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<span style="line-height: 1.5; background-color: window;"><br>
>>Actually, I don't want to modify the relative distance
between atoms and boundaries. I think journals >>would not
accept this.</span><br>
<br>
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. <br>
<br>
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.<br>
<br>
Best regards,<br>
<br>
Matic<br>
<br>
<div class="moz-cite-prefix">On 10/27/2015 01:47 PM,
<a class="moz-txt-link-abbreviated" href="mailto:liyincumt@gmail.com">liyincumt@gmail.com</a> wrote:<br>
</div>
<blockquote cite="mid:2015102714473692451475@gmail.com" type="cite">
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<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;" 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 14:27</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="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
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: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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<pre class="moz-signature" cols="72">--
Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia </pre>
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J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia </pre>
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