Skip completed LAMMPS tasks in hti/ti run (#101)

* Skip completed LAMMPS tasks in hti/ti run

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

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

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: Yi-FanLi

dpti/hti.py

@@ -1409,6 +1409,20 @@ def hti_phase_trans_analyze(job, jdata=None):
     return if_phase_trans
 
 
+def _is_completed_lammps_task(task_work_path):
+    log_file = os.path.join(task_work_path, "log.lammps")
+    if not os.path.isfile(log_file):
+        return False
+    try:
+        with open(log_file, errors="ignore") as fp:
+            lines = [line.strip() for line in fp if line.strip()]
+        if not lines:
+            return False
+        return lines[0].startswith("LAMMPS") and lines[-1].startswith("Total wall time")
+    except OSError:
+        return False
+
+
 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 + "*"))
@@ -1420,6 +1434,10 @@ def run_task(task_dir, machine_file, task_name, no_dp=False):
         job_work_dir = task_dir
     task_dir_list = glob.glob(os.path.join(job_work_dir, "task*"))
     task_dir_list = sorted(task_dir_list)
+    task_dir_list = [ii for ii in task_dir_list if not _is_completed_lammps_task(ii)]
+    if len(task_dir_list) == 0:
+        print("# all tasks already completed; nothing to submit")
+        return
     work_base_dir = os.getcwd()
     with open(machine_file) as f:
         mdata = json.load(f)

dpti/ti.py

@@ -905,9 +905,27 @@ def compute_task(job, inte_method, Eo, Eo_err, To, scheme="simpson"):
     return info
 
 
+def _is_completed_lammps_task(task_work_path):
+    log_file = os.path.join(task_work_path, "log.lammps")
+    if not os.path.isfile(log_file):
+        return False
+    try:
+        with open(log_file, errors="ignore") as fp:
+            lines = [line.strip() for line in fp if line.strip()]
+        if not lines:
+            return False
+        return lines[0].startswith("LAMMPS") and lines[-1].startswith("Total wall time")
+    except OSError:
+        return False
+
+
 def run_task(task_name, machine_file):
     task_dir_list = glob.glob(os.path.join(task_name, "task.*"))
     task_dir_list = sorted(task_dir_list)
+    task_dir_list = [ii for ii in task_dir_list if not _is_completed_lammps_task(ii)]
+    if len(task_dir_list) == 0:
+        print("# all tasks already completed; nothing to submit")
+        return
     work_base_dir = os.getcwd()
     with open(machine_file) as f:
         mdata = json.load(f)