Instructions for charge density multislice (Numis-2.0)
Jim Ciston
25 May 2009
The purpose of this program is to simulate exit waves and images of thin crystals in a
transmission electron microscope subject to the scattering potential of the fully-bonded
valence charge density as calculated by the Wien2k DFT software package.
1)
Important limitations
a. The present version of the code can only handle structures in
orthorhombic unit cells projected along principle axes. If your structure is
neither orthorhombic nor a principle projection, you must create a new
pseudo-cell for the calculation. For the example of SrTiO3 [110], a new
cell should be created with axes [110], [-110], [001]. The provision to
project along non-principal axes is currently under development.
b. The multislice projection routine computes the full scattering potential for
the unit cell along the desired direction. This effectively compresses the
entire unit cell into a single slice. If one is calculating images for very
large unit cells (e.g. surface structure supercells), the loss of threedimensionality due to this approximation may lose validity. For typical
bulk unit cells of 4-8 Å, the approximation has been tested and confirmed
to be reasonable.
2)
DFT instructions
a. Perform your DFT calculation as normal. The calculations should be well
converged (-ec 0.0001 –cc 0.0001). It should be noted that the charge
density is rather less sensitive to the choice of functional that the energy.
For SrTiO3, the difference between PBE and PBE0 is 1000x smaller than
the difference between neutral atoms and fully bonded atoms.
b. After your calculation is set up and ready to begin (i.e. after dstart), run
the following procedure:




x lapw3 (calculate x-ray structure factors)
grep –n –e ‘X – RAY STRUC’ *.output3 (get line where
structurefactors begin)
wc –l *.output3 (get total number of lines in file)
tail –[total_lines – structurefactor_line + 1] *.output3 > case.dhkl
(write only the structurefactor portion of case.output3 to a new
file called case.dhkl)
c. Once the calculation is converged, run the following procedure (comments
in parentheses):





save_lapw –a –d directory (save your calculation)
x lapw3 (calculate x-ray structure factors)
grep –n –e ‘X – RAY STRUC’ *.output3 (get line where
structurefactors begin)
wc –l *.output3 (get total numer of lines in file)
tail –[total_lines – structurefactor_line] *.output3 > case.hkl
(write only the structurefactor portion of case.output3 to a new
file called case.hkl)
d. The multislice code requires three Wien2k files as inputs:



3)
case.struct (the Wien2k structure file)
case.hkl (the charge density x-ray structurefactors)
case.dhkl (the neutral atom x-ray structurefactors)
Installation of multislice code
a. Numis is available from a CVS (concurrent version system) server hosted
at Northwestern University. The software is downloaded and installed
through a command line interface and is wrapped within the
autoconfigure/automake framework. Installation is recommended either
on Cygwin (running on Windows) or Linux platforms. It is also possible
to compile on Apple computers, but the appropriate developer tools
(compilers, libraries, etc) are not part of the standard Mac OS and must be
downloaded and installed separately.

Note: your gcc and gfortran compilers MUST be version 4.3 or
later. This can be determined by typing ‘gfortran --version’
b. Go to the directory where you want to download the Numis and Semper7
packages (e.g. /home/your_name/cvs_sources). You must set the
following environment variables for the CVS download and compilation
to function properly (this can either be done at the command line, or added
to your .bashrc)





export CVSROOT=
:ext:your_name@129.105.122.84:/export/home/cvsroot
export CVS_RSH=ssh
export F77=gfortran (or F77=gfortran-4 if you have multiple
compiler version as in Cygwin)
export CC=gcc (or possibly CC=gcc-4 for Cygwin depending
upon which compilers are linked where)
export DISPLAY=127.0.0.1:0.0 (this may or may not be needed
for Semper to launch an X-window properly)
c. Now it is time to download and install the Numis and Semper7 software.
This may be the unfortunate time when you find out that something in
your system is broken and you have to case down errors when the
compilation crashes.





cvs checkout Numis-2.0
cd Numis-2.0/
./configure (this will determine the appropriate compilation
parameters on your local machine)
make (compiles the software)
make install (puts the executables in /usr/local/numis_2.0/bin)







cd ../
cvs checkout simper-7.0beta
cd simper-7.0beta
./configure
make
make install (puts the executables in /usr/local/simper-7.0b/bin)
make help
d. If everything went successfully, all that is left is to add the appropriate
directories to your path.

export PATH=$PATH:/usr/local/numis_2.0/bin:
/usr/local/simper-7.0b/bin
e. Occasionally you may need to update your software as bugs are fixed and
features are added. The advantage of the CVS automake framework is
that only files which are new will be downloaded and re-compiled, leaving
everything else alone. This is accomplished by simply going to the
appropriate source file directory (for Numis or Semper) and executing:



4)
cvs update
make
make install
Using the Numis code
a. Numis ships with an example for Forsterite. Go to an appropriate
directory and copy the contents of Numis-2.0/examples/CD-multislice/
there. When executing cases other than the Forsterite example, you will
need to copy to your local directory and replace the case.struct, case.hkl,
and case.dhkl with your desired structure.
b. The first step is to project your structure along the relevant direction and
generate the 2-D scattering potential. This is accomplished by running the
shell script ‘ProjPotent.sh’. You must provide the header to the file names
as an input (‘Forsterite’ in this case…see below) This script will also
generate the appropriate input files for the multislice routine (case.dat,
case.d200, and case.at).
You will be prompted for the projection axes and other parameters. For
centering, enter no. All other options (yes, hexagonal, face-centered) are
untested. Enter ‘1’ to indicate that the potential has been projected. On
the last line, enter the desired temperature factor (in units of B, not u) and
an integer to divide the unit cell along the projection direction. This
integer should be chosen so that the c-axis in case.at is 1-2Å in length.
Jim@tchaikovsky ~/test_numis
$ sh ProjPotent.sh Forsterite
Enter zone _1 0 0
Enter first axis _0 1 0
Enter second axis _0 0 1
Centering (hex) used (Y/N/H/F) _n
Base.hkl (<0) or projected _1
Temperature factor, slice divide _0.25 6
Done
Enter zone _1 0 0
Enter first axis _0 1 0
Enter second axis _0 0 1
Centering (hex) used (Y/N/H/F) _n
Base.hkl (<0) or projected _1
Temperature factor, slice divide _0.25 6
Done
Jim@tchaikovsky ~/test_numis
Note that different versions of Wien2k have slightly different output
formatting for the case.struct file. This should work for the latest version.
You may have to add/remove a space for each atom in the case.struct file
here after Z: in order for the atomic number to be read correctly.
Sr1
NPT= 781 R0=.000010000 RMT= 2.36000 Z: 38.
c. Now, you must edit the case.200 file in order to tell the multislice routine
what thicknesses you would like to use. The file is printed below
Wien Test
8 8 8
00
1 2 0
8
3
1 0 0 0 1 0
1 0
4CU
0.5000 0.2500 0 MG
1.5792 1.8197 1.6576 0.5323 62.9403 12.4527 2.5042 0.3331 0.0000 12.0 2
000 0 0
200.00000 1.69833 0.00000
0 0
1
200 1
10
1 -50 -50 50 50
1 1 0 2 4 2 0 4
5 1 5 10 50100
1
0 0.0000 0.0000 0.0000 0.000 0.000 0.000 0.000 0.000 0.0000
There are a few things to note about this file. First, most of it should be
left alone as it is not used. The first number on line 10 is the microscope
asselerating voltage in units of kV. The second number on line 10 is the
slice thickness. This should match the c-axis in case.at. The first number
on line 13 is the maximum number of slices that will be calculated. Line
17 is where the user may define what thicknesses (in units of slice
number) that should be considered. The formatting of this line needs to be
(i2,30i3). This first number is the number of thicknesses (i2 format) and
the following entries are the thickness values (i3 format). Up to 30 values
may be entered.
d. Execute the multislice routine by typing ‘sh MultiSlice.sh200 Forsterite’
e. You are now ready to run the image simulation routine. Before this can be
done, you need to modify the J2200C5.pr file to tell the program what
microscope parameters to use. This is the most user-unfriendly portion of
the code and a script may be rewritten in the future to prompt the user for
these values at the command line. Here is description of the formatting for
this file:
C ****************************************************************
C DATA.
C CARD
FORMAT
VARIABLES
C 1
15A4
HEAD(I),I=1,15 A 60 CHARACTER HEADING
C
WHICH IS PUT ON THE TOP
C
OF EACH IMAGET.
C 2
A1,A1,2I5
FOUR,ROUT,IFLSK,IMODE
C 3
5F10.0
ANGIN,X1,X2,Y1,Y2
C 4
3I5
ISLSK,NTHIKS,NTILTS
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
5
2F10.0
RES,CSS
6
I5,2F10.0
TILH,TILK,IBTSET
7
2F10.0
OI,OJ
8
2F10.0,I5
DFS,DFI,NDF
9
I5,A1,F10.0 NTTTT,NQUAD,DIVGCE
10
2F10.8,I5
CHDIV,DELTA,NDIV
11
3I5
NOPTN,NOPTZ,NOPTY
12
2F10.0
AMEAN,CON
PARAMETERS.
HEAD A 60 CHARACTER HEADING WHICH IS PRINTED ON THE TOP OF
EVERY OUTPUT. (DEFAULT IS HEADING FROM MULTISLICE FILE)
FOUR
FOURIER TRANSFORM: Must be F
ROUT
OUTPUT MODE: OVERPRINT(O),
NOOVERPRINT(N),
TAPE(T),
MONITOR(M),
VDU(V),
FILE(F),
PROFILE(P).
C IMODE
C
C
C
C
C
C CSS
MODE OF OUTPUT IF <1 NORMAL IMAGES
=1 MICRODIFFRACTION OR DIFFRACTION
=2 CURRENT DENSITY
=3 DIFFraction output
=4 Reciproal space wave output
=5 Real space wave output
spherical aberration in millimeters.
C ISLSK
slice to start calculation at.
C NTHIKS
number of thicknesses (adjacent arrays) output
C NTILTS
no. of tilts (ie. thickness loops) output
C IBTSET =0 set xtal tilt wrt optic axis (ie. group of beam tilts)
C
=1
beam tilt wrt optic axis (ie. group of xtal tilts)
C TILH,TILK TILTS AS SPECIFIED BY IBTSET ABOVE
C OI,OJ
APERTURE IS CENTRED AROUND BEAM (OI,OJ).
C DFS
defocus loop start, angstroms.
C DFI
increment
C NDF
number of steps
C NTTTT number of tilts in the divergence calculation.
C
+ve if tilts come from ms.FILE (must have divgce=0.0)
C
-ve if tilts to be generated (must set divgce)
C AQUAD
C NTS
C NTI
C
C
C
Convergence symmetry
slice that the divergence calculation commences at.
every nti slice after the nts slice is used in the
divergence calculation. hence, a specific thickness
may be pick off tape 2 at varying tilts to do the
divergence sum..
C DIVGCE
Convergence (mrad) included in real space by sums
c
of tilts in objective lens only
c
requires ntttt to be the negative no. of tilts
c chdiv
c delta
c ndiv
chromatic aberration increment steps, angstroms.
standard deviation
number of steps each side
C NOPTN
2-D PROFILES OPTION. - Unsupported
C NOPTZ
C NOPTY
Unsupproted
Unsupported
c amean mean intensity for output. dark=0, light=1.
c
0.5 will centre mean intensity to the middle
c con
c
c
5)
contrast range for output. no contrast=0.0, middle
contrast=0.5, strong contrast=1.0.
Reading the Numis output into Semper
a. input 1 ms nam ‘case_J5s.img’ num (THICK*DEF)