From 066c499ddaf3ef58783092f742f70cd1207f3bf2 Mon Sep 17 00:00:00 2001 From: svdenhau Date: Sun, 11 Feb 2024 14:49:51 +0100 Subject: [PATCH] ensure topology section gets removed --- container/Dockerfile_python3.10_cuda | 2 +- psiflow/reference/_cp2k.py | 13 ++++++++----- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/container/Dockerfile_python3.10_cuda b/container/Dockerfile_python3.10_cuda index 9166319..2d43b0b 100644 --- a/container/Dockerfile_python3.10_cuda +++ b/container/Dockerfile_python3.10_cuda @@ -63,7 +63,7 @@ RUN pip install git+https://github.com/acesuit/MACE.git@55f7411 && \ RUN pip install pyscf ARG GIT_COMMIT_SHA -RUN pip install 'psiflow[parsl] @ git+https://github.com/molmod/psiflow@v3.0.3' +RUN pip install 'psiflow[parsl] @ git+https://github.com/molmod/psiflow' RUN pip cache purge ENV OMPI_MCA_plm_rsh_agent= diff --git a/psiflow/reference/_cp2k.py b/psiflow/reference/_cp2k.py index 65c42f4..16106cc 100644 --- a/psiflow/reference/_cp2k.py +++ b/psiflow/reference/_cp2k.py @@ -45,6 +45,9 @@ def dict_to_str(cp2k_input_dict: dict) -> str: def insert_atoms_in_input(cp2k_input_dict: dict, atoms: FlowAtoms): from ase.data import chemical_symbols + # get rid of topology if it's there + cp2k_input_dict["force_eval"]["subsys"].pop("topology", None) + coord = [] cell = {} for i in range(len(atoms)): @@ -54,11 +57,11 @@ def insert_atoms_in_input(cp2k_input_dict: dict, atoms: FlowAtoms): ) ) cp2k_input_dict["force_eval"]["subsys"]["coord"] = {"*": coord} - if atoms.pbc.any(): - for i, vector in enumerate(["A", "B", "C"]): - cell[vector] = "{} {} {}".format(*atoms.cell[i]) - # cell.append('{} {} {} {}'.format(vector, *atoms.cell[i])) - cp2k_input_dict["force_eval"]["subsys"]["cell"] = cell + + assert atoms.pbc.any() # CP2K needs cell info! + for i, vector in enumerate(["A", "B", "C"]): + cell[vector] = "{} {} {}".format(*atoms.cell[i]) + cp2k_input_dict["force_eval"]["subsys"]["cell"] = cell @typeguard.typechecked