repo stringlengths 1 99 | file stringlengths 13 215 | code stringlengths 12 59.2M | file_length int64 12 59.2M | avg_line_length float64 3.82 1.48M | max_line_length int64 12 2.51M | extension_type stringclasses 1
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adcgan | adcgan-main/BigGAN-PyTorch/inception_utils.py | ''' Inception utilities
This file contains methods for calculating IS and FID, using either
the original numpy code or an accelerated fully-pytorch version that
uses a fast newton-schulz approximation for the matrix sqrt. There are also
methods for acquiring a desired number of samples from the Generat... | 12,572 | 38.662461 | 136 | py |
adcgan | adcgan-main/BigGAN-PyTorch/calculate_inception_moments.py | ''' Calculate Inception Moments
This script iterates over the dataset and calculates the moments of the
activations of the Inception net (needed for FID), and also returns
the Inception Score of the training data.
Note that if you don't shuffle the data, the IS of true data will be under-
estimated as it is lab... | 5,247 | 40 | 122 | py |
adcgan | adcgan-main/BigGAN-PyTorch/train.py | """ BigGAN: The Authorized Unofficial PyTorch release
Code by A. Brock and A. Andonian
This code is an unofficial reimplementation of
"Large-Scale GAN Training for High Fidelity Natural Image Synthesis,"
by A. Brock, J. Donahue, and K. Simonyan (arXiv 1809.11096).
Let's go.
"""
import os
import fu... | 9,268 | 39.475983 | 124 | py |
adcgan | adcgan-main/BigGAN-PyTorch/sync_batchnorm/replicate.py | # -*- coding: utf-8 -*-
# File : replicate.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import functools
from torch.nn.parallel.da... | 3,226 | 32.968421 | 115 | py |
adcgan | adcgan-main/BigGAN-PyTorch/sync_batchnorm/unittest.py | # -*- coding: utf-8 -*-
# File : unittest.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import unittest
import torch
class TorchTes... | 746 | 23.9 | 59 | py |
adcgan | adcgan-main/BigGAN-PyTorch/sync_batchnorm/batchnorm.py | # -*- coding: utf-8 -*-
# File : batchnorm.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import collections
import torch
import torc... | 14,882 | 41.644699 | 159 | py |
adcgan | adcgan-main/BigGAN-PyTorch/sync_batchnorm/batchnorm_reimpl.py | #! /usr/bin/env python3
# -*- coding: utf-8 -*-
# File : batchnorm_reimpl.py
# Author : acgtyrant
# Date : 11/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import torch
import torch.nn as nn
import torch... | 2,383 | 30.786667 | 95 | py |
adcgan | adcgan-main/BigGAN-PyTorch/TFHub/biggan_v1.py | # BigGAN V1:
# This is now deprecated code used for porting the TFHub modules to pytorch,
# included here for reference only.
import numpy as np
import torch
from scipy.stats import truncnorm
from torch import nn
from torch.nn import Parameter
from torch.nn import functional as F
def l2normalize(v, eps=1e-4):
retur... | 12,173 | 30.29563 | 114 | py |
adcgan | adcgan-main/BigGAN-PyTorch/TFHub/converter.py | """Utilities for converting TFHub BigGAN generator weights to PyTorch.
Recommended usage:
To convert all BigGAN variants and generate test samples, use:
```bash
CUDA_VISIBLE_DEVICES=0 python converter.py --generate_samples
```
See `parse_args` for additional options.
"""
import argparse
import os
import sys
impor... | 17,428 | 42.355721 | 143 | py |
DeepSpectrum | DeepSpectrum-master/setup.py | #!/usr/bin/env python
import re
import sys
import warnings
warnings.filterwarnings('ignore', category=DeprecationWarning)
warnings.filterwarnings('ignore', category=FutureWarning)
from setuptools import setup, find_packages
from subprocess import CalledProcessError, check_output
PROJECT = "DeepSpectrum"
VERSION = "0.... | 2,795 | 29.064516 | 150 | py |
DeepSpectrum | DeepSpectrum-master/src/deepspectrum/cli/configuration.py | import logging
import click
import configparser
import fnmatch
import re
import decimal
from enum import Enum
from multiprocessing import cpu_count
from os import makedirs, walk
from matplotlib import cm
from os.path import abspath, join, isfile, basename, dirname, realpath, splitext
mpl_cmaps = list(cm.cmaps_listed)+... | 18,723 | 34.732824 | 194 | py |
DeepSpectrum | DeepSpectrum-master/src/deepspectrum/backend/extractor.py | import gc
from collections import namedtuple
import numpy as np
import os
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"
import tensorflow as tf
import torch
from torchvision import models, transforms
from PIL import Image
import logging
tf.compat.v1.logging.set_verbosity(logging.ERROR)
log = logging.getLogger(__name__)
... | 11,743 | 33.745562 | 115 | py |
ocp | ocp-main/scripts/preprocess_relaxed.py | """
Creates LMDB files with extracted graph features from provided *.extxyz files
for the S2EF task.
"""
import argparse
import glob
import multiprocessing as mp
import os
import pickle
import random
import sys
import ase.io
import lmdb
import numpy as np
import torch
from tqdm import tqdm
from ocpmodels.preprocessi... | 3,388 | 22.212329 | 82 | py |
ocp | ocp-main/scripts/preprocess_ef.py | """
Creates LMDB files with extracted graph features from provided *.extxyz files
for the S2EF task.
"""
import argparse
import glob
import multiprocessing as mp
import os
import pickle
import random
import sys
import ase.io
import lmdb
import numpy as np
import torch
from tqdm import tqdm
from ocpmodels.preprocessi... | 4,893 | 27.453488 | 111 | py |
ocp | ocp-main/tests/common/test_data_parallel_batch_sampler.py | import tempfile
from contextlib import contextmanager
from pathlib import Path
from typing import TypeVar
import numpy as np
import pytest
from torch.utils.data import Dataset
from ocpmodels.common.data_parallel import BalancedBatchSampler
DATA = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
SIZE_ATOMS = [1, 1, 1, 1, 1, 1, 1, 1, ... | 6,251 | 25.05 | 161 | py |
ocp | ocp-main/tests/models/test_schnet.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import os
import random
import numpy as np
import pytest
import torch
from ase.io import read
from ocpmodels.common.registry import registr... | 2,649 | 28.120879 | 79 | py |
ocp | ocp-main/tests/models/test_gemnet_oc.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import io
import logging
import os
import random
import numpy as np
import pytest
import requests
import torch
from ase.io import read
from... | 4,631 | 27.95 | 120 | py |
ocp | ocp-main/tests/models/test_gemnet.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import os
import random
import numpy as np
import pytest
import torch
from ase.io import read
from ocpmodels.common.registry... | 3,191 | 27 | 79 | py |
ocp | ocp-main/tests/models/test_dimenet.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import os
import random
import numpy as np
import pytest
import torch
from ase.io import read
from ocpmodels.common.registry import registr... | 2,693 | 27.0625 | 79 | py |
ocp | ocp-main/tests/models/test_cgcnn.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import os
import random
import numpy as np
import pytest
import torch
from ase.io import read
from ocpmodels.common.registry import registr... | 2,759 | 27.163265 | 79 | py |
ocp | ocp-main/tests/models/test_gemnet_oc_scaling_mismatch.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import io
import pytest
import requests
import torch
from ocpmodels.common.registry import registry
from ocpmodels.common.utils import load... | 9,850 | 31.511551 | 124 | py |
ocp | ocp-main/tests/models/test_dimenetpp.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import os
import random
import numpy as np
import pytest
import torch
from ase.io import read
from ocpmodels.common.registry... | 2,745 | 27.020408 | 79 | py |
ocp | ocp-main/tests/evaluator/test_evaluator.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import numpy as np
import pytest
import torch
from ocpmodels.modules.evaluator import (
Evaluator,
cosine_similarity,
magnitude_... | 3,210 | 28.731481 | 72 | py |
ocp | ocp-main/tests/preprocessing/test_radius_graph_pbc.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import os
import ase
import numpy as np
import pytest
import torch
from ase.io import read
from ase.lattice.cubic import FaceCenteredCubic
f... | 7,781 | 28.589354 | 79 | py |
ocp | ocp-main/ocpmodels/modules/normalizer.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
class Normalizer:
"""Normalize a Tensor and restore it later."""
def __init__(self, tensor=None, mean=None, std=None,... | 1,390 | 28.595745 | 78 | py |
ocp | ocp-main/ocpmodels/modules/loss.py | import logging
from typing import Optional
import torch
from torch import nn
from ocpmodels.common import distutils
class L2MAELoss(nn.Module):
def __init__(self, reduction: str = "mean") -> None:
super().__init__()
self.reduction = reduction
assert reduction in ["mean", "sum"]
def ... | 2,597 | 29.564706 | 72 | py |
ocp | ocp-main/ocpmodels/modules/exponential_moving_average.py | """
Copied (and improved) from:
https://github.com/fadel/pytorch_ema/blob/master/torch_ema/ema.py (MIT license)
"""
from __future__ import division, unicode_literals
import copy
import weakref
from typing import List, Iterable, Optional
import torch
from ocpmodels.common.typing import none_throws
# Partially based... | 7,758 | 37.410891 | 99 | py |
ocp | ocp-main/ocpmodels/modules/scheduler.py | import inspect
import torch.optim.lr_scheduler as lr_scheduler
from ocpmodels.common.utils import warmup_lr_lambda
class LRScheduler:
"""
Learning rate scheduler class for torch.optim learning rate schedulers
Notes:
If no learning rate scheduler is specified in the config the default
sc... | 2,342 | 33.970149 | 81 | py |
ocp | ocp-main/ocpmodels/modules/evaluator.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import numpy as np
import torch
from typing import Dict, Union
"""
An evaluation module for use with the OCP dataset and suite of tasks. It... | 9,085 | 28.028754 | 79 | py |
ocp | ocp-main/ocpmodels/modules/scaling/fit.py | import logging
import math
import readline
import sys
from itertools import islice
from pathlib import Path
from typing import TYPE_CHECKING, Dict, Literal
import torch
import torch.nn as nn
from torch.nn.parallel.distributed import DistributedDataParallel
from ocpmodels.common.data_parallel import OCPDataParallel
fr... | 8,347 | 33.495868 | 112 | py |
ocp | ocp-main/ocpmodels/modules/scaling/scale_factor.py | import itertools
import logging
import math
from contextlib import contextmanager
from typing import Callable, Optional, TypedDict, Union
import torch
import torch.nn as nn
class _Stats(TypedDict):
variance_in: float
variance_out: float
n_samples: int
IndexFn = Callable[[], None]
def _check_consisten... | 4,613 | 25.67052 | 89 | py |
ocp | ocp-main/ocpmodels/modules/scaling/util.py | import logging
import torch.nn as nn
from .scale_factor import ScaleFactor
def ensure_fitted(module: nn.Module, warn: bool = False) -> None:
for name, child in module.named_modules():
if not isinstance(child, ScaleFactor) or child.fitted:
continue
if child.name is not None:
... | 786 | 31.791667 | 96 | py |
ocp | ocp-main/ocpmodels/modules/scaling/compat.py | import json
import logging
from pathlib import Path
from typing import Dict, Optional, Union
import torch
import torch.nn as nn
from .scale_factor import ScaleFactor
ScaleDict = Union[Dict[str, float], Dict[str, torch.Tensor]]
def _load_scale_dict(scale_file: Optional[Union[str, ScaleDict]]):
"""
Loads sca... | 2,303 | 28.922078 | 111 | py |
ocp | ocp-main/ocpmodels/common/distutils.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import os
import subprocess
import torch
import torch.distributed as dist
from ocpmodels.common.typing import none_throws
d... | 5,803 | 32.165714 | 94 | py |
ocp | ocp-main/ocpmodels/common/data_parallel.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import heapq
import logging
from itertools import chain
from pathlib import Path
from typing import List, Literal, Protocol, Union, runtime_c... | 9,608 | 32.597902 | 126 | py |
ocp | ocp-main/ocpmodels/common/utils.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import ast
import collections
import copy
import importlib
import itertools
import json
import logging
import os
import sys
import time
from ... | 38,297 | 33.072954 | 128 | py |
ocp | ocp-main/ocpmodels/common/logger.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
from abc import ABC, abstractmethod
import torch
import wandb
from torch.utils.tensorboard import SummaryWriter
from ocpmodel... | 3,275 | 27 | 75 | py |
ocp | ocp-main/ocpmodels/common/flags.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import argparse
from pathlib import Path
class Flags:
def __init__(self) -> None:
self.parser = argparse.ArgumentParser(
... | 4,659 | 31.137931 | 93 | py |
ocp | ocp-main/ocpmodels/common/gp_utils.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
from typing import Any, Optional
import torch
from torch import distributed as dist
"""
Functions to support graph parallel trai... | 8,667 | 27.234528 | 97 | py |
ocp | ocp-main/ocpmodels/common/transforms.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
# Borrowed from https://github.com/rusty1s/pytorch_geometric/blob/master/torch_geometric/transforms/random_rotate.py
# with changes to keep t... | 3,003 | 36.55 | 116 | py |
ocp | ocp-main/ocpmodels/common/relaxation/ase_utils.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
Utilities to interface OCP models/trainers with the Atomic Simulation
Environment (ASE)
"""
import copy
import logging
import os
import torch
... | 7,362 | 33.406542 | 145 | py |
ocp | ocp-main/ocpmodels/common/relaxation/ml_relaxation.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
from collections import deque
from pathlib import Path
import torch
from torch_geometric.data import Batch
from ocpmodels.co... | 2,786 | 29.626374 | 106 | py |
ocp | ocp-main/ocpmodels/common/relaxation/optimizers/lbfgs_torch.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
from collections import deque
from pathlib import Path
from typing import Deque, Optional
import ase
import torch
from torch_... | 7,832 | 31.502075 | 79 | py |
ocp | ocp-main/ocpmodels/models/base.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import torch
import torch.nn as nn
from torch_geometric.nn import radius_graph
from ocpmodels.common.utils import (
comp... | 3,688 | 27.596899 | 94 | py |
ocp | ocp-main/ocpmodels/models/dimenet.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
from torch import nn
from torch_geometric.nn import DimeNet, radius_graph
from torch_scatter import scatter
from torch_sparse im... | 8,211 | 34.549784 | 98 | py |
ocp | ocp-main/ocpmodels/models/dimenet_plus_plus.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
---
This code borrows heavily from the DimeNet implementation as part of
pytorch-geometric: https://github.com/rusty1s/pytorch_geometric. Licens... | 15,691 | 32.175476 | 80 | py |
ocp | ocp-main/ocpmodels/models/forcenet.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from math import pi as PI
from typing import Optional
import numpy as np
import torch
import torch.nn as nn
from torch_geometric.nn import M... | 18,340 | 34.339114 | 124 | py |
ocp | ocp-main/ocpmodels/models/spinconv.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import time
from math import pi as PI
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from ... | 43,927 | 33.372457 | 137 | py |
ocp | ocp-main/ocpmodels/models/schnet.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
from torch_geometric.nn import SchNet
from torch_scatter import scatter
from ocpmodels.common.registry import registry
from ocp... | 4,755 | 32.258741 | 98 | py |
ocp | ocp-main/ocpmodels/models/cgcnn.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
import torch.nn as nn
from torch_geometric.nn import MessagePassing, global_mean_pool, radius_graph
from torch_geometric.nn.mode... | 8,190 | 33.855319 | 142 | py |
ocp | ocp-main/ocpmodels/models/gemnet/initializers.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
def _standardize(kernel):
"""
Makes sure that N*Var(W) = 1 and E[W] = 0
"""
eps = 1e-6
if len(kernel.shap... | 1,385 | 27.875 | 92 | py |
ocp | ocp-main/ocpmodels/models/gemnet/gemnet.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from typing import Optional
import numpy as np
import torch
from torch_geometric.nn import radius_graph
from torch_scatter import scatter
fr... | 20,301 | 32.724252 | 118 | py |
ocp | ocp-main/ocpmodels/models/gemnet/utils.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import json
import torch
from torch_scatter import segment_csr
def read_json(path: str):
""""""
if not path.endswith(".json"):
... | 9,228 | 31.960714 | 128 | py |
ocp | ocp-main/ocpmodels/models/gemnet/layers/base_layers.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import torch
from ..initializers import he_orthogonal_init
class Dense(torch.nn.Module):
"""
Combines dense layer wit... | 3,001 | 24.87931 | 76 | py |
ocp | ocp-main/ocpmodels/models/gemnet/layers/atom_update_block.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
from torch_scatter import scatter
from ocpmodels.modules.scaling import ScaleFactor
from ..initializers import he_orthogonal_i... | 6,443 | 30.281553 | 107 | py |
ocp | ocp-main/ocpmodels/models/gemnet/layers/embedding_block.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import numpy as np
import torch
from .base_layers import Dense
class AtomEmbedding(torch.nn.Module):
"""
Initial atom embeddings b... | 2,424 | 23.25 | 92 | py |
ocp | ocp-main/ocpmodels/models/gemnet/layers/radial_basis.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
from typing import Dict, Union
import numpy as np
import torch
from scipy.special import binom
from torch_geometric.nn.models.sc... | 6,434 | 29.353774 | 77 | py |
ocp | ocp-main/ocpmodels/models/gemnet/layers/spherical_basis.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import sympy as sym
import torch
from torch_geometric.nn.models.schnet import GaussianSmearing
from .basis_utils import real_sph_harm
from .... | 3,221 | 32.216495 | 86 | py |
ocp | ocp-main/ocpmodels/models/gemnet/layers/interaction_block.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import torch
from ocpmodels.modules.scaling.scale_factor import ScaleFactor
from .atom_update_block import AtomUpdateBlock
fro... | 10,381 | 29.356725 | 118 | py |
ocp | ocp-main/ocpmodels/models/gemnet/layers/efficient.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
from ..initializers import he_orthogonal_init
class EfficientInteractionDownProjection(torch.nn.Module):
"""
Down pro... | 5,005 | 27.770115 | 81 | py |
ocp | ocp-main/ocpmodels/models/painn/painn.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
---
MIT License
Copyright (c) 2021 www.compscience.org
Permission is hereby granted, free of charge, to any person obtaining a copy
of this so... | 21,957 | 32.472561 | 96 | py |
ocp | ocp-main/ocpmodels/models/painn/utils.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
from torch_scatter import segment_csr
def repeat_blocks(
sizes,
repeats,
continuous_indexing: bool = True,
sta... | 6,138 | 35.325444 | 128 | py |
ocp | ocp-main/ocpmodels/models/escn/so3.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import os
import torch
import torch.nn as nn
try:
from e3nn import o3
from e3nn.o3 import FromS2Grid, ToS2Grid
except ImportError:
... | 19,050 | 32.422807 | 112 | py |
ocp | ocp-main/ocpmodels/models/escn/escn.py | """
Copyright (c) Meta, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import time
from typing import List
import numpy as np
import torch
import torch.nn as nn
from pyexpat.model import XML_CQUANT_OP... | 34,881 | 33.951904 | 126 | py |
ocp | ocp-main/ocpmodels/models/scn/scn.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import sys
import time
import numpy as np
import torch
import torch.nn as nn
from torch_geometric.nn import radius_graph
fro... | 30,218 | 35.060859 | 136 | py |
ocp | ocp-main/ocpmodels/models/scn/smearing.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
import torch.nn as nn
# Different encodings for the atom distance embeddings
class GaussianSmearing(torch.nn.Module):
def ... | 2,803 | 31.229885 | 77 | py |
ocp | ocp-main/ocpmodels/models/scn/spherical_harmonics.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import math
import os
import torch
try:
from e3nn import o3
from e3nn.o3 import FromS2Grid, ToS2Grid
# Borrowed... | 14,397 | 36.397403 | 122 | py |
ocp | ocp-main/ocpmodels/models/scn/sampling.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import torch
### Methods for sample points on a sphere
def CalcSpherePoints(num_points: int, device: str = "cpu") -> torch.Ten... | 1,527 | 31.510638 | 79 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/initializers.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
def _standardize(kernel):
"""
Makes sure that N*Var(W) = 1 and E[W] = 0
"""
eps = 1e-6
if len(kernel.shap... | 1,385 | 27.875 | 92 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/gemnet.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from typing import Optional
import numpy as np
import torch
from torch_cluster import radius_graph
from torch_scatter import scatter
from to... | 22,203 | 33.16 | 118 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/utils.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import json
from typing import Optional, Tuple
import torch
from torch_scatter import segment_csr
def read_json(path: str):
""""""
... | 9,439 | 32.006993 | 128 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/layers/base_layers.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
from typing import Optional
import torch
from ..initializers import he_orthogonal_init
class Dense(torch.nn.Module):
"""
... | 3,247 | 25.406504 | 71 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/layers/atom_update_block.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from typing import Optional
import torch
from torch_scatter import scatter
from torch_scatter.utils import broadcast
from ocpmodels.common ... | 7,813 | 30.256 | 107 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/layers/embedding_block.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from typing import Optional
import numpy as np
import torch
from ocpmodels.common import gp_utils
from .base_layers import Dense
class A... | 2,621 | 23.735849 | 92 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/layers/radial_basis.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
from typing import Dict, Union
import numpy as np
import torch
from scipy.special import binom
from ocpmodels.common.typing impo... | 6,381 | 29.103774 | 77 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/layers/spherical_basis.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import sympy as sym
import torch
from torch_geometric.nn.models.schnet import GaussianSmearing
from ocpmodels.common.typing import assert_is_... | 3,221 | 32.216495 | 86 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/layers/interaction_block.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
from typing import Optional
import torch
from ocpmodels.common import gp_utils
from ocpmodels.modules.scaling import ScaleFacto... | 11,227 | 30.016575 | 118 | py |
ocp | ocp-main/ocpmodels/models/gemnet_gp/layers/efficient.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from typing import Tuple
import torch
from ..initializers import he_orthogonal_init
class EfficientInteractionDownProjection(torch.nn.Mod... | 4,957 | 27.170455 | 81 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/initializers.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from functools import partial
import torch
def _standardize(kernel):
"""
Makes sure that N*Var(W) = 1 and E[W] = 0
"""
eps ... | 2,765 | 27.8125 | 137 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/interaction_indices.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
from torch_scatter import segment_coo
from torch_sparse import SparseTensor
from .utils import get_inner_idx, masked_select_spar... | 10,507 | 32.787781 | 86 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/gemnet_oc.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import os
from typing import Dict, Optional, Union
import numpy as np
import torch
from torch_geometric.nn import radius_graph... | 48,949 | 34.834553 | 93 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/utils.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import numpy as np
import torch
from torch_scatter import segment_coo, segment_csr
from torch_sparse import SparseTensor
def ragged_range(si... | 14,529 | 33.188235 | 128 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/layers/base_layers.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import torch
from ..initializers import he_orthogonal_init
class Dense(torch.nn.Module):
"""
Combines dense layer with... | 2,826 | 25.175926 | 76 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/layers/atom_update_block.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import torch
from torch_scatter import scatter
from ocpmodels.common.utils import scatter_det
from ocpmodels.modules.scaling imp... | 5,833 | 28.614213 | 78 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/layers/embedding_block.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import numpy as np
import torch
from .base_layers import Dense
class AtomEmbedding(torch.nn.Module):
"""
Initial atom embeddings ba... | 2,622 | 24.715686 | 72 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/layers/radial_basis.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
from typing import Dict, Union
import numpy as np
import sympy as sym
import torch
from scipy.special import binom
from ocpmodel... | 7,675 | 29.827309 | 77 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/layers/basis_utils.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import numpy as np
import sympy as sym
import torch
from scipy import special as sp
from scipy.optimize import brentq
def Jn(r:... | 11,335 | 32.838806 | 121 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/layers/force_scaler.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import torch
class ForceScaler:
"""
Scales up the energy and then scales down the forces
to prevent NaNs and inf... | 3,081 | 31.442105 | 77 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/layers/spherical_basis.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
from ocpmodels.modules.scaling import ScaleFactor
from .basis_utils import get_sph_harm_basis
from .radial_basis import Gaussia... | 4,369 | 29.347222 | 79 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/layers/interaction_block.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import torch
from ocpmodels.modules.scaling import ScaleFactor
from .atom_update_block import AtomUpdateBlock
from .base_layers... | 23,476 | 29.931489 | 85 | py |
ocp | ocp-main/ocpmodels/models/gemnet_oc/layers/efficient.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from typing import Optional
import torch
from torch_scatter import scatter
from ..initializers import he_orthogonal_init
from .base_layers i... | 9,599 | 34.555556 | 89 | py |
ocp | ocp-main/ocpmodels/models/utils/activations.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
import torch.nn.functional as F
class Act(torch.nn.Module):
def __init__(self, act: str, slope: float = 0.05) -> None:
... | 1,650 | 33.395833 | 74 | py |
ocp | ocp-main/ocpmodels/models/utils/basis.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
from typing import List, Optional
import numpy as np
import torch
import torch.nn as nn
from scipy.special import sph_harm
from ... | 10,366 | 32.659091 | 122 | py |
ocp | ocp-main/ocpmodels/datasets/oc22_lmdb_dataset.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import bisect
import logging
import math
import pickle
import random
import warnings
from pathlib import Path
import lmdb
import numpy as np... | 8,611 | 35.961373 | 103 | py |
ocp | ocp-main/ocpmodels/datasets/lmdb_dataset.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import bisect
import logging
import math
import pickle
import random
import warnings
from pathlib import Path
from typing import Optional, Typ... | 9,163 | 35.07874 | 85 | py |
ocp | ocp-main/ocpmodels/datasets/ase_datasets.py | import bisect
import copy
import functools
import glob
import logging
import os
import warnings
from pathlib import Path
from abc import ABC, abstractmethod
from typing import List
import ase
import numpy as np
from torch import tensor
from torch.utils.data import Dataset
from tqdm import tqdm
from ocpmodels.common.r... | 18,646 | 36.145418 | 114 | py |
ocp | ocp-main/ocpmodels/tasks/task.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import os
from ocpmodels.common.registry import registry
from ocpmodels.trainers.forces_trainer import ForcesTrainer
class ... | 3,181 | 31.141414 | 135 | py |
ocp | ocp-main/ocpmodels/preprocessing/atoms_to_graphs.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from typing import Optional
import ase.db.sqlite
import ase.io.trajectory
import numpy as np
import torch
from torch_geometric.data import D... | 10,360 | 40.115079 | 119 | py |
ocp | ocp-main/ocpmodels/trainers/base_trainer.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import datetime
import errno
import logging
import os
import random
import subprocess
from abc import ABC, abstractmethod
from collections imp... | 29,997 | 36.264596 | 111 | py |
ocp | ocp-main/ocpmodels/trainers/energy_trainer.py | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
from typing import Optional
import torch
import torch_geometric
from tqdm import tqdm
from ocpmodels.common import distutils... | 11,855 | 33.768328 | 129 | py |
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