From b6ae4b364a2525fd20f714ae861759f45bccf743 Mon Sep 17 00:00:00 2001 From: Kamal Choudhary Date: Wed, 6 Oct 2021 07:58:14 -0400 Subject: [PATCH] Develop (#201) * 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. Co-authored-by: tavazza Co-authored-by: knc6 Co-authored-by: KAMAL CHOUDHARY --- jarvis/__init__.py | 2 +- jarvis/core/kpoints.py | 7 ++++++- jarvis/io/zeopp/inputs.py | 38 ++++++++++++++++++++++++++++++++++++++ setup.py | 2 +- 4 files changed, 46 insertions(+), 3 deletions(-) diff --git a/jarvis/__init__.py b/jarvis/__init__.py index d83c06e7..8a030e5a 100644 --- a/jarvis/__init__.py +++ b/jarvis/__init__.py @@ -1,2 +1,2 @@ """Version number.""" -__version__ = "2021.08.18" +__version__ = "2021.10.03" diff --git a/jarvis/core/kpoints.py b/jarvis/core/kpoints.py index c236d2a0..89c956c3 100644 --- a/jarvis/core/kpoints.py +++ b/jarvis/core/kpoints.py @@ -59,7 +59,12 @@ def __init__( def automatic_length_mesh(self, lattice_mat=[], length=20, header="Gamma"): """Length based automatic k-points.""" - inv_lat = Lattice(lattice_mat=lattice_mat).inv_lattice() + inv_lat = ( + Lattice(lattice_mat=lattice_mat) + .reciprocal_lattice_crystallographic() + .matrix + ) + # inv_lat = Lattice(lattice_mat=lattice_mat).inv_lattice() b1 = LA.norm(np.array(inv_lat[0])) b2 = LA.norm(np.array(inv_lat[1])) b3 = LA.norm(np.array(inv_lat[2])) diff --git a/jarvis/io/zeopp/inputs.py b/jarvis/io/zeopp/inputs.py index 04f5c827..1cf24105 100644 --- a/jarvis/io/zeopp/inputs.py +++ b/jarvis/io/zeopp/inputs.py @@ -28,6 +28,44 @@ def get_porosity(atoms=None, network_cmd="./network", output_file=None): ) +def get_surface_area( + atoms=None, + network_cmd="/home/knc6/Software/zeopp/zeo++-0.3/network", + probe_radius=1.2, + chan_radius=None, + num_samples=2000, + output_file=None, + prefix="ja_atoms", +): + """Gete surface area using zeo++.""" + # See: http://www.zeoplusplus.org/examples.html + if chan_radius is None: + chan_radius = probe_radius + filename = str(prefix) + ".cif" + atoms.write_cif(filename) + filename1 = str(prefix) + ".sa" + if os.path.exists(filename1): + os.remove(filename1) + cmd = ( + network_cmd + + " -ha -sa " + + str(probe_radius) + + " " + + str(chan_radius) + + " " + + str(num_samples) + + " " + + filename + ) + os.system(cmd) + f = open(filename1, "r") + lines = f.read().splitlines() + f.close() + ASA_m2cm3 = float(lines[0].split()[9]) + ASA_m2g = float(lines[0].split()[11]) + return ASA_m2cm3, ASA_m2g + + """ if __name__ == "__main__": from jarvis.db.figshare import get_jid_data diff --git a/setup.py b/setup.py index d6b7b40e..736447ce 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ setup( name="jarvis-tools", - version="2021.08.18", + version="2021.10.03", long_description=long_d, install_requires=[ "numpy>=1.19.5",