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.. module:: ase.calculators.openmx
======
OpenMX
======
Introduction
============
OpenMX_ (Open source package for Material eXplorer) is a software
package for nano-scale material simulations based on density functional
theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic
localized basis functions. This interface makes it possible to use
OpenMX_ as a calculator in ASE, and also to use ASE as a post-processor
for an already performed OpenMX_ calculation.
You should import the OpenMX calculator when writing ASE code.
To import into your python code,
.. code-block:: python
from ase.calculators.openmx import OpenMX
Then you can define a calculator object and set it as the calculator of an
atoms object:
.. code-block:: python
calc = OpenMX(**kwargs)
atoms.calc = calc
Environment variables
=====================
The environment variable :envvar:`ASE_OPENMX_COMMAND` must point to that file.
A directory containing the pseudopotential directories :file:`VPS`, and it
is to be put in the environment variable :envvar:`OPENMX_DFT_DATA_PATH`.
Set both environment variables in your shell configuration file:
.. highlight:: bash
::
$ export OPENMX_DFT_DATA_PATH=/openmx/DFT_DATA13
$ export ASE_OPENMX_COMMAND='openmx'
.. highlight:: python
Keyword Arguments of OpenMX objects
===================================
kwargs are categorized by integer, float, string, boolean, tuple and matrix.
Integer keyword argument(kwargs) is argument have integer value. For example,
.. code-block:: python
calc = OpenMX(scf_maxiter = 500, md_maxiter = 100, ...)
as you can see, in ASE, standard format is to use lowercase alphabet. To
follow this rule, every OpenMX keyword are changed to standard format.
Further more, since python dose not allow dot(.) as a variable name. Every dot
is changed to underbar(_). For example,::
scf.maxIter -> scf_maxiter
MD.maxIter -> md_maxiter
Some variable such like atoms_number or species_number, which can be guessed
easily, are automatically generated by the given information from atoms object.
Float keywords are keyword have float type. Standard rules are applied like
integer keywords. You can specify OpenMX float keywords by specifying,
.. code-block:: python
from ase.units import Ha
calc = OpenMX(scf_criterion = 1e-6, energy_cutoff = 150 * Ry, ...)
scf_criterion is correspond to ``scf.criterion``. The other argument
``energy_cutoff`` is a standard parameter format referencing GPAW. It acts same
as scf_energycutoff. However, units are different. ASE uses standard energy
unit as eV, and OpenMX scf.energycutoff uses the Rydburg unit. Thus, one have
to specify the unit explicitly. This keyword and unit thing is applied to every
keyword. For example, command above will be same as specifying,
.. code-block:: python
from ase.units import Ry
calc = OpenMX(scf_criterion = 1e-6, scf_energycutoff = 150, ...)
energy_cutoff is correspond to ``scf_energycutoff``. But it is written in
standard format. More standard parameters are specified in
calculators/openmx/parameter.py. Bool keywords have boolean format, True or
False. This will be translated On or Off when writing input file. For example,
.. code-block:: python
calc = OpenMX(scf_restart = True, scf_spinorbit_coupling = True, ...)
String keywords are keyword have string format. For example,
.. code-block:: python
calc = OpenMX(scf_xctype = 'LDA', xc = 'PBE', ...)
Both keyword arguments specifying exchange correlation we want to calculate.
Left is written in OpenMX format and the right one is written in standard
format. If calculator see contradicting arguments, it will use standard keyword
``xc`` and ``scf_xctype`` will be ignored. Tuple keywords are keyword that
have length 3. For example,
.. code-block:: python
calc = OpenMX(scf_kgrid = (4, 4, 4), ...)
Matrix keywords are keyword that have special format in OpenMX. For example,::
<Definition.of.Atomic.Species
H H5.0-s2p2d1 H_CA13
C C5.0-s2p2d2 C_CA13
Definition.of.Atomic.Species>
This is typical example of matrix keyword. User can specify explicitly this
argument using python list object. For example,
.. code-block:: python
calc = OpenMX(definition_of_atomic_species=[['H','H5.0-s2p2d1','H_CA13'],
['C','C5.0-s2p2d2','C_CA13']])
although user can specify it explicitly, most of the case, this matrix Arguments
are generated automatically by the information using Atoms object. information
such like cutoff radius or...
See the official `OpenMX`_ manual for more detail.
.. _OpenMX: http://www.openmx-square.org
The default setting used by the OpenMX interface is
.. autoclass:: OpenMX
Below follows a list with a selection of standard parameters
================= ======= ========== ===============================
keyword type default openmx_keyword
================= ======= ========== ===============================
``xc`` ``str`` `LDA` 'scf.XcType'
``maxiter`` ``int`` 100 'scf.maxIter'
``energy_cutoff`` ``flt`` 150\*Ry 'scf.energycutoff'
``kpts`` ``tpl`` (4, 4, 4) 'scf.Kgrid'
``kpts`` ``lst`` None 'Band.kpath'
``eigensolver`` ``str`` 'Band' 'scf.EigenvalueSolver'
``spinpol`` ``bol`` None 'scf.SpinPolarization'
``convergence`` ``flt`` 1e-6\*Ha 'scf.criterion'
``external`` ``lst`` None 'scf.Electric.Field'
``mixer`` ``str`` 'Rmm-Diis' 'scf.Mixing.Type'
``charge`` ``flt`` None 'scf.system.charge'
``smearing`` ``lst`` None 'scf.Electronic.Temperature'
================= ======= ========== ===============================
Calculator parameters
=====================
By default, calculator uses `openmx` arguments to run the code. However, single
node calculating is not a good way to run heavy DFT calculation. Parallel
computation is inevitable. In OpenMX calculator, user may choose the way to
run. There are two ways to excute the code. First is to use MPI and the second
is to use Plane Batch System. MPI method can be applied in general. To use it,
put the mpi dictionary as a kwargs. For example,
.. code-block:: python
calc = OpenMX(mpi={'processes':20, 'threads':3}, ...)
Similarly, You can use PBS method by specifying kwargs,
.. code-block:: python
calc = OpenMX(pbs={'processes':20, 'threads':3, 'walltime':'100:00:00'}, ...)
.. note::
PBS method will not be applied unless you have schedular specifically
supports PBS. If your schedular support `qsub` command and `qlist` command,
you may check pbs command is possible to use.
Below follows a list with a selection of calculator parameters
================= ======= ======= =============================================
keyword type default description
================= ======= ======= =============================================
``label`` ``str`` 'test' It will define the name of file. Also,
'System.Name' and 'System.CurrentDirectory'
will be defined by the label.
``restart`` ``str`` None Restart the calculation. While restarting,
'scf.retart' will be changed to 'On',
'scf.fixed.grid' and 'MD.Current.Iter' will
be readed from '.dat#'. Make sure '_rst' file
have same name with 'System.Name'.
``mpi`` ``dic`` None Dictionary contains the key ``processes`` and
``threads``. If user specify this variable,
calculator will calculate using
``mpirun -np (processes) -t (threads) ...``.
``pbs`` ``dic`` None Dictionary contains the key ``processes``,
``threads`` and ``walltime``. If user specify
this value, caluculator will execute
``qsub -l ppn=(procesees) -l walltime=
(walltime) ...``
``debug`` ``bol`` False Boolean value which shows the position of
code are being excuted
``nohup`` ``bol`` True If it changes to False, calculation log will
be printed
``data_path`` ``dic`` None Correspond to pseudo potential path
``DATA.PATH``. If it is None, check there is
environment variable 'OPENMX_DFT_DATA_PATH'.
``dft_data_dict`` ``dic`` None A specification of the atomic orbital basis
to be used for each atomic species e.g)
``dft_data_dict = {'C': {'cutoff radius':
8 * ase.units.Bohr, 'orbitals used': [1,1]}}``
means that for carbon species, the spatial
extent of the atomic orbitals used is limited
to 8 Bohr and one level of s orbitals are
used and one level of p orbitals are used.
The default value for this is specified in
the default_settings.py file, namely,
default_dictionary.
================= ======= ======= =============================================
Density of States
=================
================= ========= ============== ============================
keyword type default value description
================= ========= ============== ============================
``dos_fileout`` ``str`` False if True, density of states
will be calculated for an energy
range given by dos_erange.
``dos_erange`` ``tuple`` (-25, 20) Gives the density of states
energy range in eV
``dos_kgrid`` ``tuple`` None defaults to the value given by kpts.
================= ========= ============== ============================
Methods of OpenMX objects
=========================
get_dos(kwargs):
key word arguments:
==================== ========= ===============================================
keyword type description
==================== ========= ===============================================
``energy`` float The total energy of the system in eV.
``forces`` float An array of tuples describing the forces on an
each atom in eV / Ang. e.g. array([(atom1Fx,
atom1Fy, atom1Fz), (atom2Fx, atom2Fy, atom2Fz)]
'dipole': A tuple describing the total dipole
moment in Debeye 'chemical_potential':
The chemical potential of the system in eV
``atoms`` atom Needs to be specified if system hasn't been
calculated with the parameter,
dos_fileout=True.
``erange`` tuple e.g. (min_energy, max_energy) with the energy
quoted in eV. If not specified, this will be
the same as the dos_erange parameter of the
calculator.
``method`` str 'Tetrahedron' or 'Gaussian'. The method of
calculating the density of states from the
eigenvalues and eigenvectors.
``gaussian_width`` str If method='Gaussian', then the width of
broadening needs to be specified in eV. The
default is 0.1eV.
spin_polarization bool If True, each graph plotted will split
horizontally with spin up above the x-axis and
spin down below the x-axis. If not specified,
this will be True for spin polarized systems
and False for spin non-polarized systems. You
may specify this as False for a spin_polarized
system.
``density`` bool If True, the (partial) density of states will
be plotted. The default is True.
cum bool If True, the cumulative number of states from
the minimum energy specified in the dos_erange
parameter will be plotted. The default is False
``fermi_level`` bool If True, the region of the graph below the
fermi level will be highlighted in yellow.
The default is True.
``file_format`` str If specified, instead of opening a window to
the view the plot, the plot will be saved in a
specified format. The following formats are
available: 'pdf', 'png', 'ps', 'eps' or 'svg'.
``pdos`` bool If True, the partial density of states will be
calculated and plotted for the atoms specified
in atom_index_list and their orbitals specified
by orbital_list. If False, the total density of
states for the whole system will be calculated
and plotted.
``atom_index_list`` list if pdos=True, a list of reference numbers of
the atoms to have their partial density of
states calculated and plotted. If not
specified, only the first atom will be used.
``orbital_list`` list if pdos=True, a list of all the orbitals to
have their partial density of states plotted.
If is in the list, the combined partial
density of states for each desired atom will be
plotted. If 's', 'p', 'd' or 'f' is in the list
then all the corresponding orbitals of that
type will be plotted. If the list is not
specified, then only the combined density of
states will be plotted.
==================== ========= ===============================================
|
