diff --git a/.github/workflows/action_build.yml b/.github/workflows/action_build.yml index 7c7c3ff6..d4e23ea4 100644 --- a/.github/workflows/action_build.yml +++ b/.github/workflows/action_build.yml @@ -9,8 +9,8 @@ jobs: matrix: os: ["ubuntu-latest"] steps: - - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 + - uses: actions/checkout@v3 + - uses: conda-incubator/setup-miniconda@v3 with: activate-environment: test environment-file: environment.yml diff --git a/.github/workflows/deploy_nist_pages.yml b/.github/workflows/deploy_nist_pages.yml index c15488a9..1027c11e 100644 --- a/.github/workflows/deploy_nist_pages.yml +++ b/.github/workflows/deploy_nist_pages.yml @@ -43,8 +43,8 @@ jobs: matrix: os: ["ubuntu-latest"] steps: - - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 + - uses: actions/checkout@v3 + - uses: conda-incubator/setup-miniconda@v3 with: activate-environment: test environment-file: environment.yml diff --git a/docs/databases.md b/docs/databases.md index 16bc6ef2..60d51dab 100644 --- a/docs/databases.md +++ b/docs/databases.md @@ -8,71 +8,72 @@ | Database name | Number of data-points | Description | |-------------------|-----------------------|---------------------------------------------------------------------------------------------------------------------------------------| -| `dft_3d` | 75993 | Various 3D materials properties in JARVIS-DFT database computed with OptB88vdW and TBmBJ methods | +| `AGRA_CHO` | 214 | AGRA CHO catalyst dataset | +| `AGRA_COOH` | 280 | AGRA COOH catalyst dataset | +| `AGRA_CO` | 193 | AGRA CO catalyst dataset | +| `AGRA_OH` | 875 | AGRA OH catalyst dataset | +| `AGRA_O` | 1000 | AGRA Oxygen catalyst dataset | +| `aflow2` | 400k | AFLOW dataset | +| `alex_pbe_1d_all` | 100k | Alexandria DB all 1D materials with PBE | +| `alex_pbe_2d_all` | 200k | Alexandria DB all 2D materials with PBE | +| `alex_pbe_3d_all` | 5 million | Alexandria DB all 3D materials with PBE | +| `alex_pbe_hull` | 116k | Alexandria DB convex hull stable materials with PBE functional | +| `alex_pbesol_3d_all` | 500k | Alexandria DB all 3D materials with PBEsol | +| `alex_scan_3d_all` | 500k | Alexandria DB all 3D materials with SCAN | +| `alignn_ff_db` | 307113 | Energy per atom, forces and stresses for ALIGNN-FF trainig for 75k materials. | +| `arXiv` | 1796911 | arXiv dataset 1.8 million title, abstract and id dataset | +| `arxiv_summary` | 137927 | arXiv summary dataset | +| `c2db` | 3514 | Various properties in C2DB database | +| `cccbdb` | 1333 | CCCBDB dataset | +| `cfid_3d` | 55723 | Various 3D materials properties in JARVIS-DFT database computed with OptB88vdW and TBmBJ methods with CFID | +| `cod` | 431778 | Atomic structures from crystallographic open database | +| `dft_2d_2021` | 1079 | Various 2D materials properties in JARVIS-DFT database computed with OptB88vdW | | `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 | -| `stm` | 1132 | 2D materials STM images in JARVIS-STM database | -| `wtbh_electron` | 1440 | 3D and 2D materials Wannier tight-binding Hamiltonian dtaabase for electrons with spin-orbit coupling in JARVIS-WTB (Keyword: 'WANN') | -| `wtbh_phonon` | 15502 | 3D and 2D materials Wannier tight-binding Hamiltonian for phonons at Gamma with finite difference (Keyword:FD-ELAST) | -| `jff` | 2538 | Various 3D materials properties in JARVIS-FF database computed with several force-fields | -| `alignn_ff_db` | 307113 | Energy per atom, forces and stresses for ALIGNN-FF trainig for 75k materials. | +| `dft_3d` | 75993 | Various 3D materials properties in JARVIS-DFT database computed with OptB88vdW and TBmBJ methods | | `edos_pdos` | 48469 | Normalized electron and phonon density of states with interpolated values and fixed number of bins | +| `halide_peroskites` | 229 | Halide perovskite dataset | +| `hmof` | 137651 | Hypothetical MOF database | +| `hopv` | 4855 | Various properties of molecules in HOPV15 dataset | +| `interfacedb` | 593 | Interface property dataset | +| `jff` | 2538 | Various 3D materials properties in JARVIS-FF database computed with several force-fields | +| `m3gnet_mpf_1.5mil` | 1.5 million | 1.5 million structures and their energy, forces and stresses in MP | +| `m3gnet_mpf` | 168k | 168k structures and their energy, forces and stresses in MP | +| `megnet2` | 133k | 133k materials and their formation energy in MP | | `megnet` | 69239 | Formation energy and bandgaps of 3D materials properties in Materials project database as on 2018, used in megnet | +| `mlearn` | 1730 | Machine learning force-field for elements datasets | | `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 | -| `qm9_std_jctc` | 130829 | Various properties of molecules in QM9 database | -| `qm9_dgl` | 130829 | Various properties of molecules in QM9 dgl database | -| `cod` | 431778 | Atomic structures from crystallographic open database | +| `mxene275` | 275 | MXene dataset | +| `ocp100k` | 149886 | Open Catalyst 100000 training, rest validation and test dataset | +| `ocp10k` | 59886 | Open Catalyst 10000 training, rest validation and test dataset | +| `ocp_all` | 510214 | Open Catalyst 460328 training, rest validation and test dataset | +| `omdb` | 12500 | Bandgaps for organic polymers in OMDB database | | `oqmd_3d_no_cfid` | 817636 | Formation energies and bandgaps of 3D materials from OQMD database | | `oqmd_3d` | 460k | CFID descriptors for 460k materials in OQMD | -| `omdb` | 12500 | Bandgaps for organic polymers in OMDB database | -| `alex_pbe_hull` | 116k | Alexandria DB convex hull stable materials with PBE functional | -| `alex_pbe_3d_all` | 5 million | Alexandria DB all 3D materials with PBE | -| `alex_pbe_2d_all` | 200k | Alexandria DB all 2D materials with PBE | -| `alex_pbe_1d_all` | 100k | Alexandria DB all 1D materials with PBE | -| `alex_scan_3d_all` | 500k | Alexandria DB all 3D materials with SCAN | -| `alex_pbesol_3d_all` | 500k | Alexandria DB all 3D materials with PBEsol | -| `hopv` | 4855 | Various properties of molecules in HOPV15 dataset | -| `pdbbind` | 11189 | Bio-molecular complexes database from PDBBind v2015 | | `pdbbind_core` | 195 | Bio-molecular complexes database from PDBBind core | +| `pdbbind` | 11189 | Bio-molecular complexes database from PDBBind v2015 | +| `polymer_genome` | 1073 | Electronic bandgap and diecltric constants of crystall ine polymer in polymer genome database | +| `qe_tb` | 829574 | Various 3D materials properties in JARVIS-QETB database | +| `qm9_dgl` | 130829 | Various properties of molecules in QM9 dgl database | +| `qm9_std_jctc` | 130829 | Various properties of molecules in QM9 database | | `qmof` | 20425 | Bandgaps and total energies of metal organic frameowrks in QMOF database | -| `hmof` | 137651 | Hypothetical MOF database | +| `raw_files` | 144895 | Figshare links to download raw calculations VASP files from JARVIS-DFT | | `snumat` | 10481 | Bandgaps with hybrid functional | -| `arxiv_summary` | 137927 | arXiv summary dataset | -| `arXiv` | 1796911 | arXiv dataset 1.8 million title, abstract and id dataset | | `ssub` | 1726 | SSUB formation energy for chemical formula dataset | -| `mlearn` | 1730 | Machine learning force-field for elements datasets | -| `ocp10k` | 59886 | Open Catalyst 10000 training, rest validation and test dataset | -| `ocp100k` | 149886 | Open Catalyst 100000 training, rest validation and test dataset | -| `ocp_all` | 510214 | Open Catalyst 460328 training, rest validation and test dataset | +| `stm` | 1132 | 2D materials STM images in JARVIS-STM database | +| `supercon_2d` | 161 | 2D superconductor DFT dataset | +| `supercon_3d` | 1058 | 3D superconductor DFT dataset | +| `supercon_chem` | 16414 | Superconductor chemical formula dataset | +| `surfacedb` | 607 | Surface property dataset | | `tinnet_N` | 329 | TinNet Nitrogen catalyst dataset | -| `tinnet_O` | 747 | TinNet Oxygen catalyst dataset | | `tinnet_OH` | 748 | TinNet OH group catalyst dataset | -| `AGRA_O` | 1000 | AGRA Oxygen catalyst dataset | -| `AGRA_OH` | 875 | AGRA OH catalyst dataset | -| `AGRA_CO` | 193 | AGRA CO catalyst dataset | -| `AGRA_CHO` | 214 | AGRA CHO catalyst dataset | -| `AGRA_COOH` | 280 | AGRA COOH catalyst 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 | +| `tinnet_O` | 747 | TinNet Oxygen catalyst dataset | +| `twod_matpd` | 6351 | Formation energy and bandgaps of 2D materials properties in 2DMatPedia database | +| `vacancydb` | 464 | Vacancy formation energy dataset | +| `wtbh_electron` | 1440 | 3D and 2D materials Wannier tight-binding Hamiltonian dtaabase for electrons with spin-orbit coupling in JARVIS-WTB (Keyword: 'WANN') | +| `wtbh_phonon` | 15502 | 3D and 2D materials Wannier tight-binding Hamiltonian for phonons at Gamma with finite difference (Keyword:FD-ELAST) | + All these datasets can be obtained using jarvis-tools as follows, exception to `stm`, `wtbh_electron`, `wtbh_phonon` which have their own diff --git a/jarvis/__init__.py b/jarvis/__init__.py index bccb3347..aae434fd 100644 --- a/jarvis/__init__.py +++ b/jarvis/__init__.py @@ -1,6 +1,6 @@ """Version number.""" -__version__ = "2024.10.10" +__version__ = "2024.10.30" import os diff --git a/jarvis/core/lattice.py b/jarvis/core/lattice.py index a7d21802..04da1e37 100644 --- a/jarvis/core/lattice.py +++ b/jarvis/core/lattice.py @@ -63,7 +63,7 @@ def lat_lengths(self): """Return lattice vectors' lengths.""" return [ round(i, 6) - for i in (np.sqrt(np.sum(self._lat ** 2, axis=1)).tolist()) + for i in (np.sqrt(np.sum(self._lat**2, axis=1)).tolist()) ] # return [round(np.linalg.norm(v), 6) for v in self._lat] @@ -239,7 +239,9 @@ def reciprocal_lattice_crystallographic(self): """Return reciprocal Lattice without 2 * pi.""" return Lattice(self.reciprocal_lattice().matrix / (2 * np.pi)) - def get_points_in_sphere(self, frac_points, center, r): + def get_points_in_sphere( + self, frac_points, center, r, distance_vector=False + ): """ Find all points within a sphere from the point. @@ -283,11 +285,21 @@ def get_points_in_sphere(self, frac_points, center, r): tmp_img = cart_images[None, :, :, :, :] coords = cart_coords[:, None, None, None, :] + tmp_img coords -= center[None, None, None, None, :] + dist_vect = coords coords **= 2 d_2 = np.sum(coords, axis=4) # Determine which points are within `r` of `center` - within_r = np.where(d_2 <= r ** 2) + within_r = np.where(d_2 <= r**2) + if distance_vector: + return ( + shifted_coords[within_r], + np.sqrt(d_2[within_r]), + indices[within_r[0]], + images[within_r[1:]], + dist_vect[within_r], + ) + return ( shifted_coords[within_r], np.sqrt(d_2[within_r]), @@ -316,9 +328,7 @@ def find_all_matches(self, other_lattice, ltol=1e-5, atol=1): ] c_a, c_b, c_c = (cart[i] for i in inds) f_a, f_b, f_c = (frac[i] for i in inds) - l_a, l_b, l_c = ( - np.sum(c ** 2, axis=-1) ** 0.5 for c in (c_a, c_b, c_c) - ) + l_a, l_b, l_c = (np.sum(c**2, axis=-1) ** 0.5 for c in (c_a, c_b, c_c)) def get_angles(v1, v2, l1, l2): x = np.inner(v1, v2) / l1[:, None] / l2 diff --git a/setup.py b/setup.py index 119e5dbf..46b7fb6b 100644 --- a/setup.py +++ b/setup.py @@ -12,7 +12,7 @@ setup( name="jarvis-tools", - version="2024.10.10", + version="2024.10.30", long_description=long_d, install_requires=[ "numpy>=1.20.1", @@ -81,7 +81,6 @@ "Programming Language :: Python :: 3.6", "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", - "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Topic :: Scientific/Engineering", ],