DGL Graph. (#153)

* Update graphs.py

* Uncertainty module added. (#124)

* Uncertainty module added.

* Adding quantile lgbm code.

* Adding quantile lgbm code.

* Adding quantile lgbm code.

* Adding test for quantile lgbm code

* Adding quantile lgbm code.

* Magnetic setup and Uncertainty AI module update. (#125)

* Version change.

* Version change, magmom atoms added, classification models save updates.

* Update and rename LICENSE to LICENSE.rst

* Delete jarvisdft.xsl

* Delete jarvisff.xsl

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Added OQMD, MP, QM9 CFID datasets and VASP API XML update for phonons. (#130)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* Update config.yml

* Update README.rst

* 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

* XRD DB making bug fix, scattering.json update. (#131)

* 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.

* Develop (#134)

* 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.

* Update README.rst

* Wannier update.

* Version update.

* VASP task update.

* Wannier update (#136)

* 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.

* 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.

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

dev-requirements.txt

@@ -18,8 +18,8 @@ pennylane>=0.14.1
 codecov >=2.1.11
 torch >=1.8.0
 keras >=2.4.3
-tensorflow==2.4.0  
+tensorflow>=2.4.0  
 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__ = "2021.3.11"
+__version__ = "2021.3.12"

jarvis/core/atoms.py

@@ -588,7 +588,7 @@ def get_all_neighbors(self, r=5, bond_tol=0.15):
                 for i in indices[within_r]:
                     if d[i] > bond_tol:
                         neighbors[i].append([i, j, d[i], image])
-        return np.array(neighbors)
+        return np.array(neighbors, dtype="object")
 
     @property
     def raw_distance_matrix(self):

jarvis/core/graphs.py

@@ -9,6 +9,7 @@
 import warnings
 from typing import List, Tuple
 from jarvis.core.atoms import Atoms
+from collections import defaultdict
 
 try:
     import torch
@@ -54,26 +55,54 @@ def __init__(
 
     @staticmethod
     def atom_dgl_multigraph(
-        atoms=None, cutoff=8.0, max_neighbors=12, atom_features="cgcnn"
+        atoms=None,
+        cutoff=8.0,
+        max_neighbors=12,
+        atom_features="cgcnn",
+        enforce_undirected=False,
+        max_attempts=3,
+        id=None,
     ):
         """Obtain a DGLGraph for Atoms object."""
         all_neighbors = atoms.get_all_neighbors(r=cutoff)
         # if a site has too few neighbors, increase the cutoff radius
         min_nbrs = min(len(neighborlist) for neighborlist in all_neighbors)
-        if min_nbrs < max_neighbors:
+        # print('min_nbrs,max_neighbors=',min_nbrs,max_neighbors)
+        attempt = 0
+        while min_nbrs < max_neighbors:
+            print("extending cutoff radius!", attempt, cutoff, id)
             lat = atoms.lattice
             r_cut = max(cutoff, lat.a, lat.b, lat.c)
-            return Graph.atom_dgl_multigraph(
-                atoms, r_cut, max_neighbors, atom_features
-            )
+            attempt += 1
+            if attempt >= max_attempts:
+                atoms = atoms.make_supercell([2, 2, 2])
+                print(
+                    "Making supercell, exceeded,attempts",
+                    max_attempts,
+                    "cutoff",
+                    r_cut,
+                    id,
+                )
+            cutoff = r_cut
+            all_neighbors = atoms.get_all_neighbors(r=cutoff)
+            min_nbrs = min(len(neighborlist) for neighborlist in all_neighbors)
+            # return Graph.atom_dgl_multigraph(
+            #    atoms, r_cut, max_neighbors, atom_features
+            # )
 
         # build up edge list
-        # NOTE: currently there's no guarantee
-        # that this creates undirected graphs
-        # An undirected solution would build the full edge
-        # list where nodes are
-        # keyed by (index, image), and ensure
-        # each edge has a complementary edge
+        # Currently there's no guarantee that this creates undirected graphs
+        # An undirected solution would build the full edge list where nodes are
+        # keyed by (index,image), and ensure each edge has a complementary edge
+
+        # indeed,JVASP-59628 is an example of a calculation where this produces
+        # a graph where one site has no incident edges!
+
+        # build an edge dictionary u -> v
+        # so later we can run through the dictionary
+        # and remove all pairs of edges
+        # so what's left is the odd ones out
+        edges = defaultdict(list)
 
         u, v, r = [], [], []
         for site_idx, neighborlist in enumerate(all_neighbors):
@@ -83,18 +112,37 @@ def atom_dgl_multigraph(
 
             ids = np.array([nbr[1] for nbr in neighborlist])
             distances = np.array([nbr[2] for nbr in neighborlist])
+            c = np.array([nbr[3] for nbr in neighborlist])
 
             # find the distance to the k-th nearest neighbor
             max_dist = distances[max_neighbors - 1]
 
             # keep all edges out to the neighbor shell of the k-th neighbor
             ids = ids[distances <= max_dist]
+            c = c[distances <= max_dist]
             distances = distances[distances <= max_dist]
 
             u.append([site_idx] * len(ids))
             v.append(ids)
             r.append(distances)
 
+            # keep track of cell-resolved edges
+            # to enforce undirected graph construction
+            for dst, cell_id in zip(ids, c):
+                u_key = f"{site_idx}-(0.0, 0.0, 0.0)"
+                v_key = f"{dst}-{tuple(cell_id)}"
+                edge_key = tuple(sorted((u_key, v_key)))
+                edges[edge_key].append((site_idx, dst))
+
+        if enforce_undirected:
+            # add complementary edges to unpaired edges
+            for edge_pair in edges.values():
+                if len(edge_pair) == 1:
+                    src, dst = edge_pair[0]
+                    u.append(dst)  # swap the order!
+                    v.append(src)
+                    r.append(atoms.raw_distance_matrix[src, dst])
+
         u = torch.tensor(np.hstack(u))
         v = torch.tensor(np.hstack(v))
         r = torch.tensor(np.hstack(r)).type(torch.get_default_dtype())
@@ -334,33 +382,38 @@ def __init__(
         self,
         structures,
         targets,
+        ids=None,
         cutoff=8.0,
         maxrows=np.inf,
         atom_features="atomic_number",
         transform=None,
+        enforce_undirected=False,
         max_neighbors=12,
     ):
         """Initialize the class."""
         self.graphs = []
         self.labels = []
+        self.ids = []
 
-        for idx, (structure, target) in enumerate(
-            tqdm(zip(structures, targets))
+        for idx, (structure, target, id) in enumerate(
+            tqdm(zip(structures, targets, ids))
         ):
 
             if idx >= maxrows:
                 break
-
             a = Atoms.from_dict(structure)
             g = Graph.atom_dgl_multigraph(
                 a,
                 atom_features=atom_features,
+                enforce_undirected=enforce_undirected,
                 cutoff=cutoff,
                 max_neighbors=max_neighbors,
+                id=id,
             )
 
             self.graphs.append(g)
             self.labels.append(target)
+            self.ids.append(id)
 
         self.labels = torch.tensor(self.labels).type(torch.get_default_dtype())
         self.transform = transform

jarvis/db/figshare.py

@@ -185,7 +185,9 @@ def get_request_data(
         # f = open(zfile, "wb")
         # f.write(r.content)
         # f.close()
+    print("Loading the zipfile...")
     data = json.loads(zipfile.ZipFile(path).read(js_tag))
+    print("Loading completed.")
 
     #    with zipfile.ZipFile(zfile, "r") as zipObj:
     #        # zipObj.extract(path)

jarvis/tests/testfiles/core/test_graph.py

@@ -57,11 +57,13 @@ def test_dataset():
     d = data("dft_2d")
     x = []
     y = []
+    z = []
     for i in d[0:100]:
         if i["formation_energy_peratom"] != "na":
             x.append(i["atoms"])
             y.append(i["formation_energy_peratom"])
-    s = StructureDataset(x, y)
+            z.append(i["jid"])
+    s = StructureDataset(x, y, ids=z)
 
 
 # test_graph()

setup.py

@@ -11,7 +11,7 @@
 
 setup(
     name="jarvis-tools",
-    version="2021.3.11",
+    version="2021.3.12",
     long_description=long_d,
     install_requires=[
         "numpy>=1.18.5",