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Refactor and rename #4

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May 15, 2024
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Refactor and rename #4

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41cf7d8
Update to new name
cdavro May 14, 2024
1e31242
Refactor unit test paths to use arcann_training instead of deepmd_ite…
cdavro May 14, 2024
02b170b
Refactor unit test paths to use arcann_training instead of deepmd_ite…
cdavro May 14, 2024
0639875
Update README
cdavro May 14, 2024
bb76a07
Update headers
cdavro May 15, 2024
d83876c
Rename
cdavro May 15, 2024
a08da9e
Change logging filename
cdavro May 15, 2024
fd22139
Refactor
cdavro May 15, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/unittests_matrix.yml
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Expand Up @@ -63,4 +63,4 @@ jobs:

- name: Run unit tests
run: |
python -m unittest discover deepmd_iterative/unittests
python -m unittest discover arcann_training/unittests
2 changes: 1 addition & 1 deletion .github/workflows/unittests_requirements.yml
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Expand Up @@ -20,4 +20,4 @@ jobs:

- name: Run unit tests
run: |
python -m unittest discover deepmd_iterative/unittests
python -m unittest discover arcann_training/unittests
2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -3,6 +3,8 @@
<!-- PROJECT SHIELDS -->

[![GNU AGPL v3.0 License][license-shield]][license-url]
[![Unit Tests Requirements](https://github.com/arcann-chem/arcann/actions/workflows/unittests_requirements.yml/badge.svg)](https://github.com/arcann-chem/arcann/actions/workflows/unittests_requirements.yml)
[![Unit Tests Matrix](https://github.com/arcann-chem/arcann/actions/workflows/unittests_matrix.yml/badge.svg?branch=main)](https://github.com/arcann-chem/arcann/actions/workflows/unittests_matrix.yml)

<!-- TABLE OF CONTENTS -->

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0 deepmd_iterative/__init__.py → arcann_training/__init__.py
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10 changes: 5 additions & 5 deletions deepmd_iterative/__main__.py → arcann_training/__main__.py
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@@ -1,12 +1,12 @@
"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/05/01
Last modified: 2024/05/15
"""

# Standard library modules
Expand All @@ -17,7 +17,7 @@
from pathlib import Path

# Local imports
from deepmd_iterative.common.logging import setup_logging
from arcann_training.common.logging import setup_logging

# Parsing
parser = argparse.ArgumentParser(description="Deepmd iterative program suite")
Expand All @@ -41,7 +41,7 @@
# Step/Phase name
step_name: str = args.step_name
phase_name: str = args.phase_name
submodule_name: str = f"deepmd_iterative.{step_name}.{phase_name}"
submodule_name: str = f"arcann_training.{step_name}.{phase_name}"

# Input
input_fn: str = args.input
Expand All @@ -57,7 +57,7 @@
# Start
arcann_logger.info(f"-" * 88)
arcann_logger.info(f"-" * 88)
arcann_logger.info(f"DEEPMD ITERATIVE PROGRAM SUITE")
arcann_logger.info(f"ARCANN TRAINING PROGRAM SUITE")
arcann_logger.info(f"Launching: {step_name.capitalize()} - {phase_name.capitalize()}")
arcann_logger.info(f"-" * 88)
arcann_logger.info(f"-" * 88)
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0 deepmd_iterative/assets/__init__.py → arcann_training/assets/__init__.py
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0 deepmd_iterative/assets/default_config.json → arcann_training/assets/default_config.json
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0 deepmd_iterative/assets/elements.json → arcann_training/assets/elements.json
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0 deepmd_iterative/assets/others/__init__.py → arcann_training/assets/others/__init__.py
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0 ...d_iterative/assets/others/lammps_rerun.in → ...nn_training/assets/others/lammps_rerun.in
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4 changes: 2 additions & 2 deletions ...assets/others/vmd_dcd_selection_index.tcl → ...assets/others/vmd_dcd_selection_index.tcl
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@@ -1,11 +1,11 @@
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
# Created: 2022/01/01
# Last modified: 2023/08/16
# Last modified: 2024/05/15

# Load PDB file and clear all existing animations
mol new _R_PDB_FILE_
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4 changes: 2 additions & 2 deletions ...assets/others/vmd_xyz_selection_index.tcl → ...assets/others/vmd_xyz_selection_index.tcl
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#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
# Created: 2022/01/01
# Last modified: 2023/08/16
# Last modified: 2024/05/15

# Load PDB file and clear all existing animations
mol new _R_PDB_FILE_
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0 deepmd_iterative/common/__init__.py → arcann_training/common/__init__.py
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6 changes: 3 additions & 3 deletions deepmd_iterative/common/check.py → arcann_training/common/check.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/05/01
Last modified: 2024/05/15

This module contains functions for checking the availability of certain commands on the system, as well as a function for validating the current working directory during the execution of a specific step.

Expand All @@ -31,7 +31,7 @@
from pathlib import Path

# Local imports
from deepmd_iterative.common.utils import catch_errors_decorator
from arcann_training.common.utils import catch_errors_decorator


# Unittested
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6 changes: 3 additions & 3 deletions deepmd_iterative/common/filesystem.py → arcann_training/common/filesystem.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/05/01
Last modified: 2024/05/15

The filesystem module provides functions to handle file and directory management

Expand Down Expand Up @@ -42,7 +42,7 @@
from pathlib import Path

# Local imports
from deepmd_iterative.common.utils import catch_errors_decorator
from arcann_training.common.utils import catch_errors_decorator


# Unittested
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6 changes: 3 additions & 3 deletions deepmd_iterative/common/ipi.py → arcann_training/common/ipi.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/03/31
Last modified: 2024/05/15

The ipi module provides functions to manipulate i-PI data (as XML tree).

Expand All @@ -22,7 +22,7 @@
import xml.etree.ElementTree as ET

# Local imports
from deepmd_iterative.common.utils import catch_errors_decorator
from arcann_training.common.utils import catch_errors_decorator


# Unittested
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6 changes: 3 additions & 3 deletions deepmd_iterative/common/json.py → arcann_training/common/json.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/05/01
Last modified: 2024/05/15

The json module provides functions to manipulate JSON data (as dict).

Expand Down Expand Up @@ -45,7 +45,7 @@


# Local imports
from deepmd_iterative.common.utils import catch_errors_decorator
from arcann_training.common.utils import catch_errors_decorator


# Unittested
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8 changes: 4 additions & 4 deletions deepmd_iterative/common/lammps.py → arcann_training/common/lammps.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/04/01
Last modified: 2024/05/15

The lammps module provides functions to manipulate LAMMPS data (as list of strings).

Expand All @@ -26,8 +26,8 @@
import numpy as np

# Local imports
from deepmd_iterative.common.utils import catch_errors_decorator
from deepmd_iterative.common.list import textfile_to_string_list
from arcann_training.common.utils import catch_errors_decorator
from arcann_training.common.list import textfile_to_string_list


# Unittested
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6 changes: 3 additions & 3 deletions deepmd_iterative/common/list.py → arcann_training/common/list.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/03/31
Last modified: 2024/05/15

The utils module provides functions to manipulate lists.

Expand All @@ -32,7 +32,7 @@
from typing import List

# Local imports
from deepmd_iterative.common.utils import catch_errors_decorator
from arcann_training.common.utils import catch_errors_decorator


# Unittested
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6 changes: 3 additions & 3 deletions deepmd_iterative/common/logging.py → arcann_training/common/logging.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2024/05/01
Last modified: 2024/05/01
Last modified: 2024/05/15
"""
from typing import Dict

Expand Down Expand Up @@ -49,7 +49,7 @@ def setup_logging(verbose: int = 0) -> Dict:
'class': 'logging.FileHandler',
'level': 'INFO',
'formatter': 'simple_file',
'filename': 'arcann.log',
'filename': 'arcann_training.log',
'mode': 'a', # Append mode
},
},
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8 changes: 4 additions & 4 deletions deepmd_iterative/common/machine.py → arcann_training/common/machine.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/05/01
Last modified: 2024/05/15

The machine module provides functions for machine operations.

Expand Down Expand Up @@ -39,8 +39,8 @@
from typing import Any, Dict, List, Tuple, Union

# Local imports
from deepmd_iterative.common.utils import catch_errors_decorator
from deepmd_iterative.common.json import load_json_file
from arcann_training.common.utils import catch_errors_decorator
from arcann_training.common.json import load_json_file


# Unittested
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6 changes: 3 additions & 3 deletions deepmd_iterative/common/parsing_labeling.py → arcann_training/common/parsing_labeling.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2024/03/01
Last modified: 2024/05/14
Last modified: 2024/05/15
"""

# TODO: Homogenize the docstrings for this module
Expand All @@ -19,7 +19,7 @@
import numpy as np

# Local imports
from deepmd_iterative.common.utils import catch_errors_decorator
from arcann_training.common.utils import catch_errors_decorator


# TODO: Add tests for this function
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6 changes: 3 additions & 3 deletions deepmd_iterative/common/plumed.py → arcann_training/common/plumed.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/03/31
Last modified: 2024/05/15

The plumed module provides functions to manipulate PLUMED data (as list of strings).

Expand All @@ -23,7 +23,7 @@
from typing import List, Tuple, Union

# Local imports
from deepmd_iterative.common.utils import catch_errors_decorator
from arcann_training.common.utils import catch_errors_decorator


# TODO: Add tests for this function
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8 changes: 4 additions & 4 deletions deepmd_iterative/common/slurm.py → arcann_training/common/slurm.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/05/01
Last modified: 2024/05/15

The slurm module provides functions to manipulate SLURM data (as list of strings).

Expand All @@ -24,11 +24,11 @@
from typing import Dict, List

# Local imports
from deepmd_iterative.common.utils import (
from arcann_training.common.utils import (
catch_errors_decorator,
convert_seconds_to_hh_mm_ss,
)
from deepmd_iterative.common.list import (
from arcann_training.common.list import (
exclude_substring_from_string_list,
replace_substring_in_string_list,
)
Expand Down
4 changes: 2 additions & 2 deletions deepmd_iterative/common/utils.py → arcann_training/common/utils.py
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"""
#----------------------------------------------------------------------------------------------------#
# ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks #
# Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem> #
# Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem> #
# #
# SPDX-License-Identifier: AGPL-3.0-only #
#----------------------------------------------------------------------------------------------------#
Created: 2022/01/01
Last modified: 2024/05/01
Last modified: 2024/05/15

Utility module providing helper functions.

Expand Down
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