Merge branch 'main' into pre-commit-ci-update-config

.docker/cp2k-code.yml

@@ -2,7 +2,6 @@ label: cp2k
 computer: localhost
 description:
 default_calc_job_plugin: cp2k
-on_computer: True
 filepath_executable: /usr/bin/cp2k
 append_text:
 prepend_text:

.docker/opt/add-codes.sh → .docker/init/add-codes.sh

@@ -7,4 +7,4 @@ set -x
 export SHELL=/bin/bash
 
 # Install cp2k code.
-verdi code show cp2k@localhost || verdi code create core.code.installed --config /opt/aiida-cp2k/.docker/cp2k-code.yml --non-interactive
+verdi code show cp2k@localhost || verdi code create core.code.installed --config /home/aiida/aiida-cp2k/.docker/cp2k-code.yml --non-interactive

.docker/s6-rc.d/cp2k-code-setup/timeout-up

@@ -0,0 +1 @@
+0

.docker/s6-rc.d/cp2k-code-setup/type

@@ -0,0 +1 @@
+oneshot

.docker/s6-rc.d/cp2k-code-setup/up

@@ -0,0 +1,7 @@
+#!/command/execlineb -S0
+
+with-contenv
+
+foreground { s6-echo "Setting up CP2K code" }
+
+/etc/init/add-codes.sh

.github/workflows/ci.yml

@@ -47,9 +47,9 @@ jobs:
     - name: Create container from aiida_cp2k_test image and test the plugin inside
       run: |
         export DOCKERID=`docker run -d aiida_cp2k_test`
-        docker exec --tty $DOCKERID wait-for-services
+        sleep 5
         docker logs $DOCKERID
-        docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-cp2k/ && py.test --cov aiida_cp2k --cov-append .'
+        docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'cd /home/aiida/aiida-cp2k/ && py.test --cov aiida_cp2k --cov-append .'
 
 
   docs:

Dockerfile

@@ -5,13 +5,14 @@
 # For further information on the license, see the LICENSE.txt file.           #
 ###############################################################################
 
-FROM aiidateam/aiida-core:2.1.2
+
+FROM aiidateam/aiida-core-with-services:2.5.0
 
 # To prevent the container to exit prematurely.
 ENV KILL_ALL_RPOCESSES_TIMEOUT=50
 
-WORKDIR /opt/
 
+USER root
 # Install statically linked CP2K which is a considerably newer release than Debian builtin.
 # The statically linked CP2K is a non-MPI binary, but we're running all tests with 1 MPI proc.
 RUN set -ex ; \
@@ -21,16 +22,15 @@ RUN set -ex ; \
   echo "1e6fccf901873ebe9c827f45fb29331f599772f6e6281e988d8956c7a3aa143c /usr/bin/cp2k" | sha256sum -c ; \
   chmod +x /usr/bin/cp2k
 
+USER aiida
 # Install aiida-cp2k plugin.
-COPY . aiida-cp2k
+COPY --chown="${SYSTEM_UID}:${SYSTEM_GID}" . /home/aiida/aiida-cp2k
 RUN pip install ./aiida-cp2k[dev,docs]
 
 # Install coverals.
 RUN pip install coveralls
 
 # Install the cp2k code.
-COPY .docker/opt/add-codes.sh /opt/
-COPY .docker/my_init.d/add-codes.sh /etc/my_init.d/50_add-codes.sh
-
-# Add PGSQL bin folder to PATH.
-COPY .docker/my_init.d/add-pgsql-bin-to-path.sh /etc/my_init.d/50_add-pgsql-bin-to-path.sh
+COPY .docker/init/add-codes.sh /etc/init/
+COPY .docker/s6-rc.d/cp2k-code-setup /etc/s6-overlay/s6-rc.d/cp2k-code-setup
+COPY .docker/user/cp2k-code-setup /etc/s6-overlay/s6-rc.d/user/contents.d/cp2k-code-setup

README.md

@@ -31,6 +31,8 @@ pip install -e .  # Also installs aiida, if missing (but not postgres/rabbitmq).
 
 ## For maintainers
 
+### Release
+
 To create a new release, clone the repository, install development dependencies with `pip install '.[dev]'`, and then execute `bumpver update --major/--minor/--patch`.
 This will:
 
@@ -43,6 +45,33 @@ Additional notes:
   - The release tag (e.g. a/b/rc) is determined from the last release.
     Use the `--tag` option to override the release tag.
 
+### Testing
+
+To run the tests, you need to have Docker installed in your system.
+Once this is done, you can build the Docker image with the following command:
+
+```bash
+docker build -t aiida_cp2k_test .
+```
+Then, you can launch the container:
+
+```bash
+DOKERID=`docker run -d aiida_cp2k_test`
+```
+This will remeber the container ID in the variable `DOKERID`.
+You can then run the tests with the following command:
+
+```bash
+docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'cd /home/aiida/aiida-cp2k/ && pytest'
+```
+
+To enter the container for manual testing do:
+
+```bash
+docker exec -it --user aiida $DOCKERID bash
+```
+
+
 ## License
 
 MIT

aiida_cp2k/__init__.py

@@ -6,6 +6,6 @@
 ###############################################################################
 """The official AiiDA plugin for CP2K."""
 
-__version__ = "2.0.0"
+__version__ = "2.1.0b1"
 
 # EOF

aiida_cp2k/calculations/__init__.py

@@ -8,6 +8,7 @@
 
 from operator import add
 
+import numpy as np
 from aiida.common import CalcInfo, CodeInfo, InputValidationError
 from aiida.engine import CalcJob
 from aiida.orm import Dict, RemoteData, SinglefileData
@@ -25,6 +26,7 @@
 
 BandsData = DataFactory("core.array.bands")
 StructureData = DataFactory("core.structure")
+TrajectoryData = DataFactory("core.array.trajectory")
 KpointsData = DataFactory("core.array.kpoints")
 
 
@@ -40,8 +42,13 @@ class Cp2kCalculation(CalcJob):
     _DEFAULT_PROJECT_NAME = "aiida"
     _DEFAULT_RESTART_FILE_NAME = _DEFAULT_PROJECT_NAME + "-1.restart"
     _DEFAULT_TRAJECT_FILE_NAME = _DEFAULT_PROJECT_NAME + "-pos-1.dcd"
+    _DEFAULT_TRAJECT_XYZ_FILE_NAME = _DEFAULT_PROJECT_NAME + "-pos-1.xyz"
+    _DEFAULT_TRAJECT_FORCES_FILE_NAME = _DEFAULT_PROJECT_NAME + "-frc-1.xyz"
+    _DEFAULT_TRAJECT_CELL_FILE_NAME = _DEFAULT_PROJECT_NAME + "-1.cell"
     _DEFAULT_PARENT_CALC_FLDR_NAME = "parent_calc/"
-    _DEFAULT_COORDS_FILE_NAME = "aiida.coords.xyz"
+    _DEFAULT_COORDS_FILE_NAME = _DEFAULT_PROJECT_NAME + ".coords.xyz"
+    _DEFAULT_INPUT_TRAJECT_XYZ_FILE_NAME = _DEFAULT_PROJECT_NAME + "-reftraj.xyz"
+    _DEFAULT_INPUT_CELL_FILE_NAME = _DEFAULT_PROJECT_NAME + "-reftraj.cell"
     _DEFAULT_PARSER = "cp2k_base_parser"
 
     @classmethod
@@ -56,6 +63,12 @@ def define(cls, spec):
             required=False,
             help="The main input structure.",
         )
+        spec.input(
+            "trajectory",
+            valid_type=TrajectoryData,
+            required=False,
+            help="Input trajectory for a REFTRAJ simulation.",
+        )
         spec.input(
             "settings",
             valid_type=Dict,
@@ -162,6 +175,24 @@ def define(cls, spec):
             "ERROR_STRUCTURE_PARSE",
             message="The output structure could not be parsed.",
         )
+        spec.exit_code(
+            321,
+            "ERROR_COORDINATES_TRAJECTORY_READ",
+            message="The coordinates trajectory file could not be read.",
+        )
+
+        spec.exit_code(
+            323,
+            "ERROR_FORCES_TRAJECTORY_READ",
+            message="The forces trajectory file could not be read.",
+        )
+
+        spec.exit_code(
+            325,
+            "ERROR_CELLS_TRAJECTORY_READ",
+            message="The cells trajectory file could not be read.",
+        )
+
         spec.exit_code(
             350,
             "ERROR_UNEXPECTED_PARSER_EXCEPTION",
@@ -198,6 +229,12 @@ def define(cls, spec):
             required=False,
             help="The relaxed output structure.",
         )
+        spec.output(
+            "output_trajectory",
+            valid_type=TrajectoryData,
+            required=False,
+            help="The output trajectory.",
+        )
         spec.output(
             "output_bands",
             valid_type=BandsData,
@@ -249,6 +286,15 @@ def prepare_for_submission(self, folder):
                 conflicting_keys=["COORDINATE"],
             )
 
+        # Create input trajectory files
+        if "trajectory" in self.inputs:
+            self._write_trajectories(
+                self.inputs.trajectory,
+                folder,
+                self._DEFAULT_INPUT_TRAJECT_XYZ_FILE_NAME,
+                self._DEFAULT_INPUT_CELL_FILE_NAME,
+            )
+
         if "basissets" in self.inputs:
             validate_basissets(
                 inp,
@@ -329,6 +375,9 @@ def prepare_for_submission(self, folder):
             self._DEFAULT_OUTPUT_FILE,
             self._DEFAULT_RESTART_FILE_NAME,
             self._DEFAULT_TRAJECT_FILE_NAME,
+            self._DEFAULT_TRAJECT_XYZ_FILE_NAME,
+            self._DEFAULT_TRAJECT_FORCES_FILE_NAME,
+            self._DEFAULT_TRAJECT_CELL_FILE_NAME,
         ]
         calcinfo.retrieve_list += settings.pop("additional_retrieve_list", [])
 
@@ -364,6 +413,19 @@ def _write_structure(structure, folder, name):
         with open(folder.get_abs_path(name), mode="w", encoding="utf-8") as fobj:
             fobj.write(xyz)
 
+    @staticmethod
+    def _write_trajectories(trajectory, folder, name_pos, name_cell):
+        """Function that writes a structure and takes care of element tags."""
+
+        (xyz, cell) = _trajectory_to_xyz_and_cell(trajectory)
+        with open(folder.get_abs_path(name_pos), mode="w", encoding="utf-8") as fobj:
+            fobj.write(xyz)
+        if cell is not None:
+            with open(
+                folder.get_abs_path(name_cell), mode="w", encoding="utf-8"
+            ) as fobj:
+                fobj.write(cell)
+
 
 def kind_names(atoms):
     """Get atom kind names from ASE atoms based on tags.
@@ -378,7 +440,7 @@ def kind_names(atoms):
     return list(map(add, atoms.get_chemical_symbols(), elem_tags))
 
 
-def _atoms_to_xyz(atoms):
+def _atoms_to_xyz(atoms, infoline="No info"):
     """Converts ASE atoms to string, taking care of element tags.
 
     :param atoms: ASE Atoms instance
@@ -388,6 +450,33 @@ def _atoms_to_xyz(atoms):
     elem_coords = [
         f"{p[0]:25.16f} {p[1]:25.16f} {p[2]:25.16f}" for p in atoms.get_positions()
     ]
-    xyz = f"{len(elem_coords)}\n\n"
+    xyz = f"{len(elem_coords)}\n"
+    xyz += f"{infoline}\n"
     xyz += "\n".join(map(add, elem_symbols, elem_coords))
     return xyz
+
+
+def _trajectory_to_xyz_and_cell(trajectory):
+    """Converts postions and cell from a TrajectoryData  to string, taking care of element tags from ASE atoms.
+
+    :param atoms: ASE Atoms instance
+    :param trajectory: TrajectoryData instance
+    :returns: positions str (in xyz format) and cell str
+    """
+    cell = None
+    xyz = ""
+    stepids = trajectory.get_stepids()
+    for i, step in enumerate(stepids):
+        xyz += _atoms_to_xyz(
+            trajectory.get_step_structure(i).get_ase(),
+            infoline=f"i = {step+1} , time = {(step+1)*0.5}",  # reftraj trajectories cannot start from STEP 0
+        )
+        xyz += "\n"
+    if "cells" in trajectory.get_arraynames():
+        cell = "#   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"
+        cell_vecs = [
+            f"{stepid+1} {(stepid+1)*0.5:6.3f} {cellvec[0][0]:25.16f} {cellvec[0][1]:25.16f} {cellvec[0][2]:25.16f} {cellvec[1][0]:25.16f} {cellvec[1][1]:25.16f} {cellvec[1][2]:25.16f} {cellvec[2][0]:25.16f} {cellvec[2][1]:25.16f} {cellvec[2][2]:25.16f} {np.dot(cellvec[0],np.cross(cellvec[1],cellvec[2]))}"
+            for (stepid, cellvec) in zip(stepids, trajectory.get_array("cells"))
+        ]
+        cell += "\n".join(cell_vecs)
+    return xyz, cell