Re: [Wien] STM

2019-01-06 Thread Lawal Mohammed
Dear Gavin,Thank you very much for the detail explanation. I will follow the 
suggestions.With kind regards

Lawal 

 

On Saturday, January 5, 2019, 11:47:52 PM GMT+8, Gavin Abo 
 wrote:  
 
  
Not an expert on the STM, so I could be wrong about some things, but my 
comments below.
 
 
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.
 
Section 8.15.3 in the WIEN2k 18.2 usersguide has:
 
 top of file: case.in3d 
 100 100 100 # number of 3D-gridpoints in a-, b- and c-direction
 ...
 stm z 60 100 0.0001 # (optional) stmswitch, direction, start, end, density
 
 
--- bottom of file 
 
 
Looks to me that the start and end are unitless and are based on the gridpoints.
 
 What should be my start value (value above the surface atom) and end value 
(value around middle of vacuum)?
 Section 8.15.3 in the WIEN2k 18.2 usersguide has:
 
start specifies the first plane for the search of the given density (typically a
 value above the surface atom).
 
end specifies the last plane for the search of the given density (typically
 around middle of vacuum).
 
 
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.
 
 
 Also in the UG page 172, section 18.5 it's mentioned that "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." 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? 
 
 
Section 8.15 3DDENS (3D electron density plots in whole cell) in the UG has:
 
 
This program generates the charge density (or the potential) in the whole 
conventional (or primitive)
 unit cell on a three dimensional grid which can be used for plotting with an 
external program
 that can read .xsf-files (e.g., XCrysden, VESTA).
 
As the above says, the charge density case.xsf file should be generated 
automatically.
 
Section 8.15.3 in the WIEN2k 18.2 usersguide has:
 
stmswitch case_stm.xsf file is written, containing height values for the given 
density
 value.
 
As the above says, the stm image case_stm.xsf file should be generated 
automatically if the stmswitch parameter is set to "stm".
 
So if want the charge density plot, open case.xsf (in XCrySDen).  If you want 
the STM image plot, open the case_stm.xsf.
 
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 
[https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07125.html ].
 
 
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 [ http://www.numis.northwestern.edu/Software/Software.shtml ].

  
 
On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha 
 wrote:  
  
   STM simulations make only sense for a surface. You cannot make STM for a 
 bulk ???
 
 3ddens does not include tip vibrations, but is very fast and 
 conveniently lets you choose the best hight above the surface to 
 reproduce experimental images.
 
 Be careful with the STM mode of lapw5 in cases with angles differing 
 from 90 degrees !
 
 STM simulations are always a bit of an art, because the quality of the 
 experimental STM images changes a lot with group / time / 
 
 
 Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:
 > Dear Developers and Users,
 > 
 > I need some advice on using the 3ddens program. My interest is to 
 > simulate STM image of a 3D system to compare with our experimental results.
 > My questions are:
 > 
 > Whether it's possible for 3D system.
 > What determine the size of the grid points?
 > Do I have to edit any file in my case directory before x 3ddens -XX?
 > 
 > I want to test run using TiC, what are the general tips? Any hint is 
 > highly appreciated.
 > 
 > Thanks a lot for your time.
 > 
 > With kind regards.
 > 
 > */Lawal 
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Re: [Wien] STM

2019-01-05 Thread Gavin Abo
Not an expert on the STM, so I could be wrong about some things, but my 
comments below.


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.


Section 8.15.3 in the WIEN2k 18.2 usersguide has:

 top of file: case.in3d 
100 100 100 # number of 3D-gridpoints in a-, b- and c-direction
...
stm z 60 100 0.0001 # (optional) stmswitch, direction, start, end, density

--- bottom of file 

Looks to me that the start and end are unitless and are based on the 
gridpoints.


What should be my start value (value above the surface atom) and end 
value (value around middle of vacuum)?

Section 8.15.3 in the WIEN2k 18.2 usersguide has:

start specifies the first plane for the search of the given density 
(typically a

value above the surface atom).

end specifies the last plane for the search of the given density (typically
around middle of vacuum).

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.


Also in the UG page 172, section 18.5 it's mentioned that "*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*." 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?


Section 8.15 3DDENS (3D electron density plots in whole cell) in the UG has:

This program generates the charge density (or the potential) in the 
whole conventional (or primitive)
unit cell on a three dimensional grid which can be used for plotting 
with an external program

that can read .xsf-files (e.g., XCrysden, VESTA).

As the above says, the charge density case.xsf file should be generated 
automatically.


Section 8.15.3 in the WIEN2k 18.2 usersguide has:

stmswitch case_stm.xsf file is written, containing height values for the 
given density

value.

As the above says, the stm image case_stm.xsf file should be generated 
automatically if the stmswitch parameter is set to "stm".


So if want the charge density plot, open case.xsf (in XCrySDen). If you 
want the STM image plot, open the case_stm.xsf.


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 [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07125.html 
].


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 [ 
http://www.numis.northwestern.edu/Software/Software.shtml ].



On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha 
 wrote:



STM simulations make only sense for a surface. You cannot make STM for a
bulk ???

3ddens does not include tip vibrations, but is very fast and
conveniently lets you choose the best hight above the surface to
reproduce experimental images.

Be careful with the STM mode of lapw5 in cases with angles differing
from 90 degrees !

STM simulations are always a bit of an art, because the quality of the
experimental STM images changes a lot with group / time / 


Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:
> Dear Developers and Users,
>
> I need some advice on using the 3ddens program. My interest is to
> simulate STM image of a 3D system to compare with our experimental 
results.

> My questions are:
>
> Whether it's possible for 3D system.
> What determine the size of the grid points?
> Do I have to edit any file in my case directory before x 3ddens -XX?
>
> I want to test run using TiC, what are the general tips? Any hint is
> highly appreciated.
>
> Thanks a lot for your time.
>
> With kind regards.
>
> */Lawal
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Re: [Wien] STM

2019-01-05 Thread Lawal Mohammed
Dear Prof. Peter and Users,
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. What should be my start value (value above 
the surface atom) and end value (value around middle of vacuum)? Also in the UG 
page 172, section 18.5 it's mentioned that "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." 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? 

Thanks a lot for your time.
With kind regards.

Lawal 
On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha 
 wrote:  
 
 STM simulations make only sense for a surface. You cannot make STM for a 
bulk ???

3ddens does not include tip vibrations, but is very fast and 
conveniently lets you choose the best hight above the surface to 
reproduce experimental images.

Be careful with the STM mode of lapw5 in cases with angles differing 
from 90 degrees !

STM simulations are always a bit of an art, because the quality of the 
experimental STM images changes a lot with group / time / 


Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:
> Dear Developers and Users,
> 
> I need some advice on using the 3ddens program. My interest is to 
> simulate STM image of a 3D system to compare with our experimental results.
> My questions are:
> 
> Whether it's possible for 3D system.
> What determine the size of the grid points?
> Do I have to edit any file in my case directory before x 3ddens -XX?
> 
> I want to test run using TiC, what are the general tips? Any hint is 
> highly appreciated.
> 
> Thanks a lot for your time.
> 
> With kind regards.
> 
> */Lawal
> /*
> 
> 
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:  
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> 

-- 
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
WWW: 
http://www.imc.tuwien.ac.at/tc_blaha-
 

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Re: [Wien] STM

2018-12-24 Thread Lawal Mohammed
Dear Prof. Peter and Users,
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. What should be my start value (value above 
the surface atom) and end value (value around middle of vacuum)? Also in the UG 
page 172, section 18.5 it's mentioned that "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." extraction of the electron 
density is it automatic it should be done manually, and which file case.xsf or 
case_stm.xsf should be use the plotting? 

Thanks a lot for your time.
With kind regards.

Lawal 

 

On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha 
 wrote:  
 
 STM simulations make only sense for a surface. You cannot make STM for a 
bulk ???

3ddens does not include tip vibrations, but is very fast and 
conveniently lets you choose the best hight above the surface to 
reproduce experimental images.

Be careful with the STM mode of lapw5 in cases with angles differing 
from 90 degrees !

STM simulations are always a bit of an art, because the quality of the 
experimental STM images changes a lot with group / time / 


Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:
> Dear Developers and Users,
> 
> I need some advice on using the 3ddens program. My interest is to 
> simulate STM image of a 3D system to compare with our experimental results.
> My questions are:
> 
> Whether it's possible for 3D system.
> What determine the size of the grid points?
> Do I have to edit any file in my case directory before x 3ddens -XX?
> 
> I want to test run using TiC, what are the general tips? Any hint is 
> highly appreciated.
> 
> Thanks a lot for your time.
> 
> With kind regards.
> 
> */Lawal
> /*
> 
> 
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:  
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> 

-- 
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
WWW: 
http://www.imc.tuwien.ac.at/tc_blaha-
 

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Re: [Wien] STM

2018-12-07 Thread Lawal Mohammed
Dear Prof. Laurence and Peter,
 Thank you very much for making it more clear. 

It looks like I have to copy from the UG STM mode of lapw5, because in case.in5 
from SRC_templates, the STM mode lines are missing.

With kind regards.

Lawal 

 

On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha 
 wrote:  
 
 STM simulations make only sense for a surface. You cannot make STM for a 
bulk ???

3ddens does not include tip vibrations, but is very fast and 
conveniently lets you choose the best hight above the surface to 
reproduce experimental images.

Be careful with the STM mode of lapw5 in cases with angles differing 
from 90 degrees !

STM simulations are always a bit of an art, because the quality of the 
experimental STM images changes a lot with group / time / 


Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:
> Dear Developers and Users,
> 
> I need some advice on using the 3ddens program. My interest is to 
> simulate STM image of a 3D system to compare with our experimental results.
> My questions are:
> 
> Whether it's possible for 3D system.
> What determine the size of the grid points?
> Do I have to edit any file in my case directory before x 3ddens -XX?
> 
> I want to test run using TiC, what are the general tips? Any hint is 
> highly appreciated.
> 
> Thanks a lot for your time.
> 
> With kind regards.
> 
> */Lawal
> /*
> 
> 
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:  
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> 

-- 
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
WWW: 
http://www.imc.tuwien.ac.at/tc_blaha-
 

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Re: [Wien] STM

2018-12-06 Thread Peter Blaha
STM simulations make only sense for a surface. You cannot make STM for a 
bulk ???


3ddens does not include tip vibrations, but is very fast and 
conveniently lets you choose the best hight above the surface to 
reproduce experimental images.


Be careful with the STM mode of lapw5 in cases with angles differing 
from 90 degrees !


STM simulations are always a bit of an art, because the quality of the 
experimental STM images changes a lot with group / time / 



Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:

Dear Developers and Users,

I need some advice on using the 3ddens program. My interest is to 
simulate STM image of a 3D system to compare with our experimental results.

My questions are:

Whether it's possible for 3D system.
What determine the size of the grid points?
Do I have to edit any file in my case directory before x 3ddens -XX?

I want to test run using TiC, what are the general tips? Any hint is 
highly appreciated.


Thanks a lot for your time.

With kind regards.

*/Lawal
/*


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--
--
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW: 
http://www.imc.tuwien.ac.at/tc_blaha- 


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Re: [Wien] STM

2018-12-06 Thread Laurence Marks
I have no idea how good/bad 3ddens is for STM. I know lapw5 works and
agrees fairly well with experiment for insulators if you use reasonable
values for the tip vibrations. (Ignoring tip vibrations leads to images
with too high resolution.)

On Thu, Dec 6, 2018, 20:33 Lawal Mohammed  wrote:

> Dear Developers and Users,
>
> I need some advice on using the 3ddens program. My interest is to simulate
> STM image of a 3D system to compare with our experimental results.
> My questions are:
>
> Whether it's possible for 3D system.
> What determine the size of the grid points?
> Do I have to edit any file in my case directory before x 3ddens -XX?
>
> I want to test run using TiC, what are the general tips? Any hint is
> highly appreciated.
>
> Thanks a lot for your time.
>
> With kind regards.
>
>
> *Lawal *
>
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[Wien] STM

2018-12-06 Thread Lawal Mohammed
Dear Developers and Users,
I need some advice on using the 3ddens program. My interest is to simulate STM 
image of a 3D system to compare with our experimental results. My questions 
are: 

Whether it's possible for 3D system.What determine the size of the grid 
points?Do I have to edit any file in my case directory before x 3ddens -XX?
I want to test run using TiC, what are the general tips? Any hint is highly 
appreciated.
Thanks a lot for your time.
With kind regards.

Lawal 

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Re: [Wien] STM simulation in wien2k

2014-06-27 Thread Laurence Marks
The link that Gavin refers to provides information on doing STM simulations
using MATLAB; the lapw2STM code is only for large biases (insulators) and
even then probably not needed.

as Peter's email hinted, a simpler method will be in the next release.
On Jun 27, 2014 1:13 PM, "Gavin Abo"  wrote:

> Maybe "Appendix A. STM Image Simulations: Theory & Implementation" in
> the dissertation by one of Prof. Marks students at the following link is
> of interest to you:
>
> http://www.numis.northwestern.edu/thesis/ThesisAndresHD.pdf
>
> However, I don't know if the lapw2STM code is available to the public.
>
> On 6/27/2014 3:35 AM, Gang Li wrote:
> > Dear wien2k users and administrators
> >
> > I am interested to know the detailed procedure of simulating STM images
> in wien2k. I did some research on google, and learned that the key quantity
> to be calculated is the partial charge density in a given energy range.
> This range is defined by the bias voltage of the simulated STM measurement.
>  The command to be issued is “x lapw2 -emin V_bias”.
> >
> > The above is all I know for the moment. Can anyone give me a detailed
> description of “how to” step by step.  In addition to the calculation, I
> would also like to know how to plot the STM image in both experimental
> modes, i.e. constant current and constant height modes.
> >
> > Thanks in advance
> > Gang Li
>
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Re: [Wien] STM simulation in wien2k

2014-06-27 Thread Peter Blaha

The next version will include a modified lapw5 by L.Marks, such that also
constant current simulations are possible.

Am 27.06.2014 19:13, schrieb Gavin Abo:

Maybe "Appendix A. STM Image Simulations: Theory & Implementation" in the 
dissertation by one of Prof. Marks students at the following link is of interest to you:

http://www.numis.northwestern.edu/thesis/ThesisAndresHD.pdf

However, I don't know if the lapw2STM code is available to the public.

On 6/27/2014 3:35 AM, Gang Li wrote:

Dear wien2k users and administrators

I am interested to know the detailed procedure of simulating STM images in 
wien2k. I did some research on google, and learned that the key quantity to be 
calculated is
the partial charge density in a given energy range. This range is defined by 
the bias voltage of the simulated STM measurement.  The command to be issued is 
“x lapw2
-emin V_bias”.

The above is all I know for the moment. Can anyone give me a detailed 
description of “how to” step by step.  In addition to the calculation, I would 
also like to know how
to plot the STM image in both experimental modes, i.e. constant current and 
constant height modes.

Thanks in advance
Gang Li


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--
-
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Inst. Materials Chemistry, TU Vienna
Getreidemarkt 9, A-1060 Vienna, Austria
Tel: +43-1-5880115671
Fax: +43-1-5880115698
email: pbl...@theochem.tuwien.ac.at
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Re: [Wien] STM simulation in wien2k

2014-06-27 Thread Gavin Abo
Maybe "Appendix A. STM Image Simulations: Theory & Implementation" in 
the dissertation by one of Prof. Marks students at the following link is 
of interest to you:


http://www.numis.northwestern.edu/thesis/ThesisAndresHD.pdf

However, I don't know if the lapw2STM code is available to the public.

On 6/27/2014 3:35 AM, Gang Li wrote:

Dear wien2k users and administrators

I am interested to know the detailed procedure of simulating STM images in 
wien2k. I did some research on google, and learned that the key quantity to be 
calculated is the partial charge density in a given energy range. This range is 
defined by the bias voltage of the simulated STM measurement.  The command to 
be issued is “x lapw2 -emin V_bias”.

The above is all I know for the moment. Can anyone give me a detailed 
description of “how to” step by step.  In addition to the calculation, I would 
also like to know how to plot the STM image in both experimental modes, i.e. 
constant current and constant height modes.

Thanks in advance
Gang Li


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[Wien] STM simulation in wien2k

2014-06-27 Thread Gang Li
Dear wien2k users and administrators 

I am interested to know the detailed procedure of simulating STM images in 
wien2k. I did some research on google, and learned that the key quantity to be 
calculated is the partial charge density in a given energy range. This range is 
defined by the bias voltage of the simulated STM measurement.  The command to 
be issued is “x lapw2 -emin V_bias”.

The above is all I know for the moment. Can anyone give me a detailed 
description of “how to” step by step.  In addition to the calculation, I would 
also like to know how to plot the STM image in both experimental modes, i.e. 
constant current and constant height modes. 

Thanks in advance 
Gang Li


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[Wien] STM images

2009-08-07 Thread Peter Blaha
I'd check k-points! Since one gets the density from a very small 
E-interval, a crude k-mesh could miss the contributions from some k-points.

Laurence Marks schrieb:
> Has anyone done a careful study of how STM images depend upon
> convergence parameters, e.g. oversampling, step at the RMT, RKMAX,
> k-points etc?
> 


[Wien] STM images

2009-08-06 Thread Laurence Marks
Has anyone done a careful study of how STM images depend upon
convergence parameters, e.g. oversampling, step at the RMT, RKMAX,
k-points etc?

-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering to study the structure of matter.