From mashiatalaaii at gmail.com Wed Sep 1 00:03:12 2010 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Tue, 31 Aug 2010 18:03:12 -0400 Subject: [xcrysden] fermi surfaces Message-ID: Hi. I need help to get the Fermi surfaces. M Alaaii -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100831/9562a64a/attachment.htm From tone.kokalj at ijs.si Fri Sep 3 11:26:04 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 03 Sep 2010 11:26:04 +0200 Subject: [xcrysden] fermi surfaces In-Reply-To: References: Message-ID: <1283505964.4010.77.camel@walk.ijs.si> On Tue, 2010-08-31 at 18:03 -0400, mashiat alaaii wrote: > Hi. > I need help to get the Fermi surfaces. > M Alaaii Dear Alaaii, Your question is much too generic. You need to be more specific. Regards -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From startunam at yahoo.co.uk Fri Sep 3 18:36:52 2010 From: startunam at yahoo.co.uk (Ariadna Blanca Romero) Date: Fri, 3 Sep 2010 16:36:52 +0000 (GMT) Subject: [xcrysden] charge density and electrostatic potential Message-ID: <446069.78672.qm@web25805.mail.ukl.yahoo.com> Hi all I have a problem to understand what a negative isovalue means when I want to visualize the charge density and the electrostatic potential. I am using crystal06 to get these. I know that the charge density is a function dependent on three variables, namely x,y and z. I can then ask XCrysDen to collect all the points at which the density has a single specific value, the isovalue, and connect them through a three-dimensional plot. I mean rho(x,y,z)=C, where C is the isovalue.In the isosurface controlling window I get a minimum and maximum grid value. Then I chose a isovalue in this range, and I use the option Render +/-isovalue. Using this last option I get two color surfaces, one in red and other in blue. The xcrysden site (http://www.xcrysden.org/doc/isocontrol.html#render+-) gives an example: "when displaying the isosurface of a molecular orbital, then it is a good idea to display both positive and negative valued isosurface (for example the -0.02/0.02 sqrt(BOHR^3/electrons)). By default the positive isosurface is rendered in red, while negative in blue." The problem comes when I wanto to interpret it for electronic density, which is given in electrons/BHOR^3 by crystal06 and this quantity should be POSITIVE. First, the isovalue is the square root of the inverse of the electronic density (at least by the units it seems), as is shown in the xcrysden site, so what a negative isovalue means????? Does it mean less quantity of electrons????. On the other hand, when instead of surfaces we have planes, we have to specify the lowest and the higest render value. This ones are shown in the thermometer which has the label DELTA n(r), Does it means a difference between two isovalues or a difference between other quantities to get the isovalues???? and again here the question returns about negative isovalues, what does a negative isovalue means in the thermometer???? In the section for property-planes display parameters we have to select a scale function (http://www.xcrysden.org/doc/plane1control.html#__toc__5). Here is recomended: "For example for charge density plots the logarithmic scale is usually more appropriate as linear, whereas for charge density difference maps the linear scale is usually better" Why for the same property, just to see the difference maps we have to change the scale function ?????? Finally, for the electrostatic potential we have the same isosurface controlling window. So, I guess the isosurfaces color ( blue and red) have the right meaning for positive and negative charges, isn't it? Thanks before hand to help me to clarify my doubts. Regards, Ariadna -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100903/6e8cd64b/attachment.htm From tone.kokalj at ijs.si Tue Sep 7 15:03:18 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 07 Sep 2010 15:03:18 +0200 Subject: [xcrysden] charge density and electrostatic potential In-Reply-To: <446069.78672.qm@web25805.mail.ukl.yahoo.com> References: <446069.78672.qm@web25805.mail.ukl.yahoo.com> Message-ID: <1283864598.25541.279.camel@walk.ijs.si> On Fri, 2010-09-03 at 16:36 +0000, Ariadna Blanca Romero wrote: > Hi all > > I have a problem to understand what a negative isovalue means when I > want to visualize the charge density and the electrostatic potential. > I am using crystal06 to get these. As for the charge density, the negative value typically appears only for charge density difference plots, and it indicates charge deficit regions. As for the electrostatic potential (elpot), negative values indicate electron reach regions. Imagine for example a polar molecules, say HF, then you will have negative region around F and positive around H (i.e. you can consider this as a representation of dipole pointing from negative elpot region to positive elpot region). > > "when displaying the isosurface of a molecular orbital, then it is a > good idea to display both positive and negative valued isosurface (for > example the -0.02/0.02 sqrt(BOHR^3/electrons)). By default the > positive isosurface is rendered in red, while negative in blue." > > The problem comes when I wanto to interpret it for electronic density, > which is given in electrons/BHOR^3 by crystal06 and this quantity > should be POSITIVE. > First, the isovalue is the square root of the inverse of the > electronic density (at least by the units it seems), as is shown in > the xcrysden site, so what a negative isovalue means????? Does it mean > less quantity of electrons????. Don't confuse molecular orbitals and charge density! Molecular orbitals (say for molecules) can be chosen as being real; not in general true for crystals. For the latter reason, I believe (not sure) you can only plot the square moduli of molecular/crystal orbitals in CRYSTAL06 (i.e. \Phi^2, associated charge density), and in this case you only plot the "positive" isovalue. However if you would plot the real molecular orbital than the "+/-" isovalue button is useful. > > On the other hand, when instead of surfaces we have planes, we have to > specify the lowest and the higest render value. This ones are shown in > the thermometer which has the label DELTA n(r), Does it means a > difference between two isovalues No the symbol \Delta is there for convenience only (now I see it causes confusion): would you plot the charge density difference, then you would need a \Delta symbol, which cannot be input by keyword! If you plot a plain charge density, delete the \Delta symbol. > In the section for property-planes display parameters we have to > select a scale function > (http://www.xcrysden.org/doc/plane1control.html#__toc__5). Here is > recomended: > > "For example for charge density plots the logarithmic scale is usually > more appropriate as linear, whereas for charge density difference maps > the linear scale is usually better" > > > Why for the same property, just to see the difference maps we have to > change the scale function ?????? > For difference maps you simply keep the linear scale, however for plain charge density the logarithmic scale is also very useful (depends on the purpose). It is obviously up to you which scale to choose. > Finally, for the electrostatic potential we have the same isosurface > controlling window. So, I guess the isosurfaces color ( blue and > red) have the right meaning for positive and negative charges, isn't > it? Yes, blue is negative, red is positive. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From sclauzer at sissa.it Wed Sep 8 09:47:58 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 08 Sep 2010 09:47:58 +0200 Subject: [xcrysden] charge density and electrostatic potential In-Reply-To: <1283864598.25541.279.camel@walk.ijs.si> References: <446069.78672.qm@web25805.mail.ukl.yahoo.com> <1283864598.25541.279.camel@walk.ijs.si> Message-ID: <4C873FAE.80107@sissa.it> Dear Ariadna, I just want to add a few comments on top of what Tone said, hoping they will be useful to solve your problem. On 09/07/2010 03:03 PM, Tone Kokalj wrote: > On Fri, 2010-09-03 at 16:36 +0000, Ariadna Blanca Romero wrote: > >> Hi all >> >> I have a problem to understand what a negative isovalue means when I >> want to visualize the charge density and the electrostatic potential. >> I am using crystal06 to get these. >> > As for the charge density, the negative value typically appears only for > charge density difference plots, and it indicates charge deficit > regions. > I don't know much about Crystal code, but I believe this is the same for every electronic structure code employing some broadening technique: if you use smearing functions like Methfessel and Paxton's there may be some regions with (hopefully very small) negative charge densities. If you don't like them, you'll need to switch to another smearing function which is not affected by this drawback. >> "when displaying the isosurface of a molecular orbital, then it is a >> good idea to display both positive and negative valued isosurface (for >> example the -0.02/0.02 sqrt(BOHR^3/electrons)). By default the >> positive isosurface is rendered in red, while negative in blue." >> >> The problem comes when I wanto to interpret it for electronic density, >> which is given in electrons/BHOR^3 by crystal06 and this quantity >> should be POSITIVE. >> First, the isovalue is the square root of the inverse of the >> electronic density (at least by the units it seems), as is shown in >> the xcrysden site, so what a negative isovalue means????? Does it mean >> less quantity of electrons????. >> > Don't confuse molecular orbitals and charge density! > > Molecular orbitals (say for molecules) can be chosen as being real; not > in general true for crystals. For the latter reason, I believe (not > sure) you can only plot the square moduli of molecular/crystal orbitals > in CRYSTAL06 (i.e. \Phi^2, associated charge density), and in this case > you only plot the "positive" isovalue. However if you would plot the > real molecular orbital than the "+/-" isovalue button is useful. > > In crystals the wavefunctions at the Gamma point in the BZ can be chosen to be real valued, so that you can think about plotting something like: sign(\psi)*|psi|^2 where \psi is the K-S eigenstate at Gamma. In Quantum-ESPRESSO this is done by setting a flag in the postprocessing step, maybe in Crystal this is done automatically? > > Regards, Tone > > Hope this helps, GS -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne From dinogep at gmail.com Sun Sep 12 02:32:00 2010 From: dinogep at gmail.com (=?ISO-8859-1?Q?D=E9nes_Szieberth?=) Date: Sun, 12 Sep 2010 02:32:00 +0200 Subject: [xcrysden] electrostatic potential map Message-ID: Dear all, Is there any way to tell what value corresponds to a certain point on the el.pot. map (e.g. under the cursor)? Is there a way to print the contour values on the contour lines? cheers, D?nes Szieberth postdoctoral fellow University of Torino From startunam at yahoo.co.uk Mon Sep 13 11:11:20 2010 From: startunam at yahoo.co.uk (Ariadna Blanca Romero) Date: Mon, 13 Sep 2010 09:11:20 +0000 (GMT) Subject: [xcrysden] charge density and electrostatic potential Message-ID: <927027.96823.qm@web25806.mail.ukl.yahoo.com> Dr.Anton Kokalj and Dr.Gabriele Sclauzero Thanks for you soon answer, I think It will help me a lot. I wish you the best. Regards Ariadna -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100913/30dc4e1b/attachment.htm From mazar83 at gmail.com Wed Sep 15 02:09:24 2010 From: mazar83 at gmail.com (Mark Mazar) Date: Tue, 14 Sep 2010 19:09:24 -0500 Subject: [xcrysden] toggle depth from script Message-ID: Hello xcrysden users, My problem is that I'd like to turn on depth, set the fog color, set the start factor, and finally the end factor automatically with a script. I already tried "scripting::display on depth" and variations like Depth, depthcuing, depth-cuing, and Depth-Cuing. I also tried using "array set check {depthcuing 1}," which I think is the format from *.xcrysden files (when you use save current structure). To set the fog start and end factors, I tried using "set myParam(START)" and variations like FOG_START and FOG_START_FACTOR. None of my efforts were successful. Any help would be greatly appreciated. I can edit almost everything I need, but the solution to the depth/fog problem seems to elude me. Thank you, -- Mark Mazar PhD Candidate in Materials Science Chemical Engineering and Materials Science University of Minnesota From mazar83 at gmail.com Thu Sep 16 18:06:18 2010 From: mazar83 at gmail.com (Mark Mazar) Date: Thu, 16 Sep 2010 11:06:18 -0500 Subject: [xcrysden] toggle depth from script In-Reply-To: References: Message-ID: Hello xcrysden users, I'm not sure that I successfully posted this message last time. So here it is again. My problem is that I'd like to turn on depth, set the fog color, set the start factor, and finally the end factor automatically with a script. I already tried "scripting::display on depth" and variations like Depth, depthcuing, depth-cuing, and Depth-Cuing. I also tried using "array set check {depthcuing 1}," which I think is the format from *.xcrysden files (when you use save current structure). To set the fog start and end factors, I tried using "set myParam(START)" and variations like FOG_START and FOG_START_FACTOR. None of my efforts were successful. Any help would be greatly appreciated. I can edit almost everything I need, but the solution to the depth/fog problem seems to elude me. Thank you, -- Mark Mazar PhD Candidate in Materials Science Chemical Engineering and Materials Science University of Minnesota