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 <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>

jarvis/__init__.py

@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2021.07.10"
+__version__ = "2021.07.18"

jarvis/ai/descriptors/cfid.py

@@ -110,14 +110,61 @@
 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
 from jarvis.core.composition import Composition
 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]]

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)
 

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

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)

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",

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,

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():

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",