Develop (#236)

* 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. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (#197) * 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]> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. * Add installation tests (#214) * QE inputs, XANES, GHAction updates. (#210) * 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. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (#197) * 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]> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> * Add installation tests * Fix codestyle * Fix codestyle with black * Add docstrings * Fix pydocstyle error * Update __init__.py * Update __init__.py Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> * Adding QE super. * Minor changes to QE module, atoms xyz fix. * Adding qe_tb info, and version update. * Update __init__.py * WIP super QE. * Working version of ScSi. * QE inputs and task update. * Add master super. * Add master super. * Lint fix. * Lint fix. * Minor fix. * ET update. * Fix ET test. * Update sanitize atoms. * Additonal checks on supercond. * Debye bug fix. * Pressure in QE Super. * Version fix, publication update, supercond workflow update. * Lint fix. * Tensorboard fix. * Tensorboard fix. * Tensorboard fix. * Melting temp fix. * Update vasp.py (#234) * Local tetra tmp. * Version update. * Lint fix. * HSE06 Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> Co-authored-by: Saurav Maheshkar <[email protected]>
usnistgov · May 7, 2022 · 2c2241d · 2c2241d
1 parent 217eb37
commit 2c2241d
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diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -49,7 +49,7 @@ Jinja2==3.0.3
 joblib==1.1.0
 jsonschema==4.3.1
 julia==0.5.6
-keras==2.7.0
+keras
 Keras-Preprocessing==1.1.2
 kiwisolver==1.3.2
 libclang==12.0.0
@@ -63,7 +63,7 @@ mpmath==1.2.1
 multitasking==0.0.10
 networkx==2.6.3
 ntlm-auth==1.5.0
-numpy==1.21.0
+numpy==1.20.0
 oauthlib==3.1.1
 opencv-python==4.5.4.60
 opt-einsum==3.3.0
@@ -72,7 +72,7 @@ pandas==1.3.5
 pbr==5.8.0
 PennyLane==0.14.1
 phonopy==2.10.0
-Pillow==9.0.0
+Pillow==9.0.1
 pluggy==1.0.0
 ply==3.11
 protobuf==3.19.1
@@ -125,10 +125,10 @@ sphinxcontrib-serializinghtml==1.1.5
 stevedore==3.5.0
 symengine==0.8.1
 sympy==1.9
-tensorboard==2.7.0
+tensorboard
 tensorboard-data-server==0.6.1
 tensorboard-plugin-wit==1.8.0
-tensorflow==2.7.0
+tensorflow==2.8.0
 tensorflow-estimator==2.7.0
 tensorflow-io-gcs-filesystem==0.23.1
 termcolor==1.1.0
@@ -148,4 +148,4 @@ Werkzeug==2.0.2
 wrapt==1.13.3
 xmltodict==0.12.0
 yfinance==0.1.67
-zipp==3.6.0
+zipp==3.6.0
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -50,7 +50,7 @@ Jinja2==3.0.3
 joblib==1.1.0
 jsonschema==4.3.1
 julia==0.5.6
-keras==2.7.0
+keras
 Keras-Preprocessing==1.1.2
 kiwisolver==1.3.2
 libclang==12.0.0
@@ -64,7 +64,7 @@ mpmath==1.2.1
 multitasking==0.0.10
 networkx==2.6.3
 ntlm-auth==1.5.0
-numpy==1.21.0
+numpy==1.20.0
 oauthlib==3.1.1
 opencv-python==4.5.4.60
 opt-einsum==3.3.0
@@ -73,7 +73,7 @@ pandas==1.3.5
 pbr==5.8.0
 PennyLane==0.14.1
 #phonopy==2.10.0
-Pillow==9.0.0
+Pillow==9.0.1
 pluggy==1.0.0
 ply==3.11
 protobuf==3.19.1
@@ -127,7 +127,7 @@ sphinxcontrib-serializinghtml==1.1.5
 stevedore==3.5.0
 symengine==0.8.1
 sympy==1.9
-tensorboard==2.7.0
+tensorboard
 tensorboard-data-server==0.6.1
 tensorboard-plugin-wit==1.8.0
 tensorflow==2.7.0
@@ -150,4 +150,4 @@ Werkzeug==2.0.2
 wrapt==1.13.3
 xmltodict==0.12.0
 yfinance==0.1.67
-zipp==3.6.0
+zipp==3.6.0
diff --git a/docs/source/publications.rst b/docs/source/publications.rst
@@ -58,8 +58,28 @@ JARVIS-ML related
 
 [23. Enhancing materials property prediction by leveraging computational and experimental data using deep transfer learning, Nature Commun.](https://www.nature.com/articles/s41467-019-13297-w)
 
-[24. Atomistic Line Graph Neural Network for Improved Materials Property Predictions.](https://arxiv.org/abs/2106.01829)
+[24. Atomistic Line Graph Neural Network for Improved Materials Property Predictions, npj Computational Materials 7, 1 (2021)](https://www.nature.com/articles/s41524-021-00650-1)
+
+[25. Recent advances and applications of deep learning methods in materials science, npj Computational Materials 8, 1 (2022)](https://www.nature.com/articles/s41524-022-00734-6)
+
+
+[26. Graph neural network predictions of metal organic framework CO2 adsorption properties, Comp. Mat. Sci., 210, 111388 (2022)](https://www.sciencedirect.com/science/article/pii/S092702562200163X)
+
+[27. Data-Driven Multi-Scale Modeling and Optimization for Elastic Properties of Cubic Microstructures](https://link.springer.com/article/10.1007/s40192-022-00258-3)
+
+[28. Uncertainty Prediction for Machine Learning Models of Material Properties](https://pubs.acs.org/doi/abs/10.1021/acsomega.1c03752)
+
+[29. Cross-property deep transfer learning framework for enhanced predictive analytics on small materials data](https://www.nature.com/articles/s41467-021-26921-5)
+
+[30. Prediction of the Electron Density of States for Crystalline Compounds with Atomistic Line Graph Neural Networks (ALIGNN)](https://link.springer.com/article/10.1007/s11837-022-05199-y)
+
+[31. Designing High-Tc Superconductors with BCS-inspired Screening, Density Functional Theory and Deep-learning](https://arxiv.org/abs/2205.00060)
 
 JARVIS-QC related
 -----------------------------------------------------
-[25. Quantum Computation for Predicting Electron and Phonon Properties of Solids., J. Phys.: Cond. Matt.](https://iopscience.iop.org/article/10.1088/1361-648X/ac1154)
+[32. Quantum Computation for Predicting Electron and Phonon Properties of Solids., J. Phys.: Cond. Matt.](https://iopscience.iop.org/article/10.1088/1361-648X/ac1154)
+
+
+JARVIS-QETB related
+-----------------------------------------------------
+[33. Quantum Computation for Predicting Electron and Phonon Properties of Solids., J. Phys.: Cond. Matt.](https://iopscience.iop.org/article/10.1088/1361-648X/ac1154)
diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,5 +1,5 @@
 """Version number."""
-__version__ = "2022.01.10"
+__version__ = "2022.05.05"
 
 import os
 

diff --git a/jarvis/analysis/elastic/tensor.py b/jarvis/analysis/elastic/tensor.py
@@ -44,13 +44,94 @@ def reuss_modulus(self):
         )
         return [Kr, Gr]
 
+    def long_velocity(self, atoms=None):
+        """Longitudinal velocity using Navier equation."""
+        # density = atoms.density
+        weight = float(atoms.composition.weight)
+        volume = atoms.volume
+        mass_density = 1.6605e3 * weight / volume
+        avg_mod = self.average_modulus
+        k_vrh = avg_mod[0]
+        g_vrh = avg_mod[1]
+        # 1e9:= GPa to Pascal (kg/ms^2)
+        vel = np.sqrt(1e9 * (k_vrh + 4.0 / 3.0 * g_vrh) / mass_density)
+        return vel
+
+    def trans_velocity(self, atoms=None):
+        """Transverse velocity."""
+        avg_mod = self.average_modulus
+        g_vrh = avg_mod[1]
+        volume = atoms.volume
+        weight = float(atoms.composition.weight)
+        mass_density = 1.6605e3 * weight / volume
+        vel = np.sqrt(1e9 * g_vrh / mass_density)
+        return vel
+
+    def velocity_average(self, atoms=None):
+        """Average velocity."""
+        vt = self.trans_velocity(atoms=atoms)
+        vl = self.long_velocity(atoms=atoms)
+        return 1.0 / (
+            np.cbrt(
+                (1.0 / 3.0) * (2.0 / (vt * vt * vt) + 1.0 / (vl * vl * vl))
+            )
+        )
+
+    def debye_temperature(self, atoms=None):
+        """Debye temperature."""
+        const = 1.05457e-34 / 1.38065e-23  # (h/kb)
+        v0 = atoms.volume * 1e-30 / atoms.num_atoms
+        vl = self.long_velocity(atoms=atoms)
+        vt = self.trans_velocity(atoms=atoms)
+        vm = 3 ** (1.0 / 3.0) * (1 / vl ** 3 + 2 / vt ** 3) ** (-1.0 / 3.0)
+        theta = const * vm * (6 * np.pi ** 2 / v0) ** (1.0 / 3.0)
+        return theta
+
     @property
     def average_modulus(self):
         """Get average modulus."""
         return (
             np.array(self.voigt_modulus) + np.array(self.reuss_modulus)
         ) / 2
 
+    @property
+    def pugh_ratio_voigt(self):
+        """Get Voigt Pugh ratio."""
+        Kv, Gv = self.voigt_modulus
+        return Gv / Kv
+
+    @property
+    def pettifor_criteria(self):
+        """Get Pettifor criteria."""
+        c = self.et_tensor
+        return c[0][1] - c[3][3]
+
+    @property
+    def is_brittle(self):
+        """Check if brittle material."""
+        return self.pugh_ratio_voigt > 0.571 and self.pettifor_criteria < 0
+
+    @property
+    def is_ductile(self):
+        """Check if ductile material."""
+        return self.pugh_ratio_voigt < 0.571 and self.pettifor_criteria > 0
+
+    @property
+    def melting_temperature_metals(self):
+        """Get crude Melting temp. estimate."""
+        # https://doi.org/10.1016/0036-9748(84)90267-9
+        avg_mod = self.average_modulus
+        k_vrh = avg_mod[0]
+        return 607 + 9.3 * k_vrh
+
+    @property
+    def cauchy_pressure(self):
+        """Get Cauchy pressure."""
+        # >0 ionic bonding
+        # <0 covalent bonding
+        c = self.et_tensor
+        return c[0][1] - c[3][3]
+
     @property
     def poisson_ratio(self):
         """Get poisson's ratio."""

diff --git a/jarvis/core/atoms.py b/jarvis/core/atoms.py
@@ -870,7 +870,9 @@ def atomwise_angle_and_radial_distribution(
                 and nbor_info["dist"][in1][i] * nbor_info["dist"][in2][i] != 0
             ]
             ang_hist, ang_bins = np.histogram(
-                angles, bins=np.arange(1, nbins + 2, 1), density=False,
+                angles,
+                bins=np.arange(1, nbins + 2, 1),
+                density=False,
             )
             for jj, j in enumerate(angles):
                 actual_pangs[i, jj] = j
@@ -1648,13 +1650,13 @@ def pmg_to_atoms(pmg=""):
     )
 
 
-def ase_to_atoms(ase_atoms=""):
+def ase_to_atoms(ase_atoms="", cartesian=True):
     """Convert ase structure to Atoms."""
     return Atoms(
         lattice_mat=ase_atoms.get_cell(),
         elements=ase_atoms.get_chemical_symbols(),
         coords=ase_atoms.get_positions(),
-        #         pbc=True,
+        cartesian=cartesian,
     )
 
 

diff --git a/jarvis/core/utils.py b/jarvis/core/utils.py
@@ -17,6 +17,15 @@ def xml_to_dict(fname):
     return data
 
 
+def get_factors(x, start=2):
+    """Get factors of a number."""
+    facts = []
+    for i in range(start, x + 1):
+        if x % i == 0:
+            facts.append(i)
+    return facts
+
+
 def get_counts(array=["W", "W", "Mo", "Mo", "S", "S"]):
     """
     Get number of unique elements and their counts.
@@ -266,14 +275,7 @@ def digitize_array(values=[], max_len=10):
 
 
 def bond_angle(
-    dist1,
-    dist2,
-    bondx1,
-    bondx2,
-    bondy1,
-    bondy2,
-    bondz1,
-    bondz2,
+    dist1, dist2, bondx1, bondx2, bondy1, bondy2, bondz1, bondz2,
 ):
     """Get an angle."""
     nm = dist1 * dist2