pair style, a new class must
be written that is either directly or indirectly derived from the
``Pair`` class. If that class is directly derived from ``Pair``, there
are three *required* methods in addition to the constructor that must be
implemented since they are "pure" in the base class:
``Pair::compute()``, ``Pair::settings()``, ``Pair::coeff()``. All other
methods are optional and have default implementations in the base class
(most of which do nothing), but they may need to be overridden depending
on the requirements of the model.
are three methods that *must* be re-implemented, since they are "pure"
in the base class: ``Pair::compute()``, ``Pair::settings()``,
``Pair::coeff()``. In addition a custom constructor is needed. All
other methods are optional and have default implementations in the base
class (most of which do nothing), but they may need to be overridden
depending on the requirements of the model.
Case 1: a pairwise additive model
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In this section we will describe the procedure of adding a simple pair
In this section, we will describe the procedure of adding a simple pair
style to LAMMPS: an empirical model that can be used to model liquid
mercury.
@ -56,7 +56,7 @@ dependent, attractive Gaussian term.
E = A_0 \exp \left( -\alpha r \right) - A_1 \exp\left[ -\beta \left(r - r_0 \right)^2 \right]
For the application to mercury the following parameters are listed:
For the application to mercury, the following parameters are listed:
- :math:`A_0 = 8.2464 \times 10^{13} \; \textrm{eV}`
- :math:`\alpha = 12.48 \; \AA^{-1}`
@ -70,8 +70,8 @@ For the application to mercury the following parameters are listed:
- :math:`a_2 = -2.58717 \times 10^{-8} \; \textrm{eV/K}^{-2}`
With the optional cutoff, this means we have a total of 5 or 6
parameters for each pair of atom types. In addition we need to input a
default cutoff value as global setting.
parameters for each pair of atom types. Additionally, we need to input a
default cutoff value as a global setting.
Because of the combination of Born-Mayer with a Gaussian, the pair style
shall be named "born/gauss" and thus the class name would be
@ -139,22 +139,21 @@ macro.
The third segment of the header is the actual class definition of the
``PairBornGauss`` class. This has the prototypes for all member
functions that will be implemented by this pair style. This includes a
number of optional functions. All functions that were labeled in the
base class as "virtual" must be given the "override" property as it is
done in the code shown below. This helps to detect unexpected
mismatches as compile errors in case the signature of a function is
changed in the base class. For example, if this change would add an
optional argument with a default value, then all existing source code
calling the function would not need changes and still compile, but the
function in the derived class would no longer override the one in the
base class due to the different number of arguments and the behavior of
the pair style is thus changed in an unintended way. Using "override"
prevents such issues.
functions that will be implemented by this pair style. This includes
:doc:`a few required and a number of optional functions <Modify_pair>`.
All functions that were labeled in the base class as "virtual" must be
given the "override" property, as it is done in the code shown below.
Also variables and arrays for storing global settings and potential
parameters are defined. Since those are internal to the class, they are
placed after a "protected:" label.
The "override" property helps to detect unexpected mismatches because
compilation will stop with an error in case the signature of a function
is changed in the base class without also changing it in all derived
classes. For example, if this change would add an optional argument
with a default value, then all existing source code *calling* the
function would not need changes and still compile, but the function in
the derived class would no longer override the one in the base class due
to the different number of arguments and the behavior of the pair style
is thus changed in an unintended way. Using "override" keyword prevents
such issues.
.. code-block:: c++
@ -185,6 +184,12 @@ placed after a "protected:" label.
double single(int, int, int, int, double, double, double, double &) override;
void *extract(const char *, int &) override;
Also, variables and arrays for storing global settings and potential
parameters are defined. Since those are internal to the class, they are
placed after a "protected:" label.
.. code-block:: c++
protected:
double cut_global;
double **cut;
@ -204,13 +209,13 @@ Implementation file
We move on to the implementation of the ``PairBornGauss`` class in the
``pair_born_gauss.cpp`` file. This file also starts with a LAMMPS
copyright and license header. Below the notice is typically the space
copyright and license header. Below that notice is typically the space
where comments may be added with additional information about this
specific file, the author(s) and affiliation(s) and email address(es) so
the author can be easily contacted in case there are questions about the
implementation later. Since the file(s) may be around for a long time,
it is beneficial to use some kind of "permanent" email address, if
possible.
specific file, the author(s), affiliation(s), and email address(es).
This way the contributing author(s) can be easily contacted, when
there are questions about the implementation later. Since the file(s)
may be around for a long time, it is beneficial to use some kind of
"permanent" email address, if possible.
.. code-block:: c++
@ -259,6 +264,15 @@ Constructor and destructor (required)
The first two functions in the implementation source file are typically
the constructor and the destructor.
Pair styles are different from most classes in LAMMPS that define a
"style", as their constructor only uses the LAMMPS class instance
pointer as argument, but **not** the command line arguments of the
:doc:`pair_style command <pair_style>`. Instead, those arguments are
processed in the ``Pair::settings()`` function (or rather the version in
the derived class). The constructor is the place where global defaults
are set and specifically flags are set about which optional features of
a pair style are available.
.. code-block:: c++
/* ---------------------------------------------------------------------- */
@ -268,7 +282,22 @@ the constructor and the destructor.
writedata = 1;
}
/* ---------------------------------------------------------------------- */
The `writedata = 1;` statement indicates that the pair style is capable
of writing the current pair coefficient parameters to data files. That
is, the class implements specific versions for ``Pair::data()`` and
``Pair::data_all()``. Other statements that could be added here would
be `single_enable = 1;` or `respa_enable = 0;` to indicate that the
``Pair::single()`` function is present and the
``Pair::compute_(inner|middle|outer)`` are not, but those are also the
default settings and already set in the base class.
In the destructor, we need to delete all memory that was allocated by the
pair style, usually to hold force field parameters that were entered
with the :doc:`pair_coeff command <pair_coeff>`. Most of those array
pointers will need to be declared in the derived class header, but some
(e.g. setflag, cutsq) are already declared in the base class.
.. code-block:: c++
PairBornGauss::~PairBornGauss()
{
@ -285,40 +314,22 @@ the constructor and the destructor.
}
}
Pair styles are different from most classes in LAMMPS that define a
"style", as their constructor only uses the LAMMPS class instance
pointer as argument, but **not** the command line arguments of the
:doc:`pair_style command <pair_style>`. Instead, those arguments are
processed in the ``Pair::settings()`` function (or rather the version in
the derived class). The constructor is the place where global defaults
are set and specifically flags are set about which optional features of
a pair style are available. The `writedata = 1;` statement indicates
that the pair style is capable of writing the current pair coefficient
parameters to data files; in other words, that the class implements
specific versions for ``Pair::data()`` and ``Pair::data_all()``. Other
statements that could be added would be `single_enable = 1;` or
`respa_enable = 0;` to indicate that the ``Pair::single()`` function is
present and the ``Pair::compute_(inner|middle|outer)`` are not, but
those are also the default settings and already set in the base class.
In the destructor we need to delete all memory that was allocated by the
pair style, usually to hold force field parameters that were entered
with the :doc:`pair_coeff command <pair_coeff>`. Most of those array
pointers will need to be declared in the derived class header, but some
(e.g. setflag, cutsq) are already declared in the base class.
Settings and coefficients (required)
""""""""""""""""""""""""""""""""""""
To enter the global pair style settings and the pair style parameters,
the functions ``Pair::settings()`` and ``Pair::coeff()`` need to be
reimplemented. The arguments to the ``settings()`` function are the
arguments given to the :doc:`pair_style command <pair_style>`, and the
arguments to the ``coeff()`` function are the arguments to the
:doc:`pair_coeff command <pair_coeff>` but the function is also called
when processing the ``Pair Coeffs`` or ``PairIJ Coeffs`` sections of data
files. In the case of the ``Pair Coeffs`` section the first argument is
duplicated.
re-implemented. The arguments to the ``settings()`` function are the
arguments given to the :doc:`pair_style command <pair_style>`.
Normally, those would already be processed as part of the constructor,
but moving this to a separate function allows to change global settings
like the default cutoff without having to reissue all pair_coeff
commands or re-read the ``Pair Coeffs`` sections from the data file.
In the ``settings()`` function, also the arrays for storing parameters,
to define cutoffs, track with pairs of parameters have been explicitly
set are allocated and, if needed, initialized. In this case, the memory
allocation and initialization is moved to a function ``allocate()``.
.. code-block:: c++
@ -363,6 +374,19 @@ duplicated.
}
}
The arguments to the ``coeff()`` function are the arguments to the
:doc:`pair_coeff command <pair_coeff>`. The function is also called
when processing the ``Pair Coeffs`` or ``PairIJ Coeffs`` sections of
data files. In the case of the ``Pair Coeffs`` section there is only
one atom type per line and thus the first argument is duplicated. Since
the atom type arguments of the :doc:`pair_coeff command <pair_coeff>`
may be a range (e.g. \*\ 3 for atom types 1, 2, and 3), the
corresponding arguments are passed to the :cpp:func:`utils::bounds()
<LAMMPS_NS::utils::bounds>` function which will then return the low
and high end of the range.
.. code-block:: c++
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
@ -404,6 +428,21 @@ duplicated.
Initialization
""""""""""""""
The ``init()`` function is called during the :doc:`"init" phase
<Developer_flow>` of a simulation. This is where potential parameters
are checked for completeness, derived parameters computed (e.g. the
"offset" of the potential energy at the cutoff distance for use with the
:doc:`pair_modify shift yes <pair_modify>` command. If a pair style
supports generating "mixed" parameters (i.e. where both atoms of a pair
have a different atom type) from a "mixing rule" from the parameters of
the type with itself, this is the place to compute and store those mixed
values. The *born/gauss* pair style does not, so we only check for
completeness. Another purpose of the ``init()`` function is to
symmetrize the potential parameter arrays. The return value is the
cutoff for the given pair of atom types. This is used by the neighbor
list code to determine the largest cutoff and then build the neighbor
lists accordingly.
.. code-block:: c++
@ -433,10 +472,11 @@ Initialization
}
Computing forces from the neighbor list (required)
""""""""""""""""""""""""""""""""""""""""""""""""""
The ``compute()`` function is the "workhorse" of a pair style.
.. code-block:: c++

4
doc/utils/sphinx-config/false_positives.txt
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@ -270,6 +270,7 @@ Bialke
biaxial
bicrystal
Biersack
biga
bigbig
bigint
Bij
@ -631,6 +632,7 @@ cutlo
cutmax
cutoffA
cutoffC
cutsq
cuu
cv
Cv
@ -3245,6 +3247,7 @@ Sep
seqdep
Serpico
setfl
setflag
setforce
Sethna
setmask
@ -3480,6 +3483,7 @@ Sx
sy
Sy
symplectic
symmetrize
Synechococcus
sys
sysdim