fixing parser for v2024.3

aiida_cp2k/utils/parser.py

@@ -178,7 +178,7 @@ def parse_cp2k_output_advanced(
                 edens_rspace = None
                 scf_converged = True
 
-            print_now = False
+            dump_step_info = False
             data = line.split()
             # Parse general info
             if line.startswith(" CELL|"):
@@ -208,24 +208,48 @@ def parse_cp2k_output_advanced(
             # Parse specific info
             if result_dict["run_type"] in ["ENERGY", "ENERGY_FORCE"]:
                 if energy is not None and not result_dict["motion_step_info"]["step"]:
-                    print_now = True
+                    dump_step_info = True
             if result_dict["run_type"] in ["GEO_OPT", "CELL_OPT"]:
                 # Note: with CELL_OPT/LBFGS there is no "STEP 0", while there is with CELL_OPT/BFGS
+
+                # Getting the step number.
                 if re.search(r"Informations at step", line):
                     step = int(data[5])
-                if re.search(r"Max. step size             =", line):
+                elif re.search(
+                    r"OPT\| Step number ", line
+                ):  # Fix for new CP2K versions.
+                    step = int(data[-1])
+
+                # Getting the maximum step size.
+                if re.search(
+                    r"OPT\| Maximum step size\s*[-+]?\d*\.?\d+", line
+                ) or re.search(r"Max. step size\s+=", line):
                     max_step = float(data[-1])
-                if re.search(r"RMS step size              =", line):
+
+                # Getting the RMS step size.
+                if re.search(
+                    r"OPT\| RMS step size\s*[-+]?\d*\.?\d+", line
+                ) or re.search(r"RMS step size\s+=", line):
                     rms_step = float(data[-1])
-                if re.search(r"Max. gradient              =", line):
+
+                # Getting the maximum gradient.
+                if re.search(
+                    r"OPT\| Maximum gradient\s*[-+]?\d*\.?\d+", line
+                ) or re.search(r"Max. gradient\s+=", line):
                     max_grad = float(data[-1])
-                if re.search(r"RMS gradient               =", line):
+
+                # Getting the RMS gradient.
+                if re.search(
+                    r"OPT\| RMS gradient\s*[-+]?\d*\.?\d+",
+                    line,
+                ) or re.search(r"RMS gradient\s{3,}=", line):
                     rms_grad = float(data[-1])
+
                 if (
                     len(data) == 1
                     and data[0] == "---------------------------------------------------"
-                ):
-                    print_now = True  # 51('-')
+                ) or re.search(r"OPT\| Estimated peak process memory", line):
+                    dump_step_info = True  # 51('-')
                 if re.search(
                     r"Reevaluating energy at the minimum", line
                 ):  # not clear why it is doing a last one...
@@ -239,16 +263,16 @@ def parse_cp2k_output_advanced(
                     step = int(data[3])
                 if re.search(r"INITIAL PRESSURE\[bar\]", line):
                     pressure = float(data[3])
-                    print_now = True
+                    dump_step_info = True
                 if re.search(r"PRESSURE \[bar\]", line):
                     pressure = float(data[3])
-                    print_now = True
+                    dump_step_info = True
             if result_dict["run_type"] == "MD-NPT_F":
                 if re.search(r"^ STEP NUMBER", line):
                     step = int(data[3])
                 if re.search(r"^ INITIAL PRESSURE\[bar\]", line):
                     pressure = float(data[3])
-                    print_now = True
+                    dump_step_info = True
                 if re.search(r"^ PRESSURE \[bar\]", line):
                     pressure = float(data[3])
                 if re.search(r"^ VOLUME\[bohr\^3\]", line):
@@ -261,9 +285,9 @@ def parse_cp2k_output_advanced(
                     cell_alp = float(data[3])
                     cell_bet = float(data[4])
                     cell_gam = float(data[5])
-                    print_now = True
+                    dump_step_info = True
 
-            if print_now and energy is not None:
+            if dump_step_info and energy is not None:
                 result_dict["motion_step_info"]["step"].append(step)
                 result_dict["motion_step_info"]["energy_au"].append(energy)
                 result_dict["motion_step_info"]["dispersion_energy_au"].append(

aiida_cp2k/workchains/base.py

@@ -85,7 +85,7 @@ def restart_incomplete_calculation(self, calc):
         content_string = calc.outputs.retrieved.base.repository.get_object_content(calc.base.attributes.get('output_filename'))
 
         # CP2K was updating geometry - continue with that.
-        restart_geometry_transformation = "Max. gradient              =" in content_string or "MD| Step number" in content_string
+        restart_geometry_transformation = "Max. gradient              =" in content_string or "OPT| Maximum gradient                                              " in content_string or "MD| Step number" in content_string
         end_inner_scf_loop = "Total energy: " in content_string
         # The message is written in the log file when the CP2K input parameter `LOG_PRINT_KEY` is set to True.
         if not (restart_geometry_transformation or end_inner_scf_loop or "Writing RESTART" in content_string):

examples/single_calculations/example_geopt_advanced_parser.py

@@ -0,0 +1,162 @@
+###############################################################################
+# Copyright (c), The AiiDA-CP2K authors.                                      #
+# SPDX-License-Identifier: MIT                                                #
+# AiiDA-CP2K is hosted on GitHub at https://github.com/aiidateam/aiida-cp2k   #
+# For further information on the license, see the LICENSE.txt file.           #
+###############################################################################
+"""Run DFT geometry optimization."""
+
+import os
+import sys
+
+import ase.io
+import click
+from aiida.common import NotExistent
+from aiida.engine import run
+from aiida.orm import Dict, SinglefileData, load_code
+from aiida.plugins import DataFactory
+
+StructureData = DataFactory("core.structure")
+
+
+def example_geopt(cp2k_code):
+    """Run DFT geometry optimization."""
+
+    print("Testing CP2K GEO_OPT on H2O (DFT)...")
+
+    thisdir = os.path.dirname(os.path.realpath(__file__))
+
+    # Structure.
+    structure = StructureData(
+        ase=ase.io.read(os.path.join(thisdir, "..", "files", "h2.xyz"))
+    )
+
+    # Basis set.
+    basis_file = SinglefileData(
+        file=os.path.join(thisdir, "..", "files", "BASIS_MOLOPT")
+    )
+
+    # Pseudopotentials.
+    pseudo_file = SinglefileData(
+        file=os.path.join(thisdir, "..", "files", "GTH_POTENTIALS")
+    )
+
+    # Parameters.
+    parameters = Dict(
+        {
+            "GLOBAL": {
+                "RUN_TYPE": "GEO_OPT",
+            },
+            "FORCE_EVAL": {
+                "METHOD": "Quickstep",
+                "DFT": {
+                    "BASIS_SET_FILE_NAME": "BASIS_MOLOPT",
+                    "POTENTIAL_FILE_NAME": "GTH_POTENTIALS",
+                    "QS": {
+                        "EPS_DEFAULT": 1.0e-12,
+                        "WF_INTERPOLATION": "ps",
+                        "EXTRAPOLATION_ORDER": 3,
+                    },
+                    "MGRID": {
+                        "NGRIDS": 4,
+                        "CUTOFF": 280,
+                        "REL_CUTOFF": 30,
+                    },
+                    "XC": {
+                        "XC_FUNCTIONAL": {
+                            "_": "PBE",
+                        },
+                    },
+                    "POISSON": {
+                        "PERIODIC": "none",
+                        "PSOLVER": "MT",
+                    },
+                },
+                "SUBSYS": {
+                    "KIND": [
+                        {
+                            "_": "O",
+                            "BASIS_SET": "DZVP-MOLOPT-SR-GTH",
+                            "POTENTIAL": "GTH-PBE-q6",
+                        },
+                        {
+                            "_": "H",
+                            "BASIS_SET": "DZVP-MOLOPT-SR-GTH",
+                            "POTENTIAL": "GTH-PBE-q1",
+                        },
+                    ],
+                },
+            },
+        }
+    )
+
+    # Construct process builder.
+    builder = cp2k_code.get_builder()
+    builder.structure = structure
+    builder.parameters = parameters
+    builder.code = cp2k_code
+    builder.file = {
+        "basis": basis_file,
+        "pseudo": pseudo_file,
+    }
+    builder.metadata.options.resources = {
+        "num_machines": 1,
+        "num_mpiprocs_per_machine": 1,
+    }
+    builder.metadata.options.max_wallclock_seconds = 1 * 3 * 60
+    builder.metadata.options.parser_name = "cp2k_advanced_parser"
+
+    print("Submitted calculation...")
+    calc = run(builder)
+
+    # Check walltime not exceeded.
+    assert calc["output_parameters"]["exceeded_walltime"] is False
+
+    # Check energy.
+    expected_energy = -1.17212345935
+    if abs(calc["output_parameters"]["energy"] - expected_energy) < 1e-10:
+        print("OK, energy has the expected value.")
+    else:
+        print("ERROR!")
+        print(f"Expected energy value: {expected_energy}")
+        print(f"Actual energy value: {calc['output_parameters']['energy']}")
+        sys.exit(3)
+
+    # Check geometry.
+    expected_dist = 0.732594809575
+    dist = calc["output_structure"].get_ase().get_distance(0, 1)
+    if abs(dist - expected_dist) < 1e-7:
+        print("OK, H-H distance has the expected value.")
+    else:
+        print("ERROR!")
+        print(f"Expected dist value: {expected_dist}")
+        print(f"Actual dist value: {dist}")
+        sys.exit(3)
+
+    # Check motion step information.
+    assert calc["output_parameters"]["motion_step_info"]["step"] == [
+        0,
+        1,
+        2,
+    ], "ERROR: motion step info is incorrect"
+    assert calc["output_parameters"]["motion_step_info"]["cell_a_angs"] == [
+        4.0,
+        4.0,
+        4.0,
+    ], "ERROR: motion step info is incorrect"
+
+
+@click.command("cli")
+@click.argument("codelabel")
+def cli(codelabel):
+    """Click interface."""
+    try:
+        code = load_code(codelabel)
+    except NotExistent:
+        print(f"The code '{codelabel}' does not exist.")
+        sys.exit(1)
+    example_geopt(code)
+
+
+if __name__ == "__main__":
+    cli()

examples/workchains/fixme_example_base_md_reftraj_restart.py

@@ -57,7 +57,7 @@ def example_base(cp2k_code):
             "GLOBAL": {
                 "RUN_TYPE": "MD",
                 "PRINT_LEVEL": "LOW",
-                "WALLTIME": 3,
+                "WALLTIME": 2,
                 "PROJECT": "aiida",
             },
             "MOTION": {
@@ -151,9 +151,12 @@ def example_base(cp2k_code):
         "basis": basis_file,
         "pseudo": pseudo_file,
     }
-    builder.cp2k.metadata.options.resources = {
-        "num_machines": 1,
-        "num_mpiprocs_per_machine": 1,
+    builder.cp2k.metadata.options = {
+        "max_wallclock_seconds": 100,
+        "resources": {
+            "num_machines": 1,
+            "num_mpiprocs_per_machine": 1,
+        },
     }
 
     print("Submitted calculation...")