From 61b9c56ade4ea26f0945845d57e09f1a971225ca Mon Sep 17 00:00:00 2001 From: Kamal Choudhary Date: Thu, 21 Sep 2023 20:18:02 -0400 Subject: [PATCH] Develop (#303) * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (#197) * Develop (#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza Co-authored-by: knc6 Co-authored-by: KAMAL CHOUDHARY * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary Co-authored-by: tavazza Co-authored-by: knc6 Co-authored-by: KAMAL CHOUDHARY * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. * Add installation tests (#214) * QE inputs, XANES, GHAction updates. (#210) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (#197) * Develop (#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza Co-authored-by: knc6 Co-authored-by: KAMAL CHOUDHARY * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary Co-authored-by: tavazza Co-authored-by: knc6 Co-authored-by: KAMAL CHOUDHARY * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. Co-authored-by: tavazza Co-authored-by: knc6 Co-authored-by: KAMAL CHOUDHARY Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com> * Add installation tests * Fix codestyle * Fix codestyle with black * Add docstrings * Fix pydocstyle error * Update __init__.py * Update __init__.py Co-authored-by: Kamal Choudhary Co-authored-by: tavazza Co-authored-by: knc6 Co-authored-by: KAMAL CHOUDHARY Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com> * Adding QE super. * Minor changes to QE module, atoms xyz fix. * Adding qe_tb info, and version update. * Update __init__.py * WIP super QE. * Working version of ScSi. * QE inputs and task update. * Add master super. * Add master super. * Lint fix. * Lint fix. * Minor fix. * ET update. * Fix ET test. * Update sanitize atoms. * Additonal checks on supercond. * Debye bug fix. * Pressure in QE Super. * Version fix, publication update, supercond workflow update. * Lint fix. * Tensorboard fix. * Tensorboard fix. * Tensorboard fix. * Melting temp fix. * Update vasp.py (#234) * Local tetra tmp. * Version update. * Lint fix. * HSE06 * Tmp. * Vacancy update, Optimade structureand other minor lint updates. * STEM pytest fix. * Minor lint fix. * Fixed selectrive dynamics issue in Poscar, force reading for single atom system in Vasprun, np.array in core.graps, num_atoms for single atom systems in core.Atoms * Lint fix. * Added phononDos class. * fix pytorch UserWarning in build_undirected_edgedata() (#243) site-packages/jarvis/core/graphs.py:158: UserWarning: Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor. r = torch.tensor(r).type(torch.get_default_dtype()) * Add PhaseDiagram. * Add PhaseDiagram. * PhaseDiagram update. * STM image pytest increase, requirements upgrade. * STM image pytest increase, requirements upgrade. * STM image pytest increase, requirements upgrade. * Compare atoms, get spg info directly from atoms. * Flake8 fix. * Update publications.rst * Update qiskit. * Update qiskit. * Update test_hermsolver.py * FIix qiskit DOS. * Update test_hermsolver.py * Fix linting. * Develop og (#257) * Added isotope scattering rate to phonon DOS analysis script. * Linting fix. * Linting fix. * Linting fix. * Add QE convergence. * Update converg.py. * Nexus. * Super with converg. * Super with converg. * SuperCon QE update. * Figshare DB update. * Figshare DB update. * Update alignn ff link. * Lint fix. * DB docs update. * Minor fixes: delete agg in figshare, add destination path in figshare data, dtype compatibility with new numpy. * Lint fix. * Supercon workflow fix. * Add extra db entires, fix chem in cfid_chem. * Version update. * Add figshare datasets. * Update databases.rst * codecov fix. * Version update. * Lint fix. * Add FigShare datasets, DOS in QE, Uncertainty. * Add python 3.9. * Create README.md * Update README. * Add README.md. * Update action_build.yml * Update action_lint.yml * Allow md file, add mode databases. * Create NISTtheDocs2Death.yml * Allow md file, add mode databases. * Add publications. * Update publications.rst * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Create deploy_nist_pages.yml * Add mkdocs. * Update deploy_nist_pages.yml * Update md. * Update setup.py * Update readme. * Update setup.py * Remove absl. * Update dev-requirements.txt * Update index.md * Update deploy_nist_pages.yml * Update index.rst * Add redirect. * Update action_build.yml * Update dev-requirements.txt * Update dev-requirements.txt * Update setup.py * Update dev-requirements.txt * Fix __repr__ for Atoms. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Fix requirements. * Fix requirements. * Fix requirements. * Fix requirements. * Use poscar write as string. * Use poscar write as string. * Use poscar write as string. * Update action_build.yml * Use poscar write as string. * Use poscar write as string. * Update action_build.yml * Use poscar write as string. * Use poscar write as string. * Delete NISTtheDocs2Death.yml * Delete action_lint.yml * Use poscar write as string. * Fix phonopy. * Update dev-requirements.txt * Update databases. * Add eigs. * Add eigs. * Add eigs. * Fix STM test. * Delete .travis.yml * Update README. * Add python docs. * GA * Update action_build.yml * Atoms class update with props. * Atoms class update with props. * Delete .readthedocs.yaml * Update README.md --------- Co-authored-by: KAMAL CHOUDHARY Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com> Co-authored-by: tavazza Co-authored-by: knc6 Co-authored-by: Saurav Maheshkar Co-authored-by: Janosh Riebesell Co-authored-by: Ramya Gurunathan --- .readthedocs.yaml | 13 ------------- README.md | 1 - jarvis/__init__.py | 2 +- jarvis/core/atoms.py | 23 +++++++++++++++++------ setup.py | 2 +- 5 files changed, 19 insertions(+), 22 deletions(-) delete mode 100644 .readthedocs.yaml diff --git a/.readthedocs.yaml b/.readthedocs.yaml deleted file mode 100644 index c55cf367..00000000 --- a/.readthedocs.yaml +++ /dev/null @@ -1,13 +0,0 @@ -version: 2 - -python: - version: 3.8 - install: - - requirements: docs/requirements.txt - - method: pip - path: . - extra_requirements: - - docs - - method: setuptools - path: . - system_packages: true diff --git a/README.md b/README.md index 768f3e7c..026821fb 100644 --- a/README.md +++ b/README.md @@ -23,4 +23,3 @@ Detailed documentation available at: https://pages.nist.gov/jarvis/ [![image](https://img.shields.io/badge/JARVIS-Figshare-Green.svg)](https://figshare.com/authors/Kamal_Choudhary/4445539) [![image](https://img.shields.io/badge/JARVIS-ToolsDocs-Green.svg)](https://pages.nist.gov/jarvis) [![image](https://colab.research.google.com/assets/colab-badge.svg)](https://github.com/JARVIS-Materials-Design/jarvis-tools-notebooks) - diff --git a/jarvis/__init__.py b/jarvis/__init__.py index a42ca7a8..fc2dbd53 100644 --- a/jarvis/__init__.py +++ b/jarvis/__init__.py @@ -1,5 +1,5 @@ """Version number.""" -__version__ = "2023.08.10" +__version__ = "2023.09.20" import os diff --git a/jarvis/core/atoms.py b/jarvis/core/atoms.py index e88455aa..d626d902 100644 --- a/jarvis/core/atoms.py +++ b/jarvis/core/atoms.py @@ -887,9 +887,7 @@ def atomwise_angle_and_radial_distribution( and nbor_info["dist"][in1][i] * nbor_info["dist"][in2][i] != 0 ] ang_hist, ang_bins = np.histogram( - angles, - bins=np.arange(1, nbins + 2, 1), - density=False, + angles, bins=np.arange(1, nbins + 2, 1), density=False, ) for jj, j in enumerate(angles): actual_pangs[i, jj] = j @@ -944,7 +942,7 @@ def center(self, axis=2, vacuum=18.0, about=None): """ cell = self.lattice_mat p = self.cart_coords - + props = self.props dirs = np.zeros_like(cell) for i in range(3): dirs[i] = np.cross(cell[i - 1], cell[i - 2]) @@ -998,6 +996,7 @@ def center(self, axis=2, vacuum=18.0, about=None): elements=self.elements, coords=new_coords, cartesian=True, + props=props, ) return atoms @@ -1066,6 +1065,7 @@ def center_around_origin(self, new_origin=[0.0, 0.0, 0.5]): lat = self.lattice_mat typ_sp = self.elements natoms = self.num_atoms + props = self.props # abc = self.lattice.lat_lengths() COM = self.get_origin() # COM = self.get_center_of_mass() @@ -1080,7 +1080,11 @@ def center_around_origin(self, new_origin=[0.0, 0.0, 0.5]): z[i] = self.frac_coords[i][2] - COM[2] + new_origin[2] coords.append([x[i], y[i], z[i]]) struct = Atoms( - lattice_mat=lat, elements=typ_sp, coords=coords, cartesian=False + lattice_mat=lat, + elements=typ_sp, + coords=coords, + cartesian=False, + props=props, ) return struct @@ -1604,7 +1608,9 @@ def fix_pbc(atoms): ) -def add_atoms(top, bottom, distance=[0, 0, 1], apply_strain=False): +def add_atoms( + top, bottom, distance=[0, 0, 1], apply_strain=False, add_tags=True +): """ Add top and bottom Atoms with a distance array. @@ -1623,10 +1629,12 @@ def add_atoms(top, bottom, distance=[0, 0, 1], apply_strain=False): # print("strain_x,strain_y", strain_x, strain_y) elements = [] coords = [] + props = [] lattice_mat = bottom.lattice_mat for i, j in zip(bottom.elements, bottom.frac_coords): elements.append(i) coords.append(j) + props.append("bottom") top_cart_coords = lattice_coords_transformer( new_lattice_mat=top.lattice_mat, old_lattice_mat=bottom.lattice_mat, @@ -1636,6 +1644,7 @@ def add_atoms(top, bottom, distance=[0, 0, 1], apply_strain=False): for i, j in zip(top.elements, top_frac_coords): elements.append(i) coords.append(j) + props.append("top") order = np.argsort(np.array(elements)) elements = np.array(elements)[order] @@ -1651,8 +1660,10 @@ def add_atoms(top, bottom, distance=[0, 0, 1], apply_strain=False): lattice_mat=lattice_mat, coords=coords, elements=elements, + props=props, cartesian=False, ).center_around_origin() + # print('combined props',combined) return combined diff --git a/setup.py b/setup.py index 8586281c..402f29ec 100644 --- a/setup.py +++ b/setup.py @@ -12,7 +12,7 @@ setup( name="jarvis-tools", - version="2023.08.10", + version="2023.09.20", long_description=long_d, install_requires=[ "numpy>=1.20.1",