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phonopy / phono3py

A simulation package of phonon-phonon interaction related properties
http://phonopy.github.io/phono3py/
BSD 3-Clause "New" or "Revised" License
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Error arises when creating fc2.hdf/fc3.hdf and calculating thermal conductivity #8

Closed crf1989 closed 6 years ago

crf1989 commented 6 years ago

Dear Atz Togo,

I tried the example Si-PBE and I obtained the FORCES_FC3 file successfully. However, when trying to create fc2.hdf and fc3.hdf I got some errors which are shown below.

[chenrf@mic vasprun_xmls]$ phono3py --dim="2 2 2" -c POSCAR-unitcell /db/home/chenrf/.local/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type. from ._conv import register_converters as _register_converters

_ | | | / _ | ' | ' \ / | ' \ / \ | | ' | | | | | |) | | | | () | | | | () |) | |) | || | | ./|| ||_/|| ||_/__/| ./ _, | || || |/ 1.12.9

Spacegroup: Fd-3m (227) ------------------------------ primitive cell ------------------------------ Lattice vectors: a 5.466262890000000 0.000000000000000 0.000000000000000 b 0.000000000000000 5.466262890000000 0.000000000000000 c 0.000000000000000 0.000000000000000 5.466262890000000 Atomic positions (fractional): 1 Si 0.87500000000000 0.87500000000000 0.87500000000000 28.085 2 Si 0.87500000000000 0.37500000000000 0.37500000000000 28.085 3 Si 0.37500000000000 0.87500000000000 0.37500000000000 28.085 4 Si 0.37500000000000 0.37500000000000 0.87500000000000 28.085 5 Si 0.12500000000000 0.12500000000000 0.12500000000000 28.085 6 Si 0.12500000000000 0.62500000000000 0.62500000000000 28.085 7 Si 0.62500000000000 0.12500000000000 0.62500000000000 28.085 8 Si 0.62500000000000 0.62500000000000 0.12500000000000 28.085 -------------------------------- super cell -------------------------------- Lattice vectors: a 10.932525780000001 0.000000000000000 0.000000000000000 b 0.000000000000000 10.932525780000001 0.000000000000000 c 0.000000000000000 0.000000000000000 10.932525780000001 Atomic positions (fractional): 1 Si 0.43750000000000 0.43750000000000 0.43750000000000 28.085 > 1 2 Si 0.93750000000000 0.43750000000000 0.43750000000000 28.085 > 1 3 Si 0.43750000000000 0.93750000000000 0.43750000000000 28.085 > 1 4 Si 0.93750000000000 0.93750000000000 0.43750000000000 28.085 > 1 5 Si 0.43750000000000 0.43750000000000 0.93750000000000 28.085 > 1 6 Si 0.93750000000000 0.43750000000000 0.93750000000000 28.085 > 1 7 Si 0.43750000000000 0.93750000000000 0.93750000000000 28.085 > 1 8 Si 0.93750000000000 0.93750000000000 0.93750000000000 28.085 > 1 9 Si 0.43750000000000 0.18750000000000 0.18750000000000 28.085 > 9 10 Si 0.93750000000000 0.18750000000000 0.18750000000000 28.085 > 9 11 Si 0.43750000000000 0.68750000000000 0.18750000000000 28.085 > 9 12 Si 0.93750000000000 0.68750000000000 0.18750000000000 28.085 > 9 13 Si 0.43750000000000 0.18750000000000 0.68750000000000 28.085 > 9 14 Si 0.93750000000000 0.18750000000000 0.68750000000000 28.085 > 9 15 Si 0.43750000000000 0.68750000000000 0.68750000000000 28.085 > 9 16 Si 0.93750000000000 0.68750000000000 0.68750000000000 28.085 > 9 17 Si 0.18750000000000 0.43750000000000 0.18750000000000 28.085 > 17 18 Si 0.68750000000000 0.43750000000000 0.18750000000000 28.085 > 17 19 Si 0.18750000000000 0.93750000000000 0.18750000000000 28.085 > 17 20 Si 0.68750000000000 0.93750000000000 0.18750000000000 28.085 > 17 21 Si 0.18750000000000 0.43750000000000 0.68750000000000 28.085 > 17 22 Si 0.68750000000000 0.43750000000000 0.68750000000000 28.085 > 17 23 Si 0.18750000000000 0.93750000000000 0.68750000000000 28.085 > 17 24 Si 0.68750000000000 0.93750000000000 0.68750000000000 28.085 > 17 25 Si 0.18750000000000 0.18750000000000 0.43750000000000 28.085 > 25 26 Si 0.68750000000000 0.18750000000000 0.43750000000000 28.085 > 25 27 Si 0.18750000000000 0.68750000000000 0.43750000000000 28.085 > 25 28 Si 0.68750000000000 0.68750000000000 0.43750000000000 28.085 > 25 29 Si 0.18750000000000 0.18750000000000 0.93750000000000 28.085 > 25 30 Si 0.68750000000000 0.18750000000000 0.93750000000000 28.085 > 25 31 Si 0.18750000000000 0.68750000000000 0.93750000000000 28.085 > 25 32 Si 0.68750000000000 0.68750000000000 0.93750000000000 28.085 > 25 33 Si 0.06250000000000 0.06250000000000 0.06250000000000 28.085 > 33 34 Si 0.56250000000000 0.06250000000000 0.06250000000000 28.085 > 33 35 Si 0.06250000000000 0.56250000000000 0.06250000000000 28.085 > 33 36 Si 0.56250000000000 0.56250000000000 0.06250000000000 28.085 > 33 37 Si 0.06250000000000 0.06250000000000 0.56250000000000 28.085 > 33 38 Si 0.56250000000000 0.06250000000000 0.56250000000000 28.085 > 33 39 Si 0.06250000000000 0.56250000000000 0.56250000000000 28.085 > 33 40 Si 0.56250000000000 0.56250000000000 0.56250000000000 28.085 > 33 41 Si 0.06250000000000 0.31250000000000 0.31250000000000 28.085 > 41 42 Si 0.56250000000000 0.31250000000000 0.31250000000000 28.085 > 41 43 Si 0.06250000000000 0.81250000000000 0.31250000000000 28.085 > 41 44 Si 0.56250000000000 0.81250000000000 0.31250000000000 28.085 > 41 45 Si 0.06250000000000 0.31250000000000 0.81250000000000 28.085 > 41 46 Si 0.56250000000000 0.31250000000000 0.81250000000000 28.085 > 41 47 Si 0.06250000000000 0.81250000000000 0.81250000000000 28.085 > 41 48 Si 0.56250000000000 0.81250000000000 0.81250000000000 28.085 > 41 49 Si 0.31250000000000 0.06250000000000 0.31250000000000 28.085 > 49 50 Si 0.81250000000000 0.06250000000000 0.31250000000000 28.085 > 49 51 Si 0.31250000000000 0.56250000000000 0.31250000000000 28.085 > 49 52 Si 0.81250000000000 0.56250000000000 0.31250000000000 28.085 > 49 53 Si 0.31250000000000 0.06250000000000 0.81250000000000 28.085 > 49 54 Si 0.81250000000000 0.06250000000000 0.81250000000000 28.085 > 49 55 Si 0.31250000000000 0.56250000000000 0.81250000000000 28.085 > 49 56 Si 0.81250000000000 0.56250000000000 0.81250000000000 28.085 > 49 57 Si 0.31250000000000 0.31250000000000 0.06250000000000 28.085 > 57 58 Si 0.81250000000000 0.31250000000000 0.06250000000000 28.085 > 57 59 Si 0.31250000000000 0.81250000000000 0.06250000000000 28.085 > 57 60 Si 0.81250000000000 0.81250000000000 0.06250000000000 28.085 > 57 61 Si 0.31250000000000 0.31250000000000 0.56250000000000 28.085 > 57 62 Si 0.81250000000000 0.31250000000000 0.56250000000000 28.085 > 57 63 Si 0.31250000000000 0.81250000000000 0.56250000000000 28.085 > 57 64 Si 0.81250000000000 0.81250000000000 0.56250000000000 28.085 > 57 ------------------- ratio (supercell for fc)/(primitive) ------------------- 2.00 0.00 0.00 0.00 2.00 0.00 0.00 0.00 2.00 ----------------------------- Force constants ------------------------------ Imposing translational and index exchange symmetry to fc2: False Imposing translational and index exchange symmetry to fc3: False Imposing symmetry of index exchange to fc3 in reciprocal space: False Displacement dataset is read from disp_fc3.yaml. Sets of supercell forces are read from FORCES_FC3. Traceback (most recent call last): File "/db/home/chenrf/.local/bin/phono3py", line 4, in import('pkg_resources').run_script('phono3py==1.12.9.22', 'phono3py') File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 765, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1552, in run_script File "/db/home/chenrf/.local/lib/python2.7/site-packages/phono3py-1.12.9.22-py2.7-linux-x86_64.egg/EGG-INFO/scripts/phono3py", line 527, in

File "build/bdist.linux-x86_64/egg/phono3py/cui/create_force_constants.py", line 122, in create_phono3py_force_constants File "build/bdist.linux-x86_64/egg/phono3py/cui/create_force_constants.py", line 273, in _create_phono3py_fc3 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/init.py", line 278, in produce_fc3 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/init.py", line 743, in _get_fc3 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 28, in get_fc3 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 470, in _get_fc3_least_atoms File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 503, in _get_fc3_one_atom File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 234, in get_delta_fc2 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 291, in get_constrained_fc2 TypeError: distribute_force_constants() takes exactly 6 arguments (8 given)

Also, when I tried to do thermal conductivity calculation an error occurs:

[chenrf@mic vasprun_xmls]$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" -c POSCAR-unitcell --br /db/home/chenrf/.local/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type. from ._conv import register_converters as _register_converters

_ | | | / _ | ' | ' \ / | ' \ / \ | | ' | | | | | |) | | | | () | | | | () |) | |) | || | | ./|| ||_/|| ||_/__/| ./ _, | || || |/ 1.12.9

Run mode: conductivity-RTA Spacegroup: Fd-3m (227) ------------------------------ primitive cell ------------------------------ Lattice vectors: a 5.466262890000000 0.000000000000000 0.000000000000000 b 0.000000000000000 5.466262890000000 0.000000000000000 c 0.000000000000000 0.000000000000000 5.466262890000000 Atomic positions (fractional): 1 Si 0.87500000000000 0.87500000000000 0.87500000000000 28.085 2 Si 0.87500000000000 0.37500000000000 0.37500000000000 28.085 3 Si 0.37500000000000 0.87500000000000 0.37500000000000 28.085 4 Si 0.37500000000000 0.37500000000000 0.87500000000000 28.085 5 Si 0.12500000000000 0.12500000000000 0.12500000000000 28.085 6 Si 0.12500000000000 0.62500000000000 0.62500000000000 28.085 7 Si 0.62500000000000 0.12500000000000 0.62500000000000 28.085 8 Si 0.62500000000000 0.62500000000000 0.12500000000000 28.085 -------------------------------- super cell -------------------------------- Lattice vectors: a 10.932525780000001 0.000000000000000 0.000000000000000 b 0.000000000000000 10.932525780000001 0.000000000000000 c 0.000000000000000 0.000000000000000 10.932525780000001 Atomic positions (fractional): 1 Si 0.43750000000000 0.43750000000000 0.43750000000000 28.085 > 1 2 Si 0.93750000000000 0.43750000000000 0.43750000000000 28.085 > 1 3 Si 0.43750000000000 0.93750000000000 0.43750000000000 28.085 > 1 4 Si 0.93750000000000 0.93750000000000 0.43750000000000 28.085 > 1 5 Si 0.43750000000000 0.43750000000000 0.93750000000000 28.085 > 1 6 Si 0.93750000000000 0.43750000000000 0.93750000000000 28.085 > 1 7 Si 0.43750000000000 0.93750000000000 0.93750000000000 28.085 > 1 8 Si 0.93750000000000 0.93750000000000 0.93750000000000 28.085 > 1 9 Si 0.43750000000000 0.18750000000000 0.18750000000000 28.085 > 9 10 Si 0.93750000000000 0.18750000000000 0.18750000000000 28.085 > 9 11 Si 0.43750000000000 0.68750000000000 0.18750000000000 28.085 > 9 12 Si 0.93750000000000 0.68750000000000 0.18750000000000 28.085 > 9 13 Si 0.43750000000000 0.18750000000000 0.68750000000000 28.085 > 9 14 Si 0.93750000000000 0.18750000000000 0.68750000000000 28.085 > 9 15 Si 0.43750000000000 0.68750000000000 0.68750000000000 28.085 > 9 16 Si 0.93750000000000 0.68750000000000 0.68750000000000 28.085 > 9 17 Si 0.18750000000000 0.43750000000000 0.18750000000000 28.085 > 17 18 Si 0.68750000000000 0.43750000000000 0.18750000000000 28.085 > 17 19 Si 0.18750000000000 0.93750000000000 0.18750000000000 28.085 > 17 20 Si 0.68750000000000 0.93750000000000 0.18750000000000 28.085 > 17 21 Si 0.18750000000000 0.43750000000000 0.68750000000000 28.085 > 17 22 Si 0.68750000000000 0.43750000000000 0.68750000000000 28.085 > 17 23 Si 0.18750000000000 0.93750000000000 0.68750000000000 28.085 > 17 24 Si 0.68750000000000 0.93750000000000 0.68750000000000 28.085 > 17 25 Si 0.18750000000000 0.18750000000000 0.43750000000000 28.085 > 25 26 Si 0.68750000000000 0.18750000000000 0.43750000000000 28.085 > 25 27 Si 0.18750000000000 0.68750000000000 0.43750000000000 28.085 > 25 28 Si 0.68750000000000 0.68750000000000 0.43750000000000 28.085 > 25 29 Si 0.18750000000000 0.18750000000000 0.93750000000000 28.085 > 25 30 Si 0.68750000000000 0.18750000000000 0.93750000000000 28.085 > 25 31 Si 0.18750000000000 0.68750000000000 0.93750000000000 28.085 > 25 32 Si 0.68750000000000 0.68750000000000 0.93750000000000 28.085 > 25 33 Si 0.06250000000000 0.06250000000000 0.06250000000000 28.085 > 33 34 Si 0.56250000000000 0.06250000000000 0.06250000000000 28.085 > 33 35 Si 0.06250000000000 0.56250000000000 0.06250000000000 28.085 > 33 36 Si 0.56250000000000 0.56250000000000 0.06250000000000 28.085 > 33 37 Si 0.06250000000000 0.06250000000000 0.56250000000000 28.085 > 33 38 Si 0.56250000000000 0.06250000000000 0.56250000000000 28.085 > 33 39 Si 0.06250000000000 0.56250000000000 0.56250000000000 28.085 > 33 40 Si 0.56250000000000 0.56250000000000 0.56250000000000 28.085 > 33 41 Si 0.06250000000000 0.31250000000000 0.31250000000000 28.085 > 41 42 Si 0.56250000000000 0.31250000000000 0.31250000000000 28.085 > 41 43 Si 0.06250000000000 0.81250000000000 0.31250000000000 28.085 > 41 44 Si 0.56250000000000 0.81250000000000 0.31250000000000 28.085 > 41 45 Si 0.06250000000000 0.31250000000000 0.81250000000000 28.085 > 41 46 Si 0.56250000000000 0.31250000000000 0.81250000000000 28.085 > 41 47 Si 0.06250000000000 0.81250000000000 0.81250000000000 28.085 > 41 48 Si 0.56250000000000 0.81250000000000 0.81250000000000 28.085 > 41 49 Si 0.31250000000000 0.06250000000000 0.31250000000000 28.085 > 49 50 Si 0.81250000000000 0.06250000000000 0.31250000000000 28.085 > 49 51 Si 0.31250000000000 0.56250000000000 0.31250000000000 28.085 > 49 52 Si 0.81250000000000 0.56250000000000 0.31250000000000 28.085 > 49 53 Si 0.31250000000000 0.06250000000000 0.81250000000000 28.085 > 49 54 Si 0.81250000000000 0.06250000000000 0.81250000000000 28.085 > 49 55 Si 0.31250000000000 0.56250000000000 0.81250000000000 28.085 > 49 56 Si 0.81250000000000 0.56250000000000 0.81250000000000 28.085 > 49 57 Si 0.31250000000000 0.31250000000000 0.06250000000000 28.085 > 57 58 Si 0.81250000000000 0.31250000000000 0.06250000000000 28.085 > 57 59 Si 0.31250000000000 0.81250000000000 0.06250000000000 28.085 > 57 60 Si 0.81250000000000 0.81250000000000 0.06250000000000 28.085 > 57 61 Si 0.31250000000000 0.31250000000000 0.56250000000000 28.085 > 57 62 Si 0.81250000000000 0.31250000000000 0.56250000000000 28.085 > 57 63 Si 0.31250000000000 0.81250000000000 0.56250000000000 28.085 > 57 64 Si 0.81250000000000 0.81250000000000 0.56250000000000 28.085 > 57 ------------------- ratio (supercell for fc)/(primitive) ------------------- 2.00 0.00 0.00 0.00 2.00 0.00 0.00 0.00 2.00 ----------------------------- Force constants ------------------------------ Imposing translational and index exchange symmetry to fc2: False Imposing translational and index exchange symmetry to fc3: False Imposing symmetry of index exchange to fc3 in reciprocal space: False fc3.hdf5 not found.

/ \ '| '/ | '| | / | | | | (_) | | _|| || _/|_|

It seems that these errors have something to do with python. However, I searched online but found no answer. Any suggestion or hints to deal with these errors would be appreciated.

Thanks, Chen Ruofan

atztogo commented 6 years ago

Hi,

There are two issues. One is in h5py, which is just warning, you can igonore. The other is in phono3py. If you can't solve problem when you update both phonopy and phono3py to the latest version, please let me know again.

Togo

On Thu, May 17, 2018 at 5:26 PM, crf1989 notifications@github.com wrote:

Dear Atz Togo,

I tried the example Si-PBE and I obtained the FORCES_FC3 file successfully. However, when trying to create fc2.hdf and fc3.hdf I got some errors which are shown below.

[chenrf@mic vasprun_xmls]$ phono3py --dim="2 2 2" -c POSCAR-unitcell /db/home/chenrf/.local/lib/python2.7/site-packages/h5py- 2.7.1-py2.7-linux-x86_64.egg/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype fromfloattonp.floatingis deprecated. In future, it will be treated asnp.float64 == np.dtype(float).type`. from .

conv import register_converters as registerconverters __ | | | / _ | ' | ' \ / | ' \ / \ | | ' | | | | | |) | | | | () | | | | () |__) | |) | | | | | .__/|| |*|/|| ||/ /| ./ , | || |*| |___/ 1.12.9

Spacegroup: Fd-3m (227) ------------------------------ primitive cell

Lattice vectors: a 5.466262890000000 0.000000000000000 0.000000000000000 b 0.000000000000000 5.466262890000000 0.000000000000000 c 0.000000000000000 0.000000000000000 5.466262890000000 Atomic positions (fractional): 1 Si 0.87500000000000 0.87500000000000 0.87500000000000 28.085 2 Si 0.87500000000000 0.37500000000000 0.37500000000000 28.085 3 Si 0.37500000000000 0.87500000000000 0.37500000000000 28.085 4 Si 0.37500000000000 0.37500000000000 0.87500000000000 28.085 5 Si 0.12500000000000 0.12500000000000 0.12500000000000 28.085 6 Si 0.12500000000000 0.62500000000000 0.62500000000000 28.085 7 Si 0.62500000000000 0.12500000000000 0.62500000000000 28.085 8 Si 0.62500000000000 0.62500000000000 0.12500000000000 28.085 -------------------------------- super cell ------------------------------

Lattice vectors: a 10.932525780000001 0.000000000000000 0.000000000000000 b 0.000000000000000 10.932525780000001 0.000000000000000 c 0.000000000000000 0.000000000000000 10.932525780000001 Atomic positions (fractional): 1 Si 0.43750000000000 0.43750000000000 0.43750000000000 28.085 > 1 2 Si 0.93750000000000 0.43750000000000 0.43750000000000 28.085 > 1 3 Si 0.43750000000000 0.93750000000000 0.43750000000000 28.085 > 1 4 Si 0.93750000000000 0.93750000000000 0.43750000000000 28.085 > 1 5 Si 0.43750000000000 0.43750000000000 0.93750000000000 28.085 > 1 6 Si 0.93750000000000 0.43750000000000 0.93750000000000 28.085 > 1 7 Si 0.43750000000000 0.93750000000000 0.93750000000000 28.085 > 1 8 Si 0.93750000000000 0.93750000000000 0.93750000000000 28.085 > 1 9 Si 0.43750000000000 0.18750000000000 0.18750000000000 28.085 > 9 10 Si 0.93750000000000 0.18750000000000 0.18750000000000 28.085 > 9 11 Si 0.43750000000000 0.68750000000000 0.18750000000000 28.085 > 9 12 Si 0.93750000000000 0.68750000000000 0.18750000000000 28.085 > 9 13 Si 0.43750000000000 0.18750000000000 0.68750000000000 28.085 > 9 14 Si 0.93750000000000 0.18750000000000 0.68750000000000 28.085 > 9 15 Si 0.43750000000000 0.68750000000000 0.68750000000000 28.085 > 9 16 Si 0.93750000000000 0.68750000000000 0.68750000000000 28.085 > 9 17 Si 0.18750000000000 0.43750000000000 0.18750000000000 28.085 > 17 18 Si 0.68750000000000 0.43750000000000 0.18750000000000 28.085 > 17 19 Si 0.18750000000000 0.93750000000000 0.18750000000000 28.085 > 17 20 Si 0.68750000000000 0.93750000000000 0.18750000000000 28.085 > 17 21 Si 0.18750000000000 0.43750000000000 0.68750000000000 28.085 > 17 22 Si 0.68750000000000 0.43750000000000 0.68750000000000 28.085 > 17 23 Si 0.18750000000000 0.93750000000000 0.68750000000000 28.085 > 17 24 Si 0.68750000000000 0.93750000000000 0.68750000000000 28.085 > 17 25 Si 0.18750000000000 0.18750000000000 0.43750000000000 28.085 > 25 26 Si 0.68750000000000 0.18750000000000 0.43750000000000 28.085 > 25 27 Si 0.18750000000000 0.68750000000000 0.43750000000000 28.085 > 25 28 Si 0.68750000000000 0.68750000000000 0.43750000000000 28.085 > 25 29 Si 0.18750000000000 0.18750000000000 0.93750000000000 28.085 > 25 30 Si 0.68750000000000 0.18750000000000 0.93750000000000 28.085 > 25 31 Si 0.18750000000000 0.68750000000000 0.93750000000000 28.085 > 25 32 Si 0.68750000000000 0.68750000000000 0.93750000000000 28.085 > 25 33 Si 0.06250000000000 0.06250000000000 0.06250000000000 28.085 > 33 34 Si 0.56250000000000 0.06250000000000 0.06250000000000 28.085 > 33 35 Si 0.06250000000000 0.56250000000000 0.06250000000000 28.085 > 33 36 Si 0.56250000000000 0.56250000000000 0.06250000000000 28.085 > 33 37 Si 0.06250000000000 0.06250000000000 0.56250000000000 28.085 > 33 38 Si 0.56250000000000 0.06250000000000 0.56250000000000 28.085 > 33 39 Si 0.06250000000000 0.56250000000000 0.56250000000000 28.085 > 33 40 Si 0.56250000000000 0.56250000000000 0.56250000000000 28.085 > 33 41 Si 0.06250000000000 0.31250000000000 0.31250000000000 28.085 > 41 42 Si 0.56250000000000 0.31250000000000 0.31250000000000 28.085 > 41 43 Si 0.06250000000000 0.81250000000000 0.31250000000000 28.085 > 41 44 Si 0.56250000000000 0.81250000000000 0.31250000000000 28.085 > 41 45 Si 0.06250000000000 0.31250000000000 0.81250000000000 28.085 > 41 46 Si 0.56250000000000 0.31250000000000 0.81250000000000 28.085 > 41 47 Si 0.06250000000000 0.81250000000000 0.81250000000000 28.085 > 41 48 Si 0.56250000000000 0.81250000000000 0.81250000000000 28.085 > 41 49 Si 0.31250000000000 0.06250000000000 0.31250000000000 28.085 > 49 50 Si 0.81250000000000 0.06250000000000 0.31250000000000 28.085 > 49 51 Si 0.31250000000000 0.56250000000000 0.31250000000000 28.085 > 49 52 Si 0.81250000000000 0.56250000000000 0.31250000000000 28.085 > 49 53 Si 0.31250000000000 0.06250000000000 0.81250000000000 28.085 > 49 54 Si 0.81250000000000 0.06250000000000 0.81250000000000 28.085 > 49 55 Si 0.31250000000000 0.56250000000000 0.81250000000000 28.085 > 49 56 Si 0.81250000000000 0.56250000000000 0.81250000000000 28.085 > 49 57 Si 0.31250000000000 0.31250000000000 0.06250000000000 28.085 > 57 58 Si 0.81250000000000 0.31250000000000 0.06250000000000 28.085 > 57 59 Si 0.31250000000000 0.81250000000000 0.06250000000000 28.085 > 57 60 Si 0.81250000000000 0.81250000000000 0.06250000000000 28.085 > 57 61 Si 0.31250000000000 0.31250000000000 0.56250000000000 28.085 > 57 62 Si 0.81250000000000 0.31250000000000 0.56250000000000 28.085 > 57 63 Si 0.31250000000000 0.81250000000000 0.56250000000000 28.085 > 57 64 Si 0.81250000000000 0.81250000000000 0.56250000000000 28.085 > 57 ------------------- ratio (supercell for fc)/(primitive)

2.00 0.00 0.00 0.00 2.00 0.00 0.00 0.00 2.00 ----------------------------- Force constants

Imposing translational and index exchange symmetry to fc2: False Imposing translational and index exchange symmetry to fc3: False Imposing symmetry of index exchange to fc3 in reciprocal space: False Displacement dataset is read from disp_fc3.yaml. Sets of supercell forces are read from FORCES_FC3. Traceback (most recent call last): File "/db/home/chenrf/.local/bin/phono3py", line 4, in import('pkg_resources').run_script('phono3py==1.12.9.22', 'phono3py') File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 765, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1552, in run_script File "/db/home/chenrf/.local/lib/python2.7/site-packages/ phono3py-1.12.9.22-py2.7-linux-x86_64.egg/EGG-INFO/scripts/phono3py", line 527, in

File "build/bdist.linux-x86_64/egg/phono3py/cui/create_force_constants.py", line 122, in create_phono3py_force_constants File "build/bdist.linux-x86_64/egg/phono3py/cui/create_force_constants.py", line 273, in

create_phono3py_fc3 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/init.py", line 278, in produce_fc3 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/init.py", line 743, in get_fc3 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 28, in get_fc3 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 470, in get_fc3_least_atoms File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 503, in get_fc3_one_atom File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 234, in get_delta_fc2 File "build/bdist.linux-x86_64/egg/phono3py/phonon3/fc3.py", line 291, in get_constrained_fc2 TypeError: distribute_force_constants() takes exactly 6 arguments (8 given) Also, when I tried to do thermal conductivity calculation an error occurs:[chenrf@mic vasprun_xmls]$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" -c POSCAR-unitcell --br /db/home/chenrf/.local/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type. from .conv import register_converters as registerconverters __ | | | / _ _ | ' | ' \ / | ' \ / _ \ | | '_ | | | | | |) | | | | () | | | | () |__) | |) | | | | | .__/|| ||___/|| ||___/ /| ._/ , | || || |___/ 1.12.9

Run mode: conductivity-RTA Spacegroup: Fd-3m (227) ------------------------------ primitive cell

Lattice vectors: a 5.466262890000000 0.000000000000000 0.000000000000000 b 0.000000000000000 5.466262890000000 0.000000000000000 c 0.000000000000000 0.000000000000000 5.466262890000000 Atomic positions (fractional): 1 Si 0.87500000000000 0.87500000000000 0.87500000000000 28.085 2 Si 0.87500000000000 0.37500000000000 0.37500000000000 28.085 3 Si 0.37500000000000 0.87500000000000 0.37500000000000 28.085 4 Si 0.37500000000000 0.37500000000000 0.87500000000000 28.085 5 Si 0.12500000000000 0.12500000000000 0.12500000000000 28.085 6 Si 0.12500000000000 0.62500000000000 0.62500000000000 28.085 7 Si 0.62500000000000 0.12500000000000 0.62500000000000 28.085 8 Si 0.62500000000000 0.62500000000000 0.12500000000000 28.085 -------------------------------- super cell ------------------------------

Lattice vectors: a 10.932525780000001 0.000000000000000 0.000000000000000 b 0.000000000000000 10.932525780000001 0.000000000000000 c 0.000000000000000 0.000000000000000 10.932525780000001 Atomic positions (fractional): 1 Si 0.43750000000000 0.43750000000000 0.43750000000000 28.085 > 1 2 Si 0.93750000000000 0.43750000000000 0.43750000000000 28.085 > 1 3 Si 0.43750000000000 0.93750000000000 0.43750000000000 28.085 > 1 4 Si 0.93750000000000 0.93750000000000 0.43750000000000 28.085 > 1 5 Si 0.43750000000000 0.43750000000000 0.93750000000000 28.085 > 1 6 Si 0.93750000000000 0.43750000000000 0.93750000000000 28.085 > 1 7 Si 0.43750000000000 0.93750000000000 0.93750000000000 28.085 > 1 8 Si 0.93750000000000 0.93750000000000 0.93750000000000 28.085 > 1 9 Si 0.43750000000000 0.18750000000000 0.18750000000000 28.085 > 9 10 Si 0.93750000000000 0.18750000000000 0.18750000000000 28.085 > 9 11 Si 0.43750000000000 0.68750000000000 0.18750000000000 28.085 > 9 12 Si 0.93750000000000 0.68750000000000 0.18750000000000 28.085 > 9 13 Si 0.43750000000000 0.18750000000000 0.68750000000000 28.085 > 9 14 Si 0.93750000000000 0.18750000000000 0.68750000000000 28.085 > 9 15 Si 0.43750000000000 0.68750000000000 0.68750000000000 28.085 > 9 16 Si 0.93750000000000 0.68750000000000 0.68750000000000 28.085 > 9 17 Si 0.18750000000000 0.43750000000000 0.18750000000000 28.085 > 17 18 Si 0.68750000000000 0.43750000000000 0.18750000000000 28.085 > 17 19 Si 0.18750000000000 0.93750000000000 0.18750000000000 28.085 > 17 20 Si 0.68750000000000 0.93750000000000 0.18750000000000 28.085 > 17 21 Si 0.18750000000000 0.43750000000000 0.68750000000000 28.085 > 17 22 Si 0.68750000000000 0.43750000000000 0.68750000000000 28.085 > 17 23 Si 0.18750000000000 0.93750000000000 0.68750000000000 28.085 > 17 24 Si 0.68750000000000 0.93750000000000 0.68750000000000 28.085 > 17 25 Si 0.18750000000000 0.18750000000000 0.43750000000000 28.085 > 25 26 Si 0.68750000000000 0.18750000000000 0.43750000000000 28.085 > 25 27 Si 0.18750000000000 0.68750000000000 0.43750000000000 28.085 > 25 28 Si 0.68750000000000 0.68750000000000 0.43750000000000 28.085 > 25 29 Si 0.18750000000000 0.18750000000000 0.93750000000000 28.085 > 25 30 Si 0.68750000000000 0.18750000000000 0.93750000000000 28.085 > 25 31 Si 0.18750000000000 0.68750000000000 0.93750000000000 28.085 > 25 32 Si 0.68750000000000 0.68750000000000 0.93750000000000 28.085 > 25 33 Si 0.06250000000000 0.06250000000000 0.06250000000000 28.085 > 33 34 Si 0.56250000000000 0.06250000000000 0.06250000000000 28.085 > 33 35 Si 0.06250000000000 0.56250000000000 0.06250000000000 28.085 > 33 36 Si 0.56250000000000 0.56250000000000 0.06250000000000 28.085 > 33 37 Si 0.06250000000000 0.06250000000000 0.56250000000000 28.085 > 33 38 Si 0.56250000000000 0.06250000000000 0.56250000000000 28.085 > 33 39 Si 0.06250000000000 0.56250000000000 0.56250000000000 28.085 > 33 40 Si 0.56250000000000 0.56250000000000 0.56250000000000 28.085 > 33 41 Si 0.06250000000000 0.31250000000000 0.31250000000000 28.085 > 41 42 Si 0.56250000000000 0.31250000000000 0.31250000000000 28.085 > 41 43 Si 0.06250000000000 0.81250000000000 0.31250000000000 28.085 > 41 44 Si 0.56250000000000 0.81250000000000 0.31250000000000 28.085 > 41 45 Si 0.06250000000000 0.31250000000000 0.81250000000000 28.085 > 41 46 Si 0.56250000000000 0.31250000000000 0.81250000000000 28.085 > 41 47 Si 0.06250000000000 0.81250000000000 0.81250000000000 28.085 > 41 48 Si 0.56250000000000 0.81250000000000 0.81250000000000 28.085 > 41 49 Si 0.31250000000000 0.06250000000000 0.31250000000000 28.085 > 49 50 Si 0.81250000000000 0.06250000000000 0.31250000000000 28.085 > 49 51 Si 0.31250000000000 0.56250000000000 0.31250000000000 28.085 > 49 52 Si 0.81250000000000 0.56250000000000 0.31250000000000 28.085 > 49 53 Si 0.31250000000000 0.06250000000000 0.81250000000000 28.085 > 49 54 Si 0.81250000000000 0.06250000000000 0.81250000000000 28.085 > 49 55 Si 0.31250000000000 0.56250000000000 0.81250000000000 28.085 > 49 56 Si 0.81250000000000 0.56250000000000 0.81250000000000 28.085 > 49 57 Si 0.31250000000000 0.31250000000000 0.06250000000000 28.085 > 57 58 Si 0.81250000000000 0.31250000000000 0.06250000000000 28.085 > 57 59 Si 0.31250000000000 0.81250000000000 0.06250000000000 28.085 > 57 60 Si 0.81250000000000 0.81250000000000 0.06250000000000 28.085 > 57 61 Si 0.31250000000000 0.31250000000000 0.56250000000000 28.085 > 57 62 Si 0.81250000000000 0.31250000000000 0.56250000000000 28.085 > 57 63 Si 0.31250000000000 0.81250000000000 0.56250000000000 28.085 > 57 64 Si 0.81250000000000 0.81250000000000 0.56250000000000 28.085 > 57 ------------------- ratio (supercell for fc)/(primitive)

2.00 0.00 0.00 0.00 2.00 0.00 0.00 0.00 2.00 ----------------------------- Force constants

Imposing translational and index exchange symmetry to fc2: False Imposing translational and index exchange symmetry to fc3: False Imposing symmetry of index exchange to fc3 in reciprocal space: False fc3.hdf5 not found.

/ \ '| '/ | '

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`

It seems that these errors have something to do with python. However, I searched online but found no answer. Any suggestion or hints to deal with these errors would be appreciated.

Thanks, Chen Ruofan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/atztogo/phono3py/issues/8, or mute the thread https://github.com/notifications/unsubscribe-auth/AA6MPOzd4-c8NrGBHeMvO-5dmGly3m5tks5tzTQzgaJpZM4UCnp- .

-- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz.togo@gmail.com

crf1989 commented 6 years ago

Dear Atz Togo,

I update phono3py to newest verion 1.13.1, but it gives a python error at startup:

[chenrf@mic ~]$ phono3py /db/home/chenrf/.local/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type. from ._conv import register_converters as _register_converters Traceback (most recent call last): File "/db/home/chenrf/.local/bin/phono3py", line 4, in import('pkg_resources').run_script('phono3py==1.13.1', 'phono3py') File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 765, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1552, in run_script File "/db/home/chenrf/.local/lib/python2.7/site-packages/phono3py-1.13.1-py2.7-linux-x86_64.egg/EGG-INFO/scripts/phono3py", line 44, in

File "build/bdist.linux-x86_64/egg/phono3py/file_IO.py", line 5, in ImportError: cannot import name check_force_constants_indices

It seems this problem is related with python itself. It is also possible that my python is not installed properly, I'll try to run it on another computer later.

Thanks Chen Ruofan

atztogo commented 6 years ago

ImportError: cannot import name check_force_constants_indices suggests that the problem is in phono3py/phonopy. I had to release phonopy of my develop branch. I made the release now and please update to phonopy-1.13.0.28 again, and see how it goes. Sorry for inconvenience.

crf1989 commented 6 years ago

Dear Atz Togo，

Sorry to bother you again. I have updated phonopy and phono3py to newest version, but it seems phono3py would stuck at writting fc3.hdf. It stuck at the following stage all night but without CPU running

----------------------------- Force constants ------------------------------ Imposing translational and index exchange symmetry to fc2: False Imposing translational and index exchange symmetry to fc3: False Imposing symmetry of index exchange to fc3 in reciprocal space: False Displacement dataset for fc3 is read from disp_fc3.yaml. Sets of supercell forces are read from FORCES_FC3. Computing fc3[ 1, x, x ] using numpy.linalg.pinv with a displacement: [ 0.0300 0.0000 0.0000] Expanding fc3 Writing fc3 to fc3.hdf5

However, if I skip this stage to do thermal conductivity calculation directly a some error occurs:

----------------------------- Force constants ------------------------------ Imposing translational and index exchange symmetry to fc2: False Imposing translational and index exchange symmetry to fc3: False Imposing symmetry of index exchange to fc3 in reciprocal space: False fc3.hdf5 not found.

/ \ '| '/ | '| | / | | | | (_) | | _|| || _/|_|

If I terminate the hdf stage, a file fc3.hdf exists but thermal conductivity calculation would be stuck at reading hdf like:

----------------------------- Force constants ------------------------------ Imposing translational and index exchange symmetry to fc2: False Imposing translational and index exchange symmetry to fc3: False Imposing symmetry of index exchange to fc3 in reciprocal space: False Reading fc3 from fc3.hdf5

Could you please tell me what version of Python you are using? If the program runs properly in your machine, then it is possible that there exists some problem in my Python.

Thanks Chen Ruofan

atztogo commented 6 years ago

I use conda. I wrote some information here, https://atztogo.github.io/phono3py/install.html . I doubt the latest conda hdf5 package. So after installing all the latest versions of software needed from conda (e.g. conda update --all), I run conda install hdf5=1.8.18.

atztogo commented 6 years ago

If you use conda, I recommend python3 versions not python2.7.

crf1989 commented 6 years ago

Thanks, I'll try python3.

crf1989 commented 6 years ago

Thanks, Togo. It works fine now.