Version update. (#165)

* 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.

* Version update.

* Version update.

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

jarvis/__init__.py

@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2021.4.28"
+__version__ = "2021.04.29"

jarvis/core/graphs.py

@@ -52,6 +52,7 @@ def nearest_neighbor_edges(
     cutoff=8,
     max_neighbors=12,
     id=None,
+    use_canonize=False,
 ):
     """Construct k-NN edge list."""
     # returns List[List[Tuple[site, distance, index, image]]]
@@ -72,7 +73,11 @@ def nearest_neighbor_edges(
         attempt += 1
 
         return nearest_neighbor_edges(
-            atoms=atoms, cutoff=r_cut, max_neighbors=max_neighbors, id=id
+            atoms=atoms,
+            use_canonize=use_canonize,
+            cutoff=r_cut,
+            max_neighbors=max_neighbors,
+            id=id,
         )
     # build up edge list
     # NOTE: currently there's no guarantee that this creates undirected graphs
@@ -110,7 +115,10 @@ def nearest_neighbor_edges(
             src_id, dst_id, src_image, dst_image = canonize_edge(
                 site_idx, dst, (0, 0, 0), tuple(image)
             )
-            edges[(src_id, dst_id)].add(dst_image)
+            if use_canonize:
+                edges[(src_id, dst_id)].add(dst_image)
+            else:
+                edges[(site_idx, dst)].add(tuple(image))
 
     return edges
 
@@ -194,6 +202,7 @@ def atom_dgl_multigraph(
         max_attempts=3,
         id: Optional[str] = None,
         compute_line_graph: bool = True,
+        use_canonize: bool = False,
     ):
         """Obtain a DGLGraph for Atoms object."""
         if neighbor_strategy == "k-nearest":
@@ -202,6 +211,7 @@ def atom_dgl_multigraph(
                 cutoff=cutoff,
                 max_neighbors=max_neighbors,
                 id=id,
+                use_canonize=use_canonize,
             )
         else:
             raise ValueError("Not implemented yet", neighbor_strategy)

setup.py

@@ -11,7 +11,7 @@
 
 setup(
     name="jarvis-tools",
-    version="2021.4.28",
+    version="2021.04.29",
     long_description=long_d,
     install_requires=[
         "numpy>=1.18.5",