Update cp2kyaml (#212)

* update CP2kYaml Node

* remove Operating directory

* update variable names; new ZnTrack descriptors

ipsuite/analysis/model/predict.py

@@ -40,7 +40,10 @@ def run(self):
             if "stress" in calc.implemented_properties:
                 try:
                     atoms.get_stress()
-                except PropertyNotImplementedError:  # required for nequip
+                except (
+                    PropertyNotImplementedError,
+                    ValueError,
+                ):  # required for nequip, GAP
                     pass
 
             self.atoms.append(freeze_copy_atoms(atoms))

ipsuite/calculators/cp2k.py

@@ -4,6 +4,7 @@
 """
 import contextlib
 import functools
+import logging
 import os
 import pathlib
 import shutil
@@ -25,6 +26,8 @@
 
 from ipsuite import base
 
+log = logging.getLogger(__name__)
+
 
 def _update_paths(cp2k_input_dict) -> dict:
     cp2k_input_dict["force_eval"]["DFT"]["basis_set_file_name"] = (
@@ -65,17 +68,32 @@ def _update_paths(cp2k_input_dict) -> dict:
         )
 
 
+def _update_cmd(cp2k_cmd: str, env="IPSUITE_CP2K_SHELL") -> str:
+    """Update the shell command to run cp2k."""
+    if cp2k_cmd is None:
+        # Load from environment variable IPSUITE_CP2K_SHELL
+        try:
+            cp2k_cmd = os.environ[env]
+            log.info(f"Using IPSUITE_CP2K_SHELL={cp2k_cmd}")
+        except KeyError as err:
+            raise RuntimeError(
+                f"Please set the environment variable '{env}' or set the cp2k executable."
+            ) from err
+    return cp2k_cmd
+
+
 class CP2KYaml(base.ProcessSingleAtom):
     """Node for running CP2K Single point calculations."""
 
-    cp2k_bin: str = zntrack.meta.Text("cp2k.psmp")
-    cp2k_params = zntrack.dvc.params("cp2k.yaml")
-    wfn_restart: str = zntrack.dvc.deps(None)
+    cp2k_bin: str = zntrack.meta.Text(None)
+    cp2k_params = zntrack.params_path("cp2k.yaml")
+    wfn_restart: str = zntrack.deps_path(None)
 
-    cp2k_directory: pathlib.Path = zntrack.dvc.outs(zntrack.nwd / "cp2k")
+    cp2k_directory: pathlib.Path = zntrack.outs_path(zntrack.nwd / "cp2k")
 
     def run(self):
         """ZnTrack run method."""
+        self.cp2k_bin = _update_cmd(self.cp2k_bin)
         self.cp2k_directory.mkdir(exist_ok=True)
         with pathlib.Path(self.cp2k_params).open("r") as file:
             cp2k_input_dict = yaml.safe_load(file)
@@ -95,8 +113,7 @@ def run(self):
         _update_paths(cp2k_input_dict)
 
         cp2k_input_script = "\n".join(CP2KInputGenerator().line_iter(cp2k_input_dict))
-        with self.operating_directory():
-            self._run_cp2k(atoms, cp2k_input_script)
+        self._run_cp2k(atoms, cp2k_input_script)
 
     def _run_cp2k(self, atoms, cp2k_input_script):
         ase.io.write(self.cp2k_directory / "atoms.xyz", atoms)
@@ -159,26 +176,13 @@ class CP2KSinglePoint(base.ProcessAtoms):
     """
 
     cp2k_shell: str = zntrack.meta.Text(None)
-    cp2k_params = zntrack.dvc.params("cp2k.yaml")
-    cp2k_files = zntrack.dvc.deps(None)
+    cp2k_params = zntrack.params_path("cp2k.yaml")
+    cp2k_files = zntrack.deps_path(None)
 
-    wfn_restart_file: str = zntrack.dvc.deps(None)
+    wfn_restart_file: str = zntrack.deps_path(None)
     wfn_restart_node = zntrack.deps(None)
-    output_file = zntrack.dvc.outs(zntrack.nwd / "atoms.h5")
-    cp2k_directory = zntrack.dvc.outs(zntrack.nwd / "cp2k")
-
-    def _update_shell(self):
-        """Update the shell command to run cp2k."""
-        if self.cp2k_shell is None:
-            # Load from environment variable IPSUITE_CP2K_SHELL
-            try:
-                self.cp2k_shell = os.environ["IPSUITE_CP2K_SHELL"]
-                print(f"Using IPSUITE_CP2K_SHELL={self.cp2k_shell}")
-            except KeyError as err:
-                raise RuntimeError(
-                    "Please set the environment variable 'IPSUITE_CP2K_SHELL' or use the"
-                    " 'cp2k_shell' parameter."
-                ) from err
+    output_file = zntrack.outs_path(zntrack.nwd / "atoms.h5")
+    cp2k_directory = zntrack.outs_path(zntrack.nwd / "cp2k")
 
     def run(self):
         """ZnTrack run method.
@@ -189,7 +193,7 @@ def run(self):
             If the cp2k_shell is not set.
         """
 
-        self._update_shell()
+        self.cp2k_shell = _update_cmd(self.cp2k_shell)
 
         db = znh5md.io.DataWriter(self.output_file)
         db.initialize_database_groups()
@@ -245,7 +249,7 @@ def get_input_script(self):
         return "\n".join(CP2KInputGenerator().line_iter(cp2k_input_dict))
 
     def get_calculator(self, directory: str = None):
-        self._update_shell()
+        self.cp2k_shell = _update_cmd(self.cp2k_shell)
 
         if directory is None:
             directory = self.cp2k_directory