Develop (#185)

* 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.

jarvis/__init__.py

@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2021.07.04"
+__version__ = "2021.07.05"

jarvis/ai/descriptors/elemental.py

@@ -0,0 +1,14 @@
+"""Module to get elemnt fraction based array for a formula."""
+# Maximum upto 103 elements
+import numpy as np
+from jarvis.core.composition import Composition
+from jarvis.core.specie import Specie
+
+
+def get_element_fraction_desc(formula="SiO2", max_nelements=103):
+    x = np.zeros(max_nelements)
+    fracs = Composition.from_string(formula).atomic_fraction
+    for i, j in fracs.items():
+        # -1 because python array srats from 0
+        x[Specie(i).Z - 1] = j
+    return x

jarvis/core/composition.py

@@ -113,11 +113,14 @@ def reduced_formula(self):
             Z[i] = reduced[i]
         for specie, count in Z.items():
             if float(count).is_integer():
-                form = form + specie + str(int(count))
+                if count == 1:
+                    form = form + specie
+                else:
+                    form = form + specie + str(int(count))
             else:
                 form = form + specie + str(count)
 
-        return form.replace("1", "")
+        return form  # .replace("1", "")
 
     @property
     def formula(self):

jarvis/tests/testfiles/ai/test_desc.py

@@ -1,5 +1,6 @@
 from jarvis.ai.descriptors.cfid import CFID
 from jarvis.ai.descriptors.coulomb import coulomb_matrix
+from jarvis.ai.descriptors.elemental import get_element_fraction_desc
 from jarvis.core.atoms import Atoms
 
 
@@ -3141,6 +3142,7 @@ def test_desc():
     z = coulomb_matrix(Si)
     assert len(z) == 100
     assert round(z[0], 2) == round(281.62894609, 2)
+    get_element_fraction_desc()
 
 
 # test_desc()

setup.py

@@ -11,7 +11,7 @@
 
 setup(
     name="jarvis-tools",
-    version="2021.07.04",
+    version="2021.07.05",
     long_description=long_d,
     install_requires=[
         "numpy>=1.19.5",
@@ -70,6 +70,7 @@
     packages=find_packages(),
     # long_description=open(os.path.join(os.path.dirname(__file__), "README.rst")).read(),
     classifiers=[
+
         "Programming Language :: Python :: 3.6",
         "Development Status :: 4 - Beta",
         "Intended Audience :: Science/Research",