Merge pull request #2 from usnistgov/develop

Develop

README.md

@@ -1,5 +1,5 @@
 ![alt text](https://github.com/usnistgov/intermat/actions/workflows/main.yml/badge.svg)
-
+[![name](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/gist/knc6/0d9aa89f671687c6e925eea2be9b824a/intermat_gettingstarted.ipynb)
 <!-- [![name](https://colab.research.google.com/assets/colab-badge.svg)](https://gist.github.com/knc6/c00ee48c524f5000e7f80a974bc6dc71)
 [![name](https://colab.research.google.com/assets/colab-badge.svg)](https://gist.github.com/knc6/debf9cbefa9a290502d73fd3cbc4fd69)
 [![name](https://colab.research.google.com/assets/colab-badge.svg)](https://gist.github.com/knc6/7492b51b371a8e9dbaa01d76bb438467)  -->

intermat/calculators.py

@@ -11,8 +11,6 @@
 from jarvis.tasks.qe.qe import QEjob
 import numpy as np
 from jarvis.core.atoms import Atoms, ase_to_atoms
-from ase.optimize.fire import FIRE
-from ase.constraints import ExpCellFilter
 from jarvis.db.jsonutils import loadjson
 
 
@@ -216,9 +214,9 @@ def predict(
                 if "potential" not in self.extra_params:
                     # Download from
                     # https://doi.org/10.6084/m9.figshare.24187602
-                    self.extra_params["potential"] = (
-                        "Mishin-Ni-Al-Co-2013.eam.alloy"
-                    )
+                    self.extra_params[
+                        "potential"
+                    ] = "Mishin-Ni-Al-Co-2013.eam.alloy"
 
                 from ase.calculators.eam import EAM
 
@@ -308,6 +306,8 @@ def predict(
                 info["atoms"] = ase_to_atoms(atoms)
                 return info  # ,forces,stress
             elif self.relax_atoms and not self.relax_cell:
+                from ase.optimize.fire import FIRE
+
                 optimizer = FIRE
                 dyn = optimizer(atoms)
                 dyn.run(fmax=self.fmax, steps=self.steps)
@@ -317,6 +317,9 @@ def predict(
                 info["atoms"] = atoms
                 return info  # ,forces,stress
             elif self.relax_cell:
+                from ase.optimize.fire import FIRE
+                from ase.constraints import ExpCellFilter
+
                 atoms = ExpCellFilter(atoms)
                 optimizer = FIRE
                 dyn = optimizer(atoms)

intermat/config.py

@@ -126,7 +126,7 @@
     maxiter=100,
     convergence={"energy": 1},
     # convergence={"density": 1e-12, "energy": 1e-1},
-    eigensolver=Davidson(niter=2),
+    # eigensolver=Davidson(niter=2),
     out_file="gs.out",
     out_gpw="out.gpw",
     kp_length=10,

intermat/run_intermat.py

@@ -13,6 +13,7 @@
 from intermat.config import IntermatConfig
 from jarvis.db.jsonutils import loadjson
 from jarvis.db.figshare import get_jid_data
+from jarvis.db.jsonutils import dumpjson
 
 
 def main(config_file_or_dict):
@@ -21,17 +22,24 @@ def main(config_file_or_dict):
     else:
         config_dat = loadjson(config_file_or_dict)
     # A few default setting check
-    if not os.path.exists(config_dat["lammps_params"]["pair_coeff"]):
+    pprint.pprint(config_dat)
+    if "lammps_params" in config_dat and not os.path.exists(
+        config_dat["lammps_params"]["pair_coeff"]
+    ):
         config_dat["lammps_params"]["pair_coeff"] = os.path.join(
             os.path.dirname(__file__),
             "tests",
             "Mishin-Ni-Al-Co-2013.eam.alloy",
         )
-    if not os.path.exists(config_dat["lammps_params"]["control_file"]):
+    if "lammps_params" in config_dat and not os.path.exists(
+        config_dat["lammps_params"]["control_file"]
+    ):
         config_dat["lammps_params"]["control_file"] = os.path.join(
             os.path.dirname(__file__), "tests", "relax.mod"
         )
-    if not os.path.exists(config_dat["potential"]):
+    if "potential" in config_dat and not os.path.exists(
+        config_dat["potential"]
+    ):
         config_dat["potential"] = os.path.join(
             os.path.dirname(__file__),
             "tests",
@@ -87,6 +95,7 @@ def main(config_file_or_dict):
             + " It might be energetically very high/less stable."
         )
         print(combined_atoms[0])
+        combined_atoms = combined_atoms[0]
     else:
         if config.verbose:
             for ii, i in enumerate(combined_atoms):
@@ -96,7 +105,7 @@ def main(config_file_or_dict):
     wads = ""
     if config.calculator_method != "":
         # print("combined_atoms", combined_atoms)
-
+        print("config.calculator_method", config.calculator_method)
         wads = x.calculate_wad(
             method=config.calculator_method,
             do_surfaces=config.do_surfaces,
@@ -108,12 +117,14 @@ def main(config_file_or_dict):
         combined_atoms = Atoms.from_dict(
             x.generated_interfaces[index]["generated_interface"]
         )
-        print("Generated interface:\n", combined_atoms)
-        if config.plot_wads:
-
+        # print("Generated interface:\n", combined_atoms)
+        if config.plot_wads and config.disp_intvl != 0:
+            # xy = np.array(x.xy)
+            # print('xy', xy)
             X = x.X
             Y = x.Y
-
+            # X = xy[:,0]
+            # Y = xy[:,1]
             wads = np.array(wads).reshape(len(X), len(Y))
 
             fig, ax = plt.subplots(subplot_kw={"projection": "3d"})
@@ -126,13 +137,16 @@ def main(config_file_or_dict):
             # import plotly.graph_objects as go
             # fig = go.Figure(data=[go.Surface(z=wads, x=X, y=Y)])
             # fig.show()
+            wads = wads.tolist()
     t2 = time.time()
     print("Time taken:", t2 - t1)
     info = {}
-    info["syste"] = combined_atoms
+    # print("combined_atoms", combined_atoms)
+    info["systems"] = combined_atoms.to_dict()
     info["time_taken"] = t2 - t1
     info["wads"] = wads
-    return wads
+    print("info", info)
+    return info
 
 
 if __name__ == "__main__":
@@ -145,4 +159,5 @@ def main(config_file_or_dict):
         help="Settings file for intermat.",
     )
     args = parser.parse_args(sys.argv[1:])
-    main(config_file=args.config_file)
+    results = main(config_file_or_dict=args.config_file)
+    dumpjson(data=results, filename="intermat_results.json")

setup.py

@@ -13,7 +13,8 @@
         "numpy>=1.22.0",
         "scipy>=1.6.3",
         "jarvis-tools>=2021.07.19",
-        "alignn",
+        "pydantic_settings",
+        # "alignn",
     ],
     long_description=long_description,
     long_description_content_type="text/markdown",
@@ -24,5 +25,8 @@
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
+    scripts=[
+        "intermat/run_intermat.py",
+    ],
     python_requires=">=3.8",
 )