From 4fc61a43895c7a989bb2c5b16ae62d7308a31e9d Mon Sep 17 00:00:00 2001 From: Carlo Antonio Pignedoli Date: Fri, 15 Mar 2024 21:10:45 +0000 Subject: [PATCH 1/2] fix bug in creation of trajectory --- aiida_cp2k/parsers/__init__.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/aiida_cp2k/parsers/__init__.py b/aiida_cp2k/parsers/__init__.py index 440231b8..211c61bd 100644 --- a/aiida_cp2k/parsers/__init__.py +++ b/aiida_cp2k/parsers/__init__.py @@ -8,6 +8,7 @@ import ase import numpy as np +import re from aiida import common, engine, orm, parsers, plugins from .. import utils @@ -128,7 +129,7 @@ def _read_stdout(self): def _parse_trajectory(self, structure): """CP2K trajectory parser.""" - symbols = [str(site.kind_name) for site in structure.sites] + symbols = [re.sub(r"\d+", "", str(site.kind_name)) for site in structure.sites] # Handle the positions trajectory xyz_traj_fname = self.node.process_class._DEFAULT_TRAJECT_XYZ_FILE_NAME From a6d88b81cacbb251560963a429469027ca55b08d Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 15 Mar 2024 21:12:04 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- aiida_cp2k/parsers/__init__.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/aiida_cp2k/parsers/__init__.py b/aiida_cp2k/parsers/__init__.py index 211c61bd..6045ef79 100644 --- a/aiida_cp2k/parsers/__init__.py +++ b/aiida_cp2k/parsers/__init__.py @@ -6,9 +6,10 @@ ############################################################################### """AiiDA-CP2K output parser.""" +import re + import ase import numpy as np -import re from aiida import common, engine, orm, parsers, plugins from .. import utils