Build an iterative phonon flow #306
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Disclaimer: This is a small programming project that I might work on for fun in the next weeks. |
JaGeo
changed the title
JaGeo
changed the title
JaGeo
commented
Dec 22, 2024
| if volume_custom_scale_factors is None: | ||
| if volume_scale_factor_range is None: | ||
| volume_scale_factor_range = [0.90, 1.1] | ||
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add warning that default scale factor range is used
JaGeo
commented
Dec 22, 2024
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| new_atoms_list = [ | ||
| atoms | ||
| for atoms in atoms_list | ||
| if atoms.info["config_type"] != "IsolatedAtom" | ||
| ] | ||
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| ase.io.write(destination_file_path, new_atoms_list, append=True) | ||
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| logging.info( | ||
| f"File {self.pre_xyz_files[0]} has been copied to {destination_file_path}" | ||
| ) |
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is this a good universal solution? maybe, i can reduce it to just one set of isolatedAtom energies to avoid failures
JaGeo
commented
Dec 22, 2024
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| if self.pre_database_dir and os.path.exists(self.pre_database_dir): | ||
| if len(self.pre_xyz_files) == 2: | ||
| files_new = ["train.extxyz", "test.extxyz"] | ||
| for file_name, file_new in zip(self.pre_xyz_files, files_new): | ||
| with ( | ||
| open( | ||
| os.path.join(self.pre_database_dir, file_name) | ||
| ) as pre_xyz_file, | ||
| open(file_new, "a") as xyz_file, | ||
| ): | ||
| xyz_file.write(pre_xyz_file.read()) | ||
| logging.info(f"File {file_name} has been copied to {file_new}") | ||
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| elif len(self.pre_xyz_files) > 2: | ||
| raise ValueError( | ||
| "Please provide a train and a test extxyz file (two files in total) for the pre_xyz_files." | ||
| ) |
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did not keep the split ratio constant
JaGeo
commented
Dec 22, 2024
src/autoplex/fitting/common/utils.py
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| print(train_data_path) | ||
| print(test_data_path) |
JaGeo
commented
Dec 22, 2024
| @@ -1770,6 +1781,7 @@ def run_gap(num_processes_fit: int, parameters) -> None: | |||
| open("std_gap_out.log", "w", encoding="utf-8") as file_std, | |||
| open("std_gap_err.log", "w", encoding="utf-8") as file_err, | |||
| ): | |||
| print(*parameters) | |||
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autoplex/src/autoplex/auto/phonons/flows.py Line 269 in 5c231fb See #305 but we might need to investigate if the post init is really enough for this case as well |
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Very first draft for an iterative phonon flow. There are still many, many things to solve before this can work.
make sure that a new random seed is used for each step (make sure the order of the settings has been considered in the seed computation)
reuse the previous database
make sure that the phonon benchmark runs are reused as well
expose all relevant outputs to allow for an iterative procedure
random_seed + len(workflow_maker.volume_custom_scale_factors)
fix previous unit tests
fix reading mace models
improve distort_type_1
make sure random seed creation is done correctly when very similar structures are provided in "structures" - currently, this is not correctly considered (needs to be done in iterative flow as well)
fix write_benchmark_metrics
document that only 0.01 displacement is used in the benchmark
do some testing on the cluster to confirm the options and capabilities
These points will be moved into a subsequent issue.