[Wien] Unable to see Li K edges in ELOSS file. Kindly guide.
Pranjal Nandi
pnandi at ub.edu
Fri Mar 8 00:29:31 CET 2024
Dear Peter,
Thanks a lot for your explanation. It helped a lot.
Further I would like to mention that I am facing an issue when I do parallel calculation. In parallel mode, SCF runs well, Optic package runs well (version 21.1). But when I run x qtl -p -telnes (from w2web), I get the following error
running QTL in parallel mode
calculating QTL's from parallel vectors
so: Undefined variable.
0.035u 0.043s 0:00.09 77.7% 0+0k 0+24io 0pf+0w
error: command /home/WIEN2k/WIEN2k/qtlpara qtl.def failed
I checked the forum too and found the following suitable threads
http://zeus.theochem.tuwien.ac.at/pipermail/wien/2021-May/031757.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21125.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20660.html
But I am highly confused as which solution should I start first? Here are some relevant files for your convenience.
It would be helpful if you could kindly guide me on the right track.
File qtlpara_lapw
#!/bin/tcsh -f
#
set tmp = .tmp_qtlpara.$$
set tmp2 = .tmp_qtlpara.$$_2
onintr exit
set name = $0
set bin = $name:h #default directory for WIEN-executables
if !(-d $bin) set bin = .
unalias rm
alias testinput 'if (! -e \!:1 || -z \!:1) goto \!:2'
alias testerror 'if (! -z \!:1.error) goto error'
set t = time
set log = :parallel
set defmach = `hostname`
set updn # spinpolarization switch
set dnup = 'dn' # spinpolarization switch
set sc # semicore-switch
set cmplx
set remote = ssh
set init = init:
set res = residue:
############################################################################
# In this section use 0 to turn of an option, 1 to turn it on,
# respectively choose a value
set useremote = 1 # using remote shell to launch processes
setenv DELAY 0.1 # delay launching of processes by n seconds
setenv SLEEPY 1 # additional sleep before checking
set debug = 0 # set verbosity of debugging output
############################################################################
############################################################################
# and now we look if we should override the defaults
if (-e $bin/parallel_options) then
source $bin/parallel_options
endif
if ( $?USE_REMOTE ) then
set useremote = $USE_REMOTE
endif
############################################################################
if ($#argv < 1) then
echo usage: $0 deffile
exit
endif
while ($#argv)
switch ($1)
case -h:
case -H:
set help
shift; breaksw
case -up:
set updn = 'up'
set dnup = 'dn'
shift; breaksw
case -dn:
set updn = 'dn'
set dnup = 'up'
shift; breaksw
case -so:
set so = 'so'
shift; breaksw
default:
set def = $1:r
shift; breaksw
endsw
end
set exe = $bin/qtl
set exe = qtl
#are we running parallel?
testinput .processes single
echo "running QTL in parallel mode"
echo "RUNNING" >.qtlpara
#before we start, we wipe away all parallel error files
if ( -e qtl.error ) rm *qtl*.error
if ( -e upqtl.error ) rm *qtl*.error
if ( -e dnqtl.error ) rm *qtl*.error
if ( -e qtl_1.error ) rm *qtl_*.error
if ( -e upqtl_1.error ) rm *qtl_*.error
if ( -e dnqtl_1.error ) rm *qtl_*.error
if ( -e .timeq_1) rm .timeq_*
if (-e .machines.help) rm .machines.help
grep -v $init .processes|grep : | grep -v $res >$tmp2
set mist = `wc $tmp2 `
set maxproc = $mist[1]
set machine = `grep $init .processes | cut -f2 -d: | xargs`
if ($#machine > $maxproc) then
set machine = `grep $init .processes |head -$maxproc| cut -f2 -d: | xargs`
endif
set lockfile = `cut -f2 -d: $tmp2 | awk '{print $1 NR}'|xargs`
set residue = `grep $res .processes|cut -f2 -d:`
if ($residue == "") unset residue
if ($debug > 0) echo machines: $machine
echo "** " Error in Parallel QTL >$def.error
#get name of case
setenv PWD `pwd|sed "s/tmp_mnt\///"`
setenv PWD $cwd
set case = $PWD
set case = $case:t
if ($case == "") then
echo "ERROR: cannot detect working directory $cwd -> exit"
exit 1
endif
if ($debug > 0) echo Setting up case $case for parallel execution
if ($debug > 0) echo of QTL
if ($debug > 0) echo " "
#
echo "calculating QTL's from parallel vectors"
vec2old_lapw -p -local $so -$updn
$exe $def.def $maxproc
rm $tmp* >&/dev/null
echo "DONE" >.qtlpara
exit 0
error:
echo "** " QTL crashed!
echo "** " QTL crashed at `date`>>$log
echo "** " check ERROR FILES! >>$log
echo "-----------------------------------------------------------------">>$log
echo "** " Error in Parallel QTL >>$def.error
rm $tmp* >&/dev/null
echo "ERROR" >.qtlpara
exit 1
File qtlpara
#!/bin/tcsh -f
#
set tmp = .tmp_qtlpara.$$
set tmp2 = .tmp_qtlpara.$$_2
onintr exit
set name = $0
set bin = $name:h #default directory for WIEN-executables
if !(-d $bin) set bin = .
unalias rm
alias testinput 'if (! -e \!:1 || -z \!:1) goto \!:2'
alias testerror 'if (! -z \!:1.error) goto error'
set t = time
set log = :parallel
set defmach = `hostname`
set updn # spinpolarization switch
set dnup = 'dn' # spinpolarization switch
set sc # semicore-switch
set cmplx
set remote = ssh
set init = init:
set res = residue:
############################################################################
# In this section use 0 to turn of an option, 1 to turn it on,
# respectively choose a value
set useremote = 1 # using remote shell to launch processes
setenv DELAY 0.1 # delay launching of processes by n seconds
setenv SLEEPY 1 # additional sleep before checking
set debug = 0 # set verbosity of debugging output
############################################################################
############################################################################
# and now we look if we should override the defaults
if (-e $bin/parallel_options) then
source $bin/parallel_options
endif
if ( $?USE_REMOTE ) then
set useremote = $USE_REMOTE
endif
############################################################################
if ($#argv < 1) then
echo usage: $0 deffile
exit
endif
while ($#argv)
switch ($1)
case -h:
case -H:
set help
shift; breaksw
case -up:
set updn = 'up'
set dnup = 'dn'
shift; breaksw
case -dn:
set updn = 'dn'
set dnup = 'up'
shift; breaksw
case -so:
set so = 'so'
shift; breaksw
default:
set def = $1:r
shift; breaksw
endsw
end
set exe = $bin/qtl
set exe = qtl
#are we running parallel?
testinput .processes single
echo "running QTL in parallel mode"
echo "RUNNING" >.qtlpara
#before we start, we wipe away all parallel error files
if ( -e qtl.error ) rm *qtl*.error
if ( -e upqtl.error ) rm *qtl*.error
if ( -e dnqtl.error ) rm *qtl*.error
if ( -e qtl_1.error ) rm *qtl_*.error
if ( -e upqtl_1.error ) rm *qtl_*.error
if ( -e dnqtl_1.error ) rm *qtl_*.error
if ( -e .timeq_1) rm .timeq_*
if (-e .machines.help) rm .machines.help
grep -v $init .processes|grep : | grep -v $res >$tmp2
set mist = `wc $tmp2 `
set maxproc = $mist[1]
set machine = `grep $init .processes | cut -f2 -d: | xargs`
if ($#machine > $maxproc) then
set machine = `grep $init .processes |head -$maxproc| cut -f2 -d: | xargs`
endif
set lockfile = `cut -f2 -d: $tmp2 | awk '{print $1 NR}'|xargs`
set residue = `grep $res .processes|cut -f2 -d:`
if ($residue == "") unset residue
if ($debug > 0) echo machines: $machine
echo "** " Error in Parallel QTL >$def.error
#get name of case
setenv PWD `pwd|sed "s/tmp_mnt\///"`
setenv PWD $cwd
set case = $PWD
set case = $case:t
if ($case == "") then
echo "ERROR: cannot detect working directory $cwd -> exit"
exit 1
endif
if ($debug > 0) echo Setting up case $case for parallel execution
if ($debug > 0) echo of QTL
if ($debug > 0) echo " "
#
echo "calculating QTL's from parallel vectors"
vec2old_lapw -p -local $so -$updn
$exe $def.def $maxproc
rm $tmp* >&/dev/null
echo "DONE" >.qtlpara
exit 0
error:
echo "** " QTL crashed!
echo "** " QTL crashed at `date`>>$log
echo "** " check ERROR FILES! >>$log
echo "-----------------------------------------------------------------">>$log
echo "** " Error in Parallel QTL >>$def.error
rm $tmp* >&/dev/null
echo "ERROR" >.qtlpara
exit 1
File Name: qtl.def
4,'TiPO4.inso', 'unknown', 'formatted',-1
5,'TiPO4.inq', 'old', 'formatted',-1
6,'TiPO4.outputq','unknown','formatted',0
8,'TiPO4.scf2', 'old', 'formatted',-1
9,'/mnt/dades_C/WIEN2k/TiPO4.vector', 'unknown','unformatted',-1
10,'/mnt/dades_C/WIEN2k/TiPO4.vectordn', 'unknown','unformatted',-1
12,'TiPO4.dmat', 'unknown','formatted',0
16,'TiPO4.qtl', 'unknown','formatted',0
18,'TiPO4.vsp', 'old', 'formatted',-1
19,'TiPO4.vspdn', 'unknown','formatted',-1
20,'TiPO4.struct', 'old', 'formatted',-1
21,'TiPO4.scfq', 'unknown', 'formatted',0
22,'TiPO4.rotlm', 'unknown', 'formatted',0
26,'TiPO4.weight', 'old', 'formatted',-1
29,'/mnt/dades_C/WIEN2k/TiPO4.tmp','SCRATCH','unformatted',9000
30,'TiPO4.qtltext','unknown','formatted',0
31,'TiPO4.qtlatom','unknown','formatted',0
59,'TiPO4.energydn', 'unknown','formatted',-1
60,'TiPO4.energy', 'unknown','formatted',-1
32,'TiPO4.cf1','unknown','formatted',0
71,'TiPO4.int1','unknown','formatted',0
Thank you.
With warm regards,
Pranjal
-----Original Message-----
From: Wien <wien-bounces at zeus.theochem.tuwien.ac.at> On Behalf Of Peter Blaha
Sent: Sunday, March 3, 2024 8:04 PM
To: wien at zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Unable to see Li K edges in ELOSS file. Kindly guide.
I analysed your problem. It has nothing to do with WIEN2k, but is much more fundamental.
A Li-K edge is per se not a "real edge". It's energy is so low, that it may overlap with many other excitations, they could be from Fe-3p (or from other shallow core levels ), but of course also from excitations from all other valence states into the conduction band.
You can analyse the different contributions to case.joint nicely, by playing with the band-indices. Download the 4 images
http:www.wien2k.at/Depository/LiFePO4.joint-total.png
http:www.wien2k.at/Depository/LiFePO4.joint-without-Fe-3p.png
http:www.wien2k.at/Depository/LiFePO4.joint-without-Fe-3p-zoom.png
http:www.wien2k.at/Depository/Li-K-edge.png from
They show case.joint ( unbroadened eps_xx) with the following band ranges in case.injoint (1st line):
1 9999 9999 : LOWER,UPPER and (optional) UPPER-VAL BANDINDEX (total eps_xx)
13 9999 9999 : LOWER,UPPER and (optional) UPPER-VAL BANDINDEX (eps_xx without Fe-3p statesI
13 9999 16 : LOWER,UPPER and (optional) UPPER-VAL BANDINDEX (eps_xx only from Li-1s
The Li-1s plot (Li-K-edge) starts as expected only at about 50 eV and its shape follows closely the Li-2p DOS (not shown), since the Li-1s bands are really flat (around -2.9 Ry) and "JDOS = DOS". Please look at the small y-scale !!!! (Note, such a selective absorption is not possible experimentally)
The total eps-xx is very large at low energy, and around 53 eV a sharp peak appears .
However, when you cut-off the Fe-3p states (first 12 bands) this peak is gone, which identifies it as the Fe-3p ("Fe-M--2,3 edge", not the usual Fe-L-2,3 edge) contribution. Only a very shallow structure can be seen and when you zoom in, the Li-1s absorption is visible, but only a "part of the eps2".
Am 01.03.2024 um 21:50 schrieb Pranjal Nandi:
> Dear Peter,
>
> Thanks for the reply. I would like to clarify some misunderstandings.
>
> There are two files for which I am doing the simulation, they are for
> LiFePo4 and LiTi2(PO4)3. (Note the addition of Ti in the second
> sample)
>
> The image I had shared was from Optics. I am discussing both the results below.
>
> For the optics results.
>
> - For LiFePO4, I do not see any Li edge structure.
> - For LiTi2(PO4)3, I do not see any Li edge structure. What I see is a new peak compared to LiFePO4 at around 35 eV whose shape is very close to the shape of Ti and not of Li.
>
> --
> ----------------------------------------------------------------------
> ---- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060
> Vienna
> Phone: +43-1-58801-165300
> Email: peter.blaha at tuwien.ac.at WIEN2k: http://www.wien2k.at
> WWW: http://www.imc.tuwien.ac.at
> ----------------------------------------------------------------------
> ---
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