From 216e0d533e13516c0ff0a0d57b6b5792c3aef73c Mon Sep 17 00:00:00 2001 From: bananenpampe Date: Fri, 1 Mar 2024 11:33:02 +0000 Subject: [PATCH] lint --- docs/src/index.rst | 1 + examples/cp2k_run_batch/README.rst | 7 ++--- examples/cp2k_run_batch/setup_reftraj.py | 40 +++++++++++++----------- 3 files changed, 26 insertions(+), 22 deletions(-) diff --git a/docs/src/index.rst b/docs/src/index.rst index c0690894..95775b29 100644 --- a/docs/src/index.rst +++ b/docs/src/index.rst @@ -13,3 +13,4 @@ COSMO Software Cookbook examples/lode_linear/lode_tutorial examples/sample_selection/sample_selection examples/gaas_map/gaas_map + example/cp2k_run_batch/setup_reftraj diff --git a/examples/cp2k_run_batch/README.rst b/examples/cp2k_run_batch/README.rst index 160eb5cd..1231bd8e 100644 --- a/examples/cp2k_run_batch/README.rst +++ b/examples/cp2k_run_batch/README.rst @@ -2,7 +2,6 @@ CP2K bash computation ============================ This is an example of a batch calculation using CP2K. -The inputs are a set of structures in `./data/example.xyz` using the parameters defined -in `./data/reftraj_template.cp2k` importing basisset and pseudopotentials from `./data/basis/`. - - +The inputs are a set of structures in `./data/example.xyz` +using the parameters defined in `./data/reftraj_template.cp2k` +importing basisset and pseudopotentials from `./data/basis/`. diff --git a/examples/cp2k_run_batch/setup_reftraj.py b/examples/cp2k_run_batch/setup_reftraj.py index 16a286f3..083b927f 100644 --- a/examples/cp2k_run_batch/setup_reftraj.py +++ b/examples/cp2k_run_batch/setup_reftraj.py @@ -5,13 +5,17 @@ .. start-body This is an example of a batch calculation using CP2K. -The inputs are a set of structures in `./data/example.xyz` using the parameters defined -in `./data/reftraj_template.cp2k` importing basisset and pseudopotentials from `./data/basis/`. +The inputs are a set of structures in `./data/example.xyz` using the parameters defined +in `./data/reftraj_template.cp2k` importing basisset and +pseudopotentials from `./data/basis/`. -The script will create a directory `./production` containing subdirectories for each stoichiometry. -This is only necessary, because CP2K can only run calculations using a single stoichiometry at a time, using the reftraj functionality. +The script will create a directory `./production` +containing subdirectories for each stoichiometry. +This is only necessary, because CP2K can only run calculations +using a single stoichiometry at a time, using the reftraj functionality. -The reference paramaters are taken from: Cheng et al. Ab initio thermodynamics of liquid and solid water 2019. +The reference paramaters are taken from: +Cheng et al. Ab initio thermodynamics of liquid and solid water 2019. """ import os @@ -25,9 +29,7 @@ import ase.io import numpy as np -from ase.build import molecule from ase.calculators.cp2k import CP2K -from numpy.testing import assert_allclose # %% @@ -57,7 +59,7 @@ def write_reftraj(fname: str, frames: Union[ase.Atoms, List[ase.Atoms]]): f"{frames[0].get_chemical_formula()}. " "CP2K does not support changing atom types within a reftraj run!" ) - n_atoms = len(atoms) + out += f"{len(atoms):>8}\n i = {i+1:>8}, time = {0:>12.3f}\n" for atom in atoms: pos = atom.position @@ -74,7 +76,11 @@ def write_cellfile(fname: str, frames: Union[ase.Atoms, List[ase.Atoms]]): if isinstance(frames, ase.Atoms): frames = [frames] - out = "# Step Time [fs] Ax [Angstrom] Ay [Angstrom] Az [Angstrom] Bx [Angstrom] By [Angstrom] Bz [Angstrom] Cx [Angstrom] Cy [Angstrom] Cz [Angstrom] Volume [Angstrom^3]\n" + out = "# Step Time [fs] Ax [Angstrom] Ay [Angstrom]\ + Az [Angstrom] Bx [Angstrom] By [Angstrom]\ + Bz [Angstrom] Cx [Angstrom]\ + Cy [Angstrom] Cz [Angstrom]\ + Volume [Angstrom^3]\n" for i, atoms in enumerate(frames): out += f"{i+1:>8}{0:>12.3f}" out += "".join([f"{c:>20.10f}" for c in atoms.cell.flatten()]) @@ -95,9 +101,10 @@ def write_cp2k_in(fname: str, project: str, last_snapshot: int, cell: List[float cp2k_in = f.read() warnings.warn( - "Due to the small size of the test structure and convergence issues, we have\ - decreased the size of the CUTOFF_RADIUS from 6.0 to 3.0. \ - For actual production calculations adapt the template!" + "Due to the small size of the test structure and convergence issues, we have \ + decreased the size of the CUTOFF_RADIUS from 6.0 to 3.0. \ + For actual production calculations adapt the template!", + stacklevel=2, ) cp2k_in = cp2k_in.replace("//PROJECT//", project) @@ -118,7 +125,7 @@ def write_cp2k_in(fname: str, project: str, last_snapshot: int, cell: List[float def mkdir_force(*args, **kwargs): try: os.mkdir(*args, **kwargs) - except OSError as e: + except OSError: pass @@ -175,7 +182,7 @@ def mkdir_force(*args, **kwargs): # # run the bash script directly from this script -subprocess.run(f"bash run_calcs.sh", shell=True) +subprocess.run("bash run_calcs.sh", shell=True) # %% @@ -184,9 +191,6 @@ def mkdir_force(*args, **kwargs): # :language: bash # .. download:: Download the script -# alternatively do: -# subprocess.run(f"cd ./production && for i in $(find . -mindepth 1 -type d); do cd \"$i\"; cp2k.ssmp -i in.cp2k ; cd -; done", shell=True) - # %% # Load results # ============ @@ -260,7 +264,7 @@ def mkdir_force(*args, **kwargs): # multiplicity=None, poisson_solver=None, print_level=None, - command=f"./cp2k_shell.ssmp --shell", + command="./cp2k_shell.ssmp --shell", ) atoms = ase.io.read("./data/example.xyz")