small updates in examples

examples/alanine_nwchem.py

@@ -7,25 +7,23 @@
 from psiflow.learning import SequentialLearning
 from psiflow.metrics import Metrics
 from psiflow.models import NequIPConfig, NequIPModel
-from psiflow.reference import NWChemReference
+from psiflow.reference import PySCFReference
 from psiflow.walkers import BiasedDynamicWalker, DynamicWalker, PlumedBias
 
 
 def get_reference():
-    calculator_kwargs = {
-        "basis": {e: "3-21g" for e in ["H", "C", "O", "N"]},
-        "dft": {
-            "xc": "pw91lda",
-            "mult": 1,
-            "convergence": {
-                "energy": 1e-6,
-                "density": 1e-6,
-                "gradient": 1e-6,
-            },
-            #'disp': {'vdw': 3},
-        },
-    }
-    return NWChemReference(**calculator_kwargs)
+    routine = """
+from pyscf import dft
+
+mf = dft.RKS(molecule)
+mf.xc = 'pbe,pbe'
+
+energy = mf.kernel()
+forces = -mf.nuc_grad_method().kernel()
+"""
+    basis = "cc-pvtz"
+    spin = 0
+    return PySCFReference(routine, basis, spin)
 
 
 def get_bias():
@@ -93,7 +91,7 @@ def main(path_output):
 
     # this is mostly a toy script to test code paths rather
     # than an actually working example
-    data = learning.run(
+    data = learning.run(  # noqa: F841
         model=model,
         reference=reference,
         walkers=walkers_md + walkers_mtd,
@@ -104,3 +102,4 @@ def main(path_output):
     psiflow.load()
     path_output = Path.cwd() / "output"
     main(path_output)
+    psiflow.wait()

examples/copper_emt.py

@@ -1,19 +1,16 @@
-import logging
 from pathlib import Path
 
 import numpy as np
-import requests
 from ase.build import bulk, make_supercell
 
 import psiflow
 from psiflow.committee import Committee
-from psiflow.data import Dataset, FlowAtoms
-from psiflow.learning import CommitteeLearning, SequentialLearning, load_learning
+from psiflow.data import Dataset
+from psiflow.learning import CommitteeLearning, SequentialLearning
 from psiflow.metrics import Metrics
 from psiflow.models import MACEConfig, MACEModel
 from psiflow.reference import EMTReference
-from psiflow.state import load_state
-from psiflow.walkers import DynamicWalker, PlumedBias
+from psiflow.walkers import DynamicWalker
 
 
 def main(path_output):
@@ -22,7 +19,7 @@ def main(path_output):
     path_committee = path_output / "learn_committee"
     path_committee.mkdir(parents=True)
 
-    reference = EMTReference()  # CP2K; PBE-D3(BJ); TZVP
+    reference = EMTReference()
     atoms = make_supercell(bulk("Cu", "fcc", a=3.6, cubic=True), 3 * np.eye(3))
 
     config = MACEConfig()
@@ -56,7 +53,7 @@ def main(path_output):
         step=40,
         start=0,
         temperature=100,
-        temperature_threshold=300,  # reset if T > T_0 + 300 K
+        max_excess_temperature=300,  # reset if T > T_0 + 300 K
         pressure=0,
     )
     data = learning.run(
@@ -90,3 +87,4 @@ def main(path_output):
     psiflow.load()
     path_output = Path.cwd() / "output"  # stores learning results
     main(path_output)
+    psiflow.wait()

examples/mof_phase_transition.py

@@ -1,6 +1,5 @@
 from pathlib import Path
 
-import numpy as np
 import requests
 from ase.io import read
 
@@ -100,10 +99,10 @@ def main(path_output):
         step=50,
         start=0,
         temperature=300,
-        temperature_threshold=3,  # reset if T > T_0 + 3 * sigma
+        max_excess_temperature=1000,  # reset if T > T_0 + 1000
         pressure=0,
     )
-    data = learning.run(
+    data = learning.run(  # noqa: F841
         model=model,
         reference=reference,
         walkers=walkers,
@@ -126,4 +125,4 @@ def restart(path_output):
     psiflow.load()
     path_output = Path.cwd() / "output"  # stores learning results
     main(path_output)
-    # restart(path_output)
+    psiflow.wait()

examples/perovskite_defect.py

@@ -97,7 +97,7 @@ def main(path_output):
         step=50,
         start=0,
         temperature=100,
-        temperature_threshold=300,  # reset if T > T_0 + 300 K
+        max_excess_temperature=300,  # reset if T > T_0 + 300 K
         pressure=0,
     )
     metrics = Metrics("perovskite_defect", "psiflow_examples")

examples/zeolite_reaction.py

@@ -1,6 +1,5 @@
 from pathlib import Path
 
-import numpy as np
 import requests
 from ase.io import read
 
@@ -102,10 +101,10 @@ def main(path_output):
         step=50,
         start=0,
         temperature=300,
-        temperature_threshold=3,  # reset if T > T_0 + 3 * sigma
+        max_excess_temperature=1000,  # reset if T > T_0 + 1000
         pressure=0,
     )
-    data = learning.run(
+    data = learning.run(  # noqa: F841
         model=model,
         reference=reference,
         walkers=walkers,