Fix some bugs.

Author: ErjieWu

deepks/__main__.py

@@ -1,10 +1,6 @@
-import os
-import sys
+"""DeePKS package entry point."""
 
-# Add parent directory to path to import main
-sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-
-from main import main
+from deepks.main import main
 
 if __name__ == "__main__":
     main()

deepks/main.py

@@ -0,0 +1,97 @@
+#!/usr/bin/env python
+"""Unified DeePKS command-line interface."""
+
+import os
+import sys
+
+
+def _get_model_backend():
+    """Get model backend instance."""
+    from deepks.ml.backend import CorrNetModelBackend
+    return CorrNetModelBackend()
+
+
+def _get_physics_backend(scf_soft='pyscf'):
+    """Get physics backend based on scf_soft parameter.
+
+    Args:
+        scf_soft: SCF software name ('pyscf' or 'abacus')
+
+    Returns:
+        PhysicsBackend instance
+    """
+    from deepks.physics.backends import get_scf_backend
+    return get_scf_backend(scf_soft)
+
+
+def main():
+    """Main entry point for DeePKS CLI."""
+    import argparse
+    # Force line-buffered stdout/stderr so output appears in log.iter in real time
+    # even when the process is launched with >> redirection (non-TTY).
+    sys.stdout = open(sys.stdout.fileno(), mode='w', buffering=1, closefd=False)
+    sys.stderr = open(sys.stderr.fileno(), mode='w', buffering=1, closefd=False)
+
+    parser = argparse.ArgumentParser(
+        prog="deepks",
+        description="DeePKS: Deep Kohn-Sham DFT with machine learning"
+    )
+    parser.add_argument(
+        "config",
+        nargs="?",
+        default="input.yaml",
+        help="Configuration file (default: input.yaml)"
+    )
+    parser.add_argument(
+        "-v", "--version",
+        action="version",
+        version="DeePKS 1.0"
+    )
+
+    args = parser.parse_args()
+
+    # Check if config file exists
+    if not os.path.exists(args.config):
+        print(f"Error: Configuration file '{args.config}' not found", file=sys.stderr)
+        sys.exit(1)
+
+    # Load and process configuration
+    from deepks.io.input import load_config, get_default_config
+    from deepks.io.input.merger import merge_configs, apply_parameter_inheritance
+    from deepks.io.input.dispatcher import dispatch_command
+
+    try:
+        # Load configuration file
+        config = load_config(args.config)
+
+        # Determine type from config
+        if 'type' not in config:
+            print("Error: 'type' field is required in configuration file", file=sys.stderr)
+            print("Valid types: train, test, scf, stats, iterate", file=sys.stderr)
+            sys.exit(1)
+
+        task_type = config['type']
+
+        # Get defaults based on type and backend
+        scf_soft = config.get('scf_soft', 'pyscf')
+        defaults = get_default_config(task_type, scf_soft)
+
+        # Merge defaults with config
+        config = merge_configs(defaults, config)
+
+        # Apply parameter inheritance for iterate type
+        if task_type == 'iterate':
+            config = apply_parameter_inheritance(config)
+
+        # Dispatch to appropriate handler
+        dispatch_command(config)
+
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        import traceback
+        traceback.print_exc()
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

deepks/orchestration/scheduler/job/shell.py

@@ -12,11 +12,14 @@ class Shell(Batch) :
     def check_status(self) :
         if self.check_finish_tag():
             return JobStatus.finished
-        elif self.check_running() or self.check_submitted_tag():
+        elif self.check_running():
             return JobStatus.running
         else:
             return JobStatus.terminated
-        ## warn: cannont distinguish terminated from unsubmitted.
+        ## note: check_submitted_tag() only tells us the .sub file exists (was submitted),
+        ## not that the process is still running. Using it here caused an infinite loop
+        ## when a job failed: the .sub file remains, so check_status() kept returning
+        ## 'running' forever instead of 'terminated'.
 
     def check_running(self):
         uuid_names = self.context.job_uuid

deepks/physics/backends/abacus/input_generator.py

@@ -301,7 +301,7 @@ def make_abacus_scf_stru(sys_data: Dict[str, Any],
             ret += f"{valid_orb_files[atom]}\n"
 
     # DeepKS descriptor
-    if (fp_params.get("deepks_scf") and
+    if (fp_params.get("deepks_scf") == 1 or
         fp_params.get("deepks_out_labels") == 1):
         ret += "\nNUMERICAL_DESCRIPTOR\n"
         ret += f"{fp_params['proj_file'][0]}\n"