Develop (#194)

* 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. Co-authored-by: tavazza <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov>
usnistgov · Aug 7, 2021 · ad4be67 · ad4be67
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diff --git a/docs/source/databases.rst b/docs/source/databases.rst
@@ -33,7 +33,7 @@ Database name            Number of data-points       Description
 ``oqmd_3d_no_cfid``      817636                      Formation energies and bandgaps of 3D materials 
                                                      from OQMD database
 ``omdb``                 12500                       Bandgaps  for organic polymers in OMDB database
-``hpov``                 4855                        Various properties of molecules in HPOV15 dataset 
+``hopv``                 4855                        Various properties of molecules in HOPV15 dataset 
 ``pdbbind``              11189                       Bio-molecular complexes database from PDBBind v2015
 ``qmof``                 18321                       Bandgaps and total energies of metal organic frameowrks
                                                      in QMOF database

diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2021.07.19"
+__version__ = "2021.08.05"
diff --git a/jarvis/analysis/elastic/tensor.py b/jarvis/analysis/elastic/tensor.py
@@ -80,7 +80,11 @@ def to_dict(self):
         d["poisson_ratio"] = self.poisson_ratio
         d["youngs_modulus"] = self.youngs_modulus
         d["universal_ansiotropy_ratio"] = self.universal_ansiotropy_ratio
-        d["raw_et_tensor"] = self.et_tensor
+        if not isinstance(self.et_tensor, list):
+            et_tensor = self.et_tensor.tolist()
+        else:
+            et_tensor = self.et_tensor
+        d["raw_et_tensor"] = et_tensor
         return d
 
 

diff --git a/jarvis/core/image.py b/jarvis/core/image.py
@@ -10,7 +10,8 @@
     from skimage.filters import gaussian
     from PIL import Image as PIL_Image
 except Exception as exp:
-    print("Install skimage, Pillow.", exp)
+    # print("Install skimage, Pillow.", exp)
+    pass
 # from scipy.ndimage import rotate
 import scipy
 

diff --git a/jarvis/db/figshare.py b/jarvis/db/figshare.py
@@ -26,13 +26,14 @@
 def get_db_info():
     """Get DB info."""
     db_info = {
+        # https://doi.org/10.6084/m9.figshare.6815705
         "dft_2d": [
             "https://ndownloader.figshare.com/files/26808917",
             "d2-3-12-2021.json",
             "Obtaining 2D dataset 1.1k ...",
             "https://www.nature.com/articles/s41524-020-00440-1",
         ],
-        # https://doi.org/10.6084/m9.figshare.6815705
+        # https://doi.org/10.6084/m9.figshare.6815699
         "dft_3d": [
             "https://ndownloader.figshare.com/files/28034994",
             "d3-5-16-2021.json",
@@ -46,135 +47,146 @@ def get_db_info():
             "Obtaining 3D dataset 43k ...",
             "https://www.nature.com/articles/s41524-020-00440-1",
         ],
+        # https://doi.org/10.6084/m9.figshare.14213522
         "jff": [
-            "https://ndownloader.figshare.com/files/26809760",
-            "jff-3-12-2021.json",
+            "https://ndownloader.figshare.com/files/28937793",
+            # "https://ndownloader.figshare.com/files/26809760",
+            "jff-7-24-2021.json",
+            # "jff-3-12-2021.json",
             "Obtaining JARVIS-FF 2k ...",
             "https://www.nature.com/articles/s41524-020-00440-1",
         ],
-        # https://doi.org/10.6084/m9.figshare.14213522
         "mp_3d_2020": [
             "https://ndownloader.figshare.com/files/26791259",
             "all_mp.json",
             "Obtaining Materials Project-3D CFID dataset 127k...",
             "https://doi.org/10.1063/1.4812323",
         ],
+        # https://doi.org/10.6084/m9.figshare.14177630
         "megnet": [
             "https://ndownloader.figshare.com/files/26724977",
             "megnet.json",
             "Obtaining MEGNET-3D CFID dataset 69k...",
             "https://pubs.acs.org/doi/10.1021/acs.chemmater.9b01294",
         ],
-        # https://doi.org/10.6084/m9.figshare.14177630
+        # https://doi.org/10.6084/m9.figshare.14745435
         "megnet2": [
             "https://ndownloader.figshare.com/files/28332741",
             "megnet-mp-2019-04-01.json",
             "Obtaining MEGNET-3D CFID dataset 133k...",
             "https://pubs.acs.org/doi/10.1021/acs.chemmater.9b01294",
         ],
-        # https://doi.org/10.6084/m9.figshare.14745435
+        # https://doi.org/10.6084/m9.figshare.14745327
         "edos_pdos": [
             "https://ndownloader.figshare.com/files/28501764",
             "edos-up_pdos-elast_interp-6-19-2021.json",
             "Interpolated electronic total dos spin-up dataset 48k...",
             "https://www.nature.com/articles/s41524-020-00440-1",
         ],
-        # https://doi.org/10.6084/m9.figshare.14745327
+        # https://doi.org/10.6084/m9.figshare.13054247
         "mp_3d": [
             "https://ndownloader.figshare.com/files/24979850",
             "CFID_mp_desc_data_84k.json",
             "Obtaining Materials Project-3D CFID dataset 84k...",
             "https://doi.org/10.1063/1.4812323",
         ],
-        # https://doi.org/10.6084/m9.figshare.13054247
+        # https://doi.org/10.6084/m9.figshare.13055333
         "oqmd_3d": [
             "https://ndownloader.figshare.com/files/24981170",
             "CFID_OQMD_460k.json",
             "Obtaining OQMD-3D CFID dataset 460k...",
             "https://www.nature.com/articles/npjcompumats201510",
         ],
-        # https://doi.org/10.6084/m9.figshare.13055333
+        # https://doi.org/10.6084/m9.figshare.14206169
         "oqmd_3d_no_cfid": [
             "https://ndownloader.figshare.com/files/26790182",
             "all_oqmd.json",
             "Obtaining OQMD-3D  dataset 800k...",
             "https://www.nature.com/articles/npjcompumats201510",
         ],
-        # https://doi.org/10.6084/m9.figshare.14206169
+        # https://doi.org/10.6084/m9.figshare.14205083
         "twod_matpd": [
             "https://ndownloader.figshare.com/files/26789006",
             "twodmatpd.json",
             "Obtaining 2DMatPedia dataset 6k...",
             "https://www.nature.com/articles/s41597-019-0097-3",
         ],
-        # https://doi.org/10.6084/m9.figshare.14205083
+        # https://doi.org/10.6084/m9.figshare.14213603
         "polymer_genome": [
             "https://ndownloader.figshare.com/files/26809907",
             "pgnome.json",
             "Obtaining Polymer genome 1k...",
             "https://www.nature.com/articles/sdata201612",
         ],
-        # https://doi.org/10.6084/m9.figshare.14213603
         "qm9_std_jctc": [
             "https://ndownloader.figshare.com/files/28715319",
             "qm9_std_jctc.json",
             "Obtaining QM9 standardized dataset 130k,"
             + "From https://doi.org/10.1021/acs.jctc.7b00577,+",
             "https://www.nature.com/articles/sdata201422",
         ],
+        # https://doi.org/10.6084/m9.figshare.14827584
+        # Use qm9_std_jctc instaed
         "qm9_dgl": [
             "https://ndownloader.figshare.com/files/28541196",
             "qm9_dgl.json",
             "Obtaining QM9 dataset 130k, from DGL...",
             "https://www.nature.com/articles/sdata201422",
         ],
-        # https://doi.org/10.6084/m9.figshare.14827584
-        # Use qm9_std_jctc instaed
+        # https://doi.org/10.6084/m9.figshare.14912820.v1
         "cod": [
             "https://ndownloader.figshare.com/files/28715301",
             "cod_db.json",
             "Obtaining COD dataset 431k",
             "https://doi.org/10.1107/S1600576720016532",
         ],
-        # https://doi.org/10.6084/m9.figshare.14912820.v1
+        # Use qm9_std_jctc instaed
         "qm9": [
             "https://ndownloader.figshare.com/files/27627596",
             "qm9_data_cfid.json",
             "Obtaining QM9 dataset 134k...",
             "https://www.nature.com/articles/sdata201422",
         ],
-        # Use qm9_std_jctc instaed
+        # https://doi.org/10.6084/m9.figshare.15127788
         "qe_tb": [
-            "https://ndownloader.figshare.com/files/TODO",
+            "https://ndownloader.figshare.com/files/29070555",
             "jqe_tb_folder.json",
             "Obtaining QETB dataset 860k...",
             "https://www.nature.com/articles/s41524-020-00440-1",
         ],
+        # https://doi.org/10.6084/m9.figshare.14812050
         "omdb": [
             "https://ndownloader.figshare.com/files/28501761",
             "omdbv1.json",
             "Obtaining OMDB dataset 12.5k...",
             "https://doi.org/10.1002/qute.201900023",
         ],
-        # https://doi.org/10.6084/m9.figshare.14812050
+        # https://doi.org/10.6084/m9.figshare.14812044
         "qmof": [
             "https://ndownloader.figshare.com/files/28501740",
             "qmof_db.json",
             "Obtaining QMOF dataset 18k...",
             "https://www.cell.com/matter/fulltext/S2590-2385(21)00070-9",
         ],
-        # https://doi.org/10.6084/m9.figshare.14812044
+        # https://doi.org/10.6084/m9.figshare.15127758
+        "hmof": [
+            "https://ndownloader.figshare.com/files/29070516",
+            "hmof_db_7_27_2021.json",
+            "Obtaining QMOF dataset 137k...",
+            "https://doi.org/10.1021/acs.jpcc.6b08729",
+        ],
+        # https://figshare.com/account/projects/100325/articles/14960157
         "c2db": [
             "https://ndownloader.figshare.com/files/28682010",
             "c2db_atoms.json",
             "Obtaining C2DB dataset 3.5k...",
             "https://iopscience.iop.org/article/10.1088/2053-1583/aacfc1",
         ],
-        # https://figshare.com/account/projects/100325/articles/14960157
-        "hpov": [
+        # https://figshare.com/account/projects/100325/articles/14962356
+        "hopv": [
             "https://ndownloader.figshare.com/files/28814184",
             "hopv_15.json",
-            "Obtaining HPOV15 dataset 4.5k...",
+            "Obtaining HOPV15 dataset 4.5k...",
             "https://www.nature.com/articles/sdata201686",
         ],
         # https://figshare.com/account/projects/100325/articles/14962356
@@ -184,35 +196,35 @@ def get_db_info():
             "Obtaining PDBBind dataset 195...",
             "https://doi.org/10.1093/bioinformatics/btu626",
         ],
-        # https://figshare.com/account/projects/100325/articles/14962356
+        # https://doi.org/10.6084/m9.figshare.14812038
         "pdbbind": [
             "https://ndownloader.figshare.com/files/28816368",
             "pdbbind_2015.json",
             "Obtaining PDBBind dataset 11k...",
             "https://doi.org/10.1093/bioinformatics/btu626",
         ],
-        # https://doi.org/10.6084/m9.figshare.14812038
+        # https://doi.org/10.6084/m9.figshare.13215308
         "aflow2": [
             "https://ndownloader.figshare.com/files/25453265",
             "CFID_AFLOW2.json",
             "Obtaining AFLOW-2 CFID dataset 400k...",
             "https://doi.org/10.1016/j.commatsci.2012.02.005",
         ],
-        # https://doi.org/10.6084/m9.figshare.13215308
+        # https://doi.org/10.6084/m9.figshare.14211860
         "arXiv": [
             "https://ndownloader.figshare.com/files/26804795",
             "arXivdataset.json",
             "Obtaining arXiv dataset 1.8 million...",
             "https://www.kaggle.com/Cornell-University/arxiv",
         ],
-        # https://doi.org/10.6084/m9.figshare.14211860
+        # https://doi.org/10.6084/m9.figshare.14211857
         "cord19": [
             "https://ndownloader.figshare.com/files/26804798",
             "cord19.json",
             "Obtaining CORD19 dataset 223k...",
             "https://github.com/usnistgov/cord19-cdcs-nist",
         ],
-        # https://doi.org/10.6084/m9.figshare.14211857
+        # https://doi.org/10.6084/m9.figshare.13154159
         "raw_files": [
             "https://ndownloader.figshare.com/files/25295732",
             "figshare_data-10-28-2020.json",

diff --git a/jarvis/io/lammps/inputs.py b/jarvis/io/lammps/inputs.py
@@ -95,6 +95,7 @@ def read_data(
         element_order=[],
         potential_file="pot.mod",
         verbose=True,
+        has_charges=True,
     ):
         """Read Lammps data file."""
         # n_atoms = len(self._species)
@@ -128,6 +129,9 @@ def read_data(
         # print("symb=", symb)
         f = open(filename, "r")
         lines = f.read().splitlines()
+        xy = 0
+        xz = 0
+        yz = 0
         for i, line in enumerate(lines):
             if "atoms" in line.split():
                 natoms = int(line.split()[0])
@@ -160,16 +164,22 @@ def read_data(
         z = np.zeros((natoms))
         q = np.zeros((natoms))
         coords = list()
+        if has_charges:
+            it = 2
+        else:
+            it = 1
         for i, line in enumerate(lines):
             if "Atoms" in line.split():
                 for j in range(0, natoms):
                     # print int(((lines[j+2]).split()[1]))-1
                     typ[j] = symb[int(((lines[i + j + 2]).split()[1])) - 1]
-                    q[j] = (lines[i + j + 2]).split()[2]
-                    x[j] = (lines[i + j + 2]).split()[3]
-                    y[j] = (lines[i + j + 2]).split()[4]
-                    z[j] = (lines[i + j + 2]).split()[5]
+                    if has_charges:
+                        q[j] = float((lines[i + j + 2]).split()[2])
+                    x[j] = float((lines[i + j + 2]).split()[it + 1])
+                    y[j] = float((lines[i + j + 2]).split()[it + 2])
+                    z[j] = float((lines[i + j + 2]).split()[it + 3])
                     coords.append([x[j], y[j], z[j]])
+                    print(coords[-1])
         f.close()
         # print ("info",(typ),'coo',(coords),'latt',lat)
         typ_sp = [str(i, "utf-8") for i in typ]