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 <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]>
usnistgov · Oct 6, 2021 · b6ae4b3 · b6ae4b3
1 parent 21f7fde
commit b6ae4b3
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Showing 4 changed files with 46 additions and 3 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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",