[ase-users] error of using ase.calculators.vasp module

Wed May 6 16:42:41 CEST 2020

Hi Mike,

Of course I will. Please see the attachment which includes the input files
of VASP. You can rerun the scf and nscf calculations to obtain the
coresponding CHGCAR and PARCHG files.

Best,
Shuang Leung

Michael Joseph Waters via ase-users <ase-users at listserv.fysik.dtu.dk>
于2020年5月6日周三 下午10:11写道：

> Hi Shuang Leung,
>
> Do you have a minimal input that can reproduce a CHGCAR with '******' in
> it? If not, do you mind sharing which pseudo potentials, plane wave cutoff,
> and augmentation grid you are using? This info could help when designing a
> warning.
>
> Best,
> -Mike
> ------------------------------
> *From:* ase-users-bounces at listserv.fysik.dtu.dk <
> ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Offermans Willem
> via ase-users <ase-users at listserv.fysik.dtu.dk>
> *Sent:* Wednesday, May 6, 2020 8:22 AM
> *To:* ase users <ase-users at listserv.fysik.dtu.dk>
> *Subject:* Re: [ase-users] error of using ase.calculators.vasp module
>
> Hi Shuang Leung and ASE friends,
>
> Maybe this ``error`` needs to be handled in a user friendly way by ASE.
> It might make it much easier to discover what is going on.
>
>
>
> Met vriendelijke groeten,
> Mit freundlichen Grüßen,
> With kind regards,
>
>
> Willem Offermans
> Researcher Electrocatalysis SCT
> VITO NV | Boeretang 200 | 2400 Mol
> Phone:+32(0)14335263 Mobile:+32(0)492182073
>
> Willem.Offermans at Vito.be
>
>
> On 5 May 2020, at 18:02, Shuang Leung <sleung1924 at gmail.com> wrote:
>
> Hi again Mike,
>
> Sorry for replying late. I checked my PARCHG file once again and did find
> an error: "... -10.456   *********** -9.4432   -8.8059 ..."  One of  the
> grid vaules has been replaced with asterisks, and thus resulting in reading
> failure. This exception may come from the Fortran format statements of the
> VASP code which controls the output of PARCHG file. A similar example can
> be found here:
> https://stackoverflow.com/questions/15681735/fortran-splats-my-output-to-asterisks-why
> <https://urldefense.com/v3/__https://eur02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fstackoverflow.com*2Fquestions*2F15681735*2Ffortran-splats-my-output-to-asterisks-why&data=02*7C01*7Cwillem.offermans*40vito.be*7C40795f469975442f33c308d7f10dc6c1*7C9e2777ed82374ab992782c144d6f6da3*7C0*7C1*7C637242913796697956&sdata=d71ggorMh*2BOMzPfsw*2FalgHDkLZDBCv9PeU8oYLF03EU*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSU!!Dq0X2DkFhyF93HkjWTBQKhk!DCQjzM1yk9WupmH5fxDgeP-DDOU44BDrQnrgeiHSVrwbX7KrudeZrd0hXhzMzC8nii-vOrNvHjhE$>.
> My VASP version is 5.4.4.
>
> Best,
> Shuang Leung
>
>
> Michael Joseph Waters via ase-users <ase-users at listserv.fysik.dtu.dk>
> 于2020年4月21日周二 上午2:38写道：
>
> Hi Shuang Leung,
>
> This error will occur when ASE stops reading the grid values before
> getting enough to match the expected grid dimensions. Hence the mismatch.
>
> I don't know of any size limitations. Do your PARCHG files only have one
> grid in them or is there chgdiff grid too? The error is on reading the
> chgdiff part of the file. (
> https://gitlab.com/ase/ase/-/blob/master/ase/calculators/vasp/vasp.py#L883
> <https://urldefense.com/v3/__https://eur02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fgitlab.com*2Fase*2Fase*2F-*2Fblob*2Fmaster*2Fase*2Fcalculators*2Fvasp*2Fvasp.py*23L883&data=02*7C01*7Cwillem.offermans*40vito.be*7C40795f469975442f33c308d7f10dc6c1*7C9e2777ed82374ab992782c144d6f6da3*7C0*7C1*7C637242913796707949&sdata=*2BajboBKB79OQN6Rngb9TYBuBq26wg5ndZLrvKul8870*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!Dq0X2DkFhyF93HkjWTBQKhk!DCQjzM1yk9WupmH5fxDgeP-DDOU44BDrQnrgeiHSVrwbX7KrudeZrd0hXhzMzC8nii-vOgjeX7zZ$>
> )
>
> A simple thing we should check is did the file write correctly? Is it the
> expected size for this calculation? If so, what is the tail of the file?
>
> Best,
> -Mike
> ------------------------------
> *From:* ase-users-bounces at listserv.fysik.dtu.dk <
> ase-users-bounces at listserv.fysik.dtu.dk> on behalf of sleung1924 via
> ase-users <ase-users at listserv.fysik.dtu.dk>
> *Sent:* Saturday, April 18, 2020 7:29 PM
> *To:* ase-users <ase-users at listserv.fysik.dtu.dk>
> *Subject:* [ase-users] error of using ase.calculators.vasp module
>
> Hello, ASE friends.
>
> I tried to use VaspChargeDensity() function to read the 'PARCHG' file
> (which has the same format as 'CHGCAR'), but an error arised, as shown
> below:
>
> """
> Traceback (most recent call last):
>   File "STM-2Dscan.py", line 88, in <module>
>     vasp_charge = VaspChargeDensity('PARCHG')
>   File
> "/home/yinyr/.local/lib/python3.6/site-packages/ase-3.20.0b1-py3.6.egg/ase/calculators/vasp/vasp.py",
> line 789, in __init__
>     self.read(filename)
>   File
> "/home/yinyr/.local/lib/python3.6/site-packages/ase-3.20.0b1-py3.6.egg/ase/calculators/vasp/vasp.py",
> line 883, in read
>     self._read_chg(f, chgdiff, atoms.get_volume())
>   File
> "/home/yinyr/.local/lib/python3.6/site-packages/ase-3.20.0b1-py3.6.egg/ase/calculators/vasp/vasp.py",
> line 813, in _read_chg
>     sep=' ')
> ValueError: could not broadcast input array from shape (68) into shape
> (280)
> """
>
> This error only occurred when the spin polarized calculation was performed
> (ISPIN = 2 was set in INCAR). And when I closed the spin (ISPIN = 1), the
> calculated PARCHG file can be read successfully. I also tested other small
> atomic systems, however, this error didn't appeared again regardless of
> whether spin was set or not. So, is there any limitation for a large system
> (my calculated model has more than 300 atoms) when using the
> VaspChargeDensity() function? The ase-3.19.1 version was installed in my
> OS. I will be very appreciated if you could give me some advices.
>
> Best wishes,
> Shuang Leung
>
> ------------------------------
> 发自我的iPhone
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