sqs2tdb

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.