[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

dpti/__init__.py

@@ -6,10 +6,10 @@
     "equi",
     "gdi",
     "hti",
-    "hti_liq",
     "hti_ice",
+    "hti_liq",
     "hti_water",
+    "lib",
     "ti",
     "ti_water",
-    "lib",
 ]

dpti/dags/dp_ti_gdi.py

@@ -2,7 +2,7 @@
 import os
 import time
 from datetime import datetime, timedelta
-from typing import ClassVar, Dict
+from typing import ClassVar
 
 from airflow import DAG
 from airflow.api.client.local_client import Client
@@ -30,12 +30,12 @@
 
 
 class GDIDAGFactory:
-    default_args: ClassVar[Dict[str, object]] = {
+    default_args: ClassVar[dict[str, object]] = {
         "owner": "airflow",
         "start_date": datetime(2018, 1, 1),
     }
 
-    dagargs: ClassVar[Dict[str, object]] = {
+    dagargs: ClassVar[dict[str, object]] = {
         "default_args": default_args,
         "schedule_interval": None,
     }

dpti/hti.py

@@ -86,7 +86,7 @@ def _ff_deep_on(lamb, model, sparam, if_meam=False, meam_model=None, append=None
     #     ret += 'pair_coeff      * * meam /home/fengbo/4_Sn/meam_files/library_18Metal.meam Sn /home/fengbo/4_Sn/meam_files/Sn_18Metal.meam Sn \n'
     if if_meam:
         ret += f"pair_style      hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
-        ret += f'pair_coeff      * * meam {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
+        ret += f"pair_coeff      * * meam {meam_model['library']} {meam_model['element']} {meam_model['potential']} {meam_model['element']}\n"
     else:
         if append:
             ret += f"pair_style      hybrid/overlay deepmd {model:s} {append:s} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
@@ -175,7 +175,7 @@ def _ff_lj_off(lamb, model, sparam, if_meam=False, meam_model=None, append=None)
     #     ret += 'pair_coeff      * * meam /home/fengbo/4_Sn/meam_files/library_18Metal.meam Sn /home/fengbo/4_Sn/meam_files/Sn_18Metal.meam Sn\n'
     if if_meam:
         ret += f"pair_style      hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
-        ret += f'pair_coeff      * * meam {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
+        ret += f"pair_coeff      * * meam {meam_model['library']} {meam_model['element']} {meam_model['potential']} {meam_model['element']}\n"
         # ret += f'pair_coeff      * * meam {meam_model[0]} {meam_model[2]} {meam_model[1]} {meam_model[2]}\n'
     else:
         if append:
@@ -709,9 +709,9 @@ def _make_tasks(
             "sigma_" + str(t[0]) + "_" + str(t[1]) for t in sigma_key_index
         ]
         for sigma_key_name in sigma_key_name_list:
-            assert sparam.get(
-                sigma_key_name, None
-            ), f"there must be key-value for {sigma_key_name} in soft_param"
+            assert sparam.get(sigma_key_name, None), (
+                f"there must be key-value for {sigma_key_name} in soft_param"
+            )
 
     if crystal == "frenkel":
         m_spring_k = []
@@ -1412,9 +1412,9 @@ def hti_phase_trans_analyze(job, jdata=None):
 def run_task(task_dir, machine_file, task_name, no_dp=False):
     if task_name == "00" or task_name == "01" or task_name == "02":
         job_work_dir_ = glob.glob(os.path.join(task_dir, task_name + "*"))
-        assert (
-            len(job_work_dir_) == 1
-        ), f"The task_name you entered is {task_name}. It indicates that you want to run tasks for step {task_name} of the two-step or three-step HTI. Please make sure that there is one and only one {task_name}.* directory in the hti task directory."
+        assert len(job_work_dir_) == 1, (
+            f"The task_name you entered is {task_name}. It indicates that you want to run tasks for step {task_name} of the two-step or three-step HTI. Please make sure that there is one and only one {task_name}.* directory in the hti task directory."
+        )
         job_work_dir = job_work_dir_[0]
     elif task_name == "one-step":
         job_work_dir = task_dir

dpti/hti_liq.py

@@ -48,9 +48,9 @@ def parse_lj_sigma_epsilon(ret, sparam, hybrid=False):
     activation_ij = np.zeros((element_num, element_num))
 
     if epsilon is not None:
-        assert (
-            epsilon_0_0 is None
-        ), "epsilon and epsilon_0_0 cannot be set at the same time"
+        assert epsilon_0_0 is None, (
+            "epsilon and epsilon_0_0 cannot be set at the same time"
+        )
         for i, j in sigma_key_index:
             epsilon_ij[i, j] = epsilon
     else:
@@ -68,9 +68,9 @@ def parse_lj_sigma_epsilon(ret, sparam, hybrid=False):
             sigma_ij[i, j] = sparam["sigma_" + str(i) + "_" + str(j)]
 
     if activation is not None:
-        assert (
-            activation_0_0 is None
-        ), "activation and activation_0_0 cannot be set at the same time"
+        assert activation_0_0 is None, (
+            "activation and activation_0_0 cannot be set at the same time"
+        )
         for i, j in sigma_key_index:
             activation_ij[i, j] = activation
     else:
@@ -110,7 +110,7 @@ def _ff_deep_on(lamb, sparam, model, if_meam=False, meam_model=None):
     ret += "variable        ONE equal 1\n"
     if if_meam:
         ret += f"pair_style      hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
-        ret += f'pair_coeff      * * meam {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
+        ret += f"pair_coeff      * * meam {meam_model['library']} {meam_model['element']} {meam_model['potential']} {meam_model['element']}\n"
         # ret += f'pair_coeff      * * meam {meam_model[0]} {meam_model[2]} {meam_model[1]} {meam_model[2]}\n'
     else:
         ret += f"pair_style      hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
@@ -138,7 +138,7 @@ def _ff_soft_off(lamb, sparam, model, if_meam=False, meam_model=None):
     ret += "variable        INV_LAMBDA equal 1-${LAMBDA}\n"
     if if_meam:
         ret += f"pair_style      hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
-        ret += f'pair_coeff      * * meam {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
+        ret += f"pair_coeff      * * meam {meam_model['library']} {meam_model['element']} {meam_model['potential']} {meam_model['element']}\n"
         # ret += f'pair_coeff      * * meam {meam_model[0]} {meam_model[2]} {meam_model[1} {meam_model[2]} \n'
     else:
         ret += f"pair_style      hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
@@ -289,9 +289,9 @@ def _make_tasks(iter_name, jdata, step, if_meam=False, meam_model=None):
                 "sigma_" + str(t[0]) + "_" + str(t[1]) for t in sigma_key_index
             ]
             for sigma_key_name in sigma_key_name_list:
-                assert sparam.get(
-                    sigma_key_name, None
-                ), f"there must be key-value for sigma or {sigma_key_name} in soft_param"
+                assert sparam.get(sigma_key_name, None), (
+                    f"there must be key-value for sigma or {sigma_key_name} in soft_param"
+                )
 
     job_abs_dir = create_path(iter_name)
 

dpti/mti.py

@@ -165,9 +165,9 @@ def make_tasks(iter_name, jdata):
         raise RuntimeError("invalid ens")
 
     job_type = jdata["job_type"]
-    assert (
-        job_type == "nbead_convergence" or job_type == "mass_ti"
-    ), "Unknow job_type. Only nbead_convergence and mass_ti are supported."
+    assert job_type == "nbead_convergence" or job_type == "mass_ti", (
+        "Unknow job_type. Only nbead_convergence and mass_ti are supported."
+    )
     mass_scale_y_seq = get_first_matched_key_from_dict(jdata, ["mass_scale_y"])
     mass_scale_y_list = parse_seq(mass_scale_y_seq)
     mass_scales = (1.0 / np.array(mass_scale_y_list)) ** 2
@@ -176,13 +176,13 @@ def make_tasks(iter_name, jdata):
     nnode_seq = jdata.get("nnode", None)
     if nnode_seq is not None:
         nnode_list = parse_seq(nnode_seq)
-        assert (
-            len(nbead_list) == len(nnode_list)
-        ), "Lists nbead and nnode should have same length. Please specify one nnode for each nbead."
+        assert len(nbead_list) == len(nnode_list), (
+            "Lists nbead and nnode should have same length. Please specify one nnode for each nbead."
+        )
     if job_type == "mass_ti":
-        assert (
-            len(mass_scale_y_list) == len(nbead_list)
-        ), "For mass TI tasks, you must provide one value of nbead for each value of mass_scale_y."
+        assert len(mass_scale_y_list) == len(nbead_list), (
+            "For mass TI tasks, you must provide one value of nbead for each value of mass_scale_y."
+        )
 
     job_abs_dir = create_path(iter_name)
     ti_settings["equi_conf"] = relative_link_file(equi_conf, job_abs_dir)

dpti/ti.py

@@ -93,7 +93,7 @@ def _gen_lammps_input(
     #     ret += 'pair_coeff      * * /home/fengbo/4_Sn/meam_files/library_18Metal.meam Sn /home/fengbo/4_Sn/meam_files/Sn_18Metal.meam Sn\n'
     if if_meam:
         ret += "pair_style      meam\n"
-        ret += f'pair_coeff      * * {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
+        ret += f"pair_coeff      * * {meam_model['library']} {meam_model['element']} {meam_model['potential']} {meam_model['element']}\n"
     else:
         if append:
             ret += f"pair_style      deepmd {model:s} {append:s}\n"

workflow/DpFreeEnergy-aiida.py

@@ -48,18 +48,18 @@ def all_start_check(dag_run):
     )
     dag_work_dir = os.path.join(work_base_abs_dir, dag_work_dirname)
 
-    assert (
-        os.path.isdir(work_base_dir) is True
-    ), f"work_base_dir {work_base_dir} must exist "
+    assert os.path.isdir(work_base_dir) is True, (
+        f"work_base_dir {work_base_dir} must exist "
+    )
     if os.path.isdir(dag_work_dir) is False:
         os.mkdir(dag_work_dir)
     else:
         pass
 
     conf_lmp_abs_path = os.path.join(work_base_abs_dir, conf_lmp)
-    assert (
-        os.path.isfile(conf_lmp_abs_path) is True
-    ), f"structure file {conf_lmp_abs_path} must exist"
+    assert os.path.isfile(conf_lmp_abs_path) is True, (
+        f"structure file {conf_lmp_abs_path} must exist"
+    )
     assert str(ti_path) in ["t", "p"], 'value for "path" must be "t" or "p" '
     start_info = {
         "work_base_dir": work_base_dir,

workflow/DpFreeEnergy.py

@@ -33,18 +33,18 @@ def all_start_check():
     )
     dag_work_dir = os.path.join(work_base_abs_dir, dag_work_dirname)
 
-    assert (
-        os.path.isdir(work_base_dir) is True
-    ), f"work_base_dir {work_base_dir} must exist "
+    assert os.path.isdir(work_base_dir) is True, (
+        f"work_base_dir {work_base_dir} must exist "
+    )
     if os.path.isdir(dag_work_dir) is False:
         os.mkdir(dag_work_dir)
     else:
         pass
 
     conf_lmp_abs_path = os.path.join(work_base_abs_dir, conf_lmp)
-    assert (
-        os.path.isfile(conf_lmp_abs_path) is True
-    ), f"structure file {conf_lmp_abs_path} must exist"
+    assert os.path.isfile(conf_lmp_abs_path) is True, (
+        f"structure file {conf_lmp_abs_path} must exist"
+    )
     assert str(ti_path) in ["t", "p"], 'value for "path" must be "t" or "p" '
 
     start_info = {

workflow/DpFreeEnergyWater.py

@@ -57,18 +57,18 @@ def all_start_check():
     )
     dag_work_dir = os.path.join(work_base_abs_dir, dag_work_dirname)
 
-    assert (
-        os.path.isdir(work_base_dir) is True
-    ), f"work_base_dir {work_base_dir} must exist "
+    assert os.path.isdir(work_base_dir) is True, (
+        f"work_base_dir {work_base_dir} must exist "
+    )
     if os.path.isdir(dag_work_dir) is False:
         os.mkdir(dag_work_dir)
     else:
         pass
 
     conf_lmp_abs_path = os.path.join(work_base_abs_dir, conf_lmp)
-    assert (
-        os.path.isfile(conf_lmp_abs_path) is True
-    ), f"structure file {conf_lmp_abs_path} must exist"
+    assert os.path.isfile(conf_lmp_abs_path) is True, (
+        f"structure file {conf_lmp_abs_path} must exist"
+    )
     assert str(ti_path) in ["t", "p"], 'value for "path" must be "t" or "p" '
 
     start_info = {