Atomic neighbor list update (#158)

* 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.

* 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.

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

jarvis/__init__.py

@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2021.4.10"
+__version__ = "2021.4.18"

jarvis/core/atoms.py

@@ -193,6 +193,7 @@ def from_cif(
         if from_string == "":
             f = open(filename, "r")
             lines = f.read().splitlines()
+            # lines = [ii.encode('utf-8') for ii in f.read().splitlines()]
             f.close()
         else:
             lines = from_string.splitlines()
@@ -648,8 +649,8 @@ def get_all_neighbors(self, r=5, bond_tol=0.15):
         all_ranges = [np.arange(x, y) for x, y in zip(nmin, nmax)]
         matrix = self.lattice_mat
         neighbors = [list() for _ in range(len(self.cart_coords))]
-        all_fcoords = np.mod(self.frac_coords, 1)
-        coords_in_cell = np.dot(all_fcoords, matrix)
+        # all_fcoords = np.mod(self.frac_coords, 1)
+        coords_in_cell = self.cart_coords  # np.dot(all_fcoords, matrix)
         site_coords = self.cart_coords
         indices = np.arange(len(site_coords))
         for image in itertools.product(*all_ranges):
@@ -660,6 +661,7 @@ def get_all_neighbors(self, r=5, bond_tol=0.15):
             for (j, d, within_r) in zip(indices, all_dists, all_within_r):
                 for i in indices[within_r]:
                     if d[i] > bond_tol:
+                        # if d[i] > bond_tol and i!=j:
                         neighbors[i].append([i, j, d[i], image])
         return np.array(neighbors, dtype="object")