lammps/doc/src/Developer_notes.rst

Notes for developers and code maintainers
-----------------------------------------

This section documents how some of the code functionality within
LAMMPS works at a conceptual level.  Comments on code in source files
typically document what a variable stores, what a small section of
code does, or what a function does and its input/outputs.  The topics
on this page are intended to document code functionality at a higher level.

Available topics are:

- `Reading and parsing of text and text files`_
- `Requesting and accessing neighbor lists`_
- `Fix contributions to instantaneous energy, virial, and cumulative energy`_
- `KSpace PPPM FFT grids`_

----

Reading and parsing of text and text files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

It is frequently required for a class in LAMMPS to read in additional
data from a file, e.g. potential parameters from a potential file for
manybody potentials.  LAMMPS provides several custom classes and
convenience functions to simplify the process.  They offer the
following benefits:

- better code reuse and fewer lines of code needed to implement reading
  and parsing data from a file
- better detection of format errors, incompatible data, and better error messages
- exit with an error message instead of silently converting only part of the
  text to a number or returning a 0 on unrecognized text and thus reading incorrect values
- re-entrant code through avoiding global static variables (as used by ``strtok()``)
- transparent support for translating unsupported UTF-8 characters to their ASCII equivalents
  (the text-to-value conversion functions **only** accept ASCII characters)

In most cases (e.g. potential files) the same data is needed on all MPI
ranks.  Then it is best to do the reading and parsing only on MPI rank
0, and communicate the data later with one or more ``MPI_Bcast()``
calls.  For reading generic text and potential parameter files the
custom classes :cpp:class:`TextFileReader <LAMMPS_NS::TextFileReader>`
and :cpp:class:`PotentialFileReader <LAMMPS_NS::PotentialFileReader>`
are available. They allow reading the file as individual lines for which
they can return a tokenizer class (see below) for parsing the line.  Or
they can return blocks of numbers as a vector directly.  The
documentation on :ref:`File reader classes <file-reader-classes>`
contains an example for a typical case.

When reading per-atom data, the data on each line of the file usually
needs to include an atom ID so it can be associated with a particular
atom.  In that case the data can be read in multi-line chunks and
broadcast to all MPI ranks with
:cpp:func:`utils::read_lines_from_file()
<LAMMPS_NS::utils::read_lines_from_file>`.  Those chunks are then
split into lines, parsed, and applied only to atoms the MPI rank
"owns".

For splitting a string (incrementally) into words and optionally
converting those to numbers, the :cpp:class:`Tokenizer
<LAMMPS_NS::Tokenizer>` and :cpp:class:`ValueTokenizer
<LAMMPS_NS::ValueTokenizer>` can be used.  Those provide a superset of
the functionality of ``strtok()`` from the C-library and the latter
also includes conversion to different types.  Any errors while
processing the string in those classes will result in an exception,
which can be caught and the error processed as needed.  Unlike the
C-library functions ``atoi()``, ``atof()``, ``strtol()``, or
``strtod()`` the conversion will check if the converted text is a
valid integer or floating point number and will not silently return an
unexpected or incorrect value.  For example, ``atoi()`` will return 12
when converting "12.5", while the ValueTokenizer class will throw an
:cpp:class:`InvalidIntegerException
<LAMMPS_NS::InvalidIntegerException>` if
:cpp:func:`ValueTokenizer::next_int()
<LAMMPS_NS::ValueTokenizer::next_int>` is called on the same string.

Requesting and accessing neighbor lists
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

LAMMPS uses Verlet-style neighbor lists to avoid having to loop over
*all* pairs of *all* atoms when computing pairwise properties with a
cutoff (e.g. pairwise forces or radial distribution functions).  There
are three main algorithms that can be selected by the :doc:`neighbor
command <neighbor>`: `bin` (the default, uses binning to achieve linear
scaling with system size), `nsq` (without binning, quadratic scaling),
`multi` (with binning, optimized for varying cutoffs or polydisperse
granular particles).  In addition to how the neighbor lists are
constructed a number of different variants of neighbor lists need to be
created (e.g. "full" or "half") for different purposes and styles and
those may be required in every time step ("perpetual") or on some steps
("occasional").

The neighbor list creation is managed by the ``Neighbor`` class.
Individual classes can obtain a neighbor list by creating an instance of
a ``NeighRequest`` class which is stored in a list inside the
``Neighbor`` class.  The ``Neighbor`` class will then analyze the
various requests and apply optimizations where neighbor lists that have
the same settings will be created only once and then copied, or a list
may be constructed by processing a neighbor list from a different
request that is a superset of the requested list.  The neighbor list
build is then :doc:`processed in parallel <Developer_par_neigh>`.

The most commonly required neighbor list is a so-called "half" neighbor
list, where each pair of atoms is listed only once (except when the
:doc:`newton command setting <newton>` for pair is off; in that case
pairs straddling sub-domains or periodic boundaries will be listed twice).
Thus these are the default settings when a neighbor list request is created in:

.. code-block:: C++

   void Pair::init_style()
   {
     neighbor->add_request(this);
   }

   void Pair::init_list(int /*id*/, NeighList *ptr)
   {
     list = ptr;
   }

The ``this`` pointer argument is required so the neighbor list code can
access the requesting class instance to store the assembled neighbor
list with that instance by calling its ``init_list()`` member function.
The optional second argument (omitted here) contains a bitmask of flags
that determines the kind of neighbor list requested.  The default value
used here asks for a perpetual "half" neighbor list.

Non-default values of the second argument need to be used to adjust a
neighbor list request to the specific needs of a style an additional
request flag is needed.  The :doc:`tersoff <pair_tersoff>` pair style,
for example, needs a "full" neighbor list:

.. code-block:: C++

   void PairTersoff::init_style()
   {
     // [...]
     neighbor->add_request(this, NeighConst::REQ_FULL);
   }

When a pair style supports r-RESPA time integration with different cutoff regions,
the request flag may depend on the corresponding r-RESPA settings. Here an example
from pair style lj/cut:

.. code-block:: C++

   void PairLJCut::init_style()
   {
     int list_style = NeighConst::REQ_DEFAULT;

     if (update->whichflag == 1 && utils::strmatch(update->integrate_style, "^respa")) {
       auto respa = (Respa *) update->integrate;
       if (respa->level_inner >= 0) list_style = NeighConst::REQ_RESPA_INOUT;
       if (respa->level_middle >= 0) list_style = NeighConst::REQ_RESPA_ALL;
     }
     neighbor->add_request(this, list_style);
     // [...]
   }

Granular pair styles need neighbor lists based on particle sizes and not cutoff
and also may require to have the list of previous neighbors available ("history").
For example with:

.. code-block:: C++

   if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
   else neighbor->add_request(this, NeighConst::REQ_SIZE);

In case a class would need to make multiple neighbor list requests with different
settings each request can set an id which is then used in the corresponding
``init_list()`` function to assign it to the suitable pointer variable. This is
done for example by the :doc:`pair style meam <pair_meam>`:

.. code-block:: C++

   void PairMEAM::init_style()
   {
   // [...]
     neighbor->add_request(this, NeighConst::REQ_FULL)->set_id(1);
     neighbor->add_request(this)->set_id(2);
   }
   void PairMEAM::init_list(int id, NeighList *ptr)
   {
     if (id == 1) listfull = ptr;
     else if (id == 2) listhalf = ptr;
   }

Fixes may require a neighbor list that is only build occasionally (or
just once) and this can also be indicated by a flag.  As an example here
is the request from the ``FixPeriNeigh`` class which is created
internally by :doc:`Peridynamics pair styles <pair_peri>`:

.. code-block:: C++

   neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);

It is also possible to request a neighbor list that uses a different cutoff
than what is usually inferred from the pair style settings (largest cutoff of
all pair styles plus neighbor list skin).  The following is used in the
:doc:`compute rdf <compute_rdf>` command implementation:

.. code-block:: C++

  if (cutflag)
    neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
  else
    neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);

The neighbor list request function has a slightly different set of arguments
when created by a command style.  In this case the neighbor list is
*always* an occasional neighbor list, so that flag is not needed. However
for printing the neighbor list summary the name of the requesting command
should be set.  Below is the request from the :doc:`delete atoms <delete_atoms>`
command:

.. code-block:: C++

   neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);

Fix contributions to instantaneous energy, virial, and cumulative energy
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Fixes can calculate contributions to the instantaneous energy and/or
virial of the system, both in a global and peratom sense.  Fixes that
perform thermostatting or barostatting can calculate the cumulative
energy they add to or subtract from the system, which is accessed by
the *ecouple* and *econserve* thermodynamic keywords.  This subsection
explains how both work and what flags to set in a new fix to enable
this functionality.

Let's start with thermostatting and barostatting fixes.  Examples are
the :doc:`fix langevin <fix_langevin>` and :doc:`fix npt <fix_nh>`
commands.  Here is what the fix needs to do:

* Set the variable *ecouple_flag* = 1 in the constructor.  Also set
  *scalar_flag* = 1, *extscalar* = 1, and *global_freq* to a timestep
  increment which matches how often the fix is invoked.
* Implement a compute_scalar() method that returns the cumulative
  energy added or subtracted by the fix, e.g. by rescaling the
  velocity of atoms.  The sign convention is that subtracted energy is
  positive, added energy is negative.  This must be the total energy
  added to the entire system, i.e. an "extensive" quantity, not a
  per-atom energy.  Cumulative means the summed energy since the fix
  was instantiated, even across multiple runs.  This is because the
  energy is used by the *econserve* thermodynamic keyword to check
  that the fix is conserving the total energy of the system,
  i.e. potential energy + kinetic energy + coupling energy = a
  constant.

And here is how the code operates:

* The Modify class makes a list of all fixes that set *ecouple_flag* = 1.
* The :doc:`thermo_style custom <thermo_style>` command defines
  *ecouple* and *econserve* keywords.
* These keywords sum the energy contributions from all the
  *ecouple_flag* = 1 fixes by invoking the energy_couple() method in
  the Modify class, which calls the compute_scalar() method of each
  fix in the list.

------------------

Next, here is how a fix contributes to the instantaneous energy and
virial of the system.  First, it sets any or all of these flags to a
value of 1 in their constructor:

* *energy_global_flag* to contribute to global energy, example: :doc:`fix indent <fix_indent>`
* *energy_peratom_flag* to contribute to peratom energy, :doc:`fix cmap <fix_cmap>`
* *virial_global_flag* to contribute to global virial, example: :doc:`fix wall <fix_wall>`
* *virial_peratom_flag* to contribute to peratom virial, example: :doc:`fix wall <fix_wall>`

The fix must also do the following:

* For global energy, implement a compute_scalar() method that returns
  the energy added or subtracted on this timestep.  Here the sign
  convention is that added energy is positive, subtracted energy is
  negative.
* For peratom energy, invoke the ev_init(eflag,vflag) function each
  time the fix is invoked, which initializes per-atom energy storage.
  The value of eflag may need to be stored from an earlier call to the
  fix during the same timestep.  See how the :doc:`fix cmap
  <fix_cmap>` command does this in src/MOLECULE/fix_cmap.cpp.  When an
  energy for one or more atoms is calculated, invoke the ev_tally()
  function to tally the contribution to each atom.  Both the ev_init()
  and ev_tally() methods are in the parent Fix class.
* For global and/or peratom virial, invoke the v_init(vflag) function
  each time the fix is invoked, which initializes virial storage.
  When forces on one or more atoms are calculated, invoke the
  v_tally() function to tally the contribution.  Both the v_init() and
  v_tally() methods are in the parent Fix class.  Note that there are
  several variants of v_tally(); choose the one appropriate to your
  fix.

.. note::

   The ev_init() and ev_tally() methods also account for global and
   peratom virial contributions.  Thus you do not need to invoke the
   v_init() and v_tally() methods, if the fix also calculates peratom
   energies.

The fix must also specify whether (by default) to include or exclude
these contributions to the global/peratom energy/virial of the system.
For the fix to include the contributions, set either of both of these
variables in the constructor:

* *thermo_energy* = 1, for global and peratom energy
* *thermo_virial* = 1, for global and peratom virial

Note that these variables are zeroed in fix.cpp.  Thus if you don't
set the variables, the contributions will be excluded (by default)

However, the user has ultimate control over whether to include or
exclude the contributions of the fix via the :doc:`fix modify
<fix_modify>` command:

* fix modify *energy yes* to include global and peratom energy contributions
* fix modify *virial yes* to include global and peratom virial contributions

If the fix contributes to any of the global/peratom energy/virial
values for the system, it should be explained on the fix doc page,
along with the default values for the *energy yes/no* and *virial
yes/no* settings of the :doc:`fix modify <fix_modify>` command.

Finally, these 4 contributions are included in the output of 4
computes:

* global energy in :doc:`compute pe <compute_pe>`
* peratom energy in :doc:`compute pe/atom <compute_pe_atom>`
* global virial in :doc:`compute pressure <compute_pressure>`
* peratom virial in :doc:`compute stress/atom <compute_stress_atom>`

These computes invoke a method of the Modify class to include
contributions from fixes that have the corresponding flags set,
e.g. *energy_peratom_flag* and *thermo_energy* for :doc:`compute
pe/atom <compute_pe_atom>`.

Note that each compute has an optional keyword to either include or
exclude all contributions from fixes.  Also note that :doc:`compute pe
<compute_pe>` and :doc:`compute pressure <compute_pressure>` are what
is used (by default) by :doc:`thermodynamic output <thermo_style>` to
calculate values for its *pe* and *press* keywords.

KSpace PPPM FFT grids
^^^^^^^^^^^^^^^^^^^^^

The various :doc:`KSpace PPPM <kspace_style>` styles in LAMMPS use
FFTs to solve Poisson's equation.  This subsection describes:

* how FFT grids are defined
* how they are decomposed across processors
* how they are indexed by each processor
* how particle charge and electric field values are mapped to/from
  the grid

An FFT grid cell is a 3d volume; grid points are corners of a grid
cell and the code stores values assigned to grid points in vectors or
3d arrays.  A global 3d FFT grid has points indexed 0 to N-1 inclusive
in each dimension.

Each processor owns two subsets of the grid, each subset is
brick-shaped.  Depending on how it is used, these subsets are
allocated as a 1d vector or 3d array.  Either way, the ordering of
values within contiguous memory x fastest, then y, z slowest.

For the ``3d decomposition`` of the grid, the global grid is
partitioned into bricks that correspond to the sub-domains of the
simulation box that each processor owns.  Often, this is a regular 3d
array (Px by Py by Pz) of bricks, where P = number of processors =
Px * Py * Pz.  More generally it can be a tiled decomposition, where
each processor owns a brick and the union of all the bricks is the
global grid.  Tiled decompositions are produced by load balancing with
the RCB algorithm; see the :doc:`balance rcb <balance>` command.

For the ``FFT decompostion`` of the grid, each processor owns a brick
that spans the entire x dimension of the grid while the y and z
dimensions are partitioned as a regular 2d array (P1 by P2), where P =
P1 * P2.

The following indices store the inclusive bounds of the brick a
processor owns, within the global grid:

.. parsed-literal::

   nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in = 3d decomposition brick
   nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft = FFT decomposition brick
   nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out = 3d decomposition brick + ghost cells

The ``in`` and ``fft`` indices are from 0 to N-1 inclusive in each
dimension, where N is the grid size.

The ``out`` indices index an array which stores the ``in`` subset of
the grid plus ghost cells that surround it.  These indices can thus be
< 0 or >= N.

The number of ghost cells a processor owns in each of the 6 directions
is a function of:

.. parsed-literal::

   neighbor skin distance (since atoms can move outside a proc subdomain)
   qdist = offset or charge from atom due to TIP4P fictitious charge
   order = mapping stencil size
   shift = factor used when order is an even number (see below)

Here is an explanation of how the PPPM variables ``order``,
``nlower`` / ``nupper``, ``shift``, and ``OFFSET`` work. They are the
relevant variables that determine how atom charge is mapped to grid
points and how field values are mapped from grid points to atoms:

.. parsed-literal::

   order = # of nearby grid points in each dim that atom charge/field are mapped to/from
   nlower,nupper = extent of stencil around the grid point an atom is assigned to
   OFFSET = large integer added/subtracted when mapping to avoid int(-0.75) = 0 when -1 is the desired result

The particle_map() method assigns each atom to a grid point.

If order is even, say 4:

.. parsed-literal::

   atom is assigned to grid point to its left (in each dim)
   shift = OFFSET
   nlower = -1, nupper = 2, which are offsets from assigned grid point
   window of mapping grid pts is thus 2 grid points to left of atom, 2 to right

If order is odd, say 5:

.. parsed-literal::

   atom is assigned to left/right grid pt it is closest to (in each dim)
   shift = OFFSET + 0.5
   nlower = 2, nupper = 2
   if point is in left half of cell, then window of affected grid pts is 3 grid points to left of atom, 2 to right
   if point is in right half of cell, then window of affected grid pts is 2 grid points to left of atom, 3 to right

These settings apply to each dimension, so that if order = 5, an
atom's charge is mapped to 125 grid points that surround the atom.