XRD DB making bug fix, scattering.json update. (#131)

* 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
usnistgov · Oct 21, 2020 · 9601924 · 9601924
1 parent 3674038
commit 9601924
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Showing 7 changed files with 31 additions and 100 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
diff --git a/README.rst b/README.rst
@@ -1,6 +1,4 @@
 .. class:: center
-.. image:: https://circleci.com/gh/usnistgov/jarvis.svg?style=shield
-        :target: https://circleci.com/gh/usnistgov/jarvis
 .. image:: https://img.shields.io/travis/usnistgov/jarvis/master.svg?label=Travis%20CI
         :target: https://travis-ci.org/usnistgov/jarvis
 .. image:: https://ci.appveyor.com/api/projects/status/d8na8vyfm7ulya9p/branch/master?svg=true

diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2020.10.19"
+__version__ = "2020.10.20"
diff --git a/jarvis/analysis/diffraction/xrd.py b/jarvis/analysis/diffraction/xrd.py
@@ -4,8 +4,10 @@
 import collections
 import os
 from jarvis.core.specie import Specie
+
 # from jarvis.core.spectrum import Spectrum
 import itertools
+
 # from jarvis.analysis.structure.spacegroup import Spacegroup3D,
 
 
@@ -207,6 +209,7 @@ def is_perm(hkl1, hkl2):
         return pretty_unique
 
 
+"""
 if __name__ == "__main__":
     # h=create_index()
     # print (h,len(h))
@@ -221,3 +224,4 @@ def is_perm(hkl1, hkl2):
     print("a=", a)
     print("b=", b)
     print("c=", c)
+"""
diff --git a/jarvis/db/vasp_to_xml.py b/jarvis/db/vasp_to_xml.py
@@ -180,7 +180,7 @@ def encut_kp(self):
             encut_files = []
             encut_values = []
             encut_based_energies = []
-            for i in glob.glob("*.json"):
+            for i in glob.glob("ENCUT*.json"):
                 if "ENCUT" in i:
                     encut_values.append(
                         int(str(i.split("-")[-1]).split(".json")[0])
@@ -195,7 +195,7 @@ def encut_kp(self):
             kplength_files = []
             kp_values = []
             kp_based_energies = []
-            for i in glob.glob("*.json"):
+            for i in glob.glob("KPOINT*.json"):
                 if "KPOINT" in i:
                     kp_values.append(
                         int(str(i.split("-")[-1]).split(".json")[0])
@@ -330,7 +330,9 @@ def get_xrd(self, atoms):
             )
             line += '<d_hkls>"' + array_to_string(d_hkls) + '"</d_hkls>'
             line += (
-                '<intensities>"' + array_to_string(d_hkls) + '"</intensities>'
+                '<intensities>"'
+                + array_to_string(intensities)
+                + '"</intensities>'
             )
         except Exception:
             print("Cannot gt XRD pattern.")
@@ -1709,16 +1711,20 @@ def write_xml(self, filename="temp.xml"):
             """
 
 
-if __name__ == "__main__":
-    folder = "/rk2/knc6/JARVIS-DFT/Elements-bulkk/mp-149_bulk_PBEBO"
-    filename = "JVASP-1002.xml"
-    VaspToApiXmlSchema(folder=folder).write_xml(filename=filename)
-
 """
+if __name__ == "__main__":
     folder = "/rk2/knc6/JARVIS-DFT/TE-bulk/mp-541837_bulk_PBEBO"
     filename = "JVASP-1067.xml"
     VaspToApiXmlSchema(folder=folder).write_xml(filename=filename)
 
+    folder = "/rk2/knc6/JARVIS-DFT/2DSF-bulk/mp-764365_PBEBO"
+    filename = "JVASP-30266.xml"
+    VaspToApiXmlSchema(folder=folder).write_xml(filename=filename)
+
+    folder = "/rk2/knc6/JARVIS-DFT/Elements-bulkk/mp-149_bulk_PBEBO"
+    filename = "JVASP-1002.xml"
+    VaspToApiXmlSchema(folder=folder).write_xml(filename=filename)
+
     folder = "/rk2/knc6/JARVIS-DFT/2D-1L/POSCAR-mp-2815-1L.vasp_PBEBO"
     filename = "JVASP-664.xml"
     VaspToApiXmlSchema(folder=folder).write_xml(filename=filename)

diff --git a/setup.py b/setup.py
@@ -11,20 +11,17 @@
 
 setup(
     name="jarvis-tools",
-
-    version="2020.10.19",
-
+    version="2020.10.20",
     long_description=long_d,
     install_requires=[
-        "numpy",
-        "scipy",
-        "matplotlib",
-        "spglib",
-        "joblib",
-        "requests",
-        "toolz",
-        "xmltodict",
-        "pytest",
+        "numpy>=1.19.1",
+        "scipy>=1.4.1",
+        "matplotlib>=3.0.0",
+        "spglib>=1.14.1",
+        "joblib>=0.14.1",
+        "requests>=2.23.0",
+        "toolz>=0.9.0",
+        "xmltodict>=0.11.0",
     ],
     package_data={
         "jarvis.core": ["Elements.json", "element_charge.json"],
@@ -41,6 +38,8 @@
         "jarvis.io.vasp": ["default_potcars.json"],
         "jarvis.analysis.solarefficiency": ["am1.5G.dat"],
         "jarvis.io.wannier": ["default_semicore.json"],
+        "jarvis.analysis.diffraction": ["atomic_scattering_params.json"],
+        "jarvis": ["LICENSE.rst"],
     },
     extras_require={
         "ai": [

diff --git a/shell.nix b/shell.nix
@@ -20,6 +20,7 @@ in
        pytest
        bokeh
        networkx
+       xmltodict
      ];
      src=builtins.filterSource (path: type: type != "directory" || baseNameOf path != ".git") ./.;
      preShellHook = ''