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Manual downgrade
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ceriottm committed Oct 9, 2024
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678 changes: 417 additions & 261 deletions chemiscope_standalone.html

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.. rst-class:: sphx-glr-timing

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chemiscope.show_input("trajectory-md.json.gz")
.. chemiscope:: _datasets/fig_3-trajectory_004.json.gz
.. chemiscope:: _datasets/fig_3-trajectory_001.json.gz
:mode: default


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.. rst-class:: sphx-glr-timing

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.. rst-class:: sphx-glr-timing

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.. _sphx_glr_download_examples_6-explore.py:
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23 changes: 8 additions & 15 deletions docs/_sources/examples/7-explore-advanced.rst.txt
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.. code-block:: none
/home/runner/work/chemiscope/chemiscope/.tox/docs/lib/python3.11/site-packages/e3nn/o3/_wigner.py:10: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.
/home/michele/lavoro/code/chemiscope/.tox/docs/lib/python3.12/site-packages/e3nn/o3/_wigner.py:10: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.
_Jd, _W3j_flat, _W3j_indices = torch.load(os.path.join(os.path.dirname(__file__), 'constants.pt'))
Expand Down Expand Up @@ -199,14 +199,9 @@ Provide the created featurizer and the properties to :py:func:`chemiscope.explor

.. code-block:: none
Downloading MACE model from 'https://github.com/ACEsuit/mace-off/blob/main/mace_off23/MACE-OFF23_small.model?raw=true'
The model is distributed under the Academic Software License (ASL) license, see https://github.com/gabor1/ASL
To use the model you accept the terms of the license.
ASL is based on the Gnu Public License, but does not permit commercial use
Cached MACE model to /home/runner/.cache/mace/MACE-OFF23_small.model
Using MACE-OFF23 MODEL for MACECalculator with /home/runner/.cache/mace/MACE-OFF23_small.model
Using MACE-OFF23 MODEL for MACECalculator with /home/michele/.cache/mace/MACE-OFF23_small.model
Using float64 for MACECalculator, which is slower but more accurate. Recommended for geometry optimization.
/home/runner/work/chemiscope/chemiscope/.tox/docs/lib/python3.11/site-packages/mace/calculators/mace.py:128: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.
/home/michele/lavoro/code/chemiscope/.tox/docs/lib/python3.12/site-packages/mace/calculators/mace.py:128: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.
torch.load(f=model_path, map_location=device)
Expand Down Expand Up @@ -355,13 +350,11 @@ Provide the created function to :py:func:`chemiscope.explore`.

.. code-block:: none
Downloading MACE model from 'https://tinyurl.com/46jrkm3v'
Cached MACE model to /home/runner/.cache/mace/46jrkm3v
Using Materials Project MACE for MACECalculator with /home/runner/.cache/mace/46jrkm3v
Using Materials Project MACE for MACECalculator with /home/michele/.cache/mace/46jrkm3v
Using float64 for MACECalculator, which is slower but more accurate. Recommended for geometry optimization.
/home/runner/work/chemiscope/chemiscope/.tox/docs/lib/python3.11/site-packages/mace/calculators/mace.py:128: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.
/home/michele/lavoro/code/chemiscope/.tox/docs/lib/python3.12/site-packages/mace/calculators/mace.py:128: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.
torch.load(f=model_path, map_location=device)
/home/runner/work/chemiscope/chemiscope/.tox/docs/lib/python3.11/site-packages/chemiscope/structures/__init__.py:76: UserWarning: the following atomic properties are only defined for a subset of frames: ['tags']; they will be ignored
/home/michele/lavoro/code/chemiscope/.tox/docs/lib/python3.12/site-packages/chemiscope/structures/__init__.py:76: UserWarning: the following atomic properties are only defined for a subset of frames: ['tags']; they will be ignored
return _ase_list_atom_properties(frames)
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.. code-block:: none
/home/runner/work/chemiscope/chemiscope/.tox/docs/lib/python3.11/site-packages/chemiscope/structures/__init__.py:76: UserWarning: the following atomic properties are only defined for a subset of frames: ['tags']; they will be ignored
/home/michele/lavoro/code/chemiscope/.tox/docs/lib/python3.12/site-packages/chemiscope/structures/__init__.py:76: UserWarning: the following atomic properties are only defined for a subset of frames: ['tags']; they will be ignored
return _ase_list_atom_properties(frames)
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.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 11.854 seconds)
**Total running time of the script:** (0 minutes 11.924 seconds)


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.. rst-class:: sphx-glr-timing

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Computation times
=================
**00:20.656** total execution time for 9 files **from examples**:
**00:00.096** total execution time for 9 files **from examples**:

.. container::

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* - Example
- Time
- Mem (MB)
* - :ref:`sphx_glr_examples_7-explore-advanced.py` (``7-explore-advanced.py``)
- 00:11.854
* - :ref:`sphx_glr_examples_3-trajectory.py` (``3-trajectory.py``)
- 00:00.096
- 0.0
* - :ref:`sphx_glr_examples_6-explore.py` (``6-explore.py``)
- 00:06.497
* - :ref:`sphx_glr_examples_1-base.py` (``1-base.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_8-explore-with-metatensor.py` (``8-explore-with-metatensor.py``)
- 00:01.094
* - :ref:`sphx_glr_examples_2-structure_map.py` (``2-structure_map.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_9-showing_custom_bonds.py` (``9-showing_custom_bonds.py``)
- 00:01.011
* - :ref:`sphx_glr_examples_4-colors.py` (``4-colors.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_5-shapes.py` (``5-shapes.py``)
- 00:00.097
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_1-base.py` (``1-base.py``)
- 00:00.052
* - :ref:`sphx_glr_examples_6-explore.py` (``6-explore.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_3-trajectory.py` (``3-trajectory.py``)
- 00:00.021
* - :ref:`sphx_glr_examples_7-explore-advanced.py` (``7-explore-advanced.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_2-structure_map.py` (``2-structure_map.py``)
- 00:00.020
* - :ref:`sphx_glr_examples_8-explore-with-metatensor.py` (``8-explore-with-metatensor.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_4-colors.py` (``4-colors.py``)
- 00:00.008
* - :ref:`sphx_glr_examples_9-showing_custom_bonds.py` (``9-showing_custom_bonds.py``)
- 00:00.000
- 0.0
36 changes: 18 additions & 18 deletions docs/_sources/sg_execution_times.rst.txt
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Computation times
=================
**00:20.656** total execution time for 9 files **from all galleries**:
**00:00.096** total execution time for 9 files **from all galleries**:

.. container::

Expand All @@ -32,30 +32,30 @@ Computation times
* - Example
- Time
- Mem (MB)
* - :ref:`sphx_glr_examples_7-explore-advanced.py` (``../../python/examples/7-explore-advanced.py``)
- 00:11.854
* - :ref:`sphx_glr_examples_3-trajectory.py` (``../../python/examples/3-trajectory.py``)
- 00:00.096
- 0.0
* - :ref:`sphx_glr_examples_6-explore.py` (``../../python/examples/6-explore.py``)
- 00:06.497
* - :ref:`sphx_glr_examples_1-base.py` (``../../python/examples/1-base.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_8-explore-with-metatensor.py` (``../../python/examples/8-explore-with-metatensor.py``)
- 00:01.094
* - :ref:`sphx_glr_examples_2-structure_map.py` (``../../python/examples/2-structure_map.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_9-showing_custom_bonds.py` (``../../python/examples/9-showing_custom_bonds.py``)
- 00:01.011
* - :ref:`sphx_glr_examples_4-colors.py` (``../../python/examples/4-colors.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_5-shapes.py` (``../../python/examples/5-shapes.py``)
- 00:00.097
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_1-base.py` (``../../python/examples/1-base.py``)
- 00:00.052
* - :ref:`sphx_glr_examples_6-explore.py` (``../../python/examples/6-explore.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_3-trajectory.py` (``../../python/examples/3-trajectory.py``)
- 00:00.021
* - :ref:`sphx_glr_examples_7-explore-advanced.py` (``../../python/examples/7-explore-advanced.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_2-structure_map.py` (``../../python/examples/2-structure_map.py``)
- 00:00.020
* - :ref:`sphx_glr_examples_8-explore-with-metatensor.py` (``../../python/examples/8-explore-with-metatensor.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_examples_4-colors.py` (``../../python/examples/4-colors.py``)
- 00:00.008
* - :ref:`sphx_glr_examples_9-showing_custom_bonds.py` (``../../python/examples/9-showing_custom_bonds.py``)
- 00:00.000
- 0.0
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VERSION: '0.8.0',
VERSION: '0.7.3',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
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