Develop (#196)

* 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. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]>
usnistgov · Aug 19, 2021 · d261bba · d261bba
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diff --git a/README.rst b/README.rst
@@ -54,8 +54,6 @@ Documentation
 
       https://jarvis-tools.readthedocs.io
 
-      https://jarvis-materials-design.github.io/dbdocs/
-
 
 Capabilities
 -----------------------------------------

diff --git a/docs/source/databases.rst b/docs/source/databases.rst
@@ -6,7 +6,7 @@ Databases
 ====================     =========================   ======================================================= 
 Database name            Number of data-points       Description                                             
 ====================     =========================   ======================================================= 
-``dft_3d``               48527                       Various 3D materials properties in JARVIS-DFT database  
+``dft_3d``               55723                       Various 3D materials properties in JARVIS-DFT database  
                                                      computed with OptB88vdW and TBmBJ methods             
 ``dft_2d``               1079                        Various 2D materials properties in JARVIS-DFT database  
                                                      computed with OptB88vdW                                
@@ -37,6 +37,8 @@ Database name            Number of data-points       Description
 ``pdbbind``              11189                       Bio-molecular complexes database from PDBBind v2015
 ``qmof``                 18321                       Bandgaps and total energies of metal organic frameowrks
                                                      in QMOF database
+``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
 ====================     =========================   ======================================================= 

diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2021.08.05"
+__version__ = "2021.08.18"
diff --git a/jarvis/analysis/defects/substitutions.py b/jarvis/analysis/defects/substitutions.py
@@ -0,0 +1,70 @@
+"""Modules for making point-defect substituions."""
+from jarvis.analysis.structure.spacegroup import Spacegroup3D
+from jarvis.core.utils import rand_select
+from jarvis.core.atoms import Atoms, get_supercell_dims
+
+
+def generate_defect(
+    atoms=None,
+    enforce_c_size=10.0,
+    on_conventional_cell=False,
+    extend=1,
+    subs_element="Al",
+    selected_element=None,
+):
+    """Provide function to generate substitution defects."""
+    if on_conventional_cell:
+        atoms = Spacegroup3D(atoms).conventional_standard_structure
+    if enforce_c_size is not None:
+        dims = get_supercell_dims(
+            atoms, enforce_c_size=enforce_c_size, extend=extend
+        )
+        supercell_size = [dims[0], dims[1], dims[2]]
+        # atoms = atoms.make_supercell(supercell_size)
+    spg = Spacegroup3D(atoms)
+    wyckoffs = spg._dataset["wyckoffs"]
+    atoms.props = wyckoffs
+    supercell = atoms.make_supercell(supercell_size)
+    props = rand_select(supercell.props)
+    subs = []
+    # print(props)
+    for i, j in props.items():
+        info = {}
+        elements = supercell.elements.copy()
+        if selected_element is not None:
+            if elements[j] == selected_element:
+
+                elements[j] = subs_element
+
+                a = Atoms(
+                    lattice_mat=supercell.lattice_mat,
+                    coords=supercell.coords,
+                    cartesian=supercell.cartesian,
+                    elements=elements,
+                )
+                info["props"] = props
+                info["atoms"] = atoms.to_dict()
+                info["defect_atoms"] = a.to_dict()
+                info["supercell_size"] = list(supercell_size)
+                # print(a.elements)
+                subs.append(info)
+        else:
+            elements[j] = subs_element
+            a = Atoms(
+                lattice_mat=supercell.lattice_mat,
+                coords=supercell.coords,
+                cartesian=supercell.cartesian,
+                elements=elements,
+            )
+            info["props"] = props
+            info["atoms"] = atoms.to_dict()
+            info["defect_atoms"] = a.to_dict()
+            info["supercell_size"] = list(supercell_size)
+            # print(a.elements)
+            subs.append(info)
+    return subs
+
+
+"""
+x = generate_defect(atoms=a, selected_element="Br")
+"""
diff --git a/jarvis/core/atoms.py b/jarvis/core/atoms.py
@@ -642,8 +642,22 @@ def check_polar(self):
             polar = False
         return polar
 
+    def strain_atoms(self, strain):
+        """Apply volumetric strain to atoms."""
+        # strains=np.arange(0.80,1.2,0.02)
+        s = np.eye(3) + np.array(strain) * np.eye(3)
+        lattice_mat = np.array(self.lattice_mat)
+        lattice_mat = np.dot(lattice_mat, s)
+        return Atoms(
+            lattice_mat=lattice_mat,
+            elements=self.elements,
+            coords=self.coords,
+            cartesian=self.cartesian,
+        )
+
     def apply_strain(self, strain):
         """Apply a strain(e.g. 0.01, [0,0,.01]) to the lattice."""
+        print("Use strain_atoms instead.")
         s = (1 + np.array(strain)) * np.eye(3)
         self.lattice_mat = np.dot(self.lattice_mat.T, s).T
 

diff --git a/jarvis/core/image.py b/jarvis/core/image.py
@@ -9,7 +9,7 @@
     from skimage.util import random_noise
     from skimage.filters import gaussian
     from PIL import Image as PIL_Image
-except Exception as exp:
+except Exception:
     # print("Install skimage, Pillow.", exp)
     pass
 # from scipy.ndimage import rotate

diff --git a/jarvis/db/figshare.py b/jarvis/db/figshare.py
@@ -35,16 +35,16 @@ def get_db_info():
         ],
         # https://doi.org/10.6084/m9.figshare.6815699
         "dft_3d": [
-            "https://ndownloader.figshare.com/files/28034994",
-            "d3-5-16-2021.json",
-            "Obtaining 3D dataset 48k ...",
+            "https://ndownloader.figshare.com/files/29204826",
+            "jdft_3d-8-18-2021.json",
+            "Obtaining 3D dataset 55k ...",
             "https://www.nature.com/articles/s41524-020-00440-1",
         ],
         # https://doi.org/10.6084/m9.figshare.6815699
         "cfid_3d": [
-            "https://ndownloader.figshare.com/files/26808914",
-            "d3-3-12-2021.json",
-            "Obtaining 3D dataset 43k ...",
+            "https://ndownloader.figshare.com/files/29205201",
+            "cfid_3d-8-18-2021.json",
+            "Obtaining 3D dataset 55k ...",
             "https://www.nature.com/articles/s41524-020-00440-1",
         ],
         # https://doi.org/10.6084/m9.figshare.14213522
@@ -78,9 +78,9 @@ def get_db_info():
         ],
         # https://doi.org/10.6084/m9.figshare.14745327
         "edos_pdos": [
-            "https://ndownloader.figshare.com/files/28501764",
-            "edos-up_pdos-elast_interp-6-19-2021.json",
-            "Interpolated electronic total dos spin-up dataset 48k...",
+            "https://ndownloader.figshare.com/files/29216859",
+            "edos-up_pdos-elast_interp-8-18-2021.json",
+            "Interpolated electronic total dos spin-up dataset 55k...",
             "https://www.nature.com/articles/s41524-020-00440-1",
         ],
         # https://doi.org/10.6084/m9.figshare.13054247

diff --git a/jarvis/tests/testfiles/analysis/defects/test_subs.py b/jarvis/tests/testfiles/analysis/defects/test_subs.py
@@ -0,0 +1,16 @@
+from jarvis.analysis.defects.substitutions import generate_defect
+from jarvis.core.atoms import Atoms
+from jarvis.io.vasp.inputs import Poscar
+import os
+
+
+def test_subs():
+    box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]]
+    coords = [[0, 0, 0], [0.25, 0.25, 0.25]]
+    elements = ["Al", "Al"]
+    Si = Atoms(lattice_mat=box, coords=coords, elements=elements)
+    v = generate_defect(atoms=Si)
+
+
+# test_2d()
+# test_vacancy()
diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 
 setup(
     name="jarvis-tools",
-    version="2021.08.05",
+    version="2021.08.18",
     long_description=long_d,
     install_requires=[
         "numpy>=1.19.5",
-Original file line number
+Diff line change
@@ Expand Up / @@ -54,8 +54,6 @@ Documentation @@
           https://jarvis-tools.readthedocs.io
-          https://jarvis-materials-design.github.io/dbdocs/
     Capabilities
     -----------------------------------------
@@ Expand Down @@