[Gwyddion-users] Gwyddion for LDOS isosurfaces

[José Coutinho]

Dear Gwyddion users,
I am looking for a software suitable to look at simulated STM imagery from first principles codes and Gwyddion seems like a great contender.
I would like to know if Gwyddion is able to take a volume data file containing the local density of states within LDOS(E+dE,x,y,z), ie, a scalar value on a N1xN2xN3 regular grid, and produce a 2D topographical-like surface, where for each (x,y) coordinate we would have the "highest" z-coordinate (tip heigh) for which LDOS has a user-defined value? Hopefully this would result in an approximate constant-current STM image.
Many thanks,
/J

[Daniil Bratashov]

On Fri, 9 May 2014 10:48:40 +0000

Post by José Coutinho
Dear Gwyddion users,
I am looking for a software suitable to look at simulated STM imagery
from first principles codes and Gwyddion seems like a great
contender. I would like to know if Gwyddion is able to take a volume
data file containing the local density of states within
LDOS(E+dE,x,y,z), ie, a scalar value on a N1xN2xN3 regular grid, and
produce a 2D topographical-like surface, where for each (x,y)
coordinate we would have the "highest" z-coordinate (tip heigh) for
which LDOS has a user-defined value? Hopefully this would result in
an approximate constant-current STM image. Many thanks, /J

In general, yes, but some work will be required there to implement
data loading and some small work in volume data presentation code.

WBR, Daniil Bratashov.

[David Nečas (Yeti)]

Post by Daniil Bratashov
On Fri, 9 May 2014 10:48:40 +0000

Post by José Coutinho
Dear Gwyddion users,
I am looking for a software suitable to look at simulated STM imagery
from first principles codes and Gwyddion seems like a great
contender. I would like to know if Gwyddion is able to take a volume
data file containing the local density of states within
LDOS(E+dE,x,y,z), ie, a scalar value on a N1xN2xN3 regular grid, and
produce a 2D topographical-like surface, where for each (x,y)
coordinate we would have the "highest" z-coordinate (tip heigh) for
which LDOS has a user-defined value? Hopefully this would result in
an approximate constant-current STM image. Many thanks, /J

In general, yes, but some work will be required there to implement
data loading and some small work in volume data presentation code.

The visualisation module should, as intended, be able to do this but it
is a rotting bag of badgers and Petr does not seem to have much time to
develop it futher now...

If you load the data into Gwyddion as volume data (for which a relatiely
simple import module should suffice) then you can just use the Change
Preview function to get an image of the maximum value. I am not
actually sure if this is relevant because z is once described as the
grid coordinate (in which case the highest value would be constant) and
once as something to plot for (x,y). So I am probably missing
something.

Regards,

Yeti

[José Coutinho]

Post by David Nečas (Yeti)

Post by Daniil Bratashov
On Fri, 9 May 2014 10:48:40 +0000

Post by José Coutinho
Dear Gwyddion users,
I am looking for a software suitable to look at simulated STM imagery
from first principles codes and Gwyddion seems like a great
contender. I would like to know if Gwyddion is able to take a volume
data file containing the local density of states within
LDOS(E+dE,x,y,z), ie, a scalar value on a N1xN2xN3 regular grid, and
produce a 2D topographical-like surface, where for each (x,y)
coordinate we would have the "highest" z-coordinate (tip heigh) for
which LDOS has a user-defined value? Hopefully this would result in
an approximate constant-current STM image. Many thanks, /J

In general, yes, but some work will be required there to implement
data loading and some small work in volume data presentation code.

The visualisation module should, as intended, be able to do this but it
is a rotting bag of badgers and Petr does not seem to have much time to
develop it futher now...
If you load the data into Gwyddion as volume data (for which a relatiely
simple import module should suffice) then you can just use the Change
Preview function to get an image of the maximum value. I am not
actually sure if this is relevant because z is once described as the
grid coordinate (in which case the highest value would be constant) and
once as something to plot for (x,y). So I am probably missing
something.
Regards,
Yeti
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On 09 May 2014, at 20:43, David Nečas (Yeti) <***@gwyddion.net> wrote:

Thanks Yeti,
Not sure if you understood it right. I meant the maximum z-coordinate that corresponds to a user-defined (constant) LDOS(E+dE,x,y,z). Basically, in STM the tip hoovers over a landscape with approximately constant LDOS. The goal is to convert volume data to topographical data.
Hope it helped.
reg

[David Nečas (Yeti)]

Post by José Coutinho
Not sure if you understood it right. I meant the maximum z-coordinate
that corresponds to a user-defined (constant) LDOS(E+dE,x,y,z).
Basically, in STM the tip hoovers over a landscape with approximately
constant LDOS.

I admit that, being the kind of physicist preferring pencil and paper to
fickle real-world samples, I have only some basic understanding of STM.
Anyway, for me the full STM description would have 4 abscissa axes (the
fourth being voltage, electron energy, or something similar), whether we
talk about current, density of states, or anything. So please dumb it
down for me by saying explicitly what are the axes for the N1×N2×N3 grid
and what is the value (ordinate) because I am still missing one axis
somewhere.

Thanks,

Yeti

[Scott Webster]

I believe that for each X/Y grid point, the tip is moved through a series
of Z position heights. At each height a measurement is made (e.g. current).

I think what Jose wants is the following. For each X/Y grid point, find
the Z height corresponding to a certain current (or first Z height for
which current is above/below a threshold). Now you have a "normal" dataset
with a certain Z height for each X/Y point and can display as desired.

Post by David Nečas (Yeti)

Post by José Coutinho
Not sure if you understood it right. I meant the maximum z-coordinate
that corresponds to a user-defined (constant) LDOS(E+dE,x,y,z).
Basically, in STM the tip hoovers over a landscape with approximately
constant LDOS.

I admit that, being the kind of physicist preferring pencil and paper to
fickle real-world samples, I have only some basic understanding of STM.
Anyway, for me the full STM description would have 4 abscissa axes (the
fourth being voltage, electron energy, or something similar), whether we
talk about current, density of states, or anything. So please dumb it
down for me by saying explicitly what are the axes for the N1×N2×N3 grid
and what is the value (ordinate) because I am still missing one axis
somewhere.
Thanks,
Yeti
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[José Coutinho]

That is correct Scott.
Thanks for helping on casting the problem.
/J


On 09 May 2014, at 22:13, Scott Webster <***@gmail.com<mailto:***@gmail.com>> wrote:

I believe that for each X/Y grid point, the tip is moved through a series of Z position heights. At each height a measurement is made (e.g. current).

I think what Jose wants is the following. For each X/Y grid point, find the Z height corresponding to a certain current (or first Z height for which current is above/below a threshold). Now you have a "normal" dataset with a certain Z height for each X/Y point and can display as desired.

Post by José Coutinho
Not sure if you understood it right. I meant the maximum z-coordinate
that corresponds to a user-defined (constant) LDOS(E+dE,x,y,z).
Basically, in STM the tip hoovers over a landscape with approximately
constant LDOS.

I admit that, being the kind of physicist preferring pencil and paper to
fickle real-world samples, I have only some basic understanding of STM.
Anyway, for me the full STM description would have 4 abscissa axes (the
fourth being voltage, electron energy, or something similar), whether we
talk about current, density of states, or anything. So please dumb it
down for me by saying explicitly what are the axes for the N1×N2×N3 grid
and what is the value (ordinate) because I am still missing one axis
somewhere.

Thanks,

Yeti


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[Kantorovitch, Lev]

Sorry, noticed some misprints in my previous message.

==================================================


as far as I understand what is needed is to search to search through a 3D LDOS dataset
and find the value of z, for each x and y, which corresponds to the given value of the LDOS.
There are many codes doing this, including mine lev00 (the Tersoff-Hamann method):

http://www.mth.kcl.ac.uk/~lev/codes/lev00/index.html

It interpolates between the closest z-entries for the given (x,y), plots the result and is rather user-friendly.
It does many more things for DFT users, I believe it is worth looking at the above webpage.

you can currently use only vasp generated data, however, if there is demand than adding siesta
and cp2k generated datasets would be a simple thing to do, just let me know if this is required.

Cheers,
Lev




On 09 May 2014, at 22:13, Scott Webster <***@gmail.com<mailto:***@gmail.com>> wrote:

I believe that for each X/Y grid point, the tip is moved through a series of Z position heights. At each height a measurement is made (e.g. current).

I think what Jose wants is the following. For each X/Y grid point, find the Z height corresponding to a certain current (or first Z height for which current is above/below a threshold). Now you have a "normal" dataset with a certain Z height for each X/Y point and can display as desired.

Post by José Coutinho
Not sure if you understood it right. I meant the maximum z-coordinate
that corresponds to a user-defined (constant) LDOS(E+dE,x,y,z).
Basically, in STM the tip hoovers over a landscape with approximately
constant LDOS.

I admit that, being the kind of physicist preferring pencil and paper to
fickle real-world samples, I have only some basic understanding of STM.
Anyway, for me the full STM description would have 4 abscissa axes (the
fourth being voltage, electron energy, or something similar), whether we
talk about current, density of states, or anything. So please dumb it
down for me by saying explicitly what are the axes for the N1×N2×N3 grid
and what is the value (ordinate) because I am still missing one axis
somewhere.

Thanks,

Yeti


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====================================
Prof. Lev Kantorovich
Department of Physics
School of Natural and Mathematical Sciences
King' s College London
The Strand, London
WC2R 2LS
U.K.
***@kcl.ac.uk<mailto:***@kcl.ac.uk>

[José Coutinho]

Greetings Lev,
Many thanks for your kind offer. That is exactly what I was looking for. Interface with VASP will be good enough.
Hope you're doing all right.
With kind regards,
/J

On 10 May 2014, at 12:41 PM, Kantorovitch, Lev wrote:

Sorry, noticed some misprints in my previous message.

==================================================


as far as I understand what is needed is to search to search through a 3D LDOS dataset
and find the value of z, for each x and y, which corresponds to the given value of the LDOS.
There are many codes doing this, including mine lev00 (the Tersoff-Hamann method):

http://www.mth.kcl.ac.uk/~lev/codes/lev00/index.html

It interpolates between the closest z-entries for the given (x,y), plots the result and is rather user-friendly.
It does many more things for DFT users, I believe it is worth looking at the above webpage.

you can currently use only vasp generated data, however, if there is demand than adding siesta
and cp2k generated datasets would be a simple thing to do, just let me know if this is required.

Cheers,
Lev




On 09 May 2014, at 22:13, Scott Webster <***@gmail.com<mailto:***@gmail.com>> wrote:

I believe that for each X/Y grid point, the tip is moved through a series of Z position heights. At each height a measurement is made (e.g. current).

I think what Jose wants is the following. For each X/Y grid point, find the Z height corresponding to a certain current (or first Z height for which current is above/below a threshold). Now you have a "normal" dataset with a certain Z height for each X/Y point and can display as desired.

Post by José Coutinho
Not sure if you understood it right. I meant the maximum z-coordinate
that corresponds to a user-defined (constant) LDOS(E+dE,x,y,z).
Basically, in STM the tip hoovers over a landscape with approximately
constant LDOS.

I admit that, being the kind of physicist preferring pencil and paper to
fickle real-world samples, I have only some basic understanding of STM.
Anyway, for me the full STM description would have 4 abscissa axes (the
fourth being voltage, electron energy, or something similar), whether we
talk about current, density of states, or anything. So please dumb it
down for me by saying explicitly what are the axes for the N1×N2×N3 grid
and what is the value (ordinate) because I am still missing one axis
somewhere.

Thanks,

Yeti


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====================================
Prof. Lev Kantorovich
Department of Physics
School of Natural and Mathematical Sciences
King' s College London
The Strand, London
WC2R 2LS
U.K.
***@kcl.ac.uk<mailto:***@kcl.ac.uk>

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[Kantorovitch, Lev]

no problem, Jose., happy to help

On 11 May 2014, at 11:59, José Coutinho <***@ua.pt<mailto:***@ua.pt>> wrote:

Greetings Lev,
Many thanks for your kind offer. That is exactly what I was looking for. Interface with VASP will be good enough.
Hope you're doing all right.
With kind regards,
/J

On 10 May 2014, at 12:41 PM, Kantorovitch, Lev wrote:

Sorry, noticed some misprints in my previous message.

==================================================


as far as I understand what is needed is to search to search through a 3D LDOS dataset
and find the value of z, for each x and y, which corresponds to the given value of the LDOS.
There are many codes doing this, including mine lev00 (the Tersoff-Hamann method):

http://www.mth.kcl.ac.uk/~lev/codes/lev00/index.html

It interpolates between the closest z-entries for the given (x,y), plots the result and is rather user-friendly.
It does many more things for DFT users, I believe it is worth looking at the above webpage.

you can currently use only vasp generated data, however, if there is demand than adding siesta
and cp2k generated datasets would be a simple thing to do, just let me know if this is required.

Cheers,
Lev




On 09 May 2014, at 22:13, Scott Webster <***@gmail.com<mailto:***@gmail.com>> wrote:

I believe that for each X/Y grid point, the tip is moved through a series of Z position heights. At each height a measurement is made (e.g. current).

I think what Jose wants is the following. For each X/Y grid point, find the Z height corresponding to a certain current (or first Z height for which current is above/below a threshold). Now you have a "normal" dataset with a certain Z height for each X/Y point and can display as desired.

Post by José Coutinho
Not sure if you understood it right. I meant the maximum z-coordinate
that corresponds to a user-defined (constant) LDOS(E+dE,x,y,z).
Basically, in STM the tip hoovers over a landscape with approximately
constant LDOS.

I admit that, being the kind of physicist preferring pencil and paper to
fickle real-world samples, I have only some basic understanding of STM.
Anyway, for me the full STM description would have 4 abscissa axes (the
fourth being voltage, electron energy, or something similar), whether we
talk about current, density of states, or anything. So please dumb it
down for me by saying explicitly what are the axes for the N1×N2×N3 grid
and what is the value (ordinate) because I am still missing one axis
somewhere.

Thanks,

Yeti


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====================================
Prof. Lev Kantorovich
Department of Physics
School of Natural and Mathematical Sciences
King' s College London
The Strand, London
WC2R 2LS
U.K.
***@kcl.ac.uk<mailto:***@kcl.ac.uk>

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====================================
Prof. Lev Kantorovich
Department of Physics
School of Natural and Mathematical Sciences
King' s College London
The Strand, London
WC2R 2LS
U.K.
***@kcl.ac.uk<mailto:***@kcl.ac.uk>

[Daniil Bratashov]

On Fri, 9 May 2014 22:58:50 +0200

Post by David Nečas (Yeti)
So please dumb it
down for me by saying explicitly what are the axes for the N1×N2×N3
grid and what is the value (ordinate) because I am still missing one
axis somewhere.

XY is lateral coordinates, Z is either scanner-Z (i.e. height under
constant voltage) or voltage (under some sort of constant height, either
scanner, or relative to the sample) and value is electrical current
between tip and sample. So we have array of either I-V or I-Z spectra in
different XY points. I-V can be recalculated to LDoS = (dI/dU)/(I/U),
that work for small voltages below 2V, and V gives eV of sample energy
levels (we have graph module, that do exactly this).

WBR, Daniil Bratashov.

[José Coutinho]

Hi Yeti,
Thanks a lot for your email. The ordinate is LDOS.
I intend to simulate STM from density functional Kohn-Sham eigenfunctions. As I mentioned I have LDOS values on a N1xN2xN3 grid. This kind for data format is the most usual among first-principles DFT codes (VASP, SIESTA, WIEN2k, GAUSSIAN, etc).
Usually there are two ways to simulate an STM image, assuming that the tunneling current is proportional to the LDOS at the tip location. The two ways are (i) constant heigh or (ii) constant current. In constant heigh mode we simply have to produce a slice of LDOS at a specified z-value and plot LDOS(x,y). However, real STM usually records the height of the tip (z-coordinate) by scanning over a constant current isosurface over the sample. So, we need to plot z(x,y) (this is now a 2D image) so that DLOS(x,y,z)=Const.
Thanks a lot,
/J

Post by David Nečas (Yeti)

Post by José Coutinho
Not sure if you understood it right. I meant the maximum z-coordinate
that corresponds to a user-defined (constant) LDOS(E+dE,x,y,z).
Basically, in STM the tip hoovers over a landscape with approximately
constant LDOS.

I admit that, being the kind of physicist preferring pencil and paper to
fickle real-world samples, I have only some basic understanding of STM.
Anyway, for me the full STM description would have 4 abscissa axes (the
fourth being voltage, electron energy, or something similar), whether we
talk about current, density of states, or anything. So please dumb it
down for me by saying explicitly what are the axes for the N1×N2×N3 grid
and what is the value (ordinate) because I am still missing one axis
somewhere.
Thanks,
Yeti
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[David Nečas (Yeti)]

Post by José Coutinho
However, real STM usually records the
height of the tip (z-coordinate) by scanning over a constant current
isosurface over the sample. So, we need to plot z(x,y) (this is now a
2D image) so that DLOS(x,y,z)=Const.

This is something Gwyddion cannot do at present but should be reasonably
simple to implement. Anyway, the the first step is an import module for
your volume data format.

Regards,

Yeti

[Kantorovitch, Lev]

as far as I understand what is needed is to search to search through a 3D LDOS dataset
and find the value of z, for each x and y, which corresponds to the given value of the LDOS.
There are many codes doing this, including mine lev00 (the Tersoff-Hamann method):

http://www.mth.kcl.ac.uk/~lev/codes/lev00/index.html

you can currently use only gasp generated data, however, if there is demand than adding siesta
and cp2k generated datasets would be a simple thing to do, give me several days

Cheers,
Lev


On 10 May 2014, at 12:24, David Nečas (Yeti) <***@gwyddion.net<mailto:***@gwyddion.net>> wrote:

On Sat, May 10, 2014 at 07:52:14AM +0000, José Coutinho wrote:
However, real STM usually records the
height of the tip (z-coordinate) by scanning over a constant current
isosurface over the sample. So, we need to plot z(x,y) (this is now a
2D image) so that DLOS(x,y,z)=Const.

This is something Gwyddion cannot do at present but should be reasonably
simple to implement. Anyway, the the first step is an import module for
your volume data format.

Regards,

Yeti


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====================================
Prof. Lev Kantorovich
Department of Physics
School of Natural and Mathematical Sciences
King' s College London
The Strand, London
WC2R 2LS
U.K.
***@kcl.ac.uk<mailto:***@kcl.ac.uk>