[xcrysden] How to display a whole molecule in unit cell with good connection?
Matic Poberznik
matic.poberznik at gmail.com
Tue Oct 27 15:51:52 CET 2015
>>Actually, I don't want to modify the relative distance between atoms
and boundaries. I think journals >>would not accept this.
I think that modifying the relative distance, as far as the figure is
concerned, should not be a problem. The only limitation I see is that
all atoms defined in the ATOMIC_POSITIONS card should be translated by
the same vector; due to periodicity both structures are equal, what will
change is the way the program reads the structure. Without seeing the
actual output I am assuming that your optimized coordinates contain
atoms with negative values in coordinates, for example let's say the
initial positions were 0.0, 0.0, 0.0, but after optimization they
changed to -0.1,-0.1,-0.1, so assuming a cubic structure of length "1"
the program draws the optimized coordinates at 0.9, 0.9, 0.9 (equivalent
position in the crystal cell), the result being the molecule "breaks" in
the unit cell. By shifiting all positions (to positive values) by a
specific vector this problem should disappear and as stated both
structures are equivalent, so this representation should be acceptable.
Both the xsf and pwscf formats are supported by openbabel, so converting
it to other formats shouldn't be a problem, though I have no experience
regarding the dynamic matrix, so I really have no idea if information
will be lost or not.
Best regards,
Matic
On 10/27/2015 01:47 PM, liyincumt at gmail.com wrote:
> Dear Matic,
>
> Thank you very much for your help!
> Actually, I don't want to modify the relative distance between atoms
> and boundaries. I think journals would not accept this. I was thinking
> on whether Molden could display it properly as the dynamic matrix file
> can be read by Molden as well. I tried many options in molden but it
> still can't work. So far I just found material studio (Display style:
> Default) can display it properly.
> I wonder whether I can convert quantum espresso files including
> dynamic matrix file and pwo into cif or any other format which could
> be read by material studio. Even it can be converted, I am still
> worried about the loss of the information of the forces on atoms.
>
> Best Regards,
> Yin
>
> ------------------------------------------------------------------------
> Dr. Yin Li
> Department of Biophysics,Medical School, University of Pecs,
> No.12 Szigeti Street, Pecs, H-7624, HUNGARY
> Phone: +36-72-535271/36271
>
> *From:* Matic Poberznik <mailto:matic.poberznik at gmail.com>
> *Date:* 2015-10-27 14:27
> *To:* XCrySDen mailing list <mailto:xcrysden at democritos.it>
> *Subject:* Re: [xcrysden] How to display a whole molecule in unit
> cell with good connection?
> Modifying this in the pwscf output file is impossible, so I
> suggest you convert the output file to xsf format using the
> pwo2xsf.sh tool. It can be found in the Quantum Espresso
> installation directory in my case it is in
>
> /esspreso-5.1.1/PW/tools/pwo2xsf.sh
>
> To write the optimized coordinates to the xsf file the syntax
> would be :
>
> bash pwo2xsf.sh -oc name_of_pwout.out > name_of_xsf.xsf
>
> Once you have the xsf file I suggest you shift the coordinates of
> the atoms so that the molecule is in the center of the cell; If
> the molecule atoms are , for instance, at 0.0, 0.0, 0.0 you should
> shift them so that the coordinates correspond to 1/2a+1/2b+1/2c
> where a,b,c are vectors of the unit cell. You should shift all
> atomic positions accordingly and the result will hopefully be better.
>
> Best regards,
>
> Matic
>
> On 10/27/2015 11:25 AM, liyincumt at gmail.com wrote:
>> Dear Matic,
>>
>> Thanks for your kind help!
>> After setting the number of units drawn, some molecules inside
>> the supercell are displayed correctly. But there are too many
>> molecules inside the supercell. The figure would be hardly
>> accepted by journal.
>> Is it possible to just display the molecules correctly in one
>> unit cell? I have tried buttons of the display which are located
>> in the bottom center of the screen, none of them can work properly.
>>
>> Best Regards,
>> Yin
>> ------------------------------------------------------------------------
>> Dr. Yin Li
>> Department of Biophysics,Medical School, University of Pecs,
>> No.12 Szigeti Street, Pecs, H-7624, HUNGARY
>> Phone: +36-72-535271/36271
>>
>> *From:* Matic Poberznik <mailto:matic.poberznik at gmail.com>
>> *Date:* 2015-10-27 12:14
>> *To:* XCrySDen mailing list <mailto:xcrysden at democritos.it>
>> *Subject:* Re: [xcrysden] How to display a whole molecule in
>> unit cell with good connection?
>> Dear Yin,
>>
>> If I understood your problem correctly, I think the best
>> solution is to open the Modify menu and choose the Atomic
>> Radius (Shift+R) option. Once there you can modify the
>> Covalent Radius and Connectivity Factor for each atom type to
>> suit your needs.
>>
>> In order to load your custom parameters when xcrysden starts
>> you should add a line in $HOME/.xcrysden/custom-definitions
>> file, an example:
>>
>> #
>> # this line changes the default atomic radius for aluminum to 1.6
>> #
>>
>> set atmRad(13) 1.6
>>
>> The custom definitions file is described on this link:
>> http://www.xcrysden.org/doc/custom.html
>>
>> If the problem stems from the periodic boundary conditions
>> then first try the different display modes of unit cells, i.
>> e. click the button for the display of the translational
>> asymmetric unit (bottom center of the screen). Then try
>> Modify => Number of units drawn (Shift+N), if the covalent
>> radius is correct at least some molecules should be displayed
>> correctly. If that is not enough let me know, there is one
>> more workaround but it is a bit more complicated.
>>
>> Best regards,
>>
>> Matic
>>
>>
>>
>> On 10/27/2015 09:19 AM, liyincumt at gmail.com wrote:
>>> Dear Xcrysden developers,
>>>
>>> Thanks for sharing this excellent visualization software for
>>> free!
>>> I am using xcrysden to visualize the input and output files
>>> of quantum espresso. I have a problem with visualization of
>>> crystals. Due to the presence of periodic boundary
>>> condition, some of atoms which are outside of the boundary
>>> look like being non-covalently connected. Is it possible to
>>> display a whole molecule with good covalent connections in
>>> Xcrysden.
>>>
>>> Thank you very much!
>>>
>>> Best Regards,
>>> Yin
>>>
>>> ------------------------------------------------------------------------
>>> Dr. Yin Li
>>> Department of Biophysics,Medical School, University of Pecs,
>>> No.12 Szigeti Street, Pecs, H-7624, HUNGARY
>>> Phone: +36-72-535271/36271
>>>
>>>
>>> _______________________________________________
>>> XCrySDen mailing list
>>> XCrySDen at democritos.it
>>> http://www.democritos.it/mailman/listinfo/xcrysden
>>
>>
>>
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>
> --
> Matic Poberznik
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
>
>
>
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--
Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
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