day3
Day 3 tutorials
Tutorial 7: 2D systems: monolayers, slabs and surfaces
https://drive.google.com/open?id=11wHw1iQpsWCHHqQd3wPNL_5d_T_wBEQO
Tutorial 8: "a "constrain method" in EA: looking for metastable"
https://drive.google.com/open?id=1-9_nJepxFPbUGTSyR8DiU3dMrdj-NWf6
Tutorial 7: Predicting 2D materials
@Rennes 1 University
Busheng Wang, Heng Zhang & Gilles Frapper
IC2MP, Poitiers University - CNRS
OUTLINE
- Fixed-composition Prediction, -200, EX07-2D_Si
- Variable-composition Prediction, -201, EX31_2D_varcomp_SnS
- Parameters in INPUT.txt for 2D monolayer/slab
-Surface (EX23_MgO_surface)
7.1 Log in your account
ssh –oPort=86 uspexXX@thor.univ-poitiers.fr
LOGIN: uspexXX (with XX=10-32)
PWD: ?Ic2Mp;UsPeX!
Copy USPEX_Manualif you need.
cp -r /home/gfrapper/USPEX_workshop/USPEX_Manual_English.pdf .
7.2 EX07-2D_Si VASP
Copy Example07
cp -R /home/gfrapper/USPEX_workshop/Day3/EX07-2D_Si .
Edit INPUT.txt
vi INPUT.txt
One error:
% vacuumSize
8 9 10 12
% EndVacuumSize
% vacuumSize
20 20 20 20 20
% EndVacuumSize
Default: 10 Å for every step of relaxation
Note:
(1) vacuumSize in 2D structure prediction is the lattice parametercof 2D crystal along z direction, which is different from the vacuumSize in surface structure prediction(200, 201)
Edit the Queue information.
R1067861 (500 cores) for uspex01~20; R1068123 (300 cores) for uspex20-40).
vi runuspex.sh
vi Submission/submitJob_local.py
vi Submission/checkStatus_local.py
output = unicode(check_output(u'/sw/pbs/default/bin/qstat -u {}'.format('userXX') , shell=True))
# In calculation node of Thor, 'qstat jobID' jobID will be followed with '.service0' automatically, error. But 'qstat -u username' works well.
Submit job
qsub runuspex.sh
Check results
vi reference/OUTPUT.txt
vi reference/BESTIndividuals
vi reference/BESTIndividuals_POSCARS
vi reference/goodStructures
vi reference/goodStructures_POSCARS
Or
Download the reference file from Thor to local machines, then use GDIS to have a look.
scp -oPort=86 -r uspexXX@thor.univ-poitiers.fr:/directory/reference .
Password (?Ic2Mp;UsPeX!)
Note:
(1) Prediction of 2D AmBnby formula is available.
% atomType
A B
% EndAtomType
% numSpecies
m n
% EndNumSpecies
6: minAt
12: maxAt
7.3 EX31_2D_varcomp_SnS VASP
cp -R /home/gfrapper/USPEX_workshop/Day3/EX31_2D_varcomp_SnS .
vi INPUT.txt
vi reference/OUTPUT.txt
vi reference/extended_convex_hull
vi reference/extended_convex_hull_POSCARS
Open reference/extendedConvexHull.pdf in Windows
Note:
(1) Because we have confined the thickness for 2D structures, we will discard the structures with thickness after relaxation greater than thicknessS+3Å.
(2) For -201 prediction, the convex hullis calculated with respect to the energy of 2D elemental materials.
7.4 Necessary parameters in INPUT.txt (USPEX_Manual-10.2, Page 54, 75-77)
calculationType, symmetries, vacuumSize, atomType, numSpecies, minAt, maxAt
-200/-201/-s200/-s201 : calculationType
% symmetries
2-80
% endSymmetries
3.0 : thicknessS
% vacuumSize
20 20 20 20 20
% EndVacuumSize
% atomType
Si O
% EndAtomType
-200: fixed-composition prediction
-201: variable-composition prediction
% numSpecies
1 2
% EndNumSpecies
% numSpecies
1 2
% EndNumSpecies
3: minAt
9: maxAt
% numSpecies
1 0
0 1
% EndNumSpecies
4 : minAt
20 : maxAt
Note:
(1) Magnetic calculation (-s200, -s201) is only supported in VASP.
TUTORIAL Surface (EX23_MgO_surface)
1. To perform a prediction of surface reconstructions, you have to:
• Specify 200 or 201 : calculationType.
•
Provide a file containing substratein VASP5 POSCAR format.
•
5.0 : thicknessS (thickness of surface region)
3.0 : thicknessB (thickness of buffer region)
4 : reconstruct (maximum multiplications of cell)
% symmetries
2-17
% endSymmetries
% vacuumSize
10 10 15 20
% EndVacuumSize
Specify the following parameters:
Fig. 1 The surface model used in USPEX.
2. Create new folder and cd into it:
> mkdir Day3/EX23&& cd Day3/EX23
3. Copy the files for example 23:
> cp -r /home/gfrapper/USPEX_workshop/Day3/EX23_MgO_surface/* .
(Here everything is set up for submission on thor)
4. Run the calculation:
> qsub runuspex.sh
5. Download the results folder to your local machine,using the GDIS code:
(Under the local machine copy the results directory to local_dir)
> mkdirlocal_dircd local_dir
> scp -r -oPort=86 uspexXX@@thor.univ-poitiers.fr:path_to_results_dir .
> gdis results1/OUTPUT.txt