Version update (#164)

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Increase coverage. (#137)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* Wannier TB for phonons (#138)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Create CODE_OF_CONDUCT.md (#139)

* Update README.rst

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Poscar format fix. (#142)

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Minor fix in figshare and spectrum.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor fix in figshare and spectrum. (#143)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor update.

* Update figshare.py

* Fix build.

* Update README.rst

* docs update.

* Setup requirement change.

* Update version tag. (#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

* Update README.rst

* develop (#147)

* Update version tag. (#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <[email protected]>

* develop (#147)

* Update version tag. (#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <[email protected]>

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Version update.

* Version update.

* Adding Qiskit.

* Adding Qiskit.

* Fix travis.

* Fix travis.

* Fix travis.

* Fix travis.

* VASP outputs bug fix.

* Optics module and Dos module of VASP fixed.

* Fixing commit.

* Lint fix.

* Update inputs.py

* Version update.

* README update.

* Graph and dataset update.

* Graph and dataset update.

* Graph and dataset update.

* Graph module update.

* More datasets added.

* Update .travis.yml

* Update .travis.yml

* Exclude tequila tests.

* Exclude tequila tests.

* Extra tests.

* Pytest-cov added.

* Update action_build.yml

* Update action_build.yml

* Covergae update.

* Covergae update.

* StructureDataset test added.

* Graph tests fixed.

* Figshare update.

* STM image links added.

* Update test_figshare.py

* Update test_figshare.py

* Update .travis.yml

* Update .travis.yml

* Cache github action attempt.

* DB update.

* Update action.

* DB update.

* Figshare test update.

* JARVIS-FF DB added.

* Try to increase coverage.

* Polymer genome added.

* Graph update.

* Graph update.

* Graph update.

* Figshare update.

* Version update.

* Figshare update.

* Hot encoded species.

* STEM with Convolution and Pyprismatic added.

* STEM Conv update.

* Atoms module update.

* Lorentzian fix.

* Digitized features added.

* Graph angle,prdf added. QE parser update.

* Update outputs.py

* Graph angle update and cif2cell added.

* Reduced formula fix and linting fix.

* Test minor fix.

* Graph tests update.

* Pytestfix.

* See also check url in xml

* See also check url in xml

* Phonopy run update.

* Graph update with torch angle.

* Get all neighbors routine bug fix.

* Figshare lint fix.

* Version update, IR extended, graph torch fix.

* Fix IR pytest.

* IR test fix.

* Cache graph dataset (#161)

* modify graph StructureDataset to enable/disable computation of atomistic line graph.

* fix line length setting in black configuration and fix jarvis.core.specie and jarvis.core.graphs

* pin pennylane version to 0.14.1 in GH build action.

* update graph dataloader test.

* fix pennylane version pinning and fix missing pandas.DataFrame in dataloader test.

* bump version number.

* README update.

* Bandgap based on occupation tolerance added to Vasprun.

* id_tag update.

* Version update

* Remove cif2cell dependence.

Co-authored-by: Brian DeCost <[email protected]>

README.rst

@@ -82,17 +82,6 @@ or
 
 For detailed instructions, please see `Installation instructions <https://github.com/usnistgov/jarvis/blob/master/Installation.rst>`__
 
-**Do not** install like this:
-
-.. |ss| raw:: html
-
-   <strike>
-
-.. |se| raw:: html
-
-   </strike>
-
-|ss| pip install jarvis |se| 
 
 Example function
 -----------------

dev-requirements.txt

@@ -19,8 +19,9 @@ codecov >=2.1.11
 torch >=1.8.0
 keras >=2.4.3
 tensorflow>=2.4.0
-cif2cell
+cif2cell==2.0.0a3
+PyCifRW==4.4
 pytest >=6.2.2
 pytest-cov >=2.11.1
 pytest-xdist>=2.2.1
-bokeh>=2.3.0
+bokeh>=2.3.0

jarvis/__init__.py

@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2021.4.21"
+__version__ = "2021.4.28"

jarvis/core/graphs.py

@@ -520,6 +520,7 @@ def __init__(
         transform=None,
         line_graph=False,
         classification=False,
+        id_tag="jid",
     ):
         """Pytorch Dataset for atomistic graphs.
 
@@ -533,7 +534,7 @@ def __init__(
         self.line_graph = line_graph
 
         self.labels = self.df[target]
-        self.ids = self.df["jid"]
+        self.ids = self.df[id_tag]
         self.labels = torch.tensor(self.df[target]).type(
             torch.get_default_dtype()
         )

jarvis/io/vasp/outputs.py

@@ -1044,12 +1044,9 @@ def gvectors(self, ikpt=1):
                 % (Gvec.shape[0], self._nplws[ikpt - 1], np.prod(self._ngrid))
             )
         else:
-            assert (
-                Gvec.shape[0] == self._nplws[ikpt - 1]
-            ), "No. of planewaves not consistent! %d %d %d" % (
-                Gvec.shape[0],
-                self._nplws[ikpt - 1],
-                np.prod(self._ngrid),
+            assert Gvec.shape[0] == self._nplws[ikpt - 1], (
+                "No. of planewaves not consistent! %d %d %d"
+                % (Gvec.shape[0], self._nplws[ikpt - 1], np.prod(self._ngrid),)
             )
         self._gvec = np.asarray(Gvec, dtype=int)
 
@@ -1375,6 +1372,40 @@ def get_indir_gap(self):
             gap = min(cat[:, nelect]) - max(cat[:, nelect - 1])
         return gap, cbm, vbm
 
+    def bandgap_occupation_tol(self, occu_tol=0.1):
+        """Get bandgap based on occupation tolerance."""
+        eigs = np.concatenate(
+            (self.eigenvalues[0][:, :, 0], self.eigenvalues[1][:, :, 0]),
+            axis=1,
+        )
+        occs = np.concatenate(
+            (self.eigenvalues[0][:, :, 1], self.eigenvalues[1][:, :, 1]),
+            axis=1,
+        )
+
+        vbm = -np.inf
+        vbm_kpoint = None
+        cbm = np.inf
+        cbm_kpoint = None
+        k = 0
+        for i, j in zip(eigs, occs):
+            k += 1
+            for (eigenval, occu) in zip(i, j):
+                if occu > occu_tol and eigenval > vbm:
+                    vbm = eigenval
+                    vbm_kpoint = k
+                elif occu <= occu_tol and eigenval < cbm:
+                    cbm = eigenval
+                    cbm_kpoint = k
+        return (
+            max(cbm - vbm, 0),
+            cbm,
+            vbm,
+            vbm_kpoint,
+            cbm_kpoint,
+            vbm_kpoint == cbm_kpoint,
+        )
+
     @property
     def fermi_velocities(self):
         """Get fermi velocities in m/s."""

jarvis/tests/testfiles/core/test_graph.py

@@ -1,8 +1,14 @@
 from jarvis.core.atoms import Atoms
-from jarvis.core.graphs import StructureDataset, Graph
+from jarvis.core.graphs import (
+    StructureDataset,
+    Graph,
+    prepare_dgl_batch,
+    prepare_line_graph_batch,
+)
 from jarvis.db.figshare import data
 import pandas as pd
 import os
+import torch
 
 test_pos = os.path.join(
     os.path.dirname(__file__),
@@ -15,14 +21,17 @@ def test_graph():
     from jarvis.db.figshare import get_jid_data
 
     atoms = Atoms.from_poscar(test_pos)
-    g = g = Graph.atom_dgl_multigraph(atoms=atoms, atom_features="cgcnn")
+    g = Graph.atom_dgl_multigraph(atoms=atoms, atom_features="cgcnn")
     atoms = Atoms.from_dict(get_jid_data("JVASP-664")["atoms"])
     feature_sets = ("atomic_number", "basic", "cfid", "cgcnn")
     for i in feature_sets:
         g = Graph.atom_dgl_multigraph(atoms=atoms, atom_features=i)
         g = Graph.atom_dgl_multigraph(atoms=atoms, atom_features=i)
         print(i, g)
+    batch = prepare_dgl_batch(torch.tensor([1, 1]))
+    batch = prepare_line_graph_batch(torch.tensor([1, 1, 1]))
     g = Graph.from_atoms(atoms=atoms, features="atomic_number")
+    gnx = g.to_networkx()
     g = Graph.from_atoms(atoms=atoms, features="atomic_number")
     g = Graph.from_atoms(atoms=atoms, features="atomic_fraction")
     g = Graph.from_atoms(
@@ -79,8 +88,14 @@ def test_dataset():
         )
         graphs.append(g)
 
-    s = StructureDataset(d, graphs, "formation_energy_peratom")
+    s = StructureDataset(
+        d, graphs, "formation_energy_peratom", line_graph=True
+    )
     col = s.collate
+    col1 = s.collate_line_graph
+    ix = s[0]
+    sz = len(s)
+    s_std = s.setup_standardizer([1, 2])
 
 
 # test_graph()

jarvis/tests/testfiles/io/vasp/test_outputs.py

@@ -79,14 +79,12 @@
 )
 non_spinpol_vrun = Vasprun(
     filename=os.path.join(
-        os.path.dirname(__file__),
-        "vasprun.xml.JVASP-23436",
+        os.path.dirname(__file__), "vasprun.xml.JVASP-23436",
     )
 )
 vasp544_mbj_optics_vrun = Vasprun(
     filename=os.path.join(
-        os.path.dirname(__file__),
-        "vasprun.xml.JVASP-97577",
+        os.path.dirname(__file__), "vasprun.xml.JVASP-97577",
     )
 )
 opt_vrun = Vasprun(
@@ -226,11 +224,7 @@ def test_chgcar():
         chg.is_spin_polarized(),
         chg.is_spin_orbit(),
         np.array(chg.chg).shape,
-    ) == (
-        True,
-        False,
-        (4, 56, 56, 56),
-    )
+    ) == (True, False, (4, 56, 56, 56),)
     td = chg.to_dict()
     fd = Chgcar.from_dict(td)
 
@@ -241,11 +235,7 @@ def test_locpot():
         loc.is_spin_polarized(),
         loc.is_spin_orbit(),
         np.array(chg.chg).shape,
-    ) == (
-        False,
-        False,
-        (4, 56, 56, 56),
-    )
+    ) == (False, False, (4, 56, 56, 56),)
     vac = loc.vac_potential()[0]
     assert round(vac, 2) == round(7.62302803577618, 2)
 
@@ -262,6 +252,8 @@ def test_locpot():
 def test_vrun():
     # print ('gapp',round(vrun.get_indir_gap,2))
     assert (round(vrun.get_indir_gap[0], 2)) == (0.73)
+    gap2 = vrun.bandgap_occupation_tol()
+    assert round(gap2[0], 2) == 0.73
     assert (round(vrun.get_dir_gap, 2)) == (2.62)
     vrun.get_bandstructure(kpoints_file_path=band_kp, plot=True)
     assert (round(opt_vrun.get_dir_gap, 2)) == (2.62)

setup.py

@@ -11,7 +11,7 @@
 
 setup(
     name="jarvis-tools",
-    version="2021.4.21",
+    version="2021.4.28",
     long_description=long_d,
     install_requires=[
         "numpy>=1.18.5",
@@ -23,7 +23,6 @@
         "toolz>=0.9.0",
         "xmltodict>=0.11.0",
         "tqdm>=4.41.1",
-        "cif2cell>=2.0.0a3",
     ],
     package_data={
         "jarvis.core": [