usnistgov · knc6 · Aug 26, 2024 · Mar 28, 2024 · Mar 28, 2024 · Mar 31, 2024
diff --git a/docs/tutorials.md b/docs/tutorials.md
@@ -1,5 +1,9 @@
 # Tutorials
 
+## Quickstart with Jupyter/Google-colab notebooks: https://github.com/usnistgov/aims2024_workshop
+
+More detailed tutorials below:
+
 ## How to analyze an atomic structure
 
 Atomic structure act as an input to multiple simulations such as for

diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,6 +1,6 @@
 """Version number."""
 
-__version__ = "2024.5.10"
+__version__ = "2024.8.10"
 
 import os
 

diff --git a/jarvis/analysis/defects/surface.py b/jarvis/analysis/defects/surface.py
@@ -225,7 +225,7 @@ def make_surface(self):
 
         frac_coords = new_atoms.frac_coords
 
-        frac_coords[:] = frac_coords[:] % 1
+        # frac_coords[:] = frac_coords[:] % 1
         new_atoms = Atoms(
             lattice_mat=latest_lat,
             elements=surf_atoms.elements,

diff --git a/jarvis/analysis/structure/spacegroup.py b/jarvis/analysis/structure/spacegroup.py
@@ -1,19 +1,23 @@
 """Modules for handling crystallographic Spacegroup related operations."""
+
 from functools import reduce
 from jarvis.core.lattice import Lattice
 from jarvis.core.atoms import Atoms
-import spglib
 from jarvis.core.specie import Specie
 import numpy as np
 from numpy import sin, cos
 import itertools
-
-# from fractions import gcd
 from jarvis.core.utils import gcd
+import os
 
+try:
+    import spglib
+except Exception as exp:
+    print(exp)
+    pass
 # from numpy import gcd
 # from math import gcd
-import os
+# from fractions import gcd
 
 
 def unique_rows_2(a):

diff --git a/jarvis/db/figshare.py b/jarvis/db/figshare.py
@@ -12,12 +12,13 @@
 import json
 import requests
 from jarvis.db.jsonutils import loadjson
-from jarvis.io.vasp.outputs import Vasprun
-from jarvis.io.vasp.inputs import Poscar
-from jarvis.io.wannier.outputs import WannierHam
 from tqdm import tqdm
 import matplotlib.image as mpimg
-from jarvis.analysis.stm.tersoff_hamann import TersoffHamannSTM
+
+# from jarvis.analysis.stm.tersoff_hamann import TersoffHamannSTM
+# from jarvis.io.wannier.outputs import WannierHam
+# from jarvis.io.vasp.outputs import Vasprun
+# from jarvis.io.vasp.inputs import Poscar
 
 # import matplotlib.pyplot as plt
 # plt.switch_backend("agg")
@@ -79,7 +80,7 @@ def get_db_info():
             # "https://ndownloader.figshare.com/files/26809760",
             "id_prop.json",
             "Obtaining ALIGNN-FF training DB 300k ...",
-            "https://arxiv.org/abs/2209.05554",
+            "https://doi.org/10.1039/D2DD00096B",
         ],
         "mp_3d_2020": [
             "https://ndownloader.figshare.com/files/26791259",
@@ -598,6 +599,8 @@ def make_stm_from_prev_parchg(
     jid="JVASP-667", bias="Negative", filename="stm_image.png", min_size=10
 ):
     """Make STM images from previously calculated PARVHG files for 2D."""
+    from jarvis.analysis.stm.tersoff_hamann import TersoffHamannSTM
+
     fls = data("raw_files")
     for i in fls["STM"]:
         zip_name = jid + "_" + bias + ".zip"
@@ -619,6 +622,9 @@ def make_stm_from_prev_parchg(
 
 def get_wann_electron(jid="JVASP-816"):
     """Download electron WTBH if available."""
+    from jarvis.io.wannier.outputs import WannierHam
+    from jarvis.io.vasp.inputs import Poscar
+
     w = ""
     ef = ""
     fls = data("raw_files")
@@ -650,6 +656,7 @@ def get_wann_phonon(jid="JVASP-1002", factor=15.633302):
     """Download phonon WTBH if available."""
     # Requires phonopy
     from jarvis.io.phonopy.outputs import get_phonon_tb
+    from jarvis.io.vasp.outputs import Vasprun
 
     fls = data("raw_files")
 

diff --git a/setup.py b/setup.py
@@ -12,20 +12,20 @@
 
 setup(
     name="jarvis-tools",
-    version="2024.5.10",
+    version="2024.8.10",
     long_description=long_d,
     install_requires=[
         "numpy>=1.20.1",
         "scipy>=1.5.0",
         "matplotlib>=3.0.0",
-        "spglib>=1.14.1",
         "joblib>=0.14.1",
         "requests>=2.23.0",
         "toolz>=0.9.0",
         "xmltodict>=0.11.0",
         "tqdm>=4.41.1",
         "scikit-learn",
-        "inflect",
+        # "spglib>=1.14.1",
+        # "inflect",
         # "mkdocs-material>=9.0.5",
         # "markdown>=3.2.1",
         # "absl-py==1.4.0",
@@ -57,15 +57,15 @@
         "jarvis": ["LICENSE.rst"],
     },
     extras_require={
-        "ai": [
-            "torch",
-            "dgl",
-            "keras",
-            "tensorflow",
-            "flask",
-            "pandas",
-        ],
-        "babel": ["openbabel", "pybel"],
+        # "ai": [
+        #     "torch",
+        #     "dgl",
+        #     "keras",
+        #     "tensorflow",
+        #     "flask",
+        #     "pandas",
+        # ],
+        # "babel": ["openbabel", "pybel"],
         "doc": ["sphinx>=1.3.1", "sphinx-rtd-theme>=0.1.8"],
     },
     author="Kamal Choudhary",