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Hi, I'm very interested in using Psiflow to set up MD experiments but I'm trying to get it running on my local machine before plugging it into e.g. the HPC cluster I have access to. However, I have a lot of issues doing this. For example, when I try to run the H2 static/dynamic example, I get:
RuntimeError Traceback (most recent call last)
Cell In[8], [line 63](vscode-notebook-cell:?execution_count=8&line=63)
[54](vscode-notebook-cell:?execution_count=8&line=54) return frequencies[-1] * second / (100 * _c)
[58](vscode-notebook-cell:?execution_count=8&line=58) geometry = Geometry.from_data(
[59](vscode-notebook-cell:?execution_count=8&line=59) numbers=np.ones(2),
[60](vscode-notebook-cell:?execution_count=8&line=60) positions=np.array([[0, 0, 0], [0.8, 0, 0]]),
[61](vscode-notebook-cell:?execution_count=8&line=61) cell=None,
[62](vscode-notebook-cell:?execution_count=8&line=62) )
---> [63](vscode-notebook-cell:?execution_count=8&line=63) mace = MACEHamiltonian.mace_mp0()
[65](vscode-notebook-cell:?execution_count=8&line=65) dynamic = frequency_dynamic(geometry, mace)
[66](vscode-notebook-cell:?execution_count=8&line=66) static = frequency_static(geometry, mace)
File ~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:416, in MACEHamiltonian.mace_mp0(cls, size)
[411](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:411) urls = dict(
[412](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:412) small="https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2023-12-10-mace-128-L0_energy_epoch-249.model", # 2023-12-10-mace-128-L0_energy_epoch-249.model
[413](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:413) large="https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2023-12-03-mace-128-L1_epoch-199.model",
[414](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:414) )
[415](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:415) assert size in urls
--> [416](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:416) parsl_file = psiflow.context().new_file("mace_mp_", ".pth")
[417](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:417) urllib.request.urlretrieve(
[418](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:418) urls[size],
[419](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:419) parsl_file.filepath,
[420](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:420) )
[421](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/hamiltonians.py:421) return cls(parsl_file, {})
...
[598](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/execution.py:598) if cls._context is None:
--> [599](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/execution.py:599) raise RuntimeError("No ExecutionContext is currently loaded")
[600](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/execution.py:600) return cls._context
RuntimeError: No ExecutionContext is currently loaded
And when I try to run the basic geometry example, I get:
AssertionError Traceback (most recent call last)
Cell In[7], [line 7](vscode-notebook-cell:?execution_count=7&line=7)
[3](vscode-notebook-cell:?execution_count=7&line=3) from psiflow.geometry import Geometry
[6](vscode-notebook-cell:?execution_count=7&line=6) # a simple H2 molecule in vacuum
----> [7](vscode-notebook-cell:?execution_count=7&line=7) geometry = Geometry.from_string(
[8](vscode-notebook-cell:?execution_count=7&line=8) '''
[9](vscode-notebook-cell:?execution_count=7&line=9) 2
[10](vscode-notebook-cell:?execution_count=7&line=10) H 0.0 0.0 0.0
[11](vscode-notebook-cell:?execution_count=7&line=11) H 0.0 0.0 0.8
[12](vscode-notebook-cell:?execution_count=7&line=12) ''')
[14](vscode-notebook-cell:?execution_count=7&line=14) # the same H2 molecule using ase Atoms
[15](vscode-notebook-cell:?execution_count=7&line=15) atoms = ase.Atoms(
[16](vscode-notebook-cell:?execution_count=7&line=16) numbers=[1, 1, 1],
[17](vscode-notebook-cell:?execution_count=7&line=17) positions=[[0, 0, 0], [0, 0, 0.8]],
[18](vscode-notebook-cell:?execution_count=7&line=18) pbc=False,
[19](vscode-notebook-cell:?execution_count=7&line=19) )
File ~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/geometry.py:184, in Geometry.from_string(cls, s, natoms)
[180](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/geometry.py:180) else:
[181](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/geometry.py:181) lines = s.rstrip().split(
[182](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/geometry.py:182) "\n"
[183](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/geometry.py:183) ) # i-PI nonperiodic starts with empty -> rstrip!
--> [184](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/geometry.py:184) assert len(lines) == natoms + 1
[185](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/geometry.py:185) comment = lines[0]
[186](https://file+.vscode-resource.vscode-cdn.net/Users/muon/Documents/materials/curie/~/miniforge3/envs/md/lib/python3.10/site-packages/psiflow/geometry.py:186) comment_dict = key_val_str_to_dict_regex(comment)
AssertionError:
Are Psiflow scripts not intended to be developed locally? Is there any guide on how to get it working in a Jupyter notebook? I am running Python 3.10.15, a fresh Conda virtual env and installed Psiflow via pip.
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