Jonas Baltrusaitis wrote:
> Gabriele et al,
>
> I rerun input with alat and, yes , it reads nicely. I assume it will read and
> convert
> ansgtroms from geom opt to alat in the next step no prob.
>
> Last thing I want to add to my input (after or before normal modes calcs) is
> DOS calcs.
> And this is where I got stuck as it wouldn't read last optimized coordinates
> (in fact
> it would miss ATOMIC SPECIES field if I didn't add it in ncsf part in hope
> that guess
> will get read). If I added ATOMIC SPECIES in ncsf it would use those instead
> of
> converting them from the optimization run.
Sorry I cannot follow your logic, it seems to me that you are confusing things
a bit...
You must always have ATOMIC_SPECIES card if you want to include any atom in
your calcs.
>
> So my questions is how to combined DOS calcs so it uses optimized
> coordinates, so in
> one input I can 1) optimize, 2) normal modes and crossections and 3) DOS and
> PDOS calcs
> from optimized geometries
I don't see any problem, apart from the fact that in version 4.0.4
ATOMIC_POSITIONS are
read from input instead of being read from the .save directory (but now in the
CVS the
coords should be read from the scf restart files, as it seems more logical to
me, since
the charge density is read from there as well).
Anyway what I suggest to do (since you want to do everything in a single
script) is: first
the relaxation, then grep the final atomic positions with something like this
nat=5
grep -A$((nat+5)) CELL_PARAMETERS | tail -$((nat+1)) > atpos.tmp
then use the positions in this temp file to add them at the end of any
successive input
file which needs them (_after_ removing the old ones from the middle of the
file, obviously)
cat > sih4.dos.in << EOF
&control
calculation='nscf'
prefix='sih4',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2,
ecutwfc =16.0
/
&electrons
mixing_mode='plain'
mixing_beta = 0.7,
conv_thr = 1.0d-8
/
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
H 1.008 H.vbc.UPF
K_POINTS {automatic}
12 12 12 0 0 0
EOF
cat atpos.tmp >> sih4.dos.in
for instance. In this way you don't have to care about the format of the
positions. You
can do the same to build an scf run before the nscf one, if you wish. Then you
can
calculate dos, pdos, ..., whatever needs scf charge density and/or wfcs from
the relaxed
configuration.
>
> I attached the input that succeded in nm calcls but failed in DOS calcs:
> didn;t read
> coords and produced empty output files
This seems another "problem", not related with atomic positions...
Did it give you an error? Are you sure that the fildos file is not present? ...?
GS
>
> thanks
>
> Jonas
>
--
o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student |
| c/o: SISSA & CNR-INFM Democritos, |
| via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511 |
| skype: gurlonotturno |
o ------------------------------------------------ o
