[Pw_forum] Xcrysden display incorrect structure (when using angstrom units)

[Surender]

Thank you Giovanni, may I ask one more question. Earlier version (I don't
remember exactly which one) of XCrysDen  used to work from command line
using  xcrysden --pwi pwscf.in but XCrysDen-1.5.53 simply ignores all the
command line options and just show the main window, then I have to use the
file menu to load the file. It's not a very big issue but sometime it's
annoying especially when you need to visualize the structures quite
frequently.

Regards,
Surender

>
> On 1 Jun 2014, at 17:41, Paolo Giannozzi wrote:
>
>> I am not sure that xcrysden can understand the
>> "CELL_PARAMETERS {angstrom}" card, since option
>> "angstrom" was added quite recently
>>
>> P.
>
> Indeed, I also noticed that Xcrysden does not properly cope with
> "CELL_PARAMETERS angstrom" (at least the version that I have installed).
>
> As a workaround, run the calculation just for a few seconds (e.g.,
> creating a prefix.EXIT file in the same folder as the input file - where
> you have to substitute 'prefix' with the prefix you chose - that will
> automatically stop the code after the initialization part) and then open
> instead the output file with xcrysden. This should work properly in both
> cases (i.e., input file in angstrom or bohr).
>
> Best,
> Giovanni
>
>
>
> --
> Giovanni Pizzi
> Post-doctoral Research Scientist
> EPFL STI IMX THEOS
> MXC 340 (Bâtiment MXC)
> Station 12
> CH-1015 Lausanne (Switzerland)
> Phone: +41 21 69 31124
>
>
>
>> On Sun, 2014-06-01 at 14:41 +0530, Surender wrote:
>>> Dear QE Users,
>>> I don't know whether it's an issue related to XCrysDen or something is
>>> wrong wih my QE input file. Following is the first input file
>>>
>>> ================
>>> cu.scf_bohr.in
>>> ================
>>> &control
>>>    calculation='scf'
>>>    prefix='cu',
>>>    pseudo_dir='./pseudo',
>>>    outdir='./tmp'
>>> /
>>> &system
>>>    ibrav=0
>>>    ntyp= 1,
>>>    nat= 4,
>>>    ecutwfc= 50.0,
>>>    occupations='smearing',
>>>    smearing='methfessel-paxton',
>>>    degauss=0.005
>>> /
>>> &electrons
>>>    conv_thr = 1.0D-10
>>>    mixing_beta = 0.7
>>> /
>>> ATOMIC_SPECIES
>>> Cu 63.55 Cu.pz-d-rrkjus.UPF
>>> ATOMIC_POSITIONS {bohr}
>>> Cu 0.0000 0.0000 0.0000
>>> Cu 3.4155 3.4155 0.0000
>>> Cu 0.0000 3.4155 3.4155
>>> Cu 3.4155 0.0000 3.4155
>>> K_POINTS automatic
>>>   12 12 12 0 0 0
>>> CELL_PARAMETERS {bohr}
>>>   6.831 0.000 0.000
>>>   0.000 6.831 0.000
>>>   0.000 0.000 6.83
>>> ======================
>>>
>>> I can visualize cu.scf_bohr.in using XCrysDen and everything is ok (I
>>> mean
>>> no overlapping atoms). But if I specify the ATOMIC_POSITIONS and CELL
>>> PARAMETERS in ANGSTROM (see cu.scf_angstrom.in) and visualize the
>>> structure then atoms start overlapping. Following is the second input
>>> file
>>>
>>> ====================
>>> cu.scf_angstrom.in
>>> ====================
>>> &control
>>>    calculation='scf'
>>>    prefix='cu',
>>>    pseudo_dir='./pseudo',
>>>    outdir='./tmp'
>>> /
>>> &system
>>>    ibrav=0
>>>    ntyp= 1,
>>>    nat= 4,
>>>    ecutwfc= 50.0,
>>>    occupations='smearing',
>>>    smearing='methfessel-paxton',
>>>    degauss=0.005
>>> /
>>> &electrons
>>>    conv_thr = 1.0D-10
>>>    mixing_beta = 0.7
>>> /
>>> ATOMIC_SPECIES
>>> Cu 63.55 Cu.pz-d-rrkjus.UPF
>>> ATOMIC_POSITIONS {angstrom}
>>> Cu 0.0000 0.0000 0.0000
>>> Cu 1.8074 1.8074 0.0000
>>> Cu 0.0000 1.8074 1.8074
>>> Cu 1.8074 0.0000 1.8074
>>> K_POINTS automatic
>>>   12 12 12 0 0 0
>>> CELL_PARAMETERS {angstrom}
>>>   3.6148 0.0000 0.0000
>>>   0.0000 3.6148 0.0000
>>>   0.0000 0.0000 3.6148
>>> ========================
>>>
>>> I don't know what's going on or did I miss something. I am using
>>> XCrysDen
>>> Version: 1.5.53 on Ubuntu-12.04 LTS. Any help would be appreciated.
>>>
>>> Thanks,
>>> Surender
>>> IIT Bombay, India
>>>
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>>> Pw_forum at pwscf.org
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>>
>>
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