From 7f2f2bf6eb92288bac30cf32486fe702f3861c6f Mon Sep 17 00:00:00 2001 From: Kamal Choudhary Date: Sat, 7 Sep 2024 16:21:38 -0400 Subject: [PATCH] Develop (#326) * Fix repo. * Update databases.md * Update databases.md * Update databases.md * Version update. --- docs/databases.md | 94 ++++--------------------- jarvis/__init__.py | 2 +- jarvis/analysis/structure/spacegroup.py | 2 +- jarvis/core/atoms.py | 5 +- jarvis/db/figshare.py | 16 ++++- setup.py | 2 +- 6 files changed, 34 insertions(+), 87 deletions(-) diff --git a/docs/databases.md b/docs/databases.md index 9c57678d..f8b153b0 100644 --- a/docs/databases.md +++ b/docs/databases.md @@ -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 | @@ -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 | @@ -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 | @@ -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 diff --git a/jarvis/__init__.py b/jarvis/__init__.py index 42742fda..34d2ef41 100644 --- a/jarvis/__init__.py +++ b/jarvis/__init__.py @@ -1,6 +1,6 @@ """Version number.""" -__version__ = "2024.8.10" +__version__ = "2024.8.30" import os diff --git a/jarvis/analysis/structure/spacegroup.py b/jarvis/analysis/structure/spacegroup.py index 719f3964..f797071c 100644 --- a/jarvis/analysis/structure/spacegroup.py +++ b/jarvis/analysis/structure/spacegroup.py @@ -13,7 +13,7 @@ try: import spglib except Exception as exp: - print(exp) + # print(exp) pass # from numpy import gcd # from math import gcd diff --git a/jarvis/core/atoms.py b/jarvis/core/atoms.py index 7c6ca144..a31a1e38 100644 --- a/jarvis/core/atoms.py +++ b/jarvis/core/atoms.py @@ -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]): diff --git a/jarvis/db/figshare.py b/jarvis/db/figshare.py index 929bd6f8..078a7a1f 100644 --- a/jarvis/db/figshare.py +++ b/jarvis/db/figshare.py @@ -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 diff --git a/setup.py b/setup.py index 5e570c37..47400a7a 100644 --- a/setup.py +++ b/setup.py @@ -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",