Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update cp2k #10

Draft
wants to merge 2 commits into
base: main
Choose a base branch
from
Draft

Update cp2k #10

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
999e6c9
update CP2K Node
PythonFZ Nov 15, 2022
4aee77f
update CP2K Node
PythonFZ Nov 15, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
27 changes: 14 additions & 13 deletions znlib/atomistic/cp2k.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@ class CP2KNode(Node):
input_file: str = dvc.params()
# e.g. "env OMP_NUM_THREADS=2 mpiexec -np 4 cp2k_shell.psmp"
cp2k_shell: str = meta.Text("cp2k_shell.psmp")
label: str = meta.Text("ase_cp2k")

outputs: AtomsList = ZnAtoms()

Expand Down Expand Up @@ -84,34 +85,32 @@ def get_calculator(self, script) -> ase.calculators.cp2k.CP2K:
stress_tensor=self.stress_tensor,
xc=None,
print_level=None,
label="cp2k",
label=self.label,
)

def _move_cp2k_outs(self):
"""The CP2K command is executed in the cwd.
Output files will be moved to NWD afterward."""
for file in pathlib.Path(".").glob("cp2k-RESTART.wfn*"):
for file in pathlib.Path(".").glob(f"{self.label}*"):
file.rename(self.cp2k_output_dir / file)

cp2k_inp = pathlib.Path("cp2k.inp")
cp2k_inp.rename(self.cp2k_output_dir / cp2k_inp)

cp2k_out = pathlib.Path("cp2k.out")
cp2k_out.rename(self.cp2k_output_dir / cp2k_out)

@property
def wfn_restart_file(self) -> pathlib.Path:
# TODO if the file does not work return path to one of the backup files
return self.cp2k_output_dir / "cp2k-RESTART.wfn"
return self.cp2k_output_dir / f"{self.label}-RESTART.wfn"

def run(self):
if self.cp2k_output_dir.exists():
shutil.rmtree(self.cp2k_output_dir)
# ! assert there are no files starting with cp2k_...
# ! run cp2k
# ! Do checkpoints?!?
# ! move outputs
# if self.cp2k_output_dir.exists():
# shutil.rmtree(self.cp2k_output_dir)
self.cp2k_output_dir.mkdir()

if self.wfn_restart is not None:
# TODO maybe rename the file otherwise?
assert pathlib.Path(self.wfn_restart).name == "cp2k-RESTART.wfn"
assert pathlib.Path(self.wfn_restart).name == f"{self.label}-RESTART.wfn"
shutil.copy(self.wfn_restart, ".")

with open(self.input_file, "r") as file:
Expand All @@ -121,11 +120,13 @@ def run(self):

cp2k_input_script = "\n".join(CP2KInputGenerator().line_iter(cp2k_input_dict))

calc = self.get_calculator(cp2k_input_script)

self.outputs = []
for atom in self.atoms:
assert isinstance(atom, ase.Atoms)
atom = atom.copy()
atom.calc = self.get_calculator(cp2k_input_script)
atom.calc = calc
atom.get_potential_energy()
self.outputs.append(atom)

Expand Down