forked from lijiext/lammps
180 lines
5.6 KiB
Plaintext
180 lines
5.6 KiB
Plaintext
.. index:: fix external
|
|
|
|
fix external command
|
|
====================
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
fix ID group-ID external mode args
|
|
|
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
|
* external = style name of this fix command
|
|
* mode = *pf/callback* or *pf/array*
|
|
.. parsed-literal::
|
|
|
|
*pf/callback* args = Ncall Napply
|
|
Ncall = make callback every Ncall steps
|
|
Napply = apply callback forces every Napply steps
|
|
*pf/array* args = Napply
|
|
Napply = apply array forces every Napply steps
|
|
|
|
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
fix 1 all external pf/callback 1 1
|
|
fix 1 all external pf/callback 100 1
|
|
fix 1 all external pf/array 10
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
This fix allows external programs that are running LAMMPS through its
|
|
:ref:`library interface <howto_19>` to modify certain
|
|
LAMMPS properties on specific timesteps, similar to the way other
|
|
fixes do. The external driver can be a :ref:`C/C++ or Fortran program <howto_19>` or a :doc:`Python script <Section_python>`.
|
|
|
|
|
|
----------
|
|
|
|
|
|
If mode is *pf/callback* then the fix will make a callback every
|
|
*Ncall* timesteps or minimization iterations to the external program.
|
|
The external program computes forces on atoms by setting values in an
|
|
array owned by the fix. The fix then adds these forces to each atom
|
|
in the group, once every *Napply* steps, similar to the way the :doc:`fix addforce <fix_addforce>` command works. Note that if *Ncall* >
|
|
*Napply*, the force values produced by one callback will persist, and
|
|
be used multiple times to update atom forces.
|
|
|
|
The callback function "foo" is invoked by the fix as:
|
|
|
|
.. parsed-literal::
|
|
|
|
foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
|
|
|
|
The arguments are as follows:
|
|
|
|
* ptr = pointer provided by and simply passed back to external driver
|
|
* timestep = current LAMMPS timestep
|
|
* nlocal = # of atoms on this processor
|
|
* ids = list of atom IDs on this processor
|
|
* x = coordinates of atoms on this processor
|
|
* fexternal = forces to add to atoms on this processor
|
|
|
|
Note that timestep is a "bigint" which is defined in src/lmptype.h,
|
|
typically as a 64-bit integer.
|
|
|
|
Fexternal are the forces returned by the driver program.
|
|
|
|
The fix has a set_callback() method which the external driver can call
|
|
to pass a pointer to its foo() function. See the
|
|
couple/lammps_quest/lmpqst.cpp file in the LAMMPS distribution for an
|
|
example of how this is done. This sample application performs
|
|
classical MD using quantum forces computed by a density functional
|
|
code `Quest <quest_>`_.
|
|
|
|
.. _quest: http://dft.sandia.gov/Quest
|
|
|
|
|
|
|
|
|
|
----------
|
|
|
|
|
|
If mode is *pf/array* then the fix simply stores force values in an
|
|
array. The fix adds these forces to each atom in the group, once
|
|
every *Napply* steps, similar to the way the :doc:`fix addforce <fix_addforce>` command works.
|
|
|
|
The name of the public force array provided by the FixExternal
|
|
class is
|
|
|
|
.. parsed-literal::
|
|
|
|
double **fexternal;
|
|
|
|
It is allocated by the FixExternal class as an (N,3) array where N is
|
|
the number of atoms owned by a processor. The 3 corresponds to the
|
|
fx, fy, fz components of force.
|
|
|
|
It is up to the external program to set the values in this array to
|
|
the desired quantities, as often as desired. For example, the driver
|
|
program might perform an MD run in stages of 1000 timesteps each. In
|
|
between calls to the LAMMPS :doc:`run <run>` command, it could retrieve
|
|
atom coordinates from LAMMPS, compute forces, set values in fexternal,
|
|
etc.
|
|
|
|
|
|
----------
|
|
|
|
|
|
To use this fix during energy minimization, the energy corresponding
|
|
to the added forces must also be set so as to be consistent with the
|
|
added forces. Otherwise the minimization will not converge correctly.
|
|
|
|
This can be done from the external driver by calling this public
|
|
method of the FixExternal class:
|
|
|
|
.. parsed-literal::
|
|
|
|
void set_energy(double eng);
|
|
|
|
where eng is the potential energy. Eng is an extensive quantity,
|
|
meaning it should be the sum over per-atom energies of all affected
|
|
atoms. It should also be provided in :doc:`energy units <units>`
|
|
consistent with the simulation. See the details below for how to
|
|
insure this energy setting is used appropriately in a minimization.
|
|
|
|
|
|
----------
|
|
|
|
|
|
Restart, fix_modify, output, run start/stop, minimize info
|
|
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
|
|
|
No information about this fix is written to :doc:`binary restart files <restart>`.
|
|
|
|
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
|
|
fix to add the potential "energy" set by the external driver to the
|
|
system's potential energy as part of :doc:`thermodynamic output <thermo_style>`. This is a fictitious quantity but is
|
|
needed so that the :doc:`minimize <minimize>` command can include the
|
|
forces added by this fix in a consistent manner. I.e. there is a
|
|
decrease in potential energy when atoms move in the direction of the
|
|
added force.
|
|
|
|
This fix computes a global scalar which can be accessed by various
|
|
:ref:`output commands <howto_15>`. The scalar is the
|
|
potential energy discussed above. The scalar stored by this fix
|
|
is "extensive".
|
|
|
|
No parameter of this fix can be used with the *start/stop* keywords of
|
|
the :doc:`run <run>` command.
|
|
|
|
The forces due to this fix are imposed during an energy minimization,
|
|
invoked by the :doc:`minimize <minimize>` command.
|
|
|
|
.. note::
|
|
|
|
If you want the fictitious potential energy associated with the
|
|
added forces to be included in the total potential energy of the
|
|
system (the quantity being minimized), you MUST enable the
|
|
:doc:`fix_modify <fix_modify>` *energy* option for this fix.
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
none
|
|
|
|
**Related commands:** none
|
|
|
|
**Default:** none
|
|
|
|
|
|
.. _lws: http://lammps.sandia.gov
|
|
.. _ld: Manual.html
|
|
.. _lc: Section_commands.html#comm
|