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Example and documentation for the TURBOMOLE interface

This commit is contained in:
Antti Karttunen 2019-04-01 20:00:56 +03:00
parent da50c5e2bd
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5
doc/auxiliary-tools.rst
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@ -120,6 +120,11 @@ option, for example::
Analogous to ``--pwscf``, but to be used with the CRYSTAL interface.
``--turbomole``
^^^^^^^^^^^^^^^
Analogous to ``--pwscf``, but to be used with the TURBOMOLE interface
``--temperature``
^^^^^^^^^^^^^^^^^^

6
doc/command-options.rst
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@ -62,6 +62,12 @@ See the detail at :ref:`pwscf_interface`.
Using this option, CRYSTAL interface is invoked.
See the detail at :ref:`crystal_interface`.
``--turbomole``: TURBOMOLE interface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Using this option, TURBOMOLE interface is invoked.
See the details at :ref:`turbomole_interface`.
Force constants
----------------

5
doc/index.rst
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@ -31,7 +31,8 @@ written as:
- Thermal conductivity calculations are highly efficiently
distributed over nodes (see :ref:`workload_distribution`).
- User interfaces for :ref:`VASP <vasp_interface>`,
:ref:`QE <pwscf_interface>`, :ref:`CRYSTAL <crystal_interface>`, and Abinit
:ref:`QE <pwscf_interface>`, :ref:`CRYSTAL <crystal_interface>`,
:ref:`TURBOMOLE <turbomole_interface>`, and Abinit
are built in (see :ref:`calculator_interfaces`).
- API is prepared to operate from Python script (`example
<https://github.com/atztogo/phono3py/blob/master/example/Si-PBEsol/Si.py>`_)
@ -58,7 +59,7 @@ Documentation
install
examples
Interfaces to calculators (VASP, pwscf, CRYSTAL, Abinit) <interfaces>
Interfaces to calculators (VASP, pwscf, CRYSTAL, Abinit, TURBOMOLE) <interfaces>
command-options
output-files
hdf5_howto

37
doc/interfaces.rst
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@ -4,10 +4,10 @@ Interfaces to calculators
==========================
Currently the built-in interfaces for VASP, QUANTUM ESPRESSO (QE),
CRYSTAL, and Abinit are prepared. VASP is the default interface and no
CRYSTAL, Abinit, and TURBOMOLE are prepared. VASP is the default interface and no
special option is necessary to invoke it, but for the other
interfaces, each special option has to be specified, e.g. ``--qe``,
``--crystal``, or ``--abinit``.
``--crystal``, ``--abinit``, or ``--turbomole``
.. toctree::
:maxdepth: 1
@ -15,6 +15,7 @@ interfaces, each special option has to be specified, e.g. ``--qe``,
vasp
pwscf
crystal
turbomole
Calculator specific behaviors
------------------------------
@ -22,7 +23,7 @@ Calculator specific behaviors
Physical unit
^^^^^^^^^^^^^^
The interfaces for VASP, Pwscf, CRYSTAL, and Abinit are built in to
The interfaces for VASP, Pwscf, CRYSTAL, Abinit, and TURBOMOLE are built in to
the phono3py command.
For each calculator, each physical unit system is used. The physical
@ -30,12 +31,13 @@ unit systems used for the calculators are summarized below.
::
| unit-cell FORCES_FC3 disp_fc3.yaml
| unit-cell FORCES_FC3 disp_fc3.yaml
-----------------------------------------------
VASP | Angstrom eV/Angstrom Angstrom
QE | au (bohr) Ry/au au
CRYSTAL | Angstrom eV/Angstrom Angstrom
Abinit | au (bohr) eV/Angstrom au
VASP | Angstrom eV/Angstrom Angstrom
QE | au (bohr) Ry/au au
CRYSTAL | Angstrom eV/Angstrom Angstrom
Abinit | au (bohr) eV/Angstrom au
TURBOMOLE | au (bohr) hartree/au au
``FORCES_FC2`` and ``disp_fc2.yaml`` have the same physical units as
``FORCES_FC3`` and ``disp_fc3.yaml``, respectively.
@ -52,11 +54,11 @@ Default unit cell file name
Default unit cell file names are also changed according to the calculators::
VASP | POSCAR
QE | unitcell.in
CRYSTAL | crystal.o
Abinit | unitcell.in
VASP | POSCAR
QE | unitcell.in
CRYSTAL | crystal.o
Abinit | unitcell.in
TURBOMOLE | control
.. _default_displacement_distance_for_calculator:
@ -66,7 +68,8 @@ Default displacement distance created
Default displacement distances created by ``-d`` option without
``--amplitude`` option are respectively as follows::
VASP | 0.03 Angstrom
QE | 0.06 au (bohr)
CRYSTAL | 0.03 Angstrom
Abinit | 0.06 au (bohr)
VASP | 0.03 Angstrom
QE | 0.06 au (bohr)
CRYSTAL | 0.03 Angstrom
Abinit | 0.06 au (bohr)
TURBOMOLE | 0.06 au (bohr)

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@ -0,0 +1,81 @@
.. _turbomole_interface:
TURBOMOLE & phono3py calculation
==============================
The riper module of TURBOMOLE can be used to study periodic structures.
An example for TURBOMOLE is found in the ``example/Si-TURBOMOLE`` directory.
To invoke the TURBOMOLE interface, ``--turbomole`` option has to be always
specified::
% phono3py --turbomole [options] [arguments]
When the file name of the unit cell is different from the default one
(see :ref:`default_unit_cell_file_name_for_calculator`), ``-c`` option
is used to specify the file name. TURBOMOLE unit cell file parser used in
phono3py is the same as that in phonopy. It reads a limited number of
keywords that are documented in the phonopy web site
(http://atztogo.github.io/phonopy/turbomole.html#turbomole-interface).
.. _turbomole_workflow:
Workflow
---------
In the example Si-TURBOMOLE, the TURBOMOLE input file is ``control``.
This is the default file name for the TURBOMOLE interface,
so the -c control parameter is not needed.
1) Create supercells with displacements
2x2x2 conventional cell for 3rd order FC
3x3x3 conventional cell for 2nd order FC
::
% phono3py --turbomole --dim="2 2 2" --dim-fc2="3 3 3" -d
111 supercell directories (``supercell-00xxx``) for the third order
force constants are created. In addition, one supercell directory
(``supercell_fc2-00001``) is created for the second order
force constants.
2) Complete TURBOMOLE inputs need to be prepared manually in the subdirectories.
Note that supercells with displacements must not be relaxed in the
force calculations, because atomic forces induced by a small atomic
displacement are what we need for the phonon calculation. To get accurate
forces, $scfconv should be 10. Phono3py includes this data group automatically
in the ``control`` file. You also need to choose a k-point mesh for the force
calculations. TURBOMOLE data group $riper may need to be adjusted to improve
SCF convergence (see example files in subdirectory supercell-00001 for
further details)
Then, TURBOMOLE supercell calculations are executed to obtain forces on
atoms, e.g., as follows::
% riper > supercell-00001.out
3) Collect forces in ``FORCES_FC3`` and ``FORCES_FC2``::
% phono3py --turbomole --cf3 supercell-*
% phono3py --turbomole --cf2 supercell_fc2-*
``disp_fc3.yaml`` and ``disp_fc2.yaml`` are used to create ``FORCES_FC3`` and
``FORCES_FC2``, therefore they must exist in current directory. The Si-TURBOMOLE
example contains pre-calculated force files.
4) Calculate 3rd and 2nd order force constants in files ``fc3.hdf5`` and ``fc2.hdf5``::
% phono3py --turbomole --dim="2 2 2" --dim-fc2="3 3 3" --sym-fc
``--sym-fc`` is used to symmetrize second- and third-order force constants.
5) Thermal conductivity calculation::
% phono3py --turbomole --primitive-axis="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --fc3 --fc2 --dim="2 2 2" --dim-fc2="3 3 3" --mesh="20 20 20" --br
``--primitive-axis`` is used to get the results for the primitive 2-atom cell
``--br`` invokes the Relaxation Time Approximation.
Carefully test the convergence with respect to ``--mesh``!

14
example/Si-CRYSTAL/README
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@ -3,9 +3,10 @@ Si lattice thermal conductivity
CRYSTAL output file is crystal.o. This is the default file name
for the CRYSTAL interface, so the -c crystal.o parameter is not needed
1) Create displaced supercells:
(4x4x4 for 2nd order FC, 2x2x2 for 3rd order FC)
1) Create displaced supercells (4x4x4 for 2nd order FC, 2x2x2 for 3rd order FC):
phono3py --crystal --dim="2 2 2" --dim-fc2="4 4 4" -d
Complete CRYSTAL inputs can be prepared manually
or with the help of a template
(TEMPLATE for FC2-supercells, TEMPLATE3 for FC3-supercells)
@ -14,16 +15,23 @@ for the CRYSTAL interface, so the -c crystal.o parameter is not needed
Here the supercells have been pre-calculated (outputs.tar.gz).
3) Collect forces:
phono3py --crystal --cf3 supercell-*o
phono3py --crystal --cf2 supercell_fc2-*o
(Here the pre-calculated forces are available as FORCES_FC2 and FORCES_FC3)
Here the pre-calculated forces are available as FORCES_FC2 and FORCES_FC3
4) Create force constant files fc2.hdf5 and fc3.hdf5:
phono3py --crystal --dim="2 2 2" --dim-fc2="4 4 4" --sym-fc
5) Thermal conductivity calculation:
phono3py --crystal --fc3 --fc2 --dim="2 2 2" --dim-fc2="4 4 4" --mesh="20 20 20" --br
--br -> Relaxation time approximation
With 20x20x20 mesh, the lattice thermal conductivity at 300 K is 164 W m^-1 K^-1.
Add --isotope for isotope scattering
Check the effect of --nac for polar systems

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@ -0,0 +1,218 @@
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Si lattice thermal conductivity
The default file name for the TURBOMOLE interface is "control",
so the -c control parameter is not needed
1) Create displaced supercells
2x2x2 conventional cell for 3rd order FC
3x3x3 conventional cell for 2nd order FC
phono3py --turbomole --dim="2 2 2" --dim-fc2="3 3 3" -d
Complete TURBOMOLE inputs can be prepared manually
2) Run the supercell inputs with TURBOMOLE
Here the supercells have been pre-calculated (outputs.tar.gz).
3) Collect forces:
phono3py --turbomole --cf3 supercell-*
phono3py --turbomole --cf2 supercell_fc2-*
Here the pre-calculated forces are available as FORCES_FC2 and FORCES_FC3
4) Create 2nd and 3rd order force constant files fc2.hdf5 and fc3.hdf5
phono3py --turbomole --dim="2 2 2" --dim-fc2="3 3 3" --sym-fc
5) Thermal conductivity calculation
--primitive-axis is used to get the results for the primitive 2-atom cell
phono3py --turbomole --primitive-axis="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --fc3 --fc2 --dim="2 2 2" --dim-fc2="3 3 3" --mesh="20 20 20" --br
--br -> Relaxation time approximation
With 20x20x20 mesh, the lattice thermal conductivity at 300 K is 142 W m^-1 K^-1.

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$periodic 3
$lattice
10.357962933 0.0000000000 0.0000000000
0.0000000000 10.357962933 0.0000000000
0.0000000000 0.0000000000 10.357962933
$coord file=coord
$kpoints
nkpoints 6 6 6
$riper
pqmatdiag on
pqsingtol 1.0d-7
$end

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@ -0,0 +1,11 @@
$coord
2.58949092075 2.58949092075 2.58949092075 si
-2.58949092075 -2.58949092075 2.58949092075 si
-2.58949092075 2.58949092075 -2.58949092075 si
2.58949092075 -2.58949092075 -2.58949092075 si
0.00000000000 0.00000000000 0.00000000000 si
5.17898184151 5.17898184151 0.00000000000 si
5.17898184151 0.00000000000 5.17898184151 si
0.00000000000 5.17898184151 5.17898184151 si
$end

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