mirror of https://github.com/phonopy/phonopy.git
Added a siesta interface
Implemented a siesta interface. It uses regular expressions to read the siesta .fdf input file. Also added documentation and two working examples: Silicon and Graphene
This commit is contained in:
Henrique Miranda
parent
8e1a3ac0de
commit
de735912ba
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@ -114,6 +114,19 @@ input file that contains the unit cell crystal structure, e.g.,
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% phonopy --pwscf -c NaCl.in band.conf
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% phonopy --pwscf -c NaCl.in band.conf
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.. _siesta_mode:
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``--siesta``
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~~~~~~~~~~~~
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Siesta mode is invoked with this option. Usually this option is used
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with ``--cell`` (``-c``) option or ``CELL_FILENAME`` tag to read a Siesta
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input file that contains the unit cell crystal structure, e.g.,
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::
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% phonopy --siesta -c Si.fdf band.conf
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.. _elk_mode:
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.. _elk_mode:
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``--elk``
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``--elk``
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@ -0,0 +1,66 @@
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.. _siesta_interface:
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Siesta & phonopy calculation
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=========================================
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Supported Siesta tags
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---------------------------
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Currently phonopy can read the siesta tags listed below.
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More tags may be supported on request.
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::
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AtomicCoordinatesFormat, ChemicalSpeciesLabel, AtomicCoordinatesFormat,
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AtomicCoordinatesAndAtomicSpecies, LatticeVectors
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How to run
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----------
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The procedure of a Siesta-phonopy calculation is the following:
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1) Read a Siesta input file and create supercells with
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:ref:`siesta_mode` option::
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% phonopy --siesta -d --dim="2 2 2" -c Si.fdf
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In this example, 2x2x2 supercells are created. ``supercell.fdf`` and
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``supercell-xxx.fdf`` (``xxx`` are numbers) give the perfect
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supercell and supercells with displacements, respectively. In these
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supercell files, lines only relevant to crystal structures are
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generated. ``disp.yaml`` is also created. This file contains
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information on displacements. Perhaps the supercell files are
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stored in ``disp-xxx`` directories, then Siesta calculations are
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executed in these directories.
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2) Calculate forces on atoms in the supercells with
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displacements. Calculation specification tags have to be added to
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``supercell-xxx.in`` files. Crystal structure is not allowed to relax
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in the force calculations, because atomic forces induced by a small
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atomic displacement are what we need for the phonon calculation.
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3) Create ``FORCE_SETS`` by
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::
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% phonopy --siesta -f disp-001/si.FA ...
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Here ``*.FA`` files are the forces files created by Siesta.
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To run this command, ``disp.yaml`` has to be
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located in the current directory because the atomic displacements are
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written into the FORCE_SETS file. An example is found in
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``example/Si-siesta``.
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4) Run post-process of phonopy with the Siesta input file for the
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unit cell used in the step 1::
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% phonopy --siesta -c Si.fdf -p band.conf
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or::
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% phonopy --siesta -c Si.fdf --dim="2 2 2" [other-OPTIONS] [setting-file]
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.. |sflogo| image:: http://sflogo.sourceforge.net/sflogo.php?group_id=161614&type=1
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:target: http://sourceforge.net
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|sflogo|
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@ -0,0 +1,24 @@
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This is an example of the Siesta interface.
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To create supercells with displacements:
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% phonopy --siesta -c Gr.fdf -d --dim="3 3 1"
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A perfect 3x3x1 supercell (supercell.fdf) and one 3x3x1 supercells
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(supercell-xxx.in) of the conventional unit cell written in Gr.fdf are
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created. In addition, disp.yaml file is created. After force
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calculation with the crystal structure in supercell-001.fdf, it is
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needed to create FORCE_SETS file by
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% phonopy --siesta -f disp-001/Gr.FA
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Here the .FA file contains the forces on atoms calculated by Siesta. The
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disp.yaml file has to be put in the current directory. Now you can run
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phonon calculation, e.g.,
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% phonopy --siesta -c Gr.fdf -p --dim="3 3 1" --band="0.0 0.0 0.0 1/4 0.0 0.0 0.5 0.0 0.0 2/3 -1/3 1/2 1/3 -1/6 0.0 0.0 0.0 0.0"
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You can run the run_example.sh bash script to perform all the above commands
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and run the Siesta calculation (need to have Siesta installed).
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Be aware that this calculation is not converged and serves only to show the workflow
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of a siesta-phonopy calculation.
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@ -0,0 +1,19 @@
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18
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1 -0.160630715159 0.000022129661 -0.117029565525
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2 0.013904321133 -0.000635004254 -0.002783938893
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3 0.006033593624 0.003792892916 -0.002667666114
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4 -0.005302250740 -0.006540073197 -0.002712592628
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5 0.001335036108 0.011718467376 -0.002739454829
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6 0.006045158152 0.000010094262 0.001244723790
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7 -0.001439502916 -0.008841864821 -0.002768356138
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8 0.006045301078 0.000011377309 0.001262253735
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9 -0.002555148927 0.000516607376 -0.002682944816
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10 0.065463382106 0.024429002958 0.046814749865
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11 -0.001238341736 -0.004450110524 -0.007316931722
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12 0.055547885402 -0.018600739401 0.047546920213
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13 0.006428688965 -0.000567713058 0.003667294554
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14 -0.007710376636 0.003725418801 -0.007302628603
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15 -0.000022664889 0.000691178617 -0.007331859660
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16 -0.004329322223 0.006225815921 0.003668998234
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17 -0.003390917282 -0.005654737751 0.003665241986
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18 0.023243972747 -0.005473732963 0.047183550197
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@ -0,0 +1,76 @@
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# Commands to run this example
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head="
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PAO.EnergyShift 0.1 eV
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DM.Tolerance 0.0001
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DM.MixingWeight 0.2
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Use.New.Diagk .true.
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SystemLabel Gr
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PAO.BasisSize sz
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SolutionMethod diagon
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MaxSCFIterations 120
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SCF.MixAfterConvergence .false.
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MeshCutoff 400 Ry
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NumberOfSpecies 1
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DM.UseSaveDM False
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ElectronicTemperature 0.02 eV
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%block ChemicalSpeciesLabel
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1 6 C
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%endblock ChemicalSpeciesLabel
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"
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kgrid_uc="
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%block kgrid_Monkhorst_Pack
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30 0 0 0.0
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0 30 0 0.0
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0 0 1 0.0
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%endblock Kgrid_Monkhorst_Pack
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"
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kgrid_sc="
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%block kgrid_Monkhorst_Pack
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10 0 0 0.0
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0 10 0 0.0
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0 0 1 0.0
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%endblock Kgrid_Monkhorst_Pack
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"
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atoms_uc="
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NumberOfAtoms 2
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LatticeConstant 1.000000 Ang
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AtomicCoordinatesFormat NotScaledCartesianAng
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%block LatticeVectors
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2.55000000000000 0.00000000000000 0.00000000000000
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-1.27500000000000 2.20836477965032 0.00000000000000
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0.00000000000000 0.00000000000000 30.00000000000000
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%endblock LatticeVectors
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AtomicCoordinatesFormat NotScaledCartesianAng
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%block AtomicCoordinatesAndAtomicSpecies
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0.00000000000000 0.00000000000000 0.00000000000000 1 12.011000
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1.27500000000000 0.73612159321677 0.00000000000000 1 12.011000
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%endblock AtomicCoordinatesAndAtomicSpecies
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"
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echo "$head" > Gr.fdf
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echo "$kgrid_uc" >> Gr.fdf
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echo "$atoms_uc" >> Gr.fdf
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phonopy --siesta -d --dim="3 3 1" -c Gr.fdf --amplitude=0.02
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mkdir disp-001
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cp C.psf supercell-001.fdf disp-001
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cd disp-001
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echo "$head" > Gr.fdf
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echo "$kgrid_sc" >> Gr.fdf
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echo "LatticeConstant 1.0 Bohr">> Gr.fdf
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echo "%include supercell-001.fdf" >> Gr.fdf
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#siesta < Gr.fdf
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cd ..
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phonopy --siesta -f disp-001/gr.FA -c Gr.fdf
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cat > band.conf << EOF
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ATOM_NAME = C
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DIM = 3 3 1
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BAND_POINTS = 50
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BAND = 0.0 0.0 0.0 1/4 0.0 0.0 0.5 0.0 0.0 2/3 -1/3 1/2 1/3 -1/6 0.0 0.0 0.0 0.0
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EOF
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phonopy --siesta -p band.conf -c Gr.fdf
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@ -0,0 +1,24 @@
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This is an example of the Siesta interface.
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To create supercells with displacements:
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% phonopy --siesta -c Si.fdf -d --dim="3 3 3"
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A perfect 3x3x3 supercell (supercell.fdf) and one 3x3x3 supercells
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(supercell-xxx.in) of the conventional unit cell written in Si.fdf are
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created. In addition, disp.yaml file is created. After force
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calculation with the crystal structure in supercell-001.fdf, it is
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needed to create FORCE_SETS file by
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% phonopy --siesta -f disp-001/Si.FA
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Here the .FA file contains the forces on atoms calculated by Siesta. The
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disp.yaml file has to be put in the current directory. Now you can run
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phonon calculation, e.g.,
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% phonopy --siesta -c Si.fdf -p --dim="3 3 3" --band="1/2 1/2 1/2 0.0 0.0 0.0 0.0 1/2 1/2 1.0 1.0 1.0"
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You can run the run_example.sh bash script to perform all the above commands
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and run the Siesta calculation (need to have Siesta installed).
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Be aware that this calculation is not converged and serves only to show the workflow
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of a siesta-phonopy calculation.
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@ -0,0 +1,49 @@
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SystemName silicon
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SystemLabel Si
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NumberOfSpecies 1
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%block ChemicalSpeciesLabel
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1 14 Si
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%endblock ChemicalSpeciesLabel
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PAO.BasisSize sz
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MeshCutoff 400.0 Ry
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MaxSCFIterations 50
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DM.MixingWeight 0.2
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DM.NumberPulay 3
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DM.Tolerance 1.d-4
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DM.UseSaveDM
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SolutionMethod diagon
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WriteForces .true.
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ElectronicTemperature 100 K
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AtomicCoordinatesFormat Fractional
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%block kgrid_Monkhorst_Pack
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8 0 0 0.0
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0 8 0 0.0
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0 0 8 0.0
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%endblock Kgrid_Monkhorst_Pack
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NumberOfAtoms 2
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LatticeConstant 5.430 Ang
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%block LatticeVectors
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0.000 0.500 0.500
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0.500 0.000 0.500
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0.500 0.500 0.000
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%endblock LatticeVectors
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%block AtomicCoordinatesAndAtomicSpecies
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0.00 0.00 0.00 1 # Si 1
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0.25 0.25 0.25 1 # Si 2
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%endblock AtomicCoordinatesAndAtomicSpecies
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@ -0,0 +1,55 @@
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54
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1 -0.006326846769 -0.269865757978 -0.269865757978
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2 0.005151543965 0.005583616288 0.005583616288
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3 -0.004977276653 0.005408044170 0.005408044170
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4 0.000247570675 -0.003871608212 0.000115500409
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5 0.000001013377 0.001252796001 0.001246450742
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6 -0.000339901374 0.000142066028 -0.003912286238
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7 0.005303289109 -0.008964266238 0.005165263586
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8 -0.005417684456 0.005221264143 -0.008942876228
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9 -0.000004802907 0.001236186575 0.001250282992
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10 0.000247570675 0.000115500409 -0.003871608212
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11 0.000001013377 0.001246450741 0.001252796002
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12 -0.000339901374 -0.003912286238 0.000142066027
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13 0.001456557896 -0.000217456890 -0.000217456890
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14 -0.001463339652 -0.000218830516 -0.000218830516
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15 0.000005579543 0.000662351861 0.000662351861
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16 0.000006064992 -0.000163726718 -0.000172249727
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17 -0.000000826380 0.000288991743 0.000664696621
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18 0.000003538757 0.000664820231 0.000283249392
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19 0.005303289109 0.005165263585 -0.008964266238
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20 -0.005417684456 -0.008942876228 0.005221264143
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21 -0.000004802907 0.001250282992 0.001236186575
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22 0.000006064992 -0.000172249727 -0.000163726718
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23 -0.000000826380 0.000664696621 0.000288991743
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24 0.000003538757 0.000283249392 0.000664820231
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25 0.001464046517 -0.000216057239 -0.000216057239
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26 -0.000004482501 0.000667077125 0.000667077126
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27 -0.001447261482 -0.000225400452 -0.000225400453
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28 0.112159255692 0.123631298410 0.123631298410
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29 -0.000062884187 -0.000908605845 -0.000908605845
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30 -0.103778555678 0.117717678764 0.117717678764
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31 -0.000697949960 0.005426721989 -0.000224902550
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32 0.000673585888 -0.000220947908 0.005402662507
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33 -0.000025648556 -0.001830385054 -0.001894361966
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34 0.000822366299 0.012134870078 0.013401443528
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35 0.000056973811 -0.001798431230 -0.001917308947
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36 -0.000022159979 -0.001888198576 -0.001747769998
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37 -0.000697949960 -0.000224902550 0.005426721989
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38 0.000673585888 0.005402662507 -0.000220947908
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39 -0.000025648556 -0.001894361966 -0.001830385053
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40 0.000004156964 0.000463071295 0.000463071295
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41 -0.000142294256 -0.000580061073 -0.000580061073
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42 0.000141513273 -0.000577374141 -0.000577374141
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43 -0.001939576349 0.000184375211 0.000066457615
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44 0.000002858907 -0.000439650268 -0.000434048062
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45 0.001915736809 0.000064392340 0.000201320199
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46 0.000822366299 0.013401443528 0.012134870078
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47 0.000056973811 -0.001917308947 -0.001798431230
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48 -0.000022159979 -0.001747769998 -0.001888198576
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49 -0.001939576348 0.000066457615 0.000184375211
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50 0.000002858907 -0.000434048062 -0.000439650268
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||||||
|
51 0.001915736808 0.000201320199 0.000064392340
|
||||||
|
52 -0.001967316329 0.000020213564 0.000020213564
|
||||||
|
53 0.001966976723 0.000030325332 0.000030325332
|
||||||
|
54 -0.000003097174 -0.000531768850 -0.000531768850
|
||||||
|
|
@ -0,0 +1,83 @@
|
||||||
|
#Commands to run this example:
|
||||||
|
|
||||||
|
head="
|
||||||
|
SystemName silicon
|
||||||
|
SystemLabel Si
|
||||||
|
|
||||||
|
NumberOfSpecies 1
|
||||||
|
|
||||||
|
%block ChemicalSpeciesLabel
|
||||||
|
1 14 Si
|
||||||
|
%endblock ChemicalSpeciesLabel
|
||||||
|
|
||||||
|
PAO.BasisSize sz
|
||||||
|
|
||||||
|
MeshCutoff 400.0 Ry
|
||||||
|
|
||||||
|
MaxSCFIterations 50
|
||||||
|
DM.MixingWeight 0.2
|
||||||
|
DM.NumberPulay 3
|
||||||
|
DM.Tolerance 1.d-4
|
||||||
|
DM.UseSaveDM
|
||||||
|
|
||||||
|
SolutionMethod diagon
|
||||||
|
|
||||||
|
WriteForces .true.
|
||||||
|
|
||||||
|
ElectronicTemperature 100 K
|
||||||
|
|
||||||
|
AtomicCoordinatesFormat Fractional
|
||||||
|
"
|
||||||
|
|
||||||
|
kgrid_uc="
|
||||||
|
%block kgrid_Monkhorst_Pack
|
||||||
|
8 0 0 0.0
|
||||||
|
0 8 0 0.0
|
||||||
|
0 0 8 0.0
|
||||||
|
%endblock Kgrid_Monkhorst_Pack
|
||||||
|
"
|
||||||
|
|
||||||
|
kgrid_sc="
|
||||||
|
%block kgrid_Monkhorst_Pack
|
||||||
|
3 0 0 0.0
|
||||||
|
0 3 0 0.0
|
||||||
|
0 0 3 0.0
|
||||||
|
%endblock Kgrid_Monkhorst_Pack
|
||||||
|
"
|
||||||
|
|
||||||
|
atoms_uc="
|
||||||
|
NumberOfAtoms 2
|
||||||
|
LatticeConstant 5.430 Ang
|
||||||
|
%block LatticeVectors
|
||||||
|
0.000 0.500 0.500
|
||||||
|
0.500 0.000 0.500
|
||||||
|
0.500 0.500 0.000
|
||||||
|
%endblock LatticeVectors
|
||||||
|
|
||||||
|
%block AtomicCoordinatesAndAtomicSpecies
|
||||||
|
0.00 0.00 0.00 1 # Si 1
|
||||||
|
0.25 0.25 0.25 1 # Si 2
|
||||||
|
%endblock AtomicCoordinatesAndAtomicSpecies
|
||||||
|
"
|
||||||
|
|
||||||
|
echo "$head" > Si.fdf
|
||||||
|
echo "$kgrid_uc" >> Si.fdf
|
||||||
|
echo "$atoms_uc" >> Si.fdf
|
||||||
|
phonopy --siesta -d --dim="3 3 3" -c Si.fdf --amplitude=0.04
|
||||||
|
mkdir disp-001
|
||||||
|
cp Si.psf supercell-001.fdf disp-001
|
||||||
|
cd disp-001
|
||||||
|
echo "$head" > Si.fdf
|
||||||
|
echo "$kgrid_sc" >> Si.fdf
|
||||||
|
echo "LatticeConstant 1.0 Bohr">> Si.fdf
|
||||||
|
echo "%include supercell-001.fdf" >> Si.fdf
|
||||||
|
siesta < Si.fdf
|
||||||
|
cd ..
|
||||||
|
phonopy --siesta -f disp-001/Si.FA -c Si.fdf
|
||||||
|
cat > band.conf << EOF
|
||||||
|
ATOM_NAME = Si O
|
||||||
|
DIM = 3 3 3
|
||||||
|
BAND_POINTS = 100
|
||||||
|
BAND = 1/2 1/2 1/2 0.0 0.0 0.0 0.0 1/2 1/2 1.0 1.0 1.0
|
||||||
|
EOF
|
||||||
|
phonopy --siesta -p band.conf -c Si.fdf
|
||||||
|
|
@ -83,6 +83,10 @@ def read_crystal_structure(filename=None,
|
||||||
unitcell, sp_filenames = read_elk(unitcell_filename)
|
unitcell, sp_filenames = read_elk(unitcell_filename)
|
||||||
return unitcell, (unitcell_filename, sp_filenames)
|
return unitcell, (unitcell_filename, sp_filenames)
|
||||||
|
|
||||||
|
if interface_mode == 'siesta':
|
||||||
|
from phonopy.interface.siesta import read_siesta
|
||||||
|
unitcell, atypes = read_siesta(unitcell_filename)
|
||||||
|
return unitcell, (unitcell_filename, atypes)
|
||||||
|
|
||||||
def get_default_cell_filename(interface_mode, yaml_mode):
|
def get_default_cell_filename(interface_mode, yaml_mode):
|
||||||
if yaml_mode:
|
if yaml_mode:
|
||||||
|
|
@ -97,7 +101,9 @@ def get_default_cell_filename(interface_mode, yaml_mode):
|
||||||
return "case.struct"
|
return "case.struct"
|
||||||
if interface_mode == 'elk':
|
if interface_mode == 'elk':
|
||||||
return "elk.in"
|
return "elk.in"
|
||||||
|
if interface_mode == 'siesta':
|
||||||
|
return "input.fdf"
|
||||||
|
|
||||||
def create_FORCE_SETS(interface_mode,
|
def create_FORCE_SETS(interface_mode,
|
||||||
force_filenames,
|
force_filenames,
|
||||||
options,
|
options,
|
||||||
|
|
@ -107,7 +113,8 @@ def create_FORCE_SETS(interface_mode,
|
||||||
if (interface_mode == 'wien2k' or
|
if (interface_mode == 'wien2k' or
|
||||||
interface_mode == 'abinit' or
|
interface_mode == 'abinit' or
|
||||||
interface_mode == 'elk' or
|
interface_mode == 'elk' or
|
||||||
interface_mode == 'pwscf'):
|
interface_mode == 'pwscf' or
|
||||||
|
interface_mode == 'siesta'):
|
||||||
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
|
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
|
||||||
return_cell=True)
|
return_cell=True)
|
||||||
|
|
||||||
|
|
@ -173,6 +180,17 @@ def create_FORCE_SETS(interface_mode,
|
||||||
force_filenames,
|
force_filenames,
|
||||||
supercell.get_number_of_atoms())
|
supercell.get_number_of_atoms())
|
||||||
|
|
||||||
|
if interface_mode == 'siesta':
|
||||||
|
from phonopy.interface.siesta import parse_set_of_forces
|
||||||
|
print "**********************************************************"
|
||||||
|
print "**** Siesta FORCE_SETS support is experimental. ****"
|
||||||
|
print "**** Your feedback would be appreciated. ****"
|
||||||
|
print "**********************************************************"
|
||||||
|
is_parsed = parse_set_of_forces(
|
||||||
|
displacements,
|
||||||
|
force_filenames,
|
||||||
|
supercell.get_number_of_atoms())
|
||||||
|
|
||||||
if is_parsed:
|
if is_parsed:
|
||||||
write_FORCE_SETS(displacements, filename='FORCE_SETS')
|
write_FORCE_SETS(displacements, filename='FORCE_SETS')
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,201 @@
|
||||||
|
# Copyright (C) 2015 Henrique Pereira Coutada Miranda
|
||||||
|
# All rights reserved.
|
||||||
|
#
|
||||||
|
# This file is part of phonopy.
|
||||||
|
#
|
||||||
|
# Redistribution and use in source and binary forms, with or without
|
||||||
|
# modification, are permitted provided that the following conditions
|
||||||
|
# are met:
|
||||||
|
#
|
||||||
|
# * Redistributions of source code must retain the above copyright
|
||||||
|
# notice, this list of conditions and the following disclaimer.
|
||||||
|
#
|
||||||
|
# * Redistributions in binary form must reproduce the above copyright
|
||||||
|
# notice, this list of conditions and the following disclaimer in
|
||||||
|
# the documentation and/or other materials provided with the
|
||||||
|
# distribution.
|
||||||
|
#
|
||||||
|
# * Neither the name of the phonopy project nor the names of its
|
||||||
|
# contributors may be used to endorse or promote products derived
|
||||||
|
# from this software without specific prior written permission.
|
||||||
|
#
|
||||||
|
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
|
||||||
|
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
|
||||||
|
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
|
||||||
|
# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
|
||||||
|
# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
|
||||||
|
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
|
||||||
|
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
|
||||||
|
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
||||||
|
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
|
||||||
|
# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
|
||||||
|
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||||
|
# POSSIBILITY OF SUCH DAMAGE.
|
||||||
|
|
||||||
|
import sys
|
||||||
|
import numpy as np
|
||||||
|
import re
|
||||||
|
|
||||||
|
from phonopy.file_IO import iter_collect_forces, get_drift_forces
|
||||||
|
from phonopy.interface.vasp import get_scaled_positions_lines
|
||||||
|
from phonopy.units import Bohr
|
||||||
|
from phonopy.cui.settings import fracval
|
||||||
|
from phonopy.structure.atoms import Atoms, symbol_map
|
||||||
|
|
||||||
|
def parse_set_of_forces(displacements,
|
||||||
|
forces_filenames,
|
||||||
|
num_atom):
|
||||||
|
hook = ''
|
||||||
|
for siesta_filename, disp in zip(forces_filenames,
|
||||||
|
displacements['first_atoms']):
|
||||||
|
siesta_forces = iter_collect_forces(siesta_filename,
|
||||||
|
num_atom,
|
||||||
|
hook,
|
||||||
|
[1, 2, 3],
|
||||||
|
word='')
|
||||||
|
drift_force = get_drift_forces(siesta_forces)
|
||||||
|
disp['forces'] = np.array(siesta_forces) - drift_force
|
||||||
|
|
||||||
|
return True
|
||||||
|
|
||||||
|
def read_siesta(filename):
|
||||||
|
siesta_in = SiestaIn(open(filename).read())
|
||||||
|
numbers = siesta_in._tags["atomicnumbers"]
|
||||||
|
lattice = siesta_in._tags["latticevectors"]
|
||||||
|
positions = siesta_in._tags["atomiccoordinates"]
|
||||||
|
atypes = siesta_in._tags["chemicalspecieslabel"]
|
||||||
|
cell = Atoms(numbers=numbers,
|
||||||
|
cell=lattice)
|
||||||
|
|
||||||
|
coordformat = siesta_in._tags["atomiccoordinatesformat"]
|
||||||
|
if coordformat == "fractional" or coordformat == "scaledbylatticevectors":
|
||||||
|
cell.set_scaled_positions(positions)
|
||||||
|
elif coordformat == "scaledcartesian":
|
||||||
|
if siesta_in._tags['latticeconstant'] == 'ang':
|
||||||
|
cell.set_positions(np.array(positions) / Bohr)#convert from angstroem to Bohr
|
||||||
|
else:
|
||||||
|
cell.set_positions(np.array(positions))
|
||||||
|
elif coordformat == "notscaledcartesianang" or coordformat == "ang":
|
||||||
|
cell.set_positions(np.array(positions) / Bohr) #convert from angstroem to Bohr
|
||||||
|
elif coordformat == "notscaledcartesianbohr" or coordformat == "bohr":
|
||||||
|
cell.set_positions(np.array(positions))
|
||||||
|
else:
|
||||||
|
print "The format %s for the AtomicCoordinatesFormat is not implemented"%coordformat
|
||||||
|
exit()
|
||||||
|
|
||||||
|
return cell, atypes
|
||||||
|
|
||||||
|
def write_siesta(filename, cell, atypes):
|
||||||
|
f = open(filename, 'w')
|
||||||
|
f.write(get_siesta_structure(cell,atypes))
|
||||||
|
|
||||||
|
def write_supercells_with_displacements(supercell,
|
||||||
|
cells_with_displacements,
|
||||||
|
atypes):
|
||||||
|
write_siesta("supercell.fdf", supercell, atypes)
|
||||||
|
for i, cell in enumerate(cells_with_displacements):
|
||||||
|
write_siesta("supercell-%03d.fdf" % (i + 1), cell, atypes)
|
||||||
|
|
||||||
|
def get_siesta_structure(cell,atypes):
|
||||||
|
lattice = cell.get_cell()
|
||||||
|
positions = cell.get_scaled_positions()
|
||||||
|
masses = cell.get_masses()
|
||||||
|
chemical_symbols = cell.get_chemical_symbols()
|
||||||
|
|
||||||
|
lines = ""
|
||||||
|
|
||||||
|
lines += "NumberOfAtoms %d\n\n"% len(positions)
|
||||||
|
|
||||||
|
lines += "%block LatticeVectors\n"
|
||||||
|
lines += ((" %21.16f" * 3 + "\n") * 3) % tuple(lattice.ravel())
|
||||||
|
lines += "%endblock LatticeVectors\n\n"
|
||||||
|
|
||||||
|
lines += "AtomicCoordinatesFormat Fractional\n\n"
|
||||||
|
|
||||||
|
lines += "LatticeConstant 1.0 Bohr\n\n"
|
||||||
|
|
||||||
|
lines += "%block AtomicCoordinatesAndAtomicSpecies\n"
|
||||||
|
for pos, i in zip(positions,chemical_symbols):
|
||||||
|
lines += ("%21.16lf"*3+" %d\n") % tuple(pos.tolist()+[atypes[i]])
|
||||||
|
lines += "%endblock AtomicCoordinatesAndAtomicSpecies\n"
|
||||||
|
|
||||||
|
return lines
|
||||||
|
|
||||||
|
class SiestaIn:
|
||||||
|
_num_regex = '([+-]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?)'
|
||||||
|
_tags = { "latticeconstant": 1.0,
|
||||||
|
"latticeconstantunit": None,
|
||||||
|
"chemicalspecieslabel": None,
|
||||||
|
"atomiccoordinatesformat": None,
|
||||||
|
"atomicnumbers": None,
|
||||||
|
"atomicspecies": None,
|
||||||
|
"atomiccoordinates": None }
|
||||||
|
|
||||||
|
def __init__(self, lines):
|
||||||
|
self._collect(lines)
|
||||||
|
|
||||||
|
def _collect(self, lines):
|
||||||
|
""" This routine reads the following from the Siesta file:
|
||||||
|
- atomic positions
|
||||||
|
- cell_parameters
|
||||||
|
- atomic_species
|
||||||
|
"""
|
||||||
|
#capture tags
|
||||||
|
for tag,value,unit in re.findall('([\.A-Za-z]+)\s+?%s(?:[ ]+)?([A-Za-z]+)?'%self._num_regex,lines):
|
||||||
|
tag = tag.lower()
|
||||||
|
if tag == "latticeconstant":
|
||||||
|
self._tags['latticeconstantunit'] = unit.lower()
|
||||||
|
if unit == 'Ang':
|
||||||
|
self._tags[tag] = float(value) / Bohr
|
||||||
|
else:
|
||||||
|
self._tags[tag] = float(value)
|
||||||
|
|
||||||
|
for tag,value in re.findall('([\.A-Za-z]+)[ \t]+([a-zA-Z]+)',lines):
|
||||||
|
tag = tag.replace('_','').lower()
|
||||||
|
if tag == "atomiccoordinatesformat":
|
||||||
|
self._tags[tag] = value.strip().lower()
|
||||||
|
|
||||||
|
#check if the necessary tags are present
|
||||||
|
self.check_present('atomiccoordinatesformat')
|
||||||
|
acell = self._tags['latticeconstant']
|
||||||
|
|
||||||
|
#capture the blocks
|
||||||
|
blocks = re.findall('%block\s+([A-Za-z_]+)\s((?:.+\n)+?(?=(?:\s+)?%endblock))',lines,re.MULTILINE)
|
||||||
|
for tag,block in blocks:
|
||||||
|
tag = tag.replace('_','').lower()
|
||||||
|
if tag == "chemicalspecieslabel":
|
||||||
|
lines = block.split('\n')[:-1]
|
||||||
|
self._tags["atomicnumbers"] = dict([map(int,species.split()[:2]) for species in lines])
|
||||||
|
self._tags[tag] = dict([(lambda x: (x[2],int(x[0])))(species.split()) for species in lines])
|
||||||
|
elif tag == "latticevectors":
|
||||||
|
self._tags[tag] = [[ float(v)*acell for v in vector.split()] for vector in block.split('\n')[:3]]
|
||||||
|
elif tag == "atomiccoordinatesandatomicspecies":
|
||||||
|
lines = block.split('\n')[:-1]
|
||||||
|
self._tags["atomiccoordinates"] = [ [float(x) for x in atom.split()[:3]] for atom in lines ]
|
||||||
|
self._tags["atomicspecies"] = [ int(atom.split()[3]) for atom in lines]
|
||||||
|
|
||||||
|
#check if the block are present
|
||||||
|
self.check_present("atomicspecies")
|
||||||
|
self.check_present("atomiccoordinates")
|
||||||
|
self.check_present("latticevectors")
|
||||||
|
self.check_present("chemicalspecieslabel")
|
||||||
|
|
||||||
|
#translate the atomicspecies to atomic numbers
|
||||||
|
self._tags["atomicnumbers"] = [self._tags["atomicnumbers"][atype] for atype in self._tags["atomicspecies"]]
|
||||||
|
|
||||||
|
def check_present(self,tag):
|
||||||
|
if not self._tags[tag]:
|
||||||
|
print "%s not present"%tag
|
||||||
|
exit()
|
||||||
|
|
||||||
|
def __str__():
|
||||||
|
return self._tags
|
||||||
|
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
import sys
|
||||||
|
from phonopy.structure.symmetry import Symmetry
|
||||||
|
cell,atypes = read_siesta(sys.argv[1])
|
||||||
|
symmetry = Symmetry(cell)
|
||||||
|
print "#", symmetry.get_international_table()
|
||||||
|
print get_siesta_structure(cell,atypes)
|
||||||
|
|
@ -65,4 +65,5 @@ Wien2kToTHz = sqrt(Rydberg/1000*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 3.44595
|
||||||
AbinitToTHz = sqrt(EV/(AMU*Bohr))/Angstrom/(2*pi)/1e12 # [THz] 21.49068
|
AbinitToTHz = sqrt(EV/(AMU*Bohr))/Angstrom/(2*pi)/1e12 # [THz] 21.49068
|
||||||
PwscfToTHz = sqrt(Rydberg*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 108.97077
|
PwscfToTHz = sqrt(Rydberg*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 108.97077
|
||||||
ElkToTHz = sqrt(Hartree*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 154.10794
|
ElkToTHz = sqrt(Hartree*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 154.10794
|
||||||
|
SiestaToTHz = sqrt(EV/(AMU*Bohr))/Angstrom/(2*pi)/1e12 # [THz] 21.49068
|
||||||
EVAngstromToGPa = EV * 1e21
|
EVAngstromToGPa = EV * 1e21
|
||||||
|
|
|
||||||
|
|
@ -207,6 +207,7 @@ parser.set_defaults(
|
||||||
displacement_distance=None,
|
displacement_distance=None,
|
||||||
dynamical_matrix_decimals=None,
|
dynamical_matrix_decimals=None,
|
||||||
elk_mode=False,
|
elk_mode=False,
|
||||||
|
siesta_mode=False,
|
||||||
factor=None,
|
factor=None,
|
||||||
fc_symmetry=None,
|
fc_symmetry=None,
|
||||||
fc_computation_algorithm=None,
|
fc_computation_algorithm=None,
|
||||||
|
|
@ -401,6 +402,8 @@ parser.add_option("--pt", "--projected_thermal_property",
|
||||||
help="Output projected thermal properties")
|
help="Output projected thermal properties")
|
||||||
parser.add_option("--pwscf", dest="pwscf_mode",
|
parser.add_option("--pwscf", dest="pwscf_mode",
|
||||||
action="store_true", help="Invoke Pwscf mode")
|
action="store_true", help="Invoke Pwscf mode")
|
||||||
|
parser.add_option("--siesta", dest="siesta_mode",
|
||||||
|
action="store_true", help="Invoke Siesta mode")
|
||||||
parser.add_option("-q", "--quiet", dest="quiet",
|
parser.add_option("-q", "--quiet", dest="quiet",
|
||||||
action="store_true",
|
action="store_true",
|
||||||
help="Print out smallest information")
|
help="Print out smallest information")
|
||||||
|
|
@ -489,6 +492,7 @@ if options.loglevel is not None:
|
||||||
# abinit : hartree, au, AMU, eV/Angstrom
|
# abinit : hartree, au, AMU, eV/Angstrom
|
||||||
# elk : hartree, au, AMU, hartree/au
|
# elk : hartree, au, AMU, hartree/au
|
||||||
# pwscf : Ry, au, AMU, Ry/au
|
# pwscf : Ry, au, AMU, Ry/au
|
||||||
|
# siesta : eV, au, AMU, eV/Angstroem
|
||||||
#
|
#
|
||||||
if options.wien2k_mode:
|
if options.wien2k_mode:
|
||||||
interface_mode = 'wien2k'
|
interface_mode = 'wien2k'
|
||||||
|
|
@ -506,6 +510,10 @@ elif options.elk_mode:
|
||||||
interface_mode = 'elk'
|
interface_mode = 'elk'
|
||||||
from phonopy.interface.elk import write_supercells_with_displacements
|
from phonopy.interface.elk import write_supercells_with_displacements
|
||||||
factor = ElkToTHz
|
factor = ElkToTHz
|
||||||
|
elif options.siesta_mode:
|
||||||
|
interface_mode = 'siesta'
|
||||||
|
from phonopy.interface.siesta import write_supercells_with_displacements
|
||||||
|
factor = SiestaToTHz
|
||||||
else:
|
else:
|
||||||
interface_mode = 'vasp'
|
interface_mode = 'vasp'
|
||||||
from phonopy.interface.vasp import write_supercells_with_displacements
|
from phonopy.interface.vasp import write_supercells_with_displacements
|
||||||
|
|
@ -620,7 +628,8 @@ if settings.get_displacement_distance() is None:
|
||||||
if (interface_mode == 'wien2k' or
|
if (interface_mode == 'wien2k' or
|
||||||
interface_mode == 'abinit' or
|
interface_mode == 'abinit' or
|
||||||
interface_mode == 'elk' or
|
interface_mode == 'elk' or
|
||||||
interface_mode == 'pwscf'):
|
interface_mode == 'pwscf' or
|
||||||
|
interface_mode == 'siesta'):
|
||||||
displacement_distance = 0.02
|
displacement_distance = 0.02
|
||||||
else:
|
else:
|
||||||
displacement_distance = 0.01
|
displacement_distance = 0.01
|
||||||
|
|
@ -767,6 +776,11 @@ if run_mode == 'displacements':
|
||||||
write_supercells_with_displacements(supercell,
|
write_supercells_with_displacements(supercell,
|
||||||
cells_with_disps,
|
cells_with_disps,
|
||||||
sp_filenames)
|
sp_filenames)
|
||||||
|
elif interface_mode == 'siesta':
|
||||||
|
atypes = optional_structure_file_information[1]
|
||||||
|
write_supercells_with_displacements(supercell,
|
||||||
|
cells_with_disps,
|
||||||
|
atypes)
|
||||||
else:
|
else:
|
||||||
write_supercells_with_displacements(supercell, cells_with_disps)
|
write_supercells_with_displacements(supercell, cells_with_disps)
|
||||||
|
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue