Added OQMD, MP, QM9 CFID datasets and VASP API XML update for phonons. (

#130) * Added OQMD, MP, QM9 CFID datasets. * Added OQMD, MP, QM9 CFID datasets. * vasp2xml schema update.
usnistgov · Oct 20, 2020 · 66cfa96 · 66cfa96
1 parent d18dc61
commit 66cfa96
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Showing 4 changed files with 46 additions and 33 deletions.
diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2020.10.18"
+__version__ = "2020.10.19"
diff --git a/jarvis/db/figshare.py b/jarvis/db/figshare.py
@@ -20,11 +20,22 @@ def datasets(dataset=""):
         url = "https://ndownloader.figshare.com/files/22471022"
         js_tag = "jdft_3d-4-26-2020.json"
         print("Obtaining 3D dataset ...")
-
     elif dataset == "cfid_3d":
         url = "https://ndownloader.figshare.com/files/22470818"
         js_tag = "jml_3d-4-26-2020.json"
-        print("Obtaining 3D CFID dataset ...")
+        print("Obtaining JARVIS-3D CFID dataset 37k...")
+    elif dataset == "mp_3d":
+        url = "https://ndownloader.figshare.com/files/24979850"
+        js_tag = "CFID_mp_desc_data_84k.json"
+        print("Obtaining Materials Project-3D CFID dataset 84k...")
+    elif dataset == "oqmd_3d":
+        url = "https://ndownloader.figshare.com/files/24981170"
+        js_tag = "CFID_OQMD_460k.json"
+        print("Obtaining OQMD-3D CFID dataset 460k...")
+    elif dataset == "qm9":
+        url = "https://ndownloader.figshare.com/files/25159592"
+        js_tag = "qm9_data_cfid.json"
+        print("Obtaining QM9-molecule CFID dataset 134k...")
     else:
         ValueError("Dataset doesnt exist", dataset)
     return url, js_tag

diff --git a/jarvis/db/vasp_to_xml.py b/jarvis/db/vasp_to_xml.py
@@ -17,7 +17,8 @@
 from jarvis.analysis.thermodynamics.energetics import form_enp
 from jarvis.tasks.boltztrap.run import run_boltztrap
 from jarvis.tasks.phonopy.run import run_phonopy
-# from jarvis.io.phonopy.outputs import bandstructure_plot
+
+from jarvis.io.phonopy.outputs import bandstructure_plot
 from jarvis.ai.pkgs.utils import get_ml_data
 from jarvis.analysis.diffraction.xrd import XRD
 import numpy as np
@@ -1188,7 +1189,7 @@ def elastic_props(
         if os.path.isfile(totdos):
 
             mesh_yaml = outcar.replace("OUTCAR", "mesh.yaml")
-            # band_yaml = outcar.replace("OUTCAR", "band.yaml")
+            band_yaml = outcar.replace("OUTCAR", "band.yaml")
             with open(mesh_yaml, "r") as f:
                 doc = yaml.load(f)
             nmodes = doc["phonon"][0]["band"]
@@ -1231,32 +1232,32 @@ def elastic_props(
             )
 
             # Comment until 4 MB text size error
-            # frequencies, distances, labels,label_points = bandstructure_plot(
-            #    band_yaml
-            # )
-            # tmp = ""
-            # for i in range(np.array(frequencies).shape[1]):
-            #    tmp += ",".join(map(str, np.array(frequencies)[:, i])) + ";"
-            # line += (
-            #    "<phonon_bandstructure_distances>'"
-            #    + ",".join(map(str, distances))
-            #    + "'</phonon_bandstructure_distances>"
-            # )
-            # line += (
-            #    "<phonon_bandstructure_frequencies>'"
-            #    + tmp
-            #    + "'</phonon_bandstructure_frequencies>"
-            # )
-            # line += (
-            #    "<phonon_bandstructure_labels>'"
-            #    + ",".join(map(str, labels))
-            #    + "'</phonon_bandstructure_labels>"
-            # )
-            # line += (
-            #    "<phonon_bandstructure_label_points>'"
-            #    + ",".join(map(str, label_points))
-            #    + "'</phonon_bandstructure_label_points>"
-            # )
+            frequencies, distances, labels, label_points = bandstructure_plot(
+                band_yaml
+            )
+            tmp = ""
+            for i in range(np.array(frequencies).shape[1]):
+                tmp += ",".join(map(str, np.array(frequencies)[:, i])) + ";"
+            line += (
+                "<phonon_bandstructure_distances>'"
+                + ",".join(map(str, distances))
+                + "'</phonon_bandstructure_distances>"
+            )
+            line += (
+                "<phonon_bandstructure_frequencies>'"
+                + tmp
+                + "'</phonon_bandstructure_frequencies>"
+            )
+            line += (
+                "<phonon_bandstructure_labels>'"
+                + ",".join(map(str, labels))
+                + "'</phonon_bandstructure_labels>"
+            )
+            line += (
+                "<phonon_bandstructure_label_points>'"
+                + ",".join(map(str, label_points))
+                + "'</phonon_bandstructure_label_points>"
+            )
         return line
 
     def main_elastic(self):
@@ -1267,6 +1268,7 @@ def main_elastic(self):
         data = ""
 
         for i in glob.glob("MAIN-ELAST*.json"):
+
             try:
                 folder = i.split(".json")[0]
                 out = os.getcwd() + "/" + folder + "/OUTCAR"
@@ -1707,12 +1709,12 @@ 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)
 
+"""
     folder = "/rk2/knc6/JARVIS-DFT/TE-bulk/mp-541837_bulk_PBEBO"
     filename = "JVASP-1067.xml"
     VaspToApiXmlSchema(folder=folder).write_xml(filename=filename)

diff --git a/setup.py b/setup.py
@@ -12,7 +12,7 @@
 setup(
     name="jarvis-tools",
 
-    version="2020.10.18",
+    version="2020.10.19",
 
     long_description=long_d,
     install_requires=[