<html><head></head><body><div class="ydp9eed9b6fyahoo-style-wrap" style="font-family: verdana, helvetica, sans-serif; font-size: 16px;"><div><div><font size="2">Dear Gavin,</font></div><div><font size="2">Thank you very much for the detail explanation. I will follow the suggestions.</font></div><div><font size="2">With kind regards</font><br></div><div class="ydp9eed9b6fsignature"><p style="font-family:verdana, helvetica, sans-serif;font-size:16px;"><b><font size="3" face="verdana, helvetica, sans-serif"><i>Lawal <br></i></font></b></p></div></div>
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On Saturday, January 5, 2019, 11:47:52 PM GMT+8, Gavin Abo <gsabo@crimson.ua.edu> wrote:
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<p>Not an expert on the STM, so I could be wrong about some things,
but my comments below.<br clear="none">
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</span><div style="font-family:verdana, helvetica, sans-serif;font-size:16px;">Still on STM, I have a question
regarding case.in3d, please what is the unit of the
start and end value in the case.in3d file? For example,
I have a test case with a vacuum of about 13 Angstrom.</div>
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<p>Section 8.15.3 in the WIEN2k 18.2 usersguide has:</p>
<p>---------------- top of file: case.in3d --------------------<br clear="none">
<font color="#ff0000">100 100 100</font> # number of 3D-gridpoints
in a-, b- and c-direction<br clear="none">
...<br clear="none">
<font color="#993399">stm</font> z 60 <font color="#ff0000">100</font>
0.0001 # (optional) stmswitch, direction, start, end, density<br clear="none">
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<p>------------------- bottom of file ------------------------<br clear="none">
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<p>Looks to me that the start and end are unitless and are based on
the gridpoints.</p>
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</span><div style="font-family:verdana, helvetica, sans-serif;font-size:16px;"> What should be my start value (value
above the surface atom) and end value (value around
middle of vacuum)?</div>
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Section 8.15.3 in the WIEN2k 18.2 usersguide has:<br clear="none">
<p>start specifies the first plane for the <font color="#ff0000">search
of</font> <font color="#ff0000">the</font> <font color="#ff0000">given density</font> (typically a<br clear="none">
value above the surface atom).</p>
<p>end specifies the last plane for the <font color="#ff0000">search
of</font> <font color="#ff0000">the given density</font>
(typically<br clear="none">
around middle of vacuum).<br clear="none">
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<p>Sounds like something that can be found by trial and check. If
the start-end window is not able to capture the given density,
move it or make it wider. If the start-end search window is
picking up an undesirable density, narrow the window to capture
the one you want sort of thing.<br clear="none">
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</span><div style="font-family:verdana, helvetica, sans-serif;font-size:16px;"> Also in the UG page 172, section 18.5
it's mentioned that "<b><font color="#5b8828">Optionally
one can simulate a constant current STM image, where
a height profile (above a surface slab)
corresponding to a specific electron density value
can be extracted from the case.xsf-file and written
into case stm.xsf-file</font></b>." Please the
extraction of the electron density is it automatic or it
should be done manually, and which file case.xsf or
case_stm.xsf should be use for the plotting? <br clear="none">
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<p>Section 8.15 3DDENS (3D electron density plots in whole cell) in
the UG has:<br clear="none">
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<p>This <font color="#ff0000">program generates</font> the <font color="#ff0000">charge density</font> (or the potential) in the
whole conventional (or primitive)<br clear="none">
unit cell on a three dimensional grid which can be used for
plotting with an external program<br clear="none">
that can read <font color="#ff0000">.xsf-files</font> (e.g.,
XCrysden, VESTA).</p>
<p>As the above says, the charge density case.xsf file should be
generated automatically.</p>
<p>Section 8.15.3 in the WIEN2k 18.2 usersguide has:</p>
<p><font color="#ff0000"><font color="#993399">stmswitch </font>case_stm.xsf
file is written</font>, containing height values for the given
density<br clear="none">
value.</p>
<p>As the above says, the stm image case_stm.xsf file should be
generated automatically if the stmswitch parameter is set to
"stm".</p>
<p>So if want the charge density plot, open case.xsf (in XCrySDen).
If you want the STM image plot, open the case_stm.xsf.</p>
<p>If you use lapw5's STM option instead of 3ddens, I'm not sure,
but I'm thinking it outputs a case.rho file for the stm image
data. The rho file can be plotted with different programs [
<a rel="nofollow" shape="rect" class="yiv5535377032moz-txt-link-freetext" target="_blank" href="https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07125.html">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07125.html</a>
].<br clear="none">
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<p>You might have a look at the file SRC_lapw5/README_STM.docx.
That mentions it will also output a file in SEMPER format that can
be read by the semper7 code. This is probably the semper-7.0beta
image processing tool mentioned on Prof. Marks website [
<a rel="nofollow" shape="rect" class="yiv5535377032moz-txt-link-freetext" target="_blank" href="http://www.numis.northwestern.edu/Software/Software.shtml">http://www.numis.northwestern.edu/Software/Software.shtml</a> ].</p><div class="yiv5535377032yqt8682322122" id="yiv5535377032yqtfd17217"><br clear="none">
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<div> On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter
Blaha <a rel="nofollow" shape="rect" class="yiv5535377032moz-txt-link-rfc2396E" ymailto="mailto:pblaha@theochem.tuwien.ac.at" target="_blank" href="mailto:pblaha@theochem.tuwien.ac.at"><pblaha@theochem.tuwien.ac.at></a> wrote: </div>
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<div dir="ltr">STM simulations make only sense for a
surface. You cannot make STM for a <br clear="none">
bulk ???<br clear="none">
<br clear="none">
3ddens does not include tip vibrations, but is very fast
and <br clear="none">
conveniently lets you choose the best hight above the
surface to <br clear="none">
reproduce experimental images.<br clear="none">
<br clear="none">
Be careful with the STM mode of lapw5 in cases with angles
differing <br clear="none">
from 90 degrees !<br clear="none">
<br clear="none">
STM simulations are always a bit of an art, because the
quality of the <br clear="none">
experimental STM images changes a lot with group / time /
....<br clear="none">
<br clear="none">
<div class="yiv5535377032yqt3575493830" id="yiv5535377032yqtfd17651"><br clear="none">
Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:<br clear="none">
> Dear Developers and Users,<br clear="none">
> <br clear="none">
> I need some advice on using the 3ddens program. My
interest is to <br clear="none">
> simulate STM image of a 3D system to compare with
our experimental results.<br clear="none">
> My questions are:<br clear="none">
> <br clear="none">
> Whether it's possible for 3D system.<br clear="none">
> What determine the size of the grid points?<br clear="none">
> Do I have to edit any file in my case directory
before x 3ddens -XX?<br clear="none">
> <br clear="none">
> I want to test run using TiC, what are the general
tips? Any hint is <br clear="none">
> highly appreciated.<br clear="none">
> <br clear="none">
> Thanks a lot for your time.<br clear="none">
> <br clear="none">
> With kind regards.<br clear="none">
> <br clear="none">
> */Lawal</div>
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