Re: [Phonopy-users] reading forces : list index out of range
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Re: [Phonopy-users] reading forces : list index out of range
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From: Atsushi T. <atz...@gm...> - 2016-12-14 05:25:53
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OK. I will improve display output to make it easy to find which file is broken.
Togo
On Tue, Dec 13, 2016 at 10:38 PM, Vasylenko, Andrij
<A.V...@wa...> wrote:
> Dear Togo
>
> Accidentally there is *00002.out file without the forces. (deleted
> tprnfor=.true. in the input, my bad)
>
> Thank you a lot for helping to identify the problem and for taking your
> time.
>
> Best wishes,
>
> Andrij
>
>
> On 13 Dec 2016, at 12:22, Atsushi Togo <atz...@gm...> wrote:
>
> Does each file contain force lines such as below?
> atom 36 type 1 force = -0.00001834 0.00001720 0.00001456
>
> Togo
>
> On Tue, Dec 13, 2016 at 7:24 PM, Vasylenko, Andrij
> <A.V...@wa...> wrote:
>
> Dear Togo
>
> Many thanks for the reply and the update.
>
> Unfortunately it did not solve the problem. Here is a screen:
>
> _ _____
> _ __ | |__ ___ _ __ ___|___ / _ __ _ _
> | '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
> | |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
> | .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
> |_| |_| |___/
> 1.11.5
>
> Displacement dataset is read from disp_fc3.yaml.
> Number of displacements: 342
> Number of supercell files: 342
> Drift force of gete-00001.out to be subtracted
> -0.00000000 -0.00000000 0.00000000
> Traceback (most recent call last):
> File "/usr/local/bin/phono3py", line 4, in <module>
> __import__('pkg_resources').run_script('phono3py==1.11.5.39', 'phono3py')
> File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py",
> line 726, in run_script
> self.require(requires)[0].run_script(script_name, ns)
> File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py",
> line 1658, in run_script
> exec(script_code, namespace, namespace)
> File
> "/usr/local/lib/python2.7/site-packages/phono3py-1.11.5.39-py2.7-macosx-10.10-x86_64.egg/EGG-INFO/scripts/phono3py",
> line 160, in <module>
>
> File "build/bdist.macosx-10.10-x86_64/egg/phono3py/file_IO.py", line 215,
> in write_FORCES_FC3
> File "build/bdist.macosx-10.10-x86_64/egg/phono3py/file_IO.py", line 200,
> in write_FORCES_FC2
> IndexError: list index out of range
>
> The created FORCES_FC3 file breaks after the lines :
> # File: 1
> # 1 0.0600000000000000 0.0000000000000000 0.0000000000000000
>
> What would be your suggestion?
>
> Thank you in advance.
>
> Best wishes,
>
> Andrij
>
> P.S. I should also probably mention that the supercells were created with
> —dim=“1 1 2” if this might play any role. Does the *yaml file look alright
> though?
>
>
> On 13 Dec 2016, at 04:27, Atsushi Togo <atz...@gm...> wrote:
>
> Hi,
>
> I can't see what happened. I updated phonopy and phono3py to show a
> bit more log. Could you install the latest phonopy and phono3py found
> at below and show again the error output?
> https://pypi.python.org/pypi/phonopy
> https://pypi.python.org/pypi/phono3py
>
> Togo
>
> On Mon, Dec 12, 2016 at 9:31 PM, Vasylenko, Andrij
> <A.V...@wa...> wrote:
>
> Dear Togo,
>
> I attempted to collect the forces from supercell calculations (completed
> with QE)
>
> phono3py - -pwscf - - cf3 supercell*out
>
> and am receiving the following complaint
>
> Displacement dataset is read from disp_fc3.yaml.
> Drift force
> -0.00000000 -0.00000000 0.00000000
> This drift force was subtracted from forces.
> Traceback (most recent call last):
> File "/usr/local/bin/phono3py", line 4, in <module>
> __import__('pkg_resources').run_script('phono3py==1.11.3', 'phono3py')
> File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py",
> line 726, in run_script
> self.require(requires)[0].run_script(script_name, ns)
> File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py",
> line 1658, in run_script
> exec(script_code, namespace, namespace)
> File
> "/usr/local/lib/python2.7/site-packages/phono3py-1.11.3-py2.7-macosx-10.10-x86_64.egg/EGG-INFO/scripts/phono3py",
> line 131, in <module>
>
> File "build/bdist.macosx-10.10-x86_64/egg/phono3py/file_IO.py", line 215,
> in write_FORCES_FC3
> File "build/bdist.macosx-10.10-x86_64/egg/phono3py/file_IO.py", line 200,
> in write_FORCES_FC2
> IndexError: list index out of range
>
> first lines of a *.yaml file are
> natom: 16
> num_first_displacements: 6
> num_second_displacements: 336
> num_displacements_created: 342
>
> $> ls supercell*out | wc -l
> 342
>
> I would appreciate your advice.
>
> Best wishes,
> Andrij
>
> P.S. disp_fc3.yaml is attached
>
> ____________________
> Dr Andrij Vasylenko
> Research Fellow
> Department of Physics
> University of Warwick
> Coventry CV4 7AL UK
> tel. +44 (0) 24 7652 3413
>
>
>
>
>
>
>
>
>
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>
>
>
> --
> Atsushi Togo
> Elements Strategy Initiative for Structural Materials, Kyoto university
> E-mail: atz...@gm...
>
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>
>
>
> --
> Atsushi Togo
> Elements Strategy Initiative for Structural Materials, Kyoto university
> E-mail: atz...@gm...
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Phonopy-users mailing list
> Pho...@li...
> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
>
>
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> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...
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