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.

jarvis/__init__.py

@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2020.10.20"
+__version__ = "2020.11.09"

jarvis/core/atoms.py

@@ -1036,7 +1036,8 @@ def get_string(self, cart=True, sort_order="X"):
                 + cart_frac
             )
         rest = ""
-
+        if coords_ordered.ndim == 1:
+            coords_ordered = np.array([coords])
         for ii, i in enumerate(coords_ordered):
             if self.show_props:
                 rest = (

jarvis/core/kpoints.py

@@ -9,6 +9,7 @@
 from numpy import cos, sin
 from math import tan, pi
 from math import ceil
+import math
 
 
 def generate_kgrid(grid=[5, 5, 5]):
@@ -74,6 +75,18 @@ def kpts(self):
         """Return k-points arrays."""
         return self._kpoints
 
+    def kpoints_per_atom(self, atoms=None, kppa=1000):
+        """Return Kpoints object for kpoints per atom for a cell."""
+        if math.fabs((math.floor(kppa ** (1 / 3) + 0.5)) ** 3 - kppa) < 1:
+            kppa += kppa * 0.01
+        # latt = atoms.lattice_mat
+        lengths = atoms.lattice.lat_lengths()
+        ngrid = kppa / atoms.num_atoms
+        mult = (ngrid * lengths[0] * lengths[1] * lengths[2]) ** (1 / 3)
+        num_div = [int(math.floor(max(mult / lg, 1))) for lg in lengths]
+        kpts = Kpoints3D(kpoints=[num_div])
+        return kpts
+
     @property
     def labels(self):
         """Return k-points labels, used for high BZ points."""

jarvis/core/utils.py

@@ -5,8 +5,14 @@
 import random
 import numpy as np
 import math
+import xmltodict
 
-# from lxml import etree
+
+def xml_to_dict(fname):
+    """Parse XML file."""
+    with open(fname, "r") as f:
+        data = xmltodict.parse(f.read())
+    return data
 
 
 def get_counts(array=["W", "W", "Mo", "Mo", "S", "S"]):
@@ -137,6 +143,14 @@ def array_to_string(arr=[]):
     return ",".join(map(str, arr))
 
 
+def chunks(lst, n):
+    """Split successive n-sized chunks from list."""
+    x = []
+    for i in range(0, len(lst), n):
+        x.append(lst[i : i + n])
+    return x
+
+
 def check_match(a, b, tol=1e-8):
     """Check if a and b are the same, taking into account PBCs."""
     if abs(a[0] - b[0]) < tol or abs(abs(a[0] - b[0]) - 1) < tol:

jarvis/db/figshare.py

@@ -36,6 +36,18 @@ def datasets(dataset=""):
         url = "https://ndownloader.figshare.com/files/25159592"
         js_tag = "qm9_data_cfid.json"
         print("Obtaining QM9-molecule CFID dataset 134k...")
+    elif dataset == "aflow1":
+        url = "https://ndownloader.figshare.com/files/25453256"
+        js_tag = "CFID-AFLOW-1.json"
+        print("Obtaining AFLOW-1 CFID dataset 400k...")
+    elif dataset == "aflow2":
+        url = "https://ndownloader.figshare.com/files/25453265"
+        js_tag = "CFID-AFLOW-2.json"
+        print("Obtaining AFLOW-2 CFID dataset 400k...")
+    elif dataset == "raw_files":
+        url = "https://ndownloader.figshare.com/files/25295732"
+        js_tag = "figshare_data-10-28-2020.json"
+        print("Obtaining raw io files...")
     else:
         ValueError("Dataset doesnt exist", dataset)
     return url, js_tag

jarvis/db/lammps_to_xml.py

@@ -1,22 +1,43 @@
 """Module to generate XML file for LAMMPS calculation."""
 import numpy as np
 from jarvis.core.atoms import get_supercell_dims
-
+from jarvis.db.jsonutils import loadjson
 from jarvis.analysis.structure.spacegroup import Spacegroup3D
 from jarvis.core.utils import stringdict_to_xml
 
+mp_jv = loadjson("/rk2/knc6/DB/MP/mp_jv_id.json")
+
+
+def get_jvid(mp=""):
+    """Get JARVIS-ID for MPID."""
+    jvid = ""
+    try:
+        jvid = "'" + ",".join(mp_jv[mp]) + "'"
+    except Exception as exp:
+        print("No JID", exp)
+        pass
+    return jvid
+
 
 def basic_data(data={}, source="JARVIS-FF-LAMMPS"):
     """Get basic data for table."""
     info = {}
     info["id"] = data["jid"]
     info["source_folder"] = data["source_folder"]
+    info["tmp_source_folder"] = "'" + data["source_folder"] + "'"
+    info["tmp_id"] = "'" + data["jid"] + "'"
+    ref = data["source_folder"].split("/")[-1].split("@")[1].split("_")[0]
+    info["ref"] = "'" + ref + "'"
+    info["jvid"] = get_jvid(ref)
     final_atoms = data["bulk_data"]["final_str"]
     initial_atoms = data["bulk_data"]["initial_str"]
     info["formula"] = final_atoms.composition.reduced_formula
+    info["tmp_formula"] = "'" + final_atoms.composition.reduced_formula + "'"
     info["elements"] = ",".join(final_atoms.uniq_species)
+    info["tmp_elements"] = "'" + ",".join(final_atoms.uniq_species) + "'"
     info["number_uniq_species"] = len(final_atoms.uniq_species)
     info["data_source"] = source
+    info["tmp_data_source"] = "'" + source + "'"
     info["pair_style"] = data["bulk_data"]["pair_style"]
     info["pair_coeff"] = data["bulk_data"]["pair_coeff"]
     # info["pair_coeff"] = (
@@ -74,7 +95,7 @@ def basic_data(data={}, source="JARVIS-FF-LAMMPS"):
     info["final_crystal_system"] = final_spg.crystal_system
 
     et = ""
-    print(data["bulk_data"]["elastic_tensor"]["raw_et_tensor"])
+    # print(data["bulk_data"]["elastic_tensor"]["raw_et_tensor"])
     try:
         if data["bulk_data"]["elastic_tensor"] != "":
             cij = np.round(
@@ -88,8 +109,8 @@ def basic_data(data={}, source="JARVIS-FF-LAMMPS"):
                 + '"</cij>'
             )
 
-    except Exception:
-        print("Cannot obtain elastic tensor data.", info["source_folder"])
+    except Exception as exp:
+        print("Cannot obtain elastic tensor data.", info["source_folder"], exp)
         pass
 
     info["elastic_tensor"] = et
@@ -138,11 +159,11 @@ def basic_data(data={}, source="JARVIS-FF-LAMMPS"):
             + ",".join(map(str, label_points))
             + "'</phonon_bandstructure_label_points>"
         )
-    except Exception:
-        print("Cannot obtain phonon band data.")
+    except Exception as exp:
+        print("Cannot obtain phonon band data.", exp)
 
     # Comment until 4 MB text size error
-    # info["phonon_band_line"] = phonon_band_line
+    info["phonon_band_line"] = phonon_band_line
     phonon_dos_line = ""
     try:
         freq = data["dos_freq"]
@@ -190,9 +211,9 @@ def write_xml(data={}, filename="temp.xml"):
 if __name__ == "__main__":
     from jarvis.io.lammps.outputs import parse_material_calculation_folder
 
-    # fold = '/rk2/knc6/JARVIS-FF/ALLOY8/\
-    # Mishin-Ni-Al-2009.eam.alloy_nist/bulk@mp-23_fold'
-    fold = "/rk2/knc6/JARVIS-FF/COMB/ffield.TiON.comb3_nist/bulk@mp-25433_fold"
+    fold = '/rk2/knc6/JARVIS-FF/ALLOY8/
+    Mishin-Ni-Al-2009.eam.alloy_nist/bulk@mp-23_fold'
     x = parse_material_calculation_folder(fold)
     write_xml(x)
+    print('src',x["source_folder"].split('/')[-1].split('@')[1].split('_')[0])
 """