# GenLS
modeling super lattice and random polymer, and so on, in lexicographic order
Any questions pls send e-mail: longhuali@ujs.edu.cn
citation: Li, L. H.; Ge, B. X.; Han, B. L.; Shi, W. D. Journal of Physical Chemistry C 2019, 123, 14253-14260.

A) The simplest way to run GenLS is:
         ./GenLS.ne -x
where -x is option. You can use 'GenLS.ne -h' to show all options.
OPTIONS: 
   -h  : show this help message and exit
 
  -g1  : generate an example file for Stacking Mode
 
  -g2  : generate an example file for Defect Mode
 
   -1  : Enter Stacking Mode
         You should have Correct 'inpara.in' and 'addmovecontrol.in'
         As well as building blocks, such as 'POSCAR.1''POSCAR.2'...
 
   -2  : Enter Defect Mode
         You should have Correct 'inpara.in'
         As well as protype structure, such as 'POSCAR.vacan'

GenLS have Two Modes: Stacking and Defect Modes
Let's learn how to prepare those two types of calculations.

1. Stacking Mode
If you want stack numbers of structures into one super-lattice along z-directions, 
you need two input files:'inpara.in' and 'addmovecontrol.in', and POSCAR.* (VASP version 5) files that
will be stacked.

If you do not know how to prepare 'inpara.in' and 'addmovecontrol.in', you can run:
                    ./GenLS.ne -g1
templates for 'inpara.in' and 'addmovecontrol.in' could be obtained.

contents in 'inpara.in':
F       ! periodic condition? T/F
2       ! how many types of build blocks?
2 2     ! number of build blocks in each type!

contents in 'addmovecontrol.in':
15      ! specify vaccum length (Angstrom) 
1.45    ! specify required interlayer distance

Now, you can modify those two input files according your condition.
and build blocks: POSCAR.1 and POSCAR.2 (in this example, 2 types of build blocks) 
should be prepared, And finally run:
          ./GenLS.ne -1

2. Defect Mode
In this mode, point defect patterns can be constructed.
Similar to the stacking mode, 'inpara.in' can be prepared:
                   ./GenLS.ne -g2
contents in inpara.in:
8
3
POSCAR.subst

The stand VASP v5 format POSCAR ('POSCAR.subst' in this example) should be modified:
"
MergedCell
   1.00000000000000     
     3.43500000000     0.00000000000     0.00000000000
    -1.71750000000     2.97479726200     0.00000000000
     0.00000000000     0.00000000000    39.01558371223
  C   Sc  C   O 
  2   8   2   8
Selective
Direct
     0.00000000000     0.00000000000     0.58492479252  F F T M
     0.00000000000     0.00000000000     0.72581730093  F F T M
     0.66666666667     0.33333333333     0.23549154276  T T T Fe/X
     0.33333333333     0.66666666667     0.30047480737  T T T Fe/X
     0.66666666667     0.33333333333     0.38952732980  T T T Fe/X
     0.33333333333     0.66666666667     0.45409591211  T T T Fe/X
     0.66666666667     0.33333333333     0.60960416185  T T T Fe/X
     0.33333333333     0.66666666667     0.54460859447  T T T Fe/X
     0.66666666667     0.33333333333     0.76589757848  T T T Fe/X
     0.33333333333     0.66666666667     0.70133220351  T T T Fe/X
     0.00000000000     0.00000000000     0.26017091209  F F T M
     0.00000000000     0.00000000000     0.42961085652  F F T M
     0.00000000000     0.00000000000     0.21786166427  F F T M
     0.66666666667     0.33333333333     0.31689901377  T T T M
     0.33333333333     0.66666666667     0.37328673864  T T T M
     0.00000000000     0.00000000000     0.47180896597  F F T M
     0.00000000000     0.00000000000     0.62723404034  F F T M
     0.66666666667     0.33333333333     0.52819669085  T T T M
     0.00000000000     0.00000000000     0.68362176521  F F T M
     0.33333333333     0.66666666667     0.78213833573  T T T M
"
If Fe substitute Sc, the symbol 'Fe' should be placed on the positions of Sc, and others marked as 'M'.
If Sc vacances are need, the symbol 'X' should be placed on the positions of Sc, and others marked as 'M'.

Finally, run: 
                ./GenLS.ne -2


B) If you prefer the menu way, you can also type :
                 ./GenLS.ne 
without any parameters.

the menu of GenLS is shown as follows:
"
#-------------------------------------------#
#---------------    GenLS   ----------------#
#--   v1.1                                --#
#--  by arlonne                           --#
#--  longhuali@ujs.edu.cn                 --#
#-------------------------------------------#
 
Please Select the Generation Mode:
   1 : Stacking Mode (For Vertical/Lateral Superlattice)
   2 : Defect Mode (For Point Defects Strucutures)
   3 : Generate Input Files for Stacking Mode
   4 : Generate Input File  for Defect Mode
   5 : Do Nothing and Exit
-->: 
"
Simply select the task (integer number) you need. Have fun!