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learningmatter-mit / NeuralForceField

Neural Network Force Field based on PyTorch
MIT License
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NeuralFF material science modules missing #21

Closed wanfuse123 closed 9 months ago

wanfuse123 commented 10 months ago

I do not find the NeuralFF python module in the nff directory after installing with pip install . after building conda virtual env

the module for material science development for modeling mechanics of materials, I believe this is a requirement?

Can you tell me where it is?

Traceback (most recent call last): File "/tmp/ipykernel_776040/2079156642.py", line 22, in from nff import NeuralFF, AtomsBatch, EnsembleNFF ImportError: cannot import name 'NeuralFF' from 'nff' (/home/top/miniconda3/envs/nff/lib/python3.9/site-packages/nff/init.py)

wanfuse123 commented 10 months ago

%xmode Verbose

import traceback import sys

Add the path to sys.path

sys.path.append('/home/top/miniconda3/envs/nff/lib/python3.9/site-packages/') from nff import nn # Import the nn submodule

List the contents of the nn submodule

print(dir(nn))

print(sys.version) !conda activate nff !conda init !conda list !pip install . !echo $PYTHONPATH
try:

import torch
from nff import NeuralFF, AtomsBatch, EnsembleNFF
Exception reporting mode: Verbose

['AttentionPool', 'BatchedPreActivation', 'BondPrior', 'ChemPropConv', 'ChemPropInit', 'ChemPropMsgToNode', 'ConfAttention', 'CosineEnvelope', 'CpSchNetConv', 'DEFAULT_BONDPRIOR_PARAM', 'DEFAULT_DROPOUT_RATE', 'DataLoader', 'Dense', 'DiabaticReadout', 'Diagonalize', 'DimeNet', 'DimeNetDelta', 'DimeNetDiabat', 'DimeNetDiabatDelta', 'DimeNetRadialBasis', 'DimeNetSphericalBasis', 'DirectedMessage', 'DirectedMessagePP', 'EPS', 'EPSILON', 'EdgeEmbedding', 'EdgeUpdateModule', 'EmbeddingBlock', 'Envelope', 'ExpNormalBasis', 'F', 'Gaussian', 'GaussianSmearing', 'GraphAttention', 'InteractionBlock', 'LeakyReLU', 'Linear', 'LinearConfAttention', 'MeanPool', 'MessagePassingModule', 'MixedSchNetConv', 'ModuleDict', 'MolFpPool', 'NodeEmbedding', 'NodeMultiTaskReadOut', 'OutputBlock', 'PainnRadialBasis', 'PreActivation', 'RadialBasis', 'ReLU', 'ResidualBlock', 'ScaleShift', 'SchNet', 'SchNetConv', 'SchNetDiabat', 'SchNetEdgeFilter', 'SchNetEdgeUpdate', 'Sequential', 'Softmax', 'SphericalBasis', 'StochasticIncrease', 'SumPool', 'TestModules', 'builtins', 'cached', 'doc', 'file', 'loader', 'name', 'package', 'path', 'spec', 'activations', 'add_stress', 'adj_nbrs_and_z', 'att_readout_probs', 'batch_and_sum', 'bessel_basis', 'chemprop_msg_to_node', 'chemprop_msg_update', 'clean_matrix', 'collections', 'compute_angle', 'compute_grad', 'compute_hess', 'computejacobian', 'constant', 'construct_module_dict', 'construct_sequential', 'copy', 'diabat', 'dimenet', 'gaussian_smearing', 'general_batched_hessian', 'get_act', 'get_default_readout', 'get_dense', 'get_offsets', 'get_painn_hessians', 'get_rij', 'get_schnet_hessians', 'grad', 'graphconv', 'graphop', 'hess_from_atoms', 'hess_from_pad', 'hess_from_results', 'inspect', 'lattice_points_in_supercell', 'layer_types', 'layers', 'models', 'modules', 'nn', 'np', 'pad', 'partial', 'real_sph_harm', 'remove_bias', 'results_from_stack', 'scatter_add', 'schnet', 'schnet_batched_hessians', 'shifted_softplus', 'single_spec_nbrs', 'softmax', 'sum_and_grad', 'sym', 'tensorgrad', 'to_module', 'torch', 'torch_nbr_list', 'unittest', 'utils', 'xavieruniform', 'zeros_initializer'] 3.8.18 | packaged by conda-forge | (default, Oct 10 2023, 15:44:36) [GCC 12.3.0]

CondaError: Run 'conda init' before 'conda activate'

no change /home/top/miniconda3/condabin/conda no change /home/top/miniconda3/bin/conda no change /home/top/miniconda3/bin/conda-env no change /home/top/miniconda3/bin/activate no change /home/top/miniconda3/bin/deactivate no change /home/top/miniconda3/etc/profile.d/conda.sh no change /home/top/miniconda3/etc/fish/conf.d/conda.fish no change /home/top/miniconda3/shell/condabin/Conda.psm1 no change /home/top/miniconda3/shell/condabin/conda-hook.ps1 no change /home/top/miniconda3/lib/python3.11/site-packages/xontrib/conda.xsh no change /home/top/miniconda3/etc/profile.d/conda.csh no change /home/top/.bashrc No action taken. packages in environment at /home/top/VENV/conda_surface_sampling: Name Version Build Channel

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pyhd8ed1ab_0 conda-forge unicodedata2 15.1.0 py38h01eb140_0 conda-forge uri-template 1.3.0 pyhd8ed1ab_0 conda-forge urllib3 1.26.18 pyhd8ed1ab_0 conda-forge virtualenv 20.25.0 pyhd8ed1ab_0 conda-forge voro 0.4.6 h00ab1b0_0 conda-forge wcwidth 0.2.12 pyhd8ed1ab_0 conda-forge webcolors 1.13 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pyhd8ed1ab_2 conda-forge websocket-client 1.7.0 pyhd8ed1ab_0 conda-forge werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge wget 1.20.3 ha35d2d1_1 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge xarray 2022.11.0 py38h06a4308_0 xarray-einstats 0.5.1 pyhd8ed1ab_0 conda-forge xcb-util 0.4.0 hd590300_1 conda-forge xcb-util-image 0.4.0 h8ee46fc_1 conda-forge xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge xcb-util-renderutil 0.3.9 hd590300_1 conda-forge xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge xkeyboard-config 2.40 hd590300_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.7 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zeromq 4.3.5 h59595ed_0 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge ERROR: Directory '.' is not installable. Neither 'setup.py' nor 'pyproject.toml' found. /home/top/VENV/conda_surface_sampling/lib/python3.8/site-packages An error occurred: cannot import name 'NeuralFF' from 'nff' (/home/top/miniconda3/envs/nff/lib/python3.9/site-packages/nff/init.py)

Traceback (most recent call last): File "/tmp/ipykernel_776040/2079156642.py", line 22, in from nff import NeuralFF, AtomsBatch, EnsembleNFF ImportError: cannot import name 'NeuralFF' from 'nff' (/home/top/miniconda3/envs/nff/lib/python3.9/site-packages/nff/init.py)

simonaxelrod commented 10 months ago

Try inserting the path to NFF into your Python path instead of pip installing the repo. In Python, add sys.path.insert(, 0) at the top of your script or notebook. Or alternatively, in your bashrc, add export PYTHONPATH=:$PYTHONPATH

wanfuse123 commented 9 months ago

the issue is these "functions" are not included in the source. These functions are missing , perhaps you can recommend a git commit that does have them?

For all the packages used, ( don't remember but there was three packages that are used for this project--- note: I put my project to the side for a while because I couldn't find these functions in any of the three packages.

thank you in advance for the trouble.

I have an idea that is a simple solution. If I could be a pain in the back side, and ask a favor.

Since it is open source and there is no issue forking it ( as far as I am aware) , perhaps you could push the software ( three required packages ) to your git repository and share the links? Don't forget to push all the sub modules too, and make it publicly readable, and don't push anything private!

I have a very important and specific use for this software ( one world changing engineering project and this software just may provide the shortcut I need!)

Regards,

steven

On Sat, Jan 27, 2024 at 6:17 PM simonaxelrod @.***> wrote:

Closed #21 https://github.com/learningmatter-mit/NeuralForceField/issues/21 as completed.

— Reply to this email directly, view it on GitHub https://github.com/learningmatter-mit/NeuralForceField/issues/21#event-11618284120, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADDBZWJRXLWYFHAHCCFKSZDYQWDHTAVCNFSM6AAAAABAW46PUSVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRGYYTQMRYGQYTEMA . You are receiving this because you authored the thread.Message ID: <learningmatter-mit/NeuralForceField/issue/21/issue_event/11618284120@ github.com>

simonaxelrod commented 9 months ago

Try inserting the path first and see if that works