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

[Giovanni Pizzi]

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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> 
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