Develop

jarvis/__init__.py

@@ -1,6 +1,6 @@
 """Version number."""
 
-__version__ = "2024.3.24"
+__version__ = "2024.3.30"
 
 import os
 

jarvis/db/restapi.py

@@ -1,4 +1,5 @@
 """Module to access or upload data in JARVIS-API."""
+
 import requests
 import pprint
 import os
@@ -9,6 +10,25 @@
 import json
 
 
+def jarvisdft_optimade(
+    prefix="https://jarvis.nist.gov/optimade/jarvisdft/v1/structures/?filter=",
+    query="elements HAS  ALL C,Si",
+):
+    url = prefix + query
+    vals = []
+    while True:
+        if url is not None:
+            # print('url', url)
+            response = requests.get(url)
+            data = response.json()["data"]
+            for i in data:
+                vals.append(i)
+            url = response.json()["links"]["next"]
+        else:
+            break
+    return vals
+
+
 class Api(object):
     """Class for handling functions for JARVIS-API."""
 

jarvis/io/lammps/inputs.py

@@ -61,10 +61,10 @@ def atoms_to_lammps(self, atoms, origin=(0, 0, 0)):
         xhi = a + xlo
         m = atoms.lattice._lat
         xy = np.dot(m[1], m[0] / a)
-        yhi = np.sqrt(b ** 2 - xy ** 2) + ylo
+        yhi = np.sqrt(b**2 - xy**2) + ylo
         xz = np.dot(m[2], m[0] / a)
         yz = (np.dot(m[1], m[2]) - xy * xz) / (yhi - ylo)
-        zhi = np.sqrt(c ** 2 - xz ** 2 - yz ** 2) + zlo
+        zhi = np.sqrt(c**2 - xz**2 - yz**2) + zlo
         rot_matrix = np.linalg.solve(
             [[xhi - xlo, 0, 0], [xy, yhi - ylo, 0], [xz, yz, zhi - zlo]], m
         )
@@ -94,7 +94,7 @@ def read_data(
         filename="lammps.data",
         element_order=[],
         potential_file="pot.mod",
-        verbose=True,
+        verbose=False,
         has_charges=True,
     ):
         """Read Lammps data file."""
@@ -179,7 +179,7 @@ def read_data(
                     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])
+                    # print(coords[-1])
         f.close()
         # print ("info",(typ),'coo',(coords),'latt',lat)
         typ_sp = [str(i, "utf-8") for i in typ]

jarvis/io/lammps/outputs.py

@@ -1,10 +1,10 @@
 """Function to analze LAMMPS output."""
+
 import numpy as np
 import glob
 import os
 from jarvis.analysis.elastic.tensor import ElasticTensor
 from jarvis.io.lammps.inputs import LammpsData
-from jarvis.io.phonopy.outputs import bandstructure_plot, total_dos
 from jarvis.core.atoms import Atoms
 
 
@@ -251,6 +251,8 @@ def parse_material_calculation_folder(
 
     with optimization, vacancy, phonon, surface etc.
     """
+    from jarvis.io.phonopy.outputs import bandstructure_plot, total_dos
+
     cwd = os.getcwd()
     jid_file = os.path.join(path, "JARVISFF-ID")
     if os.path.exists(jid_file):
@@ -375,7 +377,9 @@ def parse_material_calculation_folder(
     return info
 
 
-def parse_full_ff_folder(path="Mishin-Ni-Al-2009.eam.alloy_nist",):
+def parse_full_ff_folder(
+    path="Mishin-Ni-Al-2009.eam.alloy_nist",
+):
     """Parse complete FF calculation folder."""
     cwd = os.getcwd()
     os.chdir(path)

jarvis/io/qe/inputs.py

@@ -41,7 +41,7 @@ def __init__(
             # Download GBRV PSPs by default
             if url is None:
                 url = (
-                    "http://www.physics.rutgers.edu/"
+                    "https://www.physics.rutgers.edu/"
                     "gbrv/all_pbesol_UPF_v1.5.tar.gz"
                 )
                 print("Please cite for PSPs:")

jarvis/tasks/lammps/lammps.py

@@ -142,11 +142,15 @@ def phonons(
         self, atoms=None, lammps_cmd="", enforce_c_size=15.0, parameters={}
     ):
         """Make Phonon calculation setup."""
-        from phonopy import Phonopy
-        from phonopy.file_IO import (
-            #    parse_FORCE_CONSTANTS,
-            write_FORCE_CONSTANTS,
-        )
+        try:
+            from phonopy import Phonopy
+            from phonopy.file_IO import (
+                #    parse_FORCE_CONSTANTS,
+                write_FORCE_CONSTANTS,
+            )
+        except Exception as exp:
+            print("Phonopy check", exp)
+            pass
 
         bulk = atoms.phonopy_converter()
 

jarvis/tests/testfiles/db/test_restapi.py

@@ -0,0 +1,8 @@
+from jarvis.db.restapi import jarvisdft_optimade
+
+
+def test_optimade():
+    x = jarvisdft_optimade()
+    print(x)
+    print(len(x))
+    assert len(x) > 1

setup.py

@@ -12,7 +12,7 @@
 
 setup(
     name="jarvis-tools",
-    version="2024.3.24",
+    version="2024.3.30",
     long_description=long_d,
     install_requires=[
         "numpy>=1.20.1",
@@ -24,8 +24,8 @@
         "toolz>=0.9.0",
         "xmltodict>=0.11.0",
         "tqdm>=4.41.1",
-        "mkdocs-material>=9.0.5",
-        "markdown>=3.2.1",
+        # "mkdocs-material>=9.0.5",
+        # "markdown>=3.2.1",
         # "absl-py==1.4.0",
     ],
     package_data={