Merge pull request #179 from usnistgov/develop

Develop

README.md

@@ -247,6 +247,9 @@ from alignn.ff.ff import AlignnAtomwiseCalculator,default_path
 from jarvis.io.vasp.inputs import Poscar
 import numpy as np
 import matplotlib.pyplot as plt
+from ase.constraints import ExpCellFilter
+from ase.optimize.fire import FIRE
+from jarvis.core.atoms import ase_to_atoms
 model_path = default_path()
 calc = AlignnAtomwiseCalculator(path=model_path)
 # Source: https://www.ctcms.nist.gov/~knc6/static/JARVIS-DFT/JVASP-1002.xml
@@ -261,9 +264,22 @@ Cartesian
 3.92483875 2.77528125 6.7980237500000005
 0.56069125 0.39646875 0.9711462500000001
 """
+def general_relaxer(atoms="", calculator="", fmax=0.05, steps=150,relax=True):
+    ase_atoms = atoms.ase_converter()
+    ase_atoms.calc = calculator
+    if not relax:
+         return ase_atoms.get_potential_energy()
+    ase_atoms = ExpCellFilter(ase_atoms)
+    dyn = FIRE(ase_atoms)
+    dyn.run(fmax=fmax, steps=steps)
+    return ase_to_atoms(ase_atoms.atoms)
+
 dx=np.arange(-0.1, 0.1, 0.01)
 atoms=Poscar.from_string(poscar).atoms
-print(atoms)
+print('Intital\n',atoms)
+atoms = general_relaxer(atoms=atoms,calculator=calc)
+print('Final\n',atoms)
+
 y = []
 vol = []
 for i in dx:
@@ -278,8 +294,8 @@ for i in dx:
 plt.plot(vol,y,'-o')
 plt.xlabel('Volume ($\AA^3$)')
 plt.ylabel('Total energy (eV)')
-plt.savefig('Si_JVASP-1002.png')
-plt.close()
+# plt.savefig('Si_JVASP-1002.png')
+# plt.close()
 ```
 
 

alignn/__init__.py

@@ -1,3 +1,3 @@
 """Version number."""
 
-__version__ = "2024.12.02"
+__version__ = "2024.12.12"

alignn/config.py

@@ -7,6 +7,7 @@
 from alignn.utils import BaseSettings
 from alignn.models.alignn import ALIGNNConfig
 from alignn.models.alignn_atomwise import ALIGNNAtomWiseConfig
+from alignn.models.ealignn_atomwise import eALIGNNAtomWiseConfig
 
 # import torch
 
@@ -188,6 +189,7 @@ class TrainingConfig(BaseSettings):
     log_tensorboard: bool = False
     standard_scalar_and_pca: bool = False
     use_canonize: bool = True
+    compute_line_graph: bool = True
     num_workers: int = 4
     cutoff: float = 8.0
     cutoff_extra: float = 3.0
@@ -210,4 +212,5 @@ class TrainingConfig(BaseSettings):
     model: Union[
         ALIGNNConfig,
         ALIGNNAtomWiseConfig,
+        eALIGNNAtomWiseConfig,
     ] = ALIGNNAtomWiseConfig(name="alignn_atomwise")

alignn/examples/sample_data_ff/econfig_example_atomwise.json

@@ -0,0 +1,56 @@
+{
+    "version": "112bbedebdaecf59fb18e11c929080fb2f358246",
+    "dataset": "user_data",
+    "target": "target",
+    "atom_features": "cgcnn",
+    "neighbor_strategy": "radius_graph",
+    "id_tag": "jid",
+    "dtype": "float32",
+    "random_seed": 123,
+    "classification_threshold": null,
+    "n_val": null,
+    "n_test": null,
+    "n_train": null,
+    "train_ratio": 0.8,
+    "val_ratio": 0.1,
+    "test_ratio": 0.1,
+    "target_multiplication_factor": null,
+    "epochs": 3,
+    "batch_size": 2,
+    "weight_decay": 1e-05,
+    "learning_rate": 0.001,
+    "warmup_steps": 2000,
+    "criterion": "l1",
+    "optimizer": "adamw",
+    "scheduler": "onecycle",
+    "pin_memory": false,
+    "save_dataloader": false,
+    "write_checkpoint": true,
+    "write_predictions": true,
+    "store_outputs": false,
+    "compute_line_graph": false,
+    "progress": true,
+    "log_tensorboard": false,
+    "standard_scalar_and_pca": false,
+    "use_canonize": true,
+    "num_workers": 0,
+    "cutoff": 4.0,
+    "max_neighbors": 12,
+    "keep_data_order": true,
+    "distributed": false,
+    "use_lmdb": true,
+    "model": {
+        "name": "ealignn_atomwise",
+        "atom_input_features": 92,
+        "calculate_gradient": true,
+        "atomwise_output_features": 0,
+        "alignn_layers": 1,
+        "gcn_layers": 1,
+        "hidden_features": 64,
+        "output_features": 1,
+        "graphwise_weight": 0.85,
+        "gradwise_weight": 0.05,
+        "atomwise_weight": 0.0,
+        "stresswise_weight": 0.05
+    }
+}

alignn/ff/all_models_alignn.json

@@ -0,0 +1,59 @@
+{
+    "jv_formation_energy_peratom_alignn": "https://figshare.com/ndownloader/files/31458679",
+    "jv_optb88vdw_total_energy_alignn": "https://figshare.com/ndownloader/files/31459642",
+    "jv_optb88vdw_bandgap_alignn": "https://figshare.com/ndownloader/files/31459636",
+    "jv_mbj_bandgap_alignn": "https://figshare.com/ndownloader/files/31458694",
+    "jv_spillage_alignn": "https://figshare.com/ndownloader/files/31458736",
+    "jv_slme_alignn": "https://figshare.com/ndownloader/files/31458727",
+    "jv_bulk_modulus_kv_alignn": "https://figshare.com/ndownloader/files/31458649",
+    "jv_shear_modulus_gv_alignn": "https://figshare.com/ndownloader/files/31458724",
+    "jv_n-Seebeck_alignn": "https://figshare.com/ndownloader/files/31458718",
+    "jv_n-powerfact_alignn": "https://figshare.com/ndownloader/files/31458712",
+    "intermat_cbm": "https://figshare.com/ndownloader/files/45392908",
+    "intermat_vbm": "https://figshare.com/ndownloader/files/45392914",
+    "intermat_phi": "https://figshare.com/ndownloader/files/45392911",
+    "jv_magmom_oszicar_alignn": "https://figshare.com/ndownloader/files/31458685",
+    "jv_kpoint_length_unit_alignn": "https://figshare.com/ndownloader/files/31458682",
+    "jv_avg_elec_mass_alignn": "https://figshare.com/ndownloader/files/31458643",
+    "jv_avg_hole_mass_alignn": "https://figshare.com/ndownloader/files/31458646",
+    "jv_epsx_alignn": "https://figshare.com/ndownloader/files/31458667",
+    "jv_mepsx_alignn": "https://figshare.com/ndownloader/files/31458703",
+    "jv_max_efg_alignn": "https://figshare.com/ndownloader/files/31458691",
+    "jv_ehull_alignn": "https://figshare.com/ndownloader/files/31458658",
+    "jv_dfpt_piezo_max_dielectric_alignn": "https://figshare.com/ndownloader/files/31458652",
+    "jv_dfpt_piezo_max_dij_alignn": "https://figshare.com/ndownloader/files/31458655",
+    "jv_exfoliation_energy_alignn": "https://figshare.com/ndownloader/files/31458676",
+    "jv_supercon_tc_alignn": "https://figshare.com/ndownloader/files/38789199",
+    "jv_supercon_edos_alignn": "https://figshare.com/ndownloader/files/39946300",
+    "jv_supercon_debye_alignn": "https://figshare.com/ndownloader/files/39946297",
+    "jv_supercon_a2F_alignn": "https://figshare.com/ndownloader/files/38801886",
+    "mp_e_form_alignn": "https://figshare.com/ndownloader/files/31458811",
+    "mp_gappbe_alignn": "https://figshare.com/ndownloader/files/31458814",
+    "tinnet_O_alignn": "https://figshare.com/ndownloader/files/41962800",
+    "tinnet_N_alignn": "https://figshare.com/ndownloader/files/41962797",
+    "tinnet_OH_alignn": "https://figshare.com/ndownloader/files/41962803",
+    "AGRA_O_alignn": "https://figshare.com/ndownloader/files/41966619",
+    "AGRA_OH_alignn": "https://figshare.com/ndownloader/files/41966610",
+    "AGRA_CHO_alignn": "https://figshare.com/ndownloader/files/41966643",
+    "AGRA_CO_alignn": "https://figshare.com/ndownloader/files/41966634",
+    "AGRA_COOH_alignn": "https://figshare.com/ndownloader/41966646",
+    "qm9_U0_alignn": "https://figshare.com/ndownloader/files/31459054",
+    "qm9_U_alignn": "https://figshare.com/ndownloader/files/31459051",
+    "qm9_alpha_alignn": "https://figshare.com/ndownloader/files/31459027",
+    "qm9_gap_alignn": "https://figshare.com/ndownloader/files/31459036",
+    "qm9_G_alignn": "https://figshare.com/ndownloader/files/31459033",
+    "qm9_HOMO_alignn": "https://figshare.com/ndownloader/files/31459042",
+    "qm9_LUMO_alignn": "https://figshare.com/ndownloader/files/31459045",
+    "qm9_ZPVE_alignn": "https://figshare.com/ndownloader/files/31459057",
+    "hmof_co2_absp_alignn": "https://figshare.com/ndownloader/files/31459198",
+    "hmof_max_co2_adsp_alignn": "https://figshare.com/ndownloader/files/31459207",
+    "hmof_surface_area_m2g_alignn": "https://figshare.com/ndownloader/files/31459222",
+    "hmof_surface_area_m2cm3_alignn": "https://figshare.com/ndownloader/files/31459219",
+    "hmof_pld_alignn": "https://figshare.com/ndownloader/files/31459216",
+    "hmof_lcd_alignn": "https://figshare.com/ndownloader/files/31459201",
+    "hmof_void_fraction_alignn": "https://figshare.com/ndownloader/files/31459228",
+    "ocp2020_all": "https://figshare.com/ndownloader/files/41411025",
+    "ocp2020_100k": "https://figshare.com/ndownloader/files/41967303",
+    "ocp2020_10k": "https://figshare.com/ndownloader/files/41967330",
+    "jv_pdos_alignn": "https://figshare.com/ndownloader/files/36757005"
+}

alignn/ff/all_models_ff.json → alignn/ff/all_models_alignn_atomwise.json

@@ -2,6 +2,14 @@
     "v12.2.2024_dft_3d_307k": "https://figshare.com/ndownloader/files/50904240",
     "v12.2.2024_mp_1.5mill": "https://figshare.com/ndownloader/files/50904783",
     "v12.2.2024_mp_187k": "https://figshare.com/ndownloader/files/50904801",
+    "v2024.12.12_dft_3d_multi_prop": "https://figshare.com/ndownloader/files/52025186",
+    "alex_band_gap": "https://figshare.com/ndownloader/files/51993641",
+    "alex_dos_pa": "https://figshare.com/ndownloader/files/51993653",
+    "alex_e_form": "https://figshare.com/ndownloader/files/51993647",
+    "alex_e_hull": "https://figshare.com/ndownloader/files/51993644",
+    "alex_e_total": "https://figshare.com/ndownloader/files/51993650",
+    "alex_mag_per_vol": "https://figshare.com/ndownloader/files/51993659",
+    "alex_vol_pa": "https://figshare.com/ndownloader/files/51993656",
     "v10.30.2024_dft_3d_307k": "https://figshare.com/ndownloader/files/50634327",
     "v10.30.2024_mp_168k": "https://figshare.com/ndownloader/files/50634318",
     "v8.29.2024_dft_3d": "https://figshare.com/ndownloader/files/48889834",