Parsing issue with MOTION/CELL_OPT/TYPE GEO_OPT #221
Description
Dear aiida-cp2k developpers,
I have been struggling for quite some time now trying to run something as simple as a structure relaxation with variable cell and atomic positions. The problem occurs when I use the following setup :
MOTION/CELL_OPT/TYPE GEO_OPT
and seems to be due to the fact that in this case CP2K runs the calculation in sort of a tree architecture, wherein each GEO_OPT is a seperate child calculation producing individual output files in the form:
aiida-GEO_OPT-N.out
aiida-GEO_OPT-N-1.cell
...
with N seemingly corresponding to the CELL_OPT step index (zero-based indexing).
The calculation also produces aiida-1_M.restart files where M also seems to correspond to the CELL_OPT step index, but in one-based indexing.
This complex file architecture of course interferes with the retrieve of files within aiida. I tried to avoid this problem by imposing fixed file names in the input parameters with the '=' sign in a syntax of the form:
{"FILENAME" : "=aiida-1.frc.xyz}
in what I hope a appropriate sections of the CP2K input.
I managed to do this to a certain extent, still have problems at parsing:
151272 1h ago Cp2kCalculation ⨯ Excepted
(aiida-2.5.0) $ verdi process report 151272
*** 151272: None
*** (empty scheduler output file)
*** (empty scheduler errors file)
*** 1 LOG MESSAGES:
+-> REPORT at 2024-12-18 15:49:45.260334+01:00
| [151272|Cp2kCalculation|on_except]: Traceback (most recent call last):
| File "/home/cadarp02/miniforge3/envs/aiida-2.5.0/lib/python3.11/site-packages/plumpy/process_states.py", line 228, in execute
| result = self.run_fn(*self.args, **self.kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/home/cadarp02/miniforge3/envs/aiida-2.5.0/lib/python3.11/site-packages/aiida/engine/processes/calcjobs/calcjob.py", line 678, in parse
| exit_code_retrieved = self.parse_retrieved_output(retrieved_temporary_folder)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/home/cadarp02/miniforge3/envs/aiida-2.5.0/lib/python3.11/site-packages/aiida/engine/processes/calcjobs/calcjob.py", line 789, in parse_retrieved_output
| exit_code = parser.parse(**parse_kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/home/cadarp02/aiida/plugin_src/aiida-cp2k/aiida_cp2k/parsers/__init__.py", line 44, in parse
| trajectory = self._parse_trajectory(last_structure)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/home/cadarp02/aiida/plugin_src/aiida-cp2k/aiida_cp2k/parsers/__init__.py", line 187, in _parse_trajectory
| trajectory.set_trajectory(
| File "/home/cadarp02/miniforge3/envs/aiida-2.5.0/lib/python3.11/site-packages/aiida/orm/nodes/data/array/trajectory.py", line 138, in set_trajectory
| self._internal_validate(stepids, cells, symbols, positions, times, velocities)
| File "/home/cadarp02/miniforge3/envs/aiida-2.5.0/lib/python3.11/site-packages/aiida/orm/nodes/data/array/trajectory.py", line 65, in _internal_validate
| raise ValueError('TrajectoryData.cells must have shape (s,3,3), with s=number of steps')
| ValueError: TrajectoryData.cells must have shape (s,3,3), with s=number of steps
Below is the parameter Dict input used for the Cp2kCalculation:
In [4]: calc.inputs.parameters.get_dict()
Out[4]:
{'GLOBAL': {'RUN_TYPE': 'CELL_OPT', 'PRINT_LEVEL': 'MEDIUM'},
'MOTION': {'PRINT': {'CELL': {'_': 'ON'},
'FORCES': {'_': 'OFF'},
'STRESS': {'_': 'OFF'},
'RESTART': {'_': 'ON', 'FILENAME': '=aiida-1.restart', 'BACKUP_COPIES': 0},
'TRAJECTORY': {'FILENAME': '=aiida-pos-1.xyz'},
'VELOCITIES': {'_': 'OFF'}},
'GEO_OPT': {'MAX_ITER': 50, 'OPTIMIZER': 'BFGS'},
'CELL_OPT': {'TYPE': 'GEO_OPT',
'PRINT': {'CELL': {'FILENAME': 'aiida-1.cell'}},
'MAX_ITER': 30,
'OPTIMIZER': 'BFGS'}},
'FORCE_EVAL': {'DFT': {'QS': {'METHOD': 'GPW',
'EPS_DEFAULT': 1e-12,
'EXTRAPOLATION': 'LINEAR_P'},
'XC': {'XC_FUNCTIONAL': {'PBE': {}}},
'SCF': {'PRINT': {'RESTART': {'_': 'OFF',
'FILENAME': 'none',
'BACKUP_COPIES': 0,
'COMMON_ITERATION_LEVELS': 0},
'RESTART_HISTORY': {'FILENAME': 'none',
'BACKUP_COPIES': 0,
'COMMON_ITERATION_LEVELS': 0}},
'SMEAR': {'_': True,
'METHOD': 'FERMI_DIRAC',
'ELECTRONIC_TEMPERATURE': 200.0},
'MIXING': {'ALPHA': 0.3, 'METHOD': 'BROYDEN_MIXING', 'NBUFFER': 8},
'EPS_SCF': 1e-06,
'MAX_SCF': 40,
'ADDED_MOS': 20,
'OUTER_SCF': {'EPS_SCF': 1e-06, 'MAX_SCF': 40},
'SCF_GUESS': 'ATOMIC'},
'MGRID': {'CUTOFF': 1000.0, 'REL_CUTOFF': 50.0},
'KPOINTS': {'SCHEME': ['MONKHORST-PACK', '3', '2', '3'],
'EPS_GEO': 1e-08,
'SYMMETRY': False,
'FULL_GRID': False},
'BASIS_SET_FILE_NAME': 'GTH_BASIS_SETS',
'POTENTIAL_FILE_NAME': 'GTH_POTENTIALS'},
'PRINT': {'FORCES': {'_': 'ON', 'FILENAME': '=aiida-frc-1.xyz'},
'STRESS_TENSOR': {'_': 'ON', 'FILENAME': '=stress_tensor'}},
'METHOD': 'QS',
'SUBSYS': {'KIND': [{'_': 'Si',
'BASIS_SET': 'DZVP-GTH-q4',
'POTENTIAL': 'GTH-PBE-q4'},
{'_': 'C', 'BASIS_SET': 'DZVP-GTH-q4', 'POTENTIAL': 'GTH-PBE-q4'},
{'_': 'N', 'BASIS_SET': 'DZVP-GTH-q5', 'POTENTIAL': 'GTH-PBE-q5'},
{'_': 'H', 'BASIS_SET': 'DZVP-GTH-q1', 'POTENTIAL': 'GTH-PBE-q1'}]},
'STRESS_TENSOR': 'ANALYTICAL'}}
Here the content of the remote folder at the end of the calculation:
$ ls
aiida-1_10.restart aiida-aiida-1.cell-1_8.Log aiida-GEO_OPT-1-BFGS.Hessian
aiida-1_11.restart aiida-aiida-1.cell-1_9.Log aiida-GEO_OPT-1.out
aiida-1_12.restart aiida-aiida-1.cell-1.Log aiida-GEO_OPT-2-1.cell
aiida-1_13.restart aiida-BFGS.Hessian aiida-GEO_OPT-2-BFGS.Hessian
aiida-1_14.restart aiida.coords.xyz aiida-GEO_OPT-2.out
aiida-1_15.restart aiida-frc-1.xyz aiida-GEO_OPT-3-1.cell
aiida-1_16.restart aiida-GEO_OPT-0-1.cell aiida-GEO_OPT-3-BFGS.Hessian
aiida-1_17.restart aiida-GEO_OPT-0-BFGS.Hessian aiida-GEO_OPT-3.out
aiida-1_18.restart aiida-GEO_OPT-0.out aiida-GEO_OPT-4-1.cell
aiida-1_1.restart aiida-GEO_OPT-10-1.cell aiida-GEO_OPT-4-BFGS.Hessian
aiida-1_2.restart aiida-GEO_OPT-10-BFGS.Hessian aiida-GEO_OPT-4.out
aiida-1_3.restart aiida-GEO_OPT-10.out aiida-GEO_OPT-5-1.cell
aiida-1_4.restart aiida-GEO_OPT-11-1.cell aiida-GEO_OPT-5-BFGS.Hessian
aiida-1_5.restart aiida-GEO_OPT-11-BFGS.Hessian aiida-GEO_OPT-5.out
aiida-1_6.restart aiida-GEO_OPT-1-1.cell aiida-GEO_OPT-6-1.cell
aiida-1_7.restart aiida-GEO_OPT-11.out aiida-GEO_OPT-6-BFGS.Hessian
aiida-1_8.restart aiida-GEO_OPT-12-1.cell aiida-GEO_OPT-6.out
aiida-1_9.restart aiida-GEO_OPT-12-BFGS.Hessian aiida-GEO_OPT-7-1.cell
aiida-1.cell aiida-GEO_OPT-12.out aiida-GEO_OPT-7-BFGS.Hessian
aiida-1.restart aiida-GEO_OPT-13-1.cell aiida-GEO_OPT-7.out
aiida-aiida-1.cell-1_0.Log aiida-GEO_OPT-13-BFGS.Hessian aiida-GEO_OPT-8-1.cell
aiida-aiida-1.cell-1_10.Log aiida-GEO_OPT-13.out aiida-GEO_OPT-8-BFGS.Hessian
aiida-aiida-1.cell-1_11.Log aiida-GEO_OPT-14-1.cell aiida-GEO_OPT-8.out
aiida-aiida-1.cell-1_12.Log aiida-GEO_OPT-14-BFGS.Hessian aiida-GEO_OPT-9-1.cell
aiida-aiida-1.cell-1_13.Log aiida-GEO_OPT-14.out aiida-GEO_OPT-9-BFGS.Hessian
aiida-aiida-1.cell-1_14.Log aiida-GEO_OPT-15-1.cell aiida-GEO_OPT-9.out
aiida-aiida-1.cell-1_15.Log aiida-GEO_OPT-15-BFGS.Hessian aiida.inp
aiida-aiida-1.cell-1_16.Log aiida-GEO_OPT-15.out aiida.out
aiida-aiida-1.cell-1_17.Log aiida-GEO_OPT-16-1.cell aiida-pos-1.xyz
aiida-aiida-1.cell-1_18.Log aiida-GEO_OPT-16-BFGS.Hessian _aiidasubmit.sh
aiida-aiida-1.cell-1_1.Log aiida-GEO_OPT-16.out GTH_BASIS_SETS
aiida-aiida-1.cell-1_2.Log aiida-GEO_OPT-17-1.cell GTH_POTENTIALS
aiida-aiida-1.cell-1_3.Log aiida-GEO_OPT-17-BFGS.Hessian _scheduler-stderr.txt
aiida-aiida-1.cell-1_4.Log aiida-GEO_OPT-17.out _scheduler-stdout.txt
aiida-aiida-1.cell-1_5.Log aiida-GEO_OPT-18-1.cell stress_tensor
aiida-aiida-1.cell-1_6.Log aiida-GEO_OPT-18-BFGS.Hessian
aiida-aiida-1.cell-1_7.Log aiida-GEO_OPT-18.out
The content of the cell files is as follows:
cat aiida-1.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]
1 0.000 6.5692964458 -0.0072670000 -0.0433940000 1.2887486077 11.0358886517 0.1229230000 -2.7377493937 1.2321923316 5.8384210740 420.9561054561
2 0.000 6.6481464154 -0.0072670000 -0.0433940000 1.2923706657 11.0867987211 0.1229230000 -2.7379253371 1.2179088244 5.9186525396 433.9213425845
3 0.000 6.6517594608 -0.0072670000 -0.0433940000 1.2950729240 11.0914514805 0.1229230000 -2.7407783747 1.2180617013 5.9229796615 434.6582644519
4 0.000 6.6549013130 -0.0072670000 -0.0433940000 1.3057628832 11.1030565459 0.1229230000 -2.7524289379 1.2208808157 5.9281413936 435.6935254360
5 0.000 6.6585920540 -0.0072670000 -0.0433940000 1.3403263448 11.1359575059 0.1229230000 -2.7899137855 1.2313114989 5.9376336987 437.9070485795
6 0.000 6.6539629118 -0.0072670000 -0.0433940000 1.3477309957 11.1388926025 0.1229230000 -2.7972722656 1.2342509968 5.9333710420 437.3950884492
7 0.000 6.6475812999 -0.0072670000 -0.0433940000 1.3528377868 11.1374281704 0.1229230000 -2.8006600574 1.2364030506 5.9254744257 436.3284136101
8 0.000 6.6471030838 -0.0072670000 -0.0433940000 1.3556674492 11.1381845902 0.1229230000 -2.8019530241 1.2368437256 5.9239327644 436.2114336096
9 0.000 6.6482547006 -0.0072670000 -0.0433940000 1.3601616312 11.1392205112 0.1229230000 -2.8022499283 1.2366774832 5.9222723622 436.2048918075
10 0.000 6.6527987324 -0.0072670000 -0.0433940000 1.3719006666 11.1402853603 0.1229230000 -2.7995567949 1.2348880321 5.9177640948 436.2143674176
11 0.000 6.6611899223 -0.0072670000 -0.0433940000 1.3937868231 11.1412762613 0.1229230000 -2.7932374202 1.2310060439 5.9093310859 436.1855253219
12 0.000 6.6609472123 -0.0072670000 -0.0433940000 1.3924142150 11.1409198666 0.1229230000 -2.7930024365 1.2308123577 5.9107163075 436.2587056110
13 0.000 6.6619721719 -0.0072670000 -0.0433940000 1.3948193861 11.1396729499 0.1229230000 -2.7904844386 1.2290636754 5.9122979828 436.3972194831
14 0.000 6.6610569685 -0.0072670000 -0.0433940000 1.3958981117 11.1382810570 0.1229230000 -2.7894498238 1.2281927703 5.9137605632 436.3922157520
15 0.000 6.6596390936 -0.0072670000 -0.0433940000 1.4022804418 11.1356954737 0.1229230000 -2.7873095775 1.2262075835 5.9155354490 436.3318747155
16 0.000 6.6590232559 -0.0072670000 -0.0433940000 1.4040232079 11.1352705056 0.1229230000 -2.7874015663 1.2262588858 5.9151994913 436.2496892777
17 0.000 6.6580267584 -0.0072670000 -0.0433940000 1.4080962317 11.1338504641 0.1229230000 -2.7867195872 1.2257666459 5.9156496125 436.1625403407
18 0.000 6.6584792940 -0.0072670000 -0.0433940000 1.4068319420 11.1342520389 0.1229230000 -2.7868868786 1.2260125869 5.9156426800 436.2072489837
Could you please help me figure out if, how and where precisely in the parameter input I can properly control the output architecture to allow AiiDA to correctly retrieve the relevant outputs and succesfully obtain in particular:
process.outputs.output_structure
process.outputs.output_trajectory
with the cell properly read from the output files.
Thank you very much for your help.
Best regards.
Sylvian.