From 08624c1ff0865002f1fc0469794609b3f232efdc Mon Sep 17 00:00:00 2001 From: Kamal Choudhary Date: Mon, 19 Jul 2021 07:41:01 -0400 Subject: [PATCH] Develop (#189) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. Co-authored-by: tavazza Co-authored-by: knc6 --- jarvis/__init__.py | 2 +- jarvis/ai/descriptors/cfid.py | 65 +++++++++++++++++++------- jarvis/analysis/defects/surface.py | 12 ++++- jarvis/core/atoms.py | 2 +- jarvis/core/magpie.json | 1 + jarvis/core/specie.py | 23 +++++++-- jarvis/db/figshare.py | 7 +++ jarvis/io/zeopp/inputs.py | 2 +- jarvis/tests/testfiles/ai/test_desc.py | 4 +- setup.py | 2 +- 10 files changed, 92 insertions(+), 28 deletions(-) create mode 100644 jarvis/core/magpie.json diff --git a/jarvis/__init__.py b/jarvis/__init__.py index a15d6a8e..8ef7228e 100644 --- a/jarvis/__init__.py +++ b/jarvis/__init__.py @@ -1,2 +1,2 @@ """Version number.""" -__version__ = "2021.07.10" +__version__ = "2021.07.18" diff --git a/jarvis/ai/descriptors/cfid.py b/jarvis/ai/descriptors/cfid.py index 880741b1..7882ba1f 100644 --- a/jarvis/ai/descriptors/cfid.py +++ b/jarvis/ai/descriptors/cfid.py @@ -110,7 +110,6 @@ https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.2.083801 """ from jarvis.analysis.structure.neighbors import NeighborsAnalysis -from jarvis.core.specie import Specie from jarvis.core.specie import get_descrp_arr_name import numpy as np from math import log @@ -118,6 +117,54 @@ from jarvis.core.specie import Specie +def get_chem_only_descriptors( + formula="Al2O3", + extra=[], + mean_only=False, + max_only=False, + min_only=False, + source="cfid", +): + """Get jarvis_cfid or magpie descriptors for each formula.""" + s = Composition.from_string(formula) + el_dict = s.to_dict() + arr = [] + sum = 0 + for k, v in el_dict.items(): + sum += v + des = v * Specie(k, source=source).get_descrp_arr + arr.append(des) + names = list(Specie("H", source=source)._data["H"].keys()) + if mean_only: + chem = np.mean(np.array(arr), axis=0) / sum + names = ["Mean_" + source + "_" + str(n) for n in names] + elif max_only: + chem = np.max(np.array(arr), axis=0) / sum + names = ["Max_" + source + "_" + str(n) for n in names] + elif min_only: + chem = np.min(np.array(arr), axis=0) / sum + names = ["Min_" + source + "_" + str(n) for n in names] + else: + chem = ( + list(np.mean(np.array(arr), axis=0) / sum) + + list(np.max(np.array(arr), axis=0) / sum) + + list(np.min(np.array(arr), axis=0) / sum) + ) + chem = np.array(chem) + names = ( + ["Mean_" + source + "_" + str(n) for n in names] + + ["Max_" + source + "_" + str(n) for n in names] + + ["Min_" + source + "_" + str(n) for n in names] + ) + chem = list(chem) + for ii, i in enumerate(extra): + chem.append(i) + nm = "extra_" + str(ii) + names.append(nm) + chem = np.array(chem) + return chem, names + + class CFID(object): """Convert Atoms class into 1557 descriptors.""" @@ -1836,22 +1883,6 @@ def feat_names(): return names -def get_chem_only_descriptor(formula="Al2O3"): - """Get 438 descriptors for a chemical formula.""" - s = Composition.from_string(formula) - # print (formula,s) - el_dict = s.to_dict() - arr = [] - tot = 0 - for k, v in el_dict.items(): - tot += v - des = v * Specie(k).get_descrp_arr - arr.append(des) - mean_chem = np.mean(np.array(arr), axis=0) / tot - names = feat_names()[0:438] - return mean_chem, names - - """ if __name__ == "__main__": box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]] diff --git a/jarvis/analysis/defects/surface.py b/jarvis/analysis/defects/surface.py index 5711f390..6290e6e4 100644 --- a/jarvis/analysis/defects/surface.py +++ b/jarvis/analysis/defects/surface.py @@ -35,6 +35,7 @@ def __init__( atoms=None, indices=[0, 0, 1], layers=3, + thickness=25, vacuum=18.0, tol=1e-10, from_conventional_structure=True, @@ -48,6 +49,8 @@ def __init__( layers: Number of surface layers + thickness: Provide thickness instead of layers + vacuum: vacuum padding tol: tolerance during dot product @@ -63,6 +66,8 @@ def __init__( self.tol = tol self.vacuum = vacuum self.layers = layers + self.thickness = thickness + # Note thickness overwrites layers def to_dict(self): """Convert to a dictionary.""" @@ -141,7 +146,12 @@ def make_surface(self): elements=atoms.elements, cartesian=True, ) - + if self.thickness is not None and (self.thickness) > 0: + self.layers = int(self.thickness / new_atoms.lattice.c) + 1 + # dims=get_supercell_dims(new_atoms,enforce_c_size=self.thickness) + # print ('dims=',dims,self.layers) + # surf_atoms = new_atoms.make_supercell_matrix([1, 1, dims[2]]) + # print('self.layers',self.layers,self.thickness,new_atoms.lattice.c) surf_atoms = new_atoms.make_supercell_matrix([1, 1, self.layers]) # print("supercell_cart_coords", surf_atoms.frac_coords) diff --git a/jarvis/core/atoms.py b/jarvis/core/atoms.py index 24962dce..09b0555a 100644 --- a/jarvis/core/atoms.py +++ b/jarvis/core/atoms.py @@ -1,7 +1,7 @@ """This module provides classes to specify atomic structure.""" import numpy as np from jarvis.core.composition import Composition -from jarvis.core.specie import Specie +from jarvis.core.specie import Specie, atomic_numbers_to_symbols from jarvis.core.lattice import Lattice, lattice_coords_transformer from collections import OrderedDict from jarvis.core.utils import get_counts diff --git a/jarvis/core/magpie.json b/jarvis/core/magpie.json new file mode 100644 index 00000000..fa694567 --- /dev/null +++ b/jarvis/core/magpie.json @@ -0,0 +1 @@ +{"H": {"AtomicWeight": 1.00794, "Column": 1.0, "CovalentRadius": 31.0, "Electronegativity": 2.2, "GSbandgap": 7.853, "GSmagmom": 0.0, "GSvolume_pa": 6.615, "MeltingT": 14.01, "MendeleevNumber": 92.0, "NUnfilled": 1.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 0.0, "NpValence": 0.0, "NsUnfilled": 1.0, "NsValence": 1.0, "Number": 1.0, "Row": 1.0, "SpaceGroupNumber": 194.0}, "He": {"AtomicWeight": 4.002602, "Column": 18.0, "CovalentRadius": 28.0, "Electronegativity": -9999, "GSbandgap": 18.098, "GSmagmom": 0.0, "GSvolume_pa": 12.305, "MeltingT": -9999, "MendeleevNumber": 98.0, "NUnfilled": 0.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 0.0, "NpValence": 0.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 2.0, "Row": 1.0, "SpaceGroupNumber": 225.0}, "Li": {"AtomicWeight": 6.941, "Column": 1.0, "CovalentRadius": 128.0, "Electronegativity": 0.98, "GSbandgap": 0.0, "GSmagmom": 0.0, "GSvolume_pa": 16.5933333333, "MeltingT": 453.69, "MendeleevNumber": 1.0, "NUnfilled": 1.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 0.0, "NpValence": 0.0, "NsUnfilled": 1.0, "NsValence": 1.0, "Number": 3.0, "Row": 2.0, "SpaceGroupNumber": 229.0}, "Be": {"AtomicWeight": 9.012182, "Column": 2.0, "CovalentRadius": 96.0, "Electronegativity": 1.57, "GSbandgap": 0.0, "GSmagmom": 0.0, "GSvolume_pa": 7.89, "MeltingT": 1560.0, "MendeleevNumber": 67.0, "NUnfilled": 0.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 0.0, "NpValence": 0.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 4.0, "Row": 2.0, "SpaceGroupNumber": 194.0}, "B": {"AtomicWeight": 10.811, "Column": 13.0, "CovalentRadius": 84.0, "Electronegativity": 2.04, "GSbandgap": 1.524, "GSmagmom": 0.0, "GSvolume_pa": 7.1725, "MeltingT": 2348.0, "MendeleevNumber": 72.0, "NUnfilled": 5.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 5.0, "NpValence": 1.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 5.0, "Row": 2.0, "SpaceGroupNumber": 166.0}, "C": {"AtomicWeight": 12.0107, "Column": 14.0, "CovalentRadius": 76.0, "Electronegativity": 2.55, "GSbandgap": 4.496, "GSmagmom": 0.0, "GSvolume_pa": 5.64, "MeltingT": 3823.0, "MendeleevNumber": 77.0, "NUnfilled": 4.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 4.0, "NpValence": 2.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 6.0, "Row": 2.0, "SpaceGroupNumber": 194.0}, "N": {"AtomicWeight": 14.0067, "Column": 15.0, "CovalentRadius": 71.0, "Electronegativity": 3.04, "GSbandgap": 6.437, "GSmagmom": 0.0, "GSvolume_pa": 14.76875, "MeltingT": 63.05, "MendeleevNumber": 82.0, "NUnfilled": 3.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 3.0, "NpValence": 3.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 7.0, "Row": 2.0, "SpaceGroupNumber": 194.0}, "O": {"AtomicWeight": 15.9994, "Column": 16.0, "CovalentRadius": 66.0, "Electronegativity": 3.44, "GSbandgap": 0.0, "GSmagmom": 0.0, "GSvolume_pa": 9.105, "MeltingT": 54.8, "MendeleevNumber": 87.0, "NUnfilled": 2.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 2.0, "NpValence": 4.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 8.0, "Row": 2.0, "SpaceGroupNumber": 12.0}, "F": {"AtomicWeight": 18.9984032, "Column": 17.0, "CovalentRadius": 57.0, "Electronegativity": 3.98, "GSbandgap": 1.97, "GSmagmom": 0.0, "GSvolume_pa": 9.7075, "MeltingT": 53.5, "MendeleevNumber": 93.0, "NUnfilled": 1.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 1.0, "NpValence": 5.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 9.0, "Row": 2.0, "SpaceGroupNumber": 15.0}, "Ne": {"AtomicWeight": 20.1791, "Column": 18.0, "CovalentRadius": 58.0, "Electronegativity": -9999, "GSbandgap": 13.088, "GSmagmom": 0.0, "GSvolume_pa": 12.64, "MeltingT": 24.56, "MendeleevNumber": 99.0, "NUnfilled": 0.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 0.0, "NpValence": 6.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 10.0, "Row": 2.0, "SpaceGroupNumber": 225.0}, "Na": {"AtomicWeight": 22.98976928, "Column": 1.0, "CovalentRadius": 166.0, "Electronegativity": 0.93, "GSbandgap": 0.0, "GSmagmom": 0.0, "GSvolume_pa": 29.2433333333, "MeltingT": 370.87, "MendeleevNumber": 2.0, "NUnfilled": 1.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 0.0, "NpValence": 0.0, "NsUnfilled": 1.0, "NsValence": 1.0, "Number": 11.0, "Row": 3.0, "SpaceGroupNumber": 229.0}, "Mg": {"AtomicWeight": 24.305, "Column": 2.0, "CovalentRadius": 141.0, "Electronegativity": 1.31, "GSbandgap": 0.0, "GSmagmom": 0.0, "GSvolume_pa": 22.89, "MeltingT": 923.0, "MendeleevNumber": 68.0, "NUnfilled": 0.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 0.0, "NpValence": 0.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 12.0, "Row": 3.0, "SpaceGroupNumber": 194.0}, "Al": {"AtomicWeight": 26.9815386, "Column": 13.0, "CovalentRadius": 121.0, "Electronegativity": 1.61, "GSbandgap": 0.0, "GSmagmom": 0.0, "GSvolume_pa": 16.48, "MeltingT": 933.47, "MendeleevNumber": 73.0, "NUnfilled": 5.0, "NdUnfilled": 0.0, "NdValence": 0.0, "NfUnfilled": 0.0, "NfValence": 0.0, "NpUnfilled": 5.0, "NpValence": 1.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 13.0, "Row": 3.0, "SpaceGroupNumber": 225.0}, "Si": {"AtomicWeight": 28.0855, "Column": 14.0, "CovalentRadius": 111.0, "Electronegativity": 1.9, "GSbandgap": 0.773, 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"GSbandgap": 0.0, "GSmagmom": 0.3180036375, "GSvolume_pa": 18.08, "MeltingT": -9999, "MendeleevNumber": -9999, "NUnfilled": 0.0, "NdUnfilled": 0.0, "NdValence": 10.0, "NfUnfilled": 0.0, "NfValence": 14.0, "NpUnfilled": 0.0, "NpValence": 0.0, "NsUnfilled": 0.0, "NsValence": 2.0, "Number": 112.0, "Row": 7.0, "SpaceGroupNumber": -9999}} \ No newline at end of file diff --git a/jarvis/core/specie.py b/jarvis/core/specie.py index 5ffb6d0a..93a36c8d 100644 --- a/jarvis/core/specie.py +++ b/jarvis/core/specie.py @@ -7,6 +7,7 @@ from jarvis.core.utils import digitize_array from collections import defaultdict from collections.abc import Iterable +from jarvis.db.jsonutils import loadjson el_chem_json_file = str( os.path.join(os.path.dirname(__file__), "Elements.json") @@ -15,6 +16,10 @@ chem_data = json.load(el_chem_json) el_chem_json.close() +chem_data_magpie = loadjson( + os.path.join(os.path.dirname(__file__), "magpie.json") +) + el_chrg_json_file = str( os.path.join(os.path.dirname(__file__), "element_charge.json") ) @@ -72,10 +77,19 @@ class Specie(object): """ - def __init__(self, symbol=""): + def __init__(self, symbol="", source="cfid"): """Initialize with periodic table element.""" self.symbol = symbol - self._data = chem_data + if source == "cfid": + # Cite reference: + # https://doi.org/10.1103/PhysRevMaterials.2.083801 + self._data = chem_data + elif source == "magpie": + # Cite reference: + # https://doi.org/10.1038/npjcompumats.2016.28 + self._data = chem_data_magpie + else: + raise ValueError("Option not available.", source) @property def Z(self): @@ -124,8 +138,9 @@ def get_descrp_arr(self): arr: array value """ arr = [] - - d = chem_data[self.symbol] + # print ('self._data') + d = self._data[self.symbol] + # d = chem_data[self.symbol] arr = [] for k, v in d.items(): arr.append(v) diff --git a/jarvis/db/figshare.py b/jarvis/db/figshare.py index 209b7769..fe244f4f 100644 --- a/jarvis/db/figshare.py +++ b/jarvis/db/figshare.py @@ -178,6 +178,13 @@ def get_db_info(): "https://www.nature.com/articles/sdata201686", ], # https://figshare.com/account/projects/100325/articles/14962356 + "pdbbind_core": [ + "https://ndownloader.figshare.com/files/28874802", + "pdbbind_2015_core.json", + "Obtaining PDBBind dataset 195...", + "https://doi.org/10.1093/bioinformatics/btu626", + ], + # https://figshare.com/account/projects/100325/articles/14962356 "pdbbind": [ "https://ndownloader.figshare.com/files/28816368", "pdbbind_2015.json", diff --git a/jarvis/io/zeopp/inputs.py b/jarvis/io/zeopp/inputs.py index c6888eb6..04f5c827 100644 --- a/jarvis/io/zeopp/inputs.py +++ b/jarvis/io/zeopp/inputs.py @@ -19,7 +19,7 @@ def get_porosity(atoms=None, network_cmd="./network", output_file=None): largest_included_sphere = lines[0].split()[1] largest_free_sphere = lines[0].split()[2] largest_included_sphere_along_free_sphere_path = lines[0].split()[3] - os.close(filename) + os.close(new_file) os.remove(filename) return ( largest_included_sphere, diff --git a/jarvis/tests/testfiles/ai/test_desc.py b/jarvis/tests/testfiles/ai/test_desc.py index ac6517b2..e87bf45b 100644 --- a/jarvis/tests/testfiles/ai/test_desc.py +++ b/jarvis/tests/testfiles/ai/test_desc.py @@ -2,11 +2,11 @@ from jarvis.ai.descriptors.coulomb import coulomb_matrix from jarvis.ai.descriptors.elemental import get_element_fraction_desc from jarvis.core.atoms import Atoms -from jarvis.ai.descriptors.cfid import get_chem_only_descriptor +from jarvis.ai.descriptors.cfid import get_chem_only_descriptors def test_formula_only(): - desc, names = get_chem_only_descriptor("Al2O3") + desc, names = get_chem_only_descriptors("Al2O3", source="magpie") def test_desc(): diff --git a/setup.py b/setup.py index fde9885c..e0375960 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ setup( name="jarvis-tools", - version="2021.07.10", + version="2021.07.18", long_description=long_d, install_requires=[ "numpy>=1.19.5",