update list of functions and add list of flags for pair styles
This commit is contained in:
Axel Kohlmeyer
@ -1,35 +1,121 @@
|
||||
Pair styles
|
||||
===========
|
||||
|
||||
Classes that compute pairwise interactions are derived from the Pair
|
||||
class. In LAMMPS, pairwise calculation include many-body potentials
|
||||
such as EAM or Tersoff where particles interact without a static bond
|
||||
topology. New styles can be created to add new pair potentials to
|
||||
LAMMPS.
|
||||
Classes that compute pairwise non-bonded interactions are derived from
|
||||
the Pair class. In LAMMPS, pairwise calculation include many-body
|
||||
potentials such as EAM, Tersoff, or ReaxFF where particles interact
|
||||
without an explicit bond topology but include interactions beyond
|
||||
pairwise non-bonded contributions. New styles can be created to add
|
||||
support for additional pair potentials to LAMMPS. When the
|
||||
modifications are small, sometimes it is more effective to derive from
|
||||
an existing pair style class. This latter approach is also used by
|
||||
:doc:`Accelerator packages <Speed_packages>` where the accelerated style
|
||||
names differ from their base classes by an appended suffix.
|
||||
|
||||
Pair_lj_cut.cpp is a simple example of a Pair class, though it
|
||||
includes some optional methods to enable its use with rRESPA.
|
||||
The file ``src/pair_lj_cut.cpp`` is an example of a Pair class with a
|
||||
very simple potential function. It includes several optional methods to
|
||||
enable its use with :doc:`run_style respa <run_style>` and :doc:`compute
|
||||
group/group <compute_group_group>`.
|
||||
|
||||
Here is a brief description of the class methods in pair.h:
|
||||
Here is a brief list of some the class methods in the Pair class that
|
||||
*must* be or *may* be overridden in a derived class.
|
||||
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
| Required | "pure" methods that *must* be overridden in a derived class |
|
||||
+=================================+=====================================================================+
|
||||
| compute | workhorse routine that computes pairwise interactions |
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
| settings | reads the input script line with arguments you define |
|
||||
| settings | processes the arguments to the pair_style command |
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
| coeff | set coefficients for one i,j type pair |
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
| init_one | perform initialization for one i,j type pair |
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
| init_style | initialization specific to this pair style |
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
| write & read_restart | write/read i,j pair coeffs to restart files |
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
| write & read_restart_settings | write/read global settings to restart files |
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
| single | force/r and energy of a single pairwise interaction between 2 atoms |
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
| compute_inner/middle/outer | versions of compute used by rRESPA |
|
||||
| coeff | set coefficients for one i,j type pair, called from pair_coeff |
|
||||
+---------------------------------+---------------------------------------------------------------------+
|
||||
|
||||
The inner/middle/outer routines are optional.
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| Optional | methods that have a default or dummy implementation |
|
||||
+=================================+======================================================================+
|
||||
| init_one | perform initialization for one i,j type pair |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| init_style | style initialization: request neighbor list(s), error checks |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| init_list | Neighbor class callback function to pass neighbor list to pair style |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| single | force/r and energy of a single pairwise interaction between 2 atoms |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| compute_inner/middle/outer | versions of compute used by rRESPA |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| memory_usage | return estimated amount of memory used by the pair style |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| modify_params | process arguments to pair_modify command |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| extract | provide access to internal scalar or per-type data like cutoffs |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| extract_peratom | provide access to internal per-atom data |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| setup | initialization at the beginning of a run |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| finish | called at the end of a run, e.g. to print |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| write & read_restart | write/read i,j pair coeffs to restart files |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| write & read_restart_settings | write/read global settings to restart files |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| write_data | write Pair Coeffs section to data file |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| write_data_all | write PairIJ Coeffs section to data file |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| pack & unpack_forward_comm | copy data to and from buffer if style uses forward communication |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| pack & unpack_reverse_comm | copy data to and from buffer if style uses reverse communication |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| reinit | reset all type-based parameters, called by fix adapt for example |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
| reset_dt | called when the time step is changed by timestep or fix reset/dt |
|
||||
+---------------------------------+----------------------------------------------------------------------+
|
||||
|
||||
Here is a list of flags or settings that should be set in the
|
||||
constructor of the derived pair class when they differ from the default
|
||||
setting.
|
||||
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| Name of flag | Description | default |
|
||||
+=================================+=============================================================+=========+
|
||||
| single_enable | 1 if single() method is implemented, 0 if missing | 1 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| respa_enable | 1 if pair style has compute_inner/middle/outer() | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| restartinfo | 1 if pair style writes its settings to a restart | 1 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| one_coeff | 1 if only a pair_coeff * * command is allowed | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| manybody_flag | 1 if pair style is a manybody potential | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| unit_convert_flag | value != 0 indicates support for unit conversion | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| no_virial_fdotr_compute | 1 if pair style does not call virial_fdotr_compute() | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| writedata | 1 if write_data() and write_data_all() are implemented | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| comm_forward | size of buffer (in doubles) for forward communication | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| comm_reverse | size of buffer (in doubles) for reverse communication | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| ghostneigh | 1 if cutghost is set and style uses neighbors of ghosts | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| finitecutflag | 1 if cutoff depends on diameter of atoms | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| reinitflag | 1 if style has reinit() and is compatible with fix adapt | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| ewaldflag | 1 if compatible with kspace_style ewald | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| pppmflag | 1 if compatible with kspace_style pppm | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| msmflag | 1 if compatible with kspace_style msm | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| dispersionflag | 1 if compatible with ewald/disp or pppm/disp | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| tip4pflag | 1 if compatible with kspace_style pppm/tip4p | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| dipoleflag | 1 if compatible with dipole kspace_style | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
| spinflag | 1 if compatible with spin kspace_style | 0 |
|
||||
+---------------------------------+-------------------------------------------------------------+---------+
|
||||
|
||||
Reference in New Issue
Block a user