Merge branch 'main' into update/docker-container

README.md

@@ -56,7 +56,7 @@ docker build -t aiida_cp2k_test .
 Then, you can launch the container:
 
 ```bash
-DOKERID=`docker run -it aiida_cp2k_test`
+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:

aiida_cp2k/parsers/__init__.py

@@ -145,12 +145,19 @@ def _parse_trajectory(self, structure):
 
         positions_traj = []
         stepids_traj = []
+        energies_traj = []
         for frame in parse(output_xyz_pos):
             _, positions = zip(*frame["atoms"])
             positions_traj.append(positions)
-            stepids_traj.append(int(frame["comment"].split()[2][:-1]))
+            comment_split = frame["comment"].split(",")
+            stepids_traj.append(int(comment_split[0].split()[-1]))
+            energy_index = next(
+                (i for i, s in enumerate(comment_split) if "E =" in s), None
+            )
+            energies_traj.append(float(comment_split[energy_index].split()[-1]))
         positions_traj = np.array(positions_traj)
         stepids_traj = np.array(stepids_traj)
+        energies_traj = np.array(energies_traj)
 
         cell_traj = None
         cell_traj_fname = self.node.process_class._DEFAULT_TRAJECT_CELL_FILE_NAME
@@ -190,6 +197,7 @@ def _parse_trajectory(self, structure):
             symbols=symbols,
             positions=positions_traj,
         )
+        trajectory.set_array("energies", energies_traj)
         if forces_traj is not None:
             trajectory.set_array("forces", forces_traj)
 

aiida_cp2k/utils/__init__.py

@@ -6,6 +6,10 @@
 ###############################################################################
 """AiiDA-CP2K utils"""
 
+from .datatype_helpers import (
+    merge_trajectory_data_non_unique,
+    merge_trajectory_data_unique,
+)
 from .input_generator import (
     Cp2kInput,
     add_ext_restart_section,
@@ -42,4 +46,6 @@
     "merge_Dict",
     "ot_has_small_bandgap",
     "resize_unit_cell",
+    "merge_trajectory_data_unique",
+    "merge_trajectory_data_non_unique",
 ]

aiida_cp2k/utils/datatype_helpers.py

@@ -9,8 +9,8 @@
 import re
 from collections.abc import Sequence
 
-from aiida.common import InputValidationError
-from aiida.plugins import DataFactory
+import numpy as np
+from aiida import common, engine, orm, plugins
 
 
 def _unpack(adict):
@@ -50,7 +50,9 @@ def _kind_element_from_kind_section(section):
     try:
         kind = section["_"]
     except KeyError:
-        raise InputValidationError("No default parameter '_' found in KIND section.")
+        raise common.InputValidationError(
+            "No default parameter '_' found in KIND section."
+        )
 
     try:
         element = section["ELEMENT"]
@@ -60,7 +62,7 @@ def _kind_element_from_kind_section(section):
         try:
             element = match["sym"]
         except TypeError:
-            raise InputValidationError(
+            raise common.InputValidationError(
                 f"Unable to figure out atomic symbol from KIND '{kind}'."
             )
 
@@ -125,7 +127,7 @@ def _write_gdt(inp, entries, folder, key, fname):
 def validate_basissets_namespace(basissets, _):
     """A input_namespace validator to ensure passed down basis sets have the correct type."""
     return _validate_gdt_namespace(
-        basissets, DataFactory("gaussian.basisset"), "basis set"
+        basissets, plugins.DataFactory("gaussian.basisset"), "basis set"
     )
 
 
@@ -176,7 +178,7 @@ def validate_basissets(inp, basissets, structure):
                 bsets = [(t, b) for t, s, b in basissets if s == element]
 
             if not bsets:
-                raise InputValidationError(
+                raise common.InputValidationError(
                     f"No basis set found for kind {kind} or element {element}"
                     f" in basissets input namespace and not explicitly set."
                 )
@@ -203,7 +205,7 @@ def validate_basissets(inp, basissets, structure):
                     bsets = [(t, b) for t, s, b in basissets if s == element]
 
                 if not bsets:
-                    raise InputValidationError(
+                    raise common.InputValidationError(
                         f"'BASIS_SET {bstype} {bsname}' for element {element} (from kind {kind})"
                         " not found in basissets input namespace"
                     )
@@ -213,7 +215,7 @@ def validate_basissets(inp, basissets, structure):
                         basissets_used.add(bset)
                         break
                 else:
-                    raise InputValidationError(
+                    raise common.InputValidationError(
                         f"'BASIS_SET {bstype} {bsname}' for element {element} (from kind {kind})"
                         " not found in basissets input namespace"
                     )
@@ -222,14 +224,14 @@ def validate_basissets(inp, basissets, structure):
     if not structure and any(
         bset not in basissets_used for bset in basissets_specified
     ):
-        raise InputValidationError(
+        raise common.InputValidationError(
             "No explicit structure given and basis sets not referenced in input"
         )
 
     if isinstance(inp["FORCE_EVAL"], Sequence) and any(
         kind.name not in explicit_kinds for kind in structure.kinds
     ):
-        raise InputValidationError(
+        raise common.InputValidationError(
             "Automated BASIS_SET keyword creation is not yet supported with multiple FORCE_EVALs."
             " Please explicitly reference a BASIS_SET for each KIND."
         )
@@ -250,13 +252,13 @@ def validate_basissets(inp, basissets, structure):
             bsets = [(t, b) for t, s, b in basissets if s == kind.symbol]
 
         if not bsets:
-            raise InputValidationError(
+            raise common.InputValidationError(
                 f"No basis set found in the given basissets for kind '{kind.name}' of your structure."
             )
 
         for _, bset in bsets:
             if bset.element != kind.symbol:
-                raise InputValidationError(
+                raise common.InputValidationError(
                     f"Basis set '{bset.name}' for '{bset.element}' specified"
                     f" for kind '{kind.name}' (of '{kind.symbol}')."
                 )
@@ -274,7 +276,7 @@ def validate_basissets(inp, basissets, structure):
 
     for bset in basissets_specified:
         if bset not in basissets_used:
-            raise InputValidationError(
+            raise common.InputValidationError(
                 f"Basis set '{bset.name}' ('{bset.element}') specified in the basissets"
                 f" input namespace but not referenced by either input or structure."
             )
@@ -287,7 +289,9 @@ def write_basissets(inp, basissets, folder):
 
 def validate_pseudos_namespace(pseudos, _):
     """A input_namespace validator to ensure passed down pseudopentials have the correct type."""
-    return _validate_gdt_namespace(pseudos, DataFactory("gaussian.pseudo"), "pseudo")
+    return _validate_gdt_namespace(
+        pseudos, plugins.DataFactory("gaussian.pseudo"), "pseudo"
+    )
 
 
 def validate_pseudos(inp, pseudos, structure):
@@ -318,7 +322,7 @@ def validate_pseudos(inp, pseudos, structure):
                 try:
                     pseudo = pseudos[element]
                 except KeyError:
-                    raise InputValidationError(
+                    raise common.InputValidationError(
                         f"No pseudopotential found for kind {kind} or element {element}"
                         f" in pseudos input namespace and not explicitly set."
                     )
@@ -335,19 +339,19 @@ def validate_pseudos(inp, pseudos, structure):
                 try:
                     pseudo = pseudos[element]
                 except KeyError:
-                    raise InputValidationError(
+                    raise common.InputValidationError(
                         f"'POTENTIAL {ptype} {pname}' for element {element} (from kind {kind})"
                         " not found in pseudos input namespace"
                     )
 
             if pname not in pseudo.aliases:
-                raise InputValidationError(
+                raise common.InputValidationError(
                     f"'POTENTIAL {ptype} {pname}' for element {element} (from kind {kind})"
                     " not found in pseudos input namespace"
                 )
 
         if pseudo.element != element:
-            raise InputValidationError(
+            raise common.InputValidationError(
                 f"Pseudopotential '{pseudo.name}' for '{pseudo.element}' specified"
                 f" for element '{element}'."
             )
@@ -358,14 +362,14 @@ def validate_pseudos(inp, pseudos, structure):
     if not structure and any(
         pseudo not in pseudos_used for pseudo in pseudos_specified
     ):
-        raise InputValidationError(
+        raise common.InputValidationError(
             "No explicit structure given and pseudo not referenced in input"
         )
 
     if isinstance(inp["FORCE_EVAL"], Sequence) and any(
         kind.name not in explicit_kinds for kind in structure.kinds
     ):
-        raise InputValidationError(
+        raise common.InputValidationError(
             "Automated POTENTIAL keyword creation is not yet supported with multiple FORCE_EVALs."
             " Please explicitly reference a POTENTIAL for each KIND."
         )
@@ -383,13 +387,13 @@ def validate_pseudos(inp, pseudos, structure):
             try:
                 pseudo = pseudos[kind.symbol]
             except KeyError:
-                raise InputValidationError(
+                raise common.InputValidationError(
                     f"No basis set found in the given basissets"
                     f" for kind '{kind.name}' (or '{kind.symbol}') of your structure."
                 )
 
         if pseudo.element != kind.symbol:
-            raise InputValidationError(
+            raise common.InputValidationError(
                 f"Pseudopotential '{pseudo.name}' for '{pseudo.element}' specified"
                 f" for kind '{kind.name}' (of '{kind.symbol}')."
             )
@@ -402,7 +406,7 @@ def validate_pseudos(inp, pseudos, structure):
 
     for pseudo in pseudos_specified:
         if pseudo not in pseudos_used:
-            raise InputValidationError(
+            raise common.InputValidationError(
                 f"Pseudopodential '{pseudo.name}' specified in the pseudos input namespace"
                 f" but not referenced by either input or structure."
             )
@@ -411,3 +415,63 @@ def validate_pseudos(inp, pseudos, structure):
 def write_pseudos(inp, pseudos, folder):
     """Writes the unified POTENTIAL file with the used pseudos"""
     _write_gdt(inp, pseudos, folder, "POTENTIAL_FILE_NAME", "POTENTIAL")
+
+
+def _merge_trajectories_into_dictionary(*trajectories, unique_stepids=False):
+    if len(trajectories) < 0:
+        return None
+    final_trajectory_dict = {}
+
+    array_names = trajectories[0].get_arraynames()
+
+    for array_name in array_names:
+        if any(array_name not in traj.get_arraynames() for traj in trajectories):
+            raise ValueError(
+                f"Array name '{array_name}' not found in all trajectories."
+            )
+        merged_array = np.concatenate(
+            [traj.get_array(array_name) for traj in trajectories], axis=0
+        )
+        final_trajectory_dict[array_name] = merged_array
+
+    # If unique_stepids is True, we only keep the unique stepids.
+    # The other arrays are then also reduced to the unique stepids.
+    if unique_stepids:
+        stepids = np.concatenate([traj.get_stepids() for traj in trajectories], axis=0)
+        final_trajectory_dict["stepids"], unique_indices = np.unique(
+            stepids, return_index=True
+        )
+
+        for array_name in array_names:
+            final_trajectory_dict[array_name] = final_trajectory_dict[array_name][
+                unique_indices
+            ]
+
+    return final_trajectory_dict
+
+
+def _dictionary_to_trajectory(trajectory_dict, symbols):
+    final_trajectory = orm.TrajectoryData()
+    final_trajectory.set_trajectory(
+        symbols=symbols, positions=trajectory_dict.pop("positions")
+    )
+    for array_name, array in trajectory_dict.items():
+        final_trajectory.set_array(array_name, array)
+
+    return final_trajectory
+
+
+@engine.calcfunction
+def merge_trajectory_data_unique(*trajectories):
+    trajectory_dict = _merge_trajectories_into_dictionary(
+        *trajectories, unique_stepids=True
+    )
+    return _dictionary_to_trajectory(trajectory_dict, trajectories[0].symbols)
+
+
+@engine.calcfunction
+def merge_trajectory_data_non_unique(*trajectories):
+    trajectory_dict = _merge_trajectories_into_dictionary(
+        *trajectories, unique_stepids=False
+    )
+    return _dictionary_to_trajectory(trajectory_dict, trajectories[0].symbols)

aiida_cp2k/workchains/base.py

@@ -46,11 +46,31 @@ def setup(self):
         super().setup()
         self.ctx.inputs = common.AttributeDict(self.exposed_inputs(Cp2kCalculation, 'cp2k'))
 
+    def _collect_all_trajetories(self):
+        """Collect all trajectories from the children calculations."""
+        trajectories = []
+        for called in self.ctx.children:
+            if isinstance(called, orm.CalcJobNode):
+                try:
+                    trajectories.append(called.outputs.output_trajectory)
+                except AttributeError:
+                    pass
+        return trajectories
+
     def results(self):
         super().results()
         if self.inputs.cp2k.parameters != self.ctx.inputs.parameters:
             self.out('final_input_parameters', self.ctx.inputs.parameters)
 
+        trajectories = self._collect_all_trajetories()
+        if trajectories:
+            self.report("Work chain completed successfully, collecting all trajectories")
+            if self.ctx.inputs.parameters.get("GLOBAL", {}).get("RUN_TYPE") == "GEO_OPT":
+                output_trajectory = utils.merge_trajectory_data_non_unique(*trajectories)
+            else:
+                output_trajectory = utils.merge_trajectory_data_unique(*trajectories)
+            self.out("output_trajectory", output_trajectory)
+
     def overwrite_input_structure(self):
         if "output_structure" in self.ctx.children[self.ctx.iteration-1].outputs:
             self.ctx.inputs.structure = self.ctx.children[self.ctx.iteration-1].outputs.output_structure