<div dir="ltr"><div><div><div>Dear Ari and Axel,<br><br></div>Thank you so much for your hints. It worked.<br><br></div>Best,<br></div>Reza<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 15, 2016 at 11:59 AM, Axel Kohlmeyer <span dir="ltr"><<a href="mailto:akohlmey@gmail.com" target="_blank">akohlmey@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:arial black,sans-serif"><br></div><div class="gmail_extra"><br><div class="gmail_quote"><span class="">On Fri, Jan 15, 2016 at 1:48 PM, Ari P Seitsonen <span dir="ltr"><<a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Dear Reza,<br>
<br>
This is actually a question on the visualisation programs, not of Quantum ESPRESSO. Yes, QE can produce the two cube files needed, then you need to find a visualisation program that can do the mapping. I have once upon a time used gOpenMol for that, but it is no longer maintained nor possibly available anymore, I do not know if VMD can do it - there is at least some discussion on the mailing list - <a href="http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/" rel="noreferrer" target="_blank">http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/</a> looks like it.</blockquote><div><br></div></span><div><div class="gmail_default" style="font-family:'arial black',sans-serif">yes, VMD can do it, if the OpenGL support in the graphics driver is sufficiently capable. these days most of them are.</div><div class="gmail_default" style="font-family:'arial black',sans-serif"><br></div><div class="gmail_default" style="font-family:'arial black',sans-serif">axel.</div><br></div><div><div class="h5"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Molekel, I do not know (and I cannot connect to '<a href="http://molekel.cscs.ch/" rel="noreferrer" target="_blank">http://molekel.cscs.ch/</a>' just now - is the project continued, does some one know?).<br>
<br>
If you do manage to do it, please let us know; Good Luck!<br>
<br>
Greetings,<br>
<br>
apsi<br>
<br>
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-<br>
Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" rel="noreferrer" target="_blank">http://www.iki.fi/~apsi/</a><br>
Ecole Normale Supérieure (ENS), Département de Chimie, Paris<br>
Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935<div><div><br>
<br>
<br>
On Fri, 15 Jan 2016, reza vatan wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Lorenzo,<br>
<br>
Many thanks for your reply.<br>
<br>
I already have the cube file of my structure obtained from pp.x calculation.<br>
I want to visualize that cube file in a 3D picture with a color scale in<br>
such a way that each color represent the intensity of charge in that<br>
specific volume or area (something like the attached picture). I can plot a<br>
plane containing different color inside the cell by using VMD and xCrySDen<br>
to visualize that cube file but I can not plot the 3D charge density plot<br>
(which I think some people call it electrostatic potential map).<br>
<br>
My first question is if I'm able to get those 3D charge density plot using<br>
the cube file obtaining from pp.x calculations.<br>
And if yes, my second question is that: How can I do it.<br>
<br>
Many thanks in advances.<br>
<br>
Best,<br>
Reza<br>
<br>
On Fri, Jan 15, 2016 at 2:28 AM, Lorenzo Paulatto<br>
<<a href="mailto:lorenzo.paulatto@impmc.upmc.fr" target="_blank">lorenzo.paulatto@impmc.upmc.fr</a>> wrote:<br>
Dear Reza,<br>
I do not know exactly what you mean by electrostatic potential<br>
map, but I<br>
think this is something you can do with pp.x after the pw.x<br>
calculation is<br>
finished. Have a look at PP/Doc/INPUT_PP.html (it takes 10<br>
minutes to read it)<br>
and you'll have an idea of the quantities you can plot (the<br>
total and hartree<br>
potentials among them) and how you can plot them (i.e. you can<br>
plot a plane<br>
inside the unit cell). Please come back to us if there is any<br>
detail you<br>
cannot understand.<br>
<br>
hth, kind regards<br>
<br>
On Thursday, January 14, 2016 11:04:47 PM reza vatan wrote:<br>
> Dear all,<br>
><br>
> I just wanted to know if the Quantum Espresso has the ability<br>
to calculate<br>
> the electrostatic potential map of a structure. If yes how I<br>
can visualize<br>
> the resulted output files?<br>
><br>
> Thanks in advances.<br>
><br>
> Best,<br>
> Reza<br>
<br>
--<br>
Dr. Lorenzo Paulatto<br>
IdR @ IMPMC -- CNRS & Université Paris 6<br>
+33 (0)1 44 275 084 / skype: paulatz<br>
<a href="http://www.impmc.upmc.fr/~paulatto/" rel="noreferrer" target="_blank">http://www.impmc.upmc.fr/~paulatto/</a><br>
23-24/4é16 Boîte courrier 115,<br>
4 place Jussieu 75252 Paris Cédex 05<br>
<br>
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</blockquote>
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