Develop (#326)

* Fix repo. * Update databases.md * Update databases.md * Update databases.md * Version update.
usnistgov · Sep 7, 2024 · 7f2f2bf · 7f2f2bf
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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",