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list post_constructor methods and modernize description

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Axel Kohlmeyer
2025-04-03 13:39:48 -04:00
parent 609b60c211
commit 999e6d95d4
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35
doc/src/Modify_compute.rst
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@ -1,19 +1,21 @@
Compute styles
==============
Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
quantities like kinetic energy and the centro-symmetry parameter
are derived from the Compute class. New styles can be created
to add new calculations to LAMMPS.
Classes that compute scalar and vector quantities like temperature and
the pressure tensor, as well as classes that compute per-atom quantities
like kinetic energy and the centro-symmetry parameter are derived from
the Compute class. New styles can be created to add new calculations to
LAMMPS.
Compute_temp.cpp is a simple example of computing a scalar
temperature. Compute_ke_atom.cpp is a simple example of computing
per-atom kinetic energy.
The ``src/compute_temp.cpp`` file is a simple example of computing a
scalar temperature. The ``src/compute_ke_atom.cpp`` file is a simple
example of computing per-atom kinetic energy.
Here is a brief description of methods you define in your new derived
class. See compute.h for details.
class. See ``src/compute.h`` for additional details.
+-----------------------+------------------------------------------------------------------+
| post_constructor | perform tasks that cannot be run in the constructor (optional) |
+-----------------------+------------------------------------------------------------------+
| init | perform one time setup (required) |
+-----------------------+------------------------------------------------------------------+
@ -50,10 +52,11 @@ class. See compute.h for details.
| memory_usage | tally memory usage (optional) |
+-----------------------+------------------------------------------------------------------+
Tally-style computes are a special case, as their computation is done
in two stages: the callback function is registered with the pair style
and then called from the Pair::ev_tally() function, which is called for
each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The :doc:`compute styles in the TALLY package <compute_tally>`
provide *examples* for utilizing this mechanism.
Tally-style computes are a special case, as their computation is done in
two stages: the callback function is registered with the pair style and
then called from the Pair::ev_tally() function, which is called for each
pair after force and energy has been computed for this pair. Then the
tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The :doc:`compute styles in
the TALLY package <compute_tally>` provide *examples* for utilizing this
mechanism.

57
doc/src/Modify_fix.rst
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@ -1,23 +1,25 @@
Fix styles
==========
In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
everything that happens during a simulation besides force computation,
neighbor list construction, and output, is a "fix". This includes
time integration (update of coordinates and velocities), force
constraints or boundary conditions (SHAKE or walls), and diagnostics
(compute a diffusion coefficient). New styles can be created to add
new options to LAMMPS.
In LAMMPS, a "fix" is any operation that is computed during timestepping
that alters some property of the system. Essentially everything that
happens during a simulation besides force computation, neighbor list
construction, and output, is a "fix". This includes time integration
(update of coordinates and velocities), force constraints or boundary
conditions (SHAKE or walls), and diagnostics (compute a diffusion
coefficient). New styles can be created to add new options to LAMMPS.
Fix_setforce.cpp is a simple example of setting forces on atoms to
prescribed values. There are dozens of fix options already in LAMMPS;
choose one as a template that is similar to what you want to
implement.
The file ``src/fix_setforce.cpp`` is a simple example of setting forces
on atoms to prescribed values. There are dozens of fix options already
in LAMMPS; choose one as a template that is similar to what you want to
implement. There also is a detailed discussion of :doc:`how to write
new fix styles <Developer_write_fix>` in LAMMPS.
Here is a brief description of methods you can define in your new
derived class. See fix.h for details.
derived class. See ``src/fix.h`` for additional details.
+---------------------------+--------------------------------------------------------------------------------------------+
| post_constructor | perform tasks that cannot be run in the constructor (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+
| setmask | determines when the fix is called during the timestep (required) |
+---------------------------+--------------------------------------------------------------------------------------------+
@ -130,10 +132,11 @@ derived class. See fix.h for details.
Typically, only a small fraction of these methods are defined for a
particular fix. Setmask is mandatory, as it determines when the fix
will be invoked during the timestep. Fixes that perform time
integration (\ *nve*, *nvt*, *npt*\ ) implement initial_integrate() and
final_integrate() to perform velocity Verlet updates. Fixes that
constrain forces implement post_force().
will be invoked during :doc:`the evolution of a timestep
<Developer_flow>`. Fixes that perform time integration (\ *nve*, *nvt*,
*npt*\ ) implement initial_integrate() and final_integrate() to perform
velocity Verlet updates. Fixes that constrain forces implement
post_force().
Fixes that perform diagnostics typically implement end_of_step(). For
an end_of_step fix, one of your fix arguments must be the variable
@ -143,13 +146,13 @@ is the first argument the fix defines (after the ID, group-ID, style).
If the fix needs to store information for each atom that persists from
timestep to timestep, it can manage that memory and migrate the info
with the atoms as they move from processors to processor by
implementing the grow_arrays, copy_arrays, pack_exchange, and
unpack_exchange methods. Similarly, the pack_restart and
unpack_restart methods can be implemented to store information about
the fix in restart files. If you wish an integrator or force
constraint fix to work with rRESPA (see the :doc:`run_style <run_style>`
command), the initial_integrate, post_force_integrate, and
final_integrate_respa methods can be implemented. The thermo method
enables a fix to contribute values to thermodynamic output, as printed
quantities and/or to be summed to the potential energy of the system.
with the atoms as they move from processors to processor by implementing
the grow_arrays, copy_arrays, pack_exchange, and unpack_exchange
methods. Similarly, the pack_restart and unpack_restart methods can be
implemented to store information about the fix in restart files. If you
wish an integrator or force constraint fix to work with rRESPA (see the
:doc:`run_style <run_style>` command), the initial_integrate,
post_force_integrate, and final_integrate_respa methods can be
implemented. The thermo method enables a fix to contribute values to
thermodynamic output, as printed quantities and/or to be summed to the
potential energy of the system.