sqs2tdb version 3.48 by Axel van de Walle and with contributions to the SQS database
from Ruoshi Sun, Qijun Hong and Sara Kadkhodaei.
Usage: sqs2tdb [options] where the available options are:
-h : More help.
-cp : Copy SQS from the database to the current directory. Must specify:
-lv=[level]
level indicates how fine of composition mesh to use (0: only end members, 1: mid points,
etc.)
-l=[lattice]
Available lattices
AUCD_B19
AUCD_B19.tar
AUCU_L10
BCC_A2
BETASN_A5
CDI2_C6
CHI_A12
CR3SI_A15
CSCL_B2
CUPRITE_C3
CUPT_B22
CUPT_L11
DIAMOND_A4
DUMMY
FCC_A1
FE3AL_D03
FLUORITE_C1
GA3PT5
GAMMA_L12
HCP_A3
HEUSLER_D022
HEUSLER_L21
hidden
LIQUID
MGCU2_C15
MGZN2_C14
NI3SN_D019
NI4MO_D1A
NIAS_D81
OMEGA_C32
PEROVSKITE_E21
PYRITE_C2
REO3_D09
ROCKSALT_B1
RUTILE_C4
SIGMA_D8B
tmp.sspp
tmp.sspp~
WURTZITE_B4
ZINCBLENDE_B3
ZINTL_B32
ZIRCONIA_TET
Optional: -sp=Element,Element,... to indicate which elements to consider
(otherwise read from species.in if it exists).
-fit : Fit solution model from SQS energies (to be run within the desired lattice directory)
The -sro option can also be specified (with -fit) to include short-range order effects.
-tdb : Combine solution models from one or multiple lattices into a single .tdb file.
add the -oc (Open Calphad) option to generate a more portable tdb file.
-mk : Generate input file for SQS generation with mcsqs. (Usually not needed - only for experts.)
To be run in the SQS database directory:
/home/avdw/avdw/atat/data/sqsdb/[lattice name]
Note that -h,-mk,-cp,-fit,-tdb are mutually exclusive.
For more information see user guide published in:
A. van de Walle, R. Sun, Q.-J. Hong, and S. Kadkhodaei.
Software tools for high-throughput calphad from first-principles data.
Calphad, 58:70, 2017.
https://doi.org/10.1016/j.calphad.2017.05.005
(Also, this paper should be cited in any publication resulting from this code's use.)
EXAMPLES
-> A simple session of sqs2tdb could be:
cp ~/atat/example/vasp.wrap .
emacs vasp.wrap #edit as needed
echo Al,Ni > species.in
sqs2tdb -cp -l=FCC_A1 -lv=1
sqs2tdb -cp -l=FCC_A1 -lv=1
cd FCC_A1
foreachfile wait pwd \; runstruct_vasp
sqs2tdb -fit
Edit the file terms.in to read
1,0
2,0
sqs2tdb -fit
cd ..
(repeat the above for other lattices if necessary)
sqs2tdb -tdb
The file AL_NI.tdb would contain a valid .tdb file.
-> In a more advanced example, the runstruct_vasp command could be replaced
by a job script submission containing the runstruct_vasp command.
-> When there are lattice instabilities, the runstruct_vasp could be replaced by
robustrelax_vasp -mk #this is to be run only once (see robustrelax_vasp -h for instructions)
robustrelax_vasp -id
-> If phonons are to be included (for end members) one could do:
foreachfile endmem pwd \; fitfc -si=str_relax.out -ernn=4 -ns=1 -nrr
foreachfile -d 3 wait \; runstruct_vasp -lu -w vaspf.wrap
where vaspf.wrap contains parameters for a static run to calculate forces.
foreachfile endmem pwd \; fitfc -si=str_relax.out -f -frnn=2
foreachfile endmem pwd \; robustrelax_vasp -vib
sqs2tdb -fit
OPTIONAL input files (to placed in the topmost directory):
exfromsgte.in : specify which phases should NOT be copied from SGTE database
(by default all phases for each relevant element are included,
but you may want to use ab initio data for virtual phase)
subref.sed : substitution rule (sed command to be applied to final tdb file)
OUTPUT FILES
In addition to the *.tdb files, there is some diagnostic info available in the files
fit_[property].out where property could be
energy, svib_ht, etc.
ADVANCED FEATURES
In each sqs subdirectory created, there may be a file called link that contains the path to
another directory where energy data can be found. This is useful if another structure is
known be equivalent by symmetry. This file is created by default for equivalence within a
given structure type can even find symmetries across structure types.
You can also create the file yourself and the code will follow your link.
There may also be a file called bump which indicates that a structure must be moved up in energy
by the
amount specified by the -bv option (or 5e-3 by default) to avoid degeneracy with an equivalent
higher symmetry structure.
This file is created by default (during the -cp step) when the code detects higher symmetry
(e.g. a GAMMA_L12 phase with all sites occupied
with the same type of atom is just FCC). You can delete this file if the higher-symmetry
structure is not in your
set of structures. This file is read during the -fit step.
In summary, if you see a bump file, ask yourself if you have that structure elsewhere and put an
appropriate link file.
If you don't have that structure elsewhere, you can delete the bump file.
The code will still work and give the right answer if you don't do this, but it will spend more
computer time.
During the -fit step, one can specify the -sro option to include a low-order CVM approximation
to the short range order.
One can also specify the weights used to enforce better fit of the end members with the -ew
option (a weight of 10 is the default).
The default lower and upper temperature limits of 298.15K and 10000K can be changed with the
-Tl=... and -Tu=... options, respectively.
This code now allows for the input free energies to general CALPHAD-compatible T-dependent
functions. To use this feature, place your functions
in 'func' files and do not specify 'energy' or 'svib_ht' files.
avdw@alum.mit.edu Wed, Dec 6, 2023 12:55:16 PM