Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Develop #326

Merged
merged 5 commits into from
Sep 7, 2024
Merged

Develop #326

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
ef1b383
Fix repo.
knc6 Sep 5, 2024
5ffb6ab
Update databases.md
knc6 Sep 5, 2024
fdf62c0
Update databases.md
knc6 Sep 6, 2024
dfc23c1
Update databases.md
knc6 Sep 7, 2024
723a6bd
Version update.
knc6 Sep 7, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
94 changes: 12 additions & 82 deletions docs/databases.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,12 @@
|-------------------|-----------------------|---------------------------------------------------------------------------------------------------------------------------------------|
| `dft_3d` | 75993 | Various 3D materials properties in JARVIS-DFT database computed with OptB88vdW and TBmBJ methods |
| `dft_2d` | 1109 | Various 2D materials properties in JARVIS-DFT database computed with OptB88vdW |
| `supercon_3d` | 1058 | 3D superconductor DFT dataset |
| `supercon_2d` | 161 | 2D superconductor DFT dataset |
| `supercon_chem` | 16414 | Superconductor chemical formula dataset |
| `vacancydb` | 464 | Vacancy formation energy dataset |
| `surfacedb` | 607 | Surface property dataset |
| `interfacedb` | 593 | Interface property dataset |
| `dft_3d_2021` | 55723 | Various 3D materials properties in JARVIS-DFT database computed with OptB88vdW and TBmBJ methods |
| `dft_2d_2021` | 1079 | Various 2D materials properties in JARVIS-DFT database computed with OptB88vdW |
| `qe_tb` | 829574 | Various 3D materials properties in JARVIS-QETB database |
Expand All @@ -19,6 +25,8 @@
| `mp_3d_2020` | 127k | CFID descriptors for materials project |
| `mp_3d` | 84k | CFID descriptors for 84k materials project |
| `megnet2` | 133k | 133k materials and their formation energy in MP |
| `m3gnet_mpf` | 168k | 168k structures and their energy, forces and stresses in MP |
| `m3gnet_mpf_1.5mil` | 1.5 million | 1.5 million structures and their energy, forces and stresses in MP |
| `twod_matpd` | 6351 | Formation energy and bandgaps of 2D materials properties in 2DMatPedia database |
| `c2db` | 3514 | Various properties in C2DB database |
| `polymer_genome` | 1073 | Electronic bandgap and diecltric constants of crystall ine polymer in polymer genome database |
Expand Down Expand Up @@ -49,10 +57,10 @@
| `AGRA_CO` | 193 | AGRA CO catalyst dataset |
| `AGRA_CHO` | 214 | AGRA CHO catalyst dataset |
| `AGRA_COOH` | 280 | AGRA COOH catalyst dataset |
| `supercon_3d` | 1058 | 3D superconductor DFT dataset |
| `supercon_2d` | 161 | 2D superconductor DFT dataset |
| `supercon_chem` | 16414 | Superconductor chemical formula dataset |
| `vacancydb` | 464 | Vacancy formation energy dataset |
| `halide_peroskites` | 229 | Halide perovskite dataset |
| `aflow2` | 400k | AFLOW dataset |
| `mxene275` | 275 | MXene dataset |
| `cccbdb` | 1333 | CCCBDB dataset |
| `cfid_3d` | 55723 | Various 3D materials properties in JARVIS-DFT database computed with OptB88vdW and TBmBJ methods with CFID |
| `raw_files` | 144895 | Figshare links to download raw calculations VASP files from JARVIS-DFT |

Expand Down Expand Up @@ -80,82 +88,4 @@ df = pd.DataFrame(d)
print(df)
```

## JARVIS-DFT

Description coming soon!

### JARVIS-Formation energy and bandgap

### JARVIS-2D Exfoliation energies

### JARVIS-MetaGGA (dielectric function and SLME, solar cells)

### JARVIS-STM and STEM

### JARVIS-WannierTB

### JARVIS-Elastic constants

### JARVIS-Topological materials (Spin-orbit Spillage)

### JARVIS-DFPT (Piezoelectric, IR, Raman, dielectric, BEC)

### JARVIS-BoltzTrap (Thermoelectrics coeff, eff. mass)

### JARVIS-Magnetic moments

### JARVIS-DFPT (Piezoelectric, IR, dielectric)

### JARVIS-EFG

### JARVIS-PBE0 and HSE06

### JARVIS-Heterostructure

### JARVIS-EDOS-PDOS

### JARVIS-Kpoint and cut-off

## JARVIS-FF

### Energetics

### Elastic constants

### Vacancy formation energy

### Surface energy and Wulff-plots

### Phonon DOS

## JARVIS-RAW Files

### JARVIS-DFT structure relaxation

### JARVIS-DFT Elastic constants/finite difference

### JARVIS-WannierTB

### JARVIS-STM and STEM

## External datasets used for ML training

### Materials project dataset

### QM9 dataset

### OQMD dataset

### AFLOW dataset

### Polymer genome dataset

### COD dataset

### OMDB dataset

### QMOF dataset

### C2DB dataset

### HPOV dataset
2 changes: 1 addition & 1 deletion jarvis/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
"""Version number."""

__version__ = "2024.8.10"
__version__ = "2024.8.30"

import os

Expand Down
2 changes: 1 addition & 1 deletion jarvis/analysis/structure/spacegroup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
try:
import spglib
except Exception as exp:
print(exp)
# print(exp)
pass
# from numpy import gcd
# from math import gcd
Expand Down
5 changes: 4 additions & 1 deletion jarvis/core/atoms.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1776,16 +1776,19 @@ def make_supercell_matrix(self, scaling_matrix):

new_sites = []
new_elements = []
for site, el in zip(self.cart_coords, self.elements):
new_props = []
for site, el, p in zip(self.cart_coords, self.elements, self.props):
for v in c_lat:
new_elements.append(el)
tmp = site + v
new_sites.append(tmp)
new_props.append(p)
return Atoms(
lattice_mat=new_lattice.lattice(),
elements=new_elements,
coords=new_sites,
cartesian=True,
props=new_props,
)

def make_supercell(self, dim=[2, 2, 2]):
Expand Down
16 changes: 15 additions & 1 deletion jarvis/db/figshare.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -328,7 +328,21 @@ def get_db_info():
"https://figshare.com/ndownloader/files/40750811",
"vacancydb.json",
"Obtaining vacancy dataset 464...",
"https://arxiv.org/abs/2205.08366",
"https://doi.org/10.1063/5.0135382",
],
# https://doi.org/10.6084/m9.figshare.25832614
"surfacedb": [
"https://figshare.com/ndownloader/files/46355689",
"surface_db_dd.json",
"Obtaining vacancy dataset 607...",
"https://doi.org/10.1039/D4DD00031E",
],
# https://doi.org/10.6084/m9.figshare.25832614
"interfacedb": [
"https://figshare.com/ndownloader/files/46355692",
"interface_db_dd.json",
"Obtaining vacancy dataset 607...",
"https://doi.org/10.1039/D4DD00031E",
],
# Contains repeats
# https://doi.org/10.6084/m9.figshare.23206193
Expand Down
2 changes: 1 addition & 1 deletion setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@

setup(
name="jarvis-tools",
version="2024.8.10",
version="2024.8.30",
long_description=long_d,
install_requires=[
"numpy>=1.20.1",
Expand Down
Loading