<html><head><meta http-equiv="content-type" content="text/html; charset=ISO-8859-1"><style>body { line-height: 1.5; }blockquote { margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em; }div.foxdiv20151027143411640253 { }body { font-family: 'Segoe UI'; color: rgb(0, 0, 0); line-height: 1.5; }</style></head><body>
<div><span></span>Dear Matic,</div><div><br></div><div><span style="line-height: 1.5; background-color: window;">Thank you very much for your help!</span></div><div><span style="line-height: 1.5; background-color: window;">Actually, I don't want to modify the relative distance between atoms and boundaries. I think journals would not accept this. </span><span style="background-color: window; line-height: 1.5;">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. </span></div><div><span style="background-color: window; line-height: 1.5;">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.</span></div><div><span style="background-color: window; line-height: 1.5;"><br></span></div><div><span style="background-color: window; line-height: 1.5;">Best Regards,</span></div><div><span style="background-color: window; line-height: 1.5;">Yin</span></div>
<div><br></div><hr style="width: 210px; height: 1px;" color="#b5c4df" size="1" align="left">
<div><span><div style="margin: 10px; font-family: verdana; font-size: 15px;"><span style="color: rgb(0, 0, 0); background-color: rgba(0, 0, 0, 0);">Dr. Yin Li <br>Department of Biophysics,Medical School, University of Pecs,<br>No.12 Szigeti Street, Pecs, H-7624, HUNGARY<br>Phone: +36-72-535271/36271</span></div></span></div>
<blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;"><div> </div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"><div style="PADDING-RIGHT: 8px; PADDING-LEFT: 8px; FONT-SIZE: 12px;FONT-FAMILY:tahoma;COLOR:#000000; BACKGROUND: #efefef; PADDING-BOTTOM: 8px; PADDING-TOP: 8px"><div><b>From:</b> <a href="mailto:matic.poberznik@gmail.com">Matic Poberznik</a></div><div><b>Date:</b> 2015-10-27 14:27</div><div><b>To:</b> <a href="mailto:xcrysden@democritos.it">XCrySDen mailing list</a></div><div><b>Subject:</b> Re: [xcrysden] How to display a whole molecule in unit cell with good connection?</div></div></div><div><div class="FoxDiv20151027143411640253">
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 <br>
<br>
/esspreso-5.1.1/PW/tools/pwo2xsf.sh<br>
<br>
To write the optimized coordinates to the xsf file the syntax would
be :<br>
<br>
bash pwo2xsf.sh -oc name_of_pwout.out > name_of_xsf.xsf <br>
<br>
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. <br>
<br>
Best regards,<br>
<br>
Matic<br>
<br>
<div class="moz-cite-prefix">On 10/27/2015 11:25 AM,
<a class="moz-txt-link-abbreviated" href="mailto:liyincumt@gmail.com">liyincumt@gmail.com</a> wrote:<br>
</div>
<blockquote cite="mid:2015102712253113411864@gmail.com" type="cite" style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;">
<div><span></span>Dear <span style="line-height: 1.5;
background-color: window;">Matic,</span></div>
<div><span style="line-height: 1.5; background-color: window;"><br>
</span></div>
<div><span style="line-height: 1.5; background-color: window;">Thanks
for your kind help! </span></div>
<div><span style="line-height: 1.5; background-color: window;">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.</span></div>
<div><span style="line-height: 1.5; background-color: window;">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. </span></div>
<div><br>
</div>
<div><span style="line-height: 1.5; background-color: window;">Best
Regards,</span></div>
<div>Yin</div>
<hr style="width: 210px; height: 1px;" align="left" size="1" color="#b5c4df">
<div><span>
<div style="margin: 10px; font-family: verdana; font-size:
15px;"><span style="color: rgb(0, 0, 0); background-color:
rgba(0, 0, 0, 0);">Dr. Yin Li <br>
Department of Biophysics,Medical School, University of Pecs,<br>
No.12 Szigeti Street, Pecs, H-7624, HUNGARY<br>
Phone: +36-72-535271/36271</span></div>
</span></div>
<blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;">
<div> </div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<div style="PADDING-RIGHT: 8px; PADDING-LEFT: 8px; FONT-SIZE:
12px;FONT-FAMILY:tahoma;COLOR:#000000; BACKGROUND: #efefef;
PADDING-BOTTOM: 8px; PADDING-TOP: 8px">
<div><b>From:</b> <a moz-do-not-send="true" href="mailto:matic.poberznik@gmail.com">Matic Poberznik</a></div>
<div><b>Date:</b> 2015-10-27 12:14</div>
<div><b>To:</b> <a moz-do-not-send="true" href="mailto:xcrysden@democritos.it">XCrySDen mailing
list</a></div>
<div><b>Subject:</b> Re: [xcrysden] How to display a whole
molecule in unit cell with good connection?</div>
</div>
</div>
<div>
<div class="FoxDiv20151027121916502830"> Dear Yin,<br>
<br>
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. <br>
<br>
In order to load your custom parameters when xcrysden starts
you should add a line in $HOME/.xcrysden/custom-definitions
file, an example:<br>
<br>
#<br>
# this line changes the default atomic radius for aluminum
to 1.6<br>
#<br>
<br>
set atmRad(13) 1.6<br>
<br>
The custom definitions file is described on this link: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.xcrysden.org/doc/custom.html">http://www.xcrysden.org/doc/custom.html</a><br>
<br>
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.<br>
<br>
Best regards,<br>
<br>
Matic<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 10/27/2015 09:19 AM, <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:liyincumt@gmail.com">liyincumt@gmail.com</a>
wrote:<br>
</div>
<blockquote cite="mid:2015102710192009085257@gmail.com" type="cite" style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;">
<div><span style="line-height: 1.5; background-color:
window;">Dear Xcrysden developers,</span></div>
<div><br>
</div>
<div>Thanks for sharing this excellent visualization
software for free! </div>
<div><span style="line-height: 1.5; background-color:
window;">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.</span></div>
<div><span style="line-height: 1.5; background-color:
window;"><br>
</span></div>
<div><span style="line-height: 1.5; background-color:
window;">Thank you very much!</span></div>
<div><span style="line-height: 1.5; background-color:
window;"><br>
</span></div>
<div><span style="line-height: 1.5; background-color:
window;">Best Regards,</span></div>
<div><span style="line-height: 1.5; background-color:
window;">Yin</span></div>
<div><br>
</div>
<hr style="width: 210px; height: 1px;" align="left" size="1" color="#b5c4df">
<div><span>
<div style="margin: 10px; font-family: verdana;
font-size: 15px;"><span style="color: rgb(0, 0, 0);
background-color: rgba(0, 0, 0, 0);">Dr. Yin Li <br>
Department of Biophysics,Medical School, University of Pecs,<br>
No.12 Szigeti Street, Pecs, H-7624, HUNGARY<br>
Phone: +36-72-535271/36271</span></div>
</span></div>
<br>
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<br>
</div>
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<br>
<pre class="moz-signature" cols="72">--
Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia </pre>
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