Develop

environment.yml

@@ -246,19 +246,19 @@ dependencies:
       - python-dateutil==2.8.2
       - pyyaml==6.0.1
       - pyyaml-env-tag==0.1
-      - qiskit==0.41.1
-      - qiskit-aer==0.11.2
-      - qiskit-ibmq-provider==0.20.1
-      - qiskit-terra==0.23.2
+      - qiskit>=2.3.1
+      - qiskit-aer>=0.17.2
+      - qiskit_algorithms>=0.4.1
+      - rustworkx
       - regex==2023.12.25
       - requests==2.28.2
       - requests-ntlm==1.1.0
       - rustworkx==0.14.2
       - scikit-learn==1.4.1.post1
       - scipy==1.12.0
       - semantic-version==2.6.0
-      - spglib==2.3.1
-      - stevedore==5.2.0
+      - spglib==2.7.0
+      - stevedore==5.7.0
       - symengine==0.11.0
       - sympy==1.12
       - threadpoolctl==3.3.0

jarvis/__init__.py

@@ -1,6 +1,6 @@
 """Version number."""
 
-__version__ = "2026.4.2"
+__version__ = "2026.6.12"
 
 import os
 

jarvis/core/atoms.py

@@ -1361,17 +1361,19 @@ def pymatgen_converter(self):
     def phonopy_converter(self, pbc=True):
         """Get phonopy representation of the atoms object."""
         try:
-            from phonopy.structure.atoms import Atoms as PhonopyAtoms
-
-            return PhonopyAtoms(
-                symbols=self.elements,
-                positions=self.cart_coords,
-                pbc=pbc,
-                cell=self.lattice_mat,
-            )
+            from phonopy.structure.atoms import PhonopyAtoms
         except Exception:
             print("Requires phonopy for this functionality.")
-            pass
+            return
+        kw = dict(
+            symbols=self.elements,
+            positions=self.cart_coords,
+            cell=self.lattice_mat,
+        )
+        try:
+            return PhonopyAtoms(pbc=pbc, **kw)   # phonopy < 4
+        except TypeError:
+            return PhonopyAtoms(**kw)            # phonopy >= 4 dropped pbc=
 
     def ase_converter(self, pbc=True):
         """Get ASE representation of the atoms object."""

jarvis/core/specie.py

@@ -316,14 +316,11 @@ def get_node_attributes(species, atom_features="atomic_number"):
             # For alternative features use
             # get_digitized_feats_hot_encoded()
             i = json.load(f)
-        try:
-            return i[key]
-        except KeyError:
-            print(f"warning: could not load CGCNN features for {key}")
-            print("Setting it to max atomic number available here, 103")
-            # TODO Check for the error in oqmd_3d_no_cfid dataset
-            # return i['Lr']
-            return i["100"]
+        # cgcnn.json defines elements 1-100; species outside that set
+        # (trans-fermium placeholders, or an unrecognized 'nan' symbol)
+        # fall back to element 100's features silently -- these never occur
+        # in real structures, so the old print was pure noise.
+        return i.get(key, i["100"])
 
 
 keys = [

jarvis/db/figshare.py

@@ -40,9 +40,9 @@ def get_db_info():
         ],
         # https://doi.org/10.6084/m9.figshare.6815699
         "dft_3d": [
-            "https://ndownloader.figshare.com/files/38521619",
-            "jdft_3d-12-12-2022.json",
-            "Obtaining 3D dataset 76k ...",
+            "https://ndownloader.figshare.com/files/64391379",
+            "jdft_3d-9-24-2025.json",
+            "Obtaining 3D dataset 94k ...",
             "https://doi.org/10.1016/j.commatsci.2025.114063"
             # "https://www.nature.com/articles/s41524-020-00440-1"
             + "\nOther versions:https://doi.org/10.6084/m9.figshare.6815699",
@@ -55,6 +55,15 @@ def get_db_info():
             "https://www.nature.com/articles/s41524-020-00440-1",
         ],
         # https://doi.org/10.6084/m9.figshare.6815699
+        "dft_3d_2022": [
+            "https://ndownloader.figshare.com/files/38521619",
+            "jdft_3d-12-12-2022.json",
+            "Obtaining 3D dataset 76k ...",
+            "https://doi.org/10.1016/j.commatsci.2025.114063"
+            # "https://www.nature.com/articles/s41524-020-00440-1"
+            + "\nOther versions:https://doi.org/10.6084/m9.figshare.6815699",
+        ],
+        # https://doi.org/10.6084/m9.figshare.6815699
         "dft_3d_2021": [
             "https://ndownloader.figshare.com/files/29204826",
             "jdft_3d-8-18-2021.json",
@@ -86,6 +95,84 @@ def get_db_info():
             "Obtaining ALIGNN-FF training DB 300k ...",
             "https://doi.org/10.1039/D2DD00096B",
         ],
+        # ALIGNN2 datasets (Figshare project 279395)
+        # https://doi.org/10.6084/m9.figshare.33325302
+        "alignn_ff_db2": [
+            "https://ndownloader.figshare.com/files/67810098",
+            "fd_id_prop.json",
+            "Obtaining ALIGNN-FF finite-difference (FD) training DB 1.18M ...",
+            "https://doi.org/10.6084/m9.figshare.33325302",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33325272
+        "dfpt_tensors": [
+            "https://ndownloader.figshare.com/files/67810035",
+            "dfpt.json",
+            "Obtaining JARVIS-DFT DFPT tensors (Born charges, dielectric, piezo) ...",
+            "https://doi.org/10.6084/m9.figshare.33325272",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33325275
+        "a2f": [
+            "https://ndownloader.figshare.com/files/67810083",
+            "a2f_id_prop.json",
+            "Obtaining Eliashberg alpha^2F(omega) spectral-function dataset ...",
+            "https://doi.org/10.6084/m9.figshare.33325275",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33325278
+        "elastic_tensor": [
+            "https://ndownloader.figshare.com/files/67810041",
+            "id_prop_elastic.json",
+            "Obtaining JARVIS-DFT elastic stiffness tensor (Cij, 6x6) ...",
+            "https://doi.org/10.6084/m9.figshare.33325278",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33325281
+        "multitask_eps": [
+            "https://ndownloader.figshare.com/files/67810086",
+            "eps_id_prop.json",
+            "Obtaining JARVIS-DFT multitask dielectric (eps) dataset ...",
+            "https://doi.org/10.6084/m9.figshare.33325281",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33325284
+        "chg_mag": [
+            "https://ndownloader.figshare.com/files/67810089",
+            "chg_mag_id_prop.json",
+            "Obtaining JARVIS-DFT per-atom charge (Bader) + magnetic-moment ...",
+            "https://doi.org/10.6084/m9.figshare.33325284",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33325287
+        "ir_alignn": [
+            "https://ndownloader.figshare.com/files/67810092",
+            "ir_id_prop.json",
+            "Obtaining JARVIS-DFT DFPT infrared (IR) spectra dataset ...",
+            "https://doi.org/10.6084/m9.figshare.33325287",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33325290
+        "raman_alignn": [
+            "https://ndownloader.figshare.com/files/67810095",
+            "raman_id_prop.json",
+            "Obtaining JARVIS Raman spectra dataset (ALIGNN2 form) ...",
+            "https://doi.org/10.6084/m9.figshare.33325290",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33325293
+        "edos_alignn": [
+            "https://ndownloader.figshare.com/files/67810056",
+            "edos.json",
+            "Obtaining JARVIS-DFT electronic DOS (300-bin) dataset ...",
+            "https://doi.org/10.6084/m9.figshare.33325293",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33325299
+        "pdos_alignn": [
+            "https://ndownloader.figshare.com/files/67810062",
+            "pdos.json",
+            "Obtaining JARVIS-DFT phonon DOS (200-bin) dataset ...",
+            "https://doi.org/10.6084/m9.figshare.33325299",
+        ],
+        # https://doi.org/10.6084/m9.figshare.33336759
+        "ltc_alignn": [
+            "https://ndownloader.figshare.com/files/67841763",
+            "ltc_id_prop.json",
+            "Obtaining lattice thermal conductivity (log10 kappa_L) dataset on OQMD structures ...",
+            "https://doi.org/10.6084/m9.figshare.33336759",
+        ],
         "mp_3d_2020": [
             "https://ndownloader.figshare.com/files/26791259",
             "all_mp.json",
@@ -99,6 +186,12 @@ def get_db_info():
             "Obtaining MEGNET-3D CFID dataset 69k...",
             "https://pubs.acs.org/doi/10.1021/acs.chemmater.9b01294",
         ],
+        "matpes": [
+            "https://ndownloader.figshare.com/files/66983876",
+            "matpes.json",
+            "Obtaining MATPES-PBE dataset 434k...",
+            "https://matpes.ai",
+        ],
         # https://doi.org/10.6084/m9.figshare.14745435
         "megnet2": [
             "https://ndownloader.figshare.com/files/28332741",
@@ -172,7 +265,7 @@ def get_db_info():
         ],
         # https://doi.org/10.6084/m9.figshare.14912820.v1
         "cod_200": [
-            "https://figshare.com/ndownloader/files/63463986",
+            "https://ndownloader.figshare.com/files/63463986",
             "cod_200.json",
             "Obtaining COD dataset 237k",
             "https://doi.org/10.1107/S1600576720016532",