keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
2D | cbouy/mols2grid | DEVELOPMENT.md | .md | 2,333 | 71 | This is a short guide to setup a dev environment for mols2grid.
1. Install [uv](https://docs.astral.sh/uv/)
2. Create a new environment and install:
```
uv sync --python 3.11
```
We use [poethepoet](https://poethepoet.natn.io/) to define tasks to run in development environments.
You can run all of the checks... | Markdown |
2D | cbouy/mols2grid | mols2grid/datafiles.py | .py | 331 | 11 | import atexit
from contextlib import ExitStack
from importlib import resources
_file_manager = ExitStack()
atexit.register(_file_manager.close)
_data_resource = resources.files("mols2grid") / "data/"
datapath = _file_manager.enter_context(resources.as_file(_data_resource))
SOLUBILITY_SDF = str(datapath / "solubility.... | Python |
2D | cbouy/mols2grid | mols2grid/__init__.py | .py | 619 | 17 | from mols2grid import datafiles as datafiles
from mols2grid._version import __version__ as __version__
from mols2grid.callbacks import make_popup_callback as make_popup_callback
from mols2grid.dispatch import display as display
from mols2grid.dispatch import save as save
from mols2grid.molgrid import MolGrid as MolGrid... | Python |
2D | cbouy/mols2grid | mols2grid/callbacks.py | .py | 6,334 | 183 | from typing import NamedTuple
from mols2grid.utils import env
class _JSCallback(NamedTuple):
"""Class that holds JavaScript code for running a callback function. If an external
library is required for the callback to function correctly, it can be passed in
the optional ``library_src`` as a ``<script>`` t... | Python |
2D | cbouy/mols2grid | mols2grid/select.py | .py | 1,810 | 64 | import warnings
from ast import literal_eval
from mols2grid.utils import is_running_within_marimo
class SelectionRegister:
"""Register for grid selections
Attributes
----------
SELECTIONS : dict
Stores each grid selection according to their name
current_selection : str
Name of th... | Python |
2D | cbouy/mols2grid | mols2grid/utils.py | .py | 3,946 | 146 | import gzip
import re
from ast import literal_eval
from functools import partial, wraps
from importlib.util import find_spec
from pathlib import Path
import pandas as pd
from jinja2 import Environment, FileSystemLoader
from rdkit import Chem
env = Environment(
loader=FileSystemLoader(Path(__file__).parent / "temp... | Python |
2D | cbouy/mols2grid | mols2grid/dispatch.py | .py | 12,747 | 303 | import inspect
from functools import singledispatch
from pathlib import Path
from pandas import DataFrame, Series
from mols2grid.molgrid import MolGrid
_SIGNATURE = {
method: dict(inspect.signature(getattr(MolGrid, method)).parameters.items())
for method in ["render", "to_interactive", "to_static", "display"... | Python |
2D | cbouy/mols2grid | mols2grid/widget.py | .py | 1,108 | 36 | from pathlib import Path
import anywidget
from traitlets import Bool, List, Unicode
from mols2grid._version import __version__ # noqa: F401
BUNDLER_OUTPUT_DIR = Path(__file__).parent / "static"
class MolGridWidget(anywidget.AnyWidget):
"""A custom widget for the MolGrid class. Handles selections and callbacks... | Python |
2D | cbouy/mols2grid | mols2grid/_version.py | .py | 22 | 2 | __version__ = "2.2.0"
| Python |
2D | cbouy/mols2grid | mols2grid/molgrid.py | .py | 43,650 | 1,137 | import ast
import json
import warnings
from base64 import b64encode
from functools import partial
from html import escape
import numpy as np
import pandas as pd
from rdkit import Chem
from rdkit.Chem import Draw
from mols2grid.callbacks import _JSCallback
from mols2grid.select import register
from mols2grid.utils imp... | Python |
2D | cbouy/mols2grid | mols2grid/templates/__init__.py | .py | 0 | 0 | null | Python |
2D | cbouy/mols2grid | docs/contents.md | .md | 6,489 | 116 | # 💡 Introduction
- [](https://pypi.python.org/pypi/mols2grid)
[](https://anaconda.org/conda-forge/mols2grid)
- [![Tests status](https://github.com/cbouy/mols2grid/workflows/CI/badge.sv... | Markdown |
2D | cbouy/mols2grid | docs/conf.py | .py | 4,097 | 133 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... | Python |
2D | cbouy/mols2grid | docs/notebooks/customization.ipynb | .ipynb | 5,589 | 176 | {
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"# Customization\n",
"\n",
"[](https://colab.research.google.com/github/cbouy/mols2grid/blob/master/docs/notebooks/customization.ipy... | Unknown |
2D | cbouy/mols2grid | docs/notebooks/callbacks.ipynb | .ipynb | 10,486 | 316 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Callbacks\n",
"\n",
"[](https://colab.research.google.com/github/cbouy/mols2grid/blob/master/docs/notebooks/callbacks.ipynb)\n",
"\n",
"Callbac... | Unknown |
2D | cbouy/mols2grid | docs/notebooks/quickstart.ipynb | .ipynb | 4,711 | 175 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Quickstart\n",
"\n",
"[](https://colab.research.google.com/github/cbouy/mols2grid/blob/master/docs/notebooks/quickstart.ipynb)\n",
"\n",
"The e... | Unknown |
2D | cbouy/mols2grid | docs/notebooks/filtering.ipynb | .ipynb | 3,481 | 121 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Filtering\n",
"\n",
"[](https://colab.research.google.com/github/cbouy/mols2grid/blob/master/docs/notebooks/filtering.ipynb)\n",
"\n",
"It's po... | Unknown |
2D | cbouy/mols2grid | scripts/marimo_example.py | .py | 2,983 | 104 | import marimo
__generated_with = "0.18.4"
app = marimo.App(width="medium")
@app.cell
def import_libraries():
import marimo as mo
import mols2grid
from mols2grid.datafiles import SOLUBILITY_SDF
return SOLUBILITY_SDF, mo, mols2grid
@app.cell
def prepare(mo):
from rdkit.Chem.Draw import rdMolDra... | Python |
2D | cbouy/mols2grid | tests/webdriver_utils.py | .py | 5,453 | 137 | from ast import literal_eval
from base64 import b64decode
from io import BytesIO
import imagehash
from cairosvg import svg2png
from PIL import Image
from selenium import webdriver
from selenium.common.exceptions import StaleElementReferenceException
from selenium.webdriver.common.action_chains import ActionChains
from... | Python |
2D | cbouy/mols2grid | tests/test_select.py | .py | 1,528 | 59 | from types import SimpleNamespace
import pytest
import mols2grid as mg
from mols2grid.select import register
@pytest.fixture(autouse=True)
def clear_register_between_tests():
register._clear()
register._init_grid("foo")
yield
register._clear()
def test_clear_register():
register._clear()
a... | Python |
2D | cbouy/mols2grid | tests/test_marimo_integration.py | .py | 4,250 | 137 | import sys
from unittest.mock import MagicMock, patch
import pandas as pd
import pytest
from mols2grid import MolGrid
from mols2grid.utils import is_running_within_marimo
@pytest.fixture
def mock_marimo_module():
with patch.dict(sys.modules, {"marimo": MagicMock()}):
yield
@pytest.mark.usefixtures("mo... | Python |
2D | cbouy/mols2grid | tests/__init__.py | .py | 0 | 0 | null | Python |
2D | cbouy/mols2grid | tests/test_callbacks.py | .py | 921 | 34 | import pytest
from mols2grid import callbacks
def test_make_popup_callback():
popup = callbacks.make_popup_callback(
title="${title}",
subtitle="${title}",
svg="<svg><rect width='10' height='10'/></svg>",
html='<span id="foo">${title}</span>',
js='var title = "FOOBAR";',
... | Python |
2D | cbouy/mols2grid | tests/test_molgrid.py | .py | 10,533 | 345 | from types import SimpleNamespace
import pytest
from numpy.testing import assert_equal
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.rdDepictor import Compute2DCoords
from mols2grid import MolGrid
from mols2grid.select import register
def get_grid(df, **kwargs):
kwargs.setdefault("mol_col",... | Python |
2D | cbouy/mols2grid | tests/test_interface.py | .py | 27,392 | 859 | import json
import os
import sys
from base64 import b64encode
from datetime import datetime, timezone
from pathlib import Path
from types import SimpleNamespace
import imagehash
import pytest
from rdkit import Chem
from rdkit.Chem import AllChem
from selenium import webdriver
from selenium.webdriver.common.action_chai... | Python |
2D | cbouy/mols2grid | tests/test_utils.py | .py | 5,656 | 205 | import gzip
from types import SimpleNamespace
from unittest.mock import Mock, patch
import pandas as pd
import pytest
from rdkit import Chem
from rdkit.Chem.rdDepictor import Compute2DCoords
from mols2grid import utils
def test_requires():
@utils.requires("_not_a_module")
def func():
pass
with ... | Python |
2D | cbouy/mols2grid | tests/conftest.py | .py | 890 | 46 | from pathlib import Path
import pytest
from mols2grid import MolGrid, datafiles, sdf_to_dataframe
@pytest.fixture(scope="module")
def sdf_path():
return Path(datafiles.SOLUBILITY_SDF)
@pytest.fixture(scope="module")
def sdf_file(sdf_path):
return str(sdf_path)
@pytest.fixture(scope="module")
def smiles_... | Python |
2D | thesourcerer8/OpenSourceTCAD | install-ubuntu.sh | .sh | 220 | 17 | echo Installation routine for Ubuntu:
sudo apt-get install docker.io
cd Charon
sudo bash build.sh
cd ..
cd Genius
sudo bash build.sh
cd ..
cd DevSim
sudo bash build.sh
cd ..
echo "All Docker images have been built."
| Shell |
2D | thesourcerer8/OpenSourceTCAD | DevSim/DockerUsage.md | .md | 1,028 | 34 | # DevSim TCAD Docker Usage
DevSim-TCAD uses a number of old versions of libraries, this makes it increasingly difficult to compile and run on the latest Linux distributions. To work around this a Docker image of an older Ubuntu 20.04 distribution is used.
## Installation
### Docker Installation
Search for instruct... | Markdown |
2D | thesourcerer8/OpenSourceTCAD | DevSim/build.sh | .sh | 30 | 2 | docker build -t devsim-tcad .
| Shell |
2D | thesourcerer8/OpenSourceTCAD | DevSim/bash.sh | .sh | 37 | 2 | docker run -it devsim-tcad /bin/bash
| Shell |
2D | thesourcerer8/OpenSourceTCAD | Genius/DockerUsage.md | .md | 1,028 | 34 | # Genius TCAD Docker Usage
Genius-TCAD uses a number of old versions of libraries, this makes it increasingly difficult to compile and run on the latest Linux distributions. To work around this a Docker image of an older Ubuntu 14.04 distribution is used.
## Installation
### Docker Installation
Search for instruct... | Markdown |
2D | thesourcerer8/OpenSourceTCAD | Genius/build.sh | .sh | 30 | 2 | docker build -t genius-tcad .
| Shell |
2D | thesourcerer8/OpenSourceTCAD | Genius/bash.sh | .sh | 160 | 7 | xhost +local:
docker run -it \
--env="DISPLAY" \
--env="QT_X11_NO_MITSHM=1" \
--volume="/tmp/.X11-unix:/tmp/.X11-unix:rw" \
genius-tcad /bin/bash
| Shell |
2D | thesourcerer8/OpenSourceTCAD | Charon/DockerUsage.md | .md | 1,028 | 34 | # Charon TCAD Docker Usage
Charon-TCAD uses a number of old versions of libraries, this makes it increasingly difficult to compile and run on the latest Linux distributions. To work around this a Docker image of an older Ubuntu 18.04 distribution is used.
## Installation
### Docker Installation
Search for instruct... | Markdown |
2D | thesourcerer8/OpenSourceTCAD | Charon/build.sh | .sh | 30 | 2 | docker build -t charon-tcad .
| Shell |
2D | thesourcerer8/OpenSourceTCAD | Charon/bash.sh | .sh | 37 | 2 | docker run -it charon-tcad /bin/bash
| Shell |
2D | thesourcerer8/OpenSourceTCAD | Vienna/DockerUsage.md | .md | 1,025 | 34 | # Vienna TCAD Docker Usage
Vienna-* uses a number of old versions of libraries, this makes it increasingly difficult to compile and run on the latest Linux distributions. To work around this a Docker image of an older Ubuntu 18.04 distribution is used.
## Installation
### Docker Installation
Search for instruction... | Markdown |
2D | thesourcerer8/OpenSourceTCAD | Vienna/build.sh | .sh | 30 | 2 | docker build -t vienna-tcad .
| Shell |
2D | thesourcerer8/OpenSourceTCAD | Vienna/bash.sh | .sh | 37 | 2 | docker run -it vienna-tcad /bin/bash
| Shell |
2D | brownjm/gpe | spectral.py | .py | 3,694 | 137 | """Spectral method for evolving GPE for BEC's"""
from numpy import exp, pi, arange, meshgrid, sqrt, linspace
from numpy.fft import fft2, ifft2, fftshift
import matplotlib
import matplotlib.pyplot as plt
from matplotlib import animation
matplotlib.rcParams['figure.dpi'] = 200
from timestep2d import QHO
class Simula... | Python |
2D | brownjm/gpe | timestep2d.py | .py | 10,691 | 374 | """Modified Visscher's method for Gross-Pitaevskii equation for BEC's
Original paper:
A fast explicit algorithm for the time-dependent Schroedinger equation
P. B. Visscher
Computers in Physics 5, 596 (1991)
doi: 10.1063/1.168415
"""
from math import factorial
from numpy import pi, sqrt, exp, linspace, meshgrid, zeros... | Python |
2D | brownjm/gpe | timestep.py | .py | 7,844 | 287 | """Modified Visscher's method for Gross-Pitaevskii equation for BEC's
Original paper:
A fast explicit algorithm for the time-dependent Schroedinger equation
P. B. Visscher
Computers in Physics 5, 596 (1991)
doi: 10.1063/1.168415
"""
from math import factorial
from numpy import pi, sqrt, exp, linspace, zeros, empty, c... | Python |
2D | ma-compbio/SNIPER | sniper_train.py | .py | 438 | 23 | """
Main training file
Calls helper functions from utilities
"""
import numpy as np
import sys
from scipy.io import loadmat
from utilities.input import get_params
from pipeline.training import train_with_hic, train_with_mat
if __name__ == '__main__':
params = get_params()
rowMap = params['cropMap']['rowMap']
co... | Python |
2D | ma-compbio/SNIPER | sniper.py | .py | 378 | 20 | """
Application file
Calls helper functions from utilities
"""
import numpy as np
import sys
from scipy.io import loadmat
from utilities.input import get_application_params
from pipeline.application import apply_on_hic, apply_on_mat
if __name__ == '__main__':
params = get_application_params()
if not params['usem... | Python |
2D | ma-compbio/SNIPER | utilities/interchromosome_matrix.py | .py | 1,608 | 69 | import os
import numpy as np
import pandas as pd
import pickle as pkl
from scipy.sparse import coo_matrix, hstack, vstack
from scipy.io import savemat
from utilities.data_processing import chrom_sizes
def construct(hic_dir='.',prefix='hic',hic_res=100000,sizes_file='data/hg19.chrom.sizes',verbose=False):
fullSM = No... | Python |
2D | ma-compbio/SNIPER | utilities/input.py | .py | 3,474 | 138 | import sys
from scipy.io import loadmat
def get_params():
# set defaults
if len(sys.argv) < 4:
raise Exception('Must specify input and target .hic or .mat files and a label file')
params = {
'usemat' : False,
'input_file': sys.argv[1],
'target_file': sys.argv[2],
'label_file': sys.argv[3],
}
if para... | Python |
2D | ma-compbio/SNIPER | utilities/data_processing.py | .py | 4,488 | 158 | import os
import numpy as np
from subprocess import call
from scipy.io import loadmat, savemat
def chrom_sizes(f,length=np.inf):
data = open(f,'r')
sizes = {}
for line in data:
ldata = line.split()
if len(ldata[0]) > length:
continue
size... | Python |
2D | ma-compbio/SNIPER | pipeline/training.py | .py | 4,102 | 112 | import os
import tensorflow as tf
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
from scipy.io import loadmat
from utilities.data_processing import hicToMat, trimMat, contactProbabilities, bootstrap, Sigmoid
from pipeline.models import DenoisingAutoencoder, Classifier
from keras.utils import to_categorical
def trainNN(in... | Python |
2D | ma-compbio/SNIPER | pipeline/models.py | .py | 1,563 | 51 | import keras.backend as K
from keras.layers import Dense, Input, Dropout
from keras.models import Sequential, Model
def DenoisingAutoencoder(input,target):
Ninput = input.shape[1]
Noutput = target.shape[1]
hidden_dims = [1024,512,256]
latent_dim = 128
encodeInput = Input(shape=(Ninput,))
encodeModel = Sequentia... | Python |
2D | ma-compbio/SNIPER | pipeline/application.py | .py | 2,092 | 61 | import os
import tensorflow as tf
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
from scipy.io import loadmat, savemat
from keras.models import load_model
from utilities.data_processing import hicToMat, trimMat, contactProbabilities, Sigmoid, predictionsToBed
def apply_on_hic(params):
inputM = hicToMat(params['input_file... | Python |
2D | ITV-Stuttgart/loadBalancedChemistryModel | PrepareOpenFOAM.sh | .sh | 731 | 18 | #!/bin/bash
cd ${0%/*} || exit 1 # run from this directory
cat << EOF
The TDACChemistryModel of OpenFOAM uses a private scope for the variables
and member functions. This however prevents other classes, such as the
LoadBalancedTDACChemistryModel to derive from this class without replicating
all functionality. Furt... | Shell |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/chemistrySolver/makeLoadBalancedChemistrySolvers.C | .C | 5,418 | 227 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/chemistrySolver/makeLoadBalancedChemistrySolverTypes.H | .H | 6,270 | 107 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | Unknown |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/chemistryModel/LoadBalancedTDACChemistryModel/LoadBalancedTDACChemistryModel.C | .C | 31,732 | 1,081 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/chemistryModel/LoadBalancedTDACChemistryModel/LoadBalancedTDACChemistryModel.H | .H | 9,233 | 290 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | Unknown |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/chemistryModel/LoadBalancedTDACChemistryModel/makeLoadBalancedTDACChemistryModels.C | .C | 6,255 | 276 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/chemistryModel/LoadBalancedChemistryModel/LoadBalancedChemistryModel.C | .C | 20,786 | 733 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/chemistryModel/LoadBalancedChemistryModel/makeLoadBalancedChemistryModels.C | .C | 6,123 | 276 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/chemistryModel/LoadBalancedChemistryModel/LoadBalancedChemistryModel.H | .H | 8,189 | 259 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | Unknown |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/pointToPointBuffer/pointToPointBuffer.C | .C | 7,605 | 270 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/pointToPointBuffer/pointToPointBuffer.H | .H | 4,877 | 158 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | Unknown |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/dataContainer/baseDataContainer/baseDataContainer.H | .H | 6,280 | 220 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | Unknown |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/dataContainer/baseDataContainer/baseDataContainer.C | .C | 2,683 | 100 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/dataContainer/TDACDataContainer/TDACDataContainer.H | .H | 7,136 | 246 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | Unknown |
2D | ITV-Stuttgart/loadBalancedChemistryModel | src/dataContainer/TDACDataContainer/TDACDataContainer.C | .C | 2,826 | 105 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | tests/src/main.C | .C | 4,013 | 117 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | tests/src/TDACChemistryModel-Test.C | .C | 3,508 | 105 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | tests/src/pointToPointBuffer-Test.C | .C | 7,551 | 293 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | tests/src/standardChemistryModel-Test.C | .C | 3,507 | 105 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | C |
2D | ITV-Stuttgart/loadBalancedChemistryModel | tests/src/globalFoamArgs.H | .H | 1,757 | 58 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-----------------------------------... | Unknown |
2D | abhinavroy1999/grain-growth-phase-field-code | GrainGrowth.m | .m | 12,068 | 256 | function GrainGrowth(Nx, Ny, dx, dy, end_time, time_step)
% Phase-field simulation code for grain growth in 2D, using the Allen-Cahn
% equation (for non-conserved order parameters).
%
% The model is developed by Fan & Chen (http://www.mmm.psu.edu/DNFan1997Actamater_Graingrowth1phase2D.pdf)
%
% Function ca... | MATLAB |
2D | pyNLSE/bpm | 1D.py | .py | 4,478 | 155 | import numpy as np
import matplotlib.pyplot as plt
import os
from matplotlib import cm
import shutil
import platform
def grid(Nx,Ny,xmax,ymax):
x = np.linspace(-xmax, xmax-2*xmax/Nx, Nx) # x variable
y = 0 # not used, but a value must be given
return x,y;
# Builds the Laplacian in Fourier spac... | Python |
2D | pyNLSE/bpm | bpm.py | .py | 3,154 | 71 | # Integrating a 1+1D or 1+2D NLSE with different initial conditions and for different potentials.
# To run this code type the command:
# python3 bpm.py example 1D for a 1D example (1D.py file needed)
# python3 bpm.py example 2D for a 2D example (2D.py file needed)
# where example.py contains the details for... | Python |
2D | pyNLSE/bpm | 2D.py | .py | 6,458 | 211 | import numpy as np
import matplotlib.pyplot as plt
import os
from matplotlib import cm
import shutil
import platform
# Builds the (x,y) grid
def grid(Nx,Ny,xmax,ymax):
x = np.linspace(-xmax, xmax-2*xmax/Nx, Nx) # x variable
y = np.linspace(-ymax, ymax-2*ymax/Ny, Ny) # y variable
y,x=np.meshgrid(y, x)
retu... | Python |
2D | pyNLSE/bpm | examples2D/Diffraction_Circle_2D.py | .py | 926 | 36 | # File: ./examples2D/Diffraction_Circle_2D.py
# Run as python3 bpm.py Diffraction_Circle_2D 2D
# Diffraction by a circular aperture
import numpy as np
Nx = 500 # Grid points
Ny = Nx
dt = 0.001 # Evolution step
tmax = 60 # End of propagation
xmax = 100 # x-window size
ymax = xmax # y-window s... | Python |
2D | pyNLSE/bpm | examples2D/Vortex_Precession_2D.py | .py | 1,012 | 36 | # File: ./examples2D/Vortex_Precession_2D.py
# Run as python3 bpm.py Vortex_Precession_2D 2D
# Vortex precession within a harmonic potential
import numpy as np
Nx = 300 # Grid points
Ny = Nx
dt = 0.001 # Evolution step
tmax = 80 # End of propagation
xmax = 8 # x-window size
ymax = xma... | Python |
2D | pyNLSE/bpm | examples2D/Vortices_Pattern_2D.py | .py | 1,678 | 51 | # File: ./examples2D/Vortices_Pattern_2D.py
# Run as python3 bpm.py Vortices_Pattern_2D 2D
# A Gaussian beam impinges on a mask that generates a diffaction pattern with
# vortices of different topological charges.
# NOTICE: This example uses a fine computational grid, it uses a lot of memory
# and takes some time... | Python |
2D | pyNLSE/bpm | examples2D/Vortex_2D.py | .py | 1,146 | 37 | # File: ./examples2D/Vortex_2D.py
# Run as python3 bpm.py Vortex_2D 2D
# A vortex beam propagating in free space
import numpy as np
Nx = 300 # Grid points
Ny = Nx
dt = 0.001 # Evolution step
tmax = 10 # End of propagation
xmax = 20 # x-window size
ymax = xmax # y-window... | Python |
2D | pyNLSE/bpm | examples2D/Vortex_Breaking_2D.py | .py | 1,182 | 37 | # File: ./examples2D/Vortex_Breaking_2D.py
# Run as python3 bpm.py Vortex_Breaking_2D 2D
# Azimuthal instability of a vortex because of an attractive nonlinearity
import numpy as np
Nx = 300 # Grid points
Ny = Nx
dt = 0.001 # Evolution step
tmax = 500 # End of propagation
xmax = 120 # x-... | Python |
2D | pyNLSE/bpm | examples2D/Collapse_2D.py | .py | 1,527 | 52 | # File: ./examples2D/Collapse_2D.py
# Run as python3 bpm.py Collapse_2D 2D
# Self-similar collapse of the Townes' profile
import numpy as np
Nx = 500 # Grid points
Ny = 500
dt = 0.005 # Evolution step
tmax = 7 # End of propagation
xmax = 20 # x-window size
ymax = xmax # y-window size
... | Python |
2D | pyNLSE/bpm | examples2D/Liquid_Droplet_2D.py | .py | 1,370 | 50 | # File: ./examples2D/Liquid_Droplet_2D.py
# Run as python3 bpm.py Liquid_Droplet_2D 2D
# A droplet of "liquid light" collides with a barrier
import numpy as np
Nx = 400 # Grid points
Ny = 240
dt = 0.001 # Evolution step
tmax = 140 # End of propagation
xmax = 160 # x-window size
ymax = 10... | Python |
2D | pyNLSE/bpm | examples2D/Gaussian_Vortex_interf_2D.py | .py | 1,608 | 57 | # File: ./examples2D/Gaussian_Vortex_interf_2D.py
# Run as python3 bpm.py Gaussian_Vortex_interf_2D 2D
# A Gaussian beam and a vortex cross each other generating the typical fork-like
# pattern
import numpy as np
Nx = 600 # Grid points
Ny = 300
dt = 0.001 # Evolution step
tmax = 7 # End of ... | Python |
2D | pyNLSE/bpm | examples2D/Gaussian_Beam_2D.py | .py | 1,082 | 34 | # File: ./examples2D/Gaussian_Beam_2D.py
# Run as python3 bpm.py Gaussian_Beam_2D 2D
# A Gaussian beam propagating in free space
import numpy as np
Nx = 300 # Grid points
Ny = Nx
dt = 0.001 # Evolution step
tmax = 10 # End of propagation
xmax = 20 # x-window size
ymax = xmax # y-win... | Python |
2D | pyNLSE/bpm | examples2D/Filamentation_2D.py | .py | 1,319 | 39 | # File: ./examples2D/Filamentation.py
# Run as python3 bpm.py Filamentation 2D
# Filamentation: an initially constant energy distribution results in the
# formation of filaments. The nonlinearities drive the evolution.
import numpy as np
Nx = 400 # Grid points
Ny = Nx
dt = 0.001 # Evolution step
tmax = ... | Python |
2D | pyNLSE/bpm | examples1D/Thomas_Fermi_1D.py | .py | 1,428 | 49 | # File: ./examples1D/Thomas_Fermi_1D.py
# Run as python3 bpm.py Thomas_Fermi_1D 1D
# Initially, a nonlinear wave packet is confined within a harmonic well, and
# it is well approximated by a Thomas-Fermi profile (in which the Laplacian
# is neglected). At t=5, the strength of the nonlinearity is changed and an
# osc... | Python |
2D | pyNLSE/bpm | examples1D/Diffraction_Slit_1D.py | .py | 1,139 | 34 | # File: ./examples1D/Diffraction_Slit_1D.py
# Run as python3 bpm.py Diffraction_Slit_1D 1D
# Diffraction by a slit
# The initial condition is a flat function within a finite domain, modeling
# the passage of a wide wave through a slit. The evolution generates the typical
# diffraction pattern
import numpy as np
Nx... | Python |
2D | pyNLSE/bpm | examples1D/Solitons_phase_opp_1D.py | .py | 1,276 | 42 | # File: ./examples1D/Solitons_phase_opp_1D.py
# Run as python3 bpm.py Solitons_phase_opp_1D 1D
# Encounter of two solitons in phase opposition. The process can be interpreted
# as two robust wave packets that bounce back from each other.
import numpy as np
Nx = 500 # Grid points
Ny = Nx
dt = 0.001 # Evo... | Python |
2D | pyNLSE/bpm | examples1D/Soliton_Emission_B_1D.py | .py | 1,656 | 48 | # File: ./examples1D/Soliton_Emission_B_1D.py
# Run as python3 bpm.py Soliton_Emission_B_1D 1D
# Initially, a Gaussian wave packet is confined within a shallow trap. At a given
# time, a repulsive interaction is turned on and the wave starts expanding. Then,
# the sign of the nonlinear term is changed and the intera... | Python |
2D | pyNLSE/bpm | examples1D/Interference_Gaussians_1D.py | .py | 1,243 | 35 | # File: ./examples1D/Interference_Gaussians_1D.py
# Run as python3 bpm.py Interference_Gaussians_1D 1D
# Interference of two Gaussian wave packets.
# The initial condition consists of two separate Gaussians. Each of them grows
# wider because of diffraction due to the Laplacian term. Eventually, they are
# wide eno... | Python |
2D | pyNLSE/bpm | examples1D/Double_Well_1D.py | .py | 1,132 | 34 | # File: ./examples1D/Double_Well_1D.py
# Run as python3 bpm.py Double_Well_1D 1D
# Beating in a double well potential
# A double well potential is defined. The initial condition concentrates the
# wavefunction around one of the minima. The simulation shows that, periodically, the
# energy tunnels between the two wel... | Python |
2D | pyNLSE/bpm | examples1D/Solitons_in_phase_1D.py | .py | 1,237 | 41 | # File: ./examples1D/Solitons_in_phase_1D.py
# Run as python3 bpm.py Solitons_in_phase_1D 1D
# Encounter of two solitons in phase, which traverse each other unaffected.
# During the collision, an interference pattern is generated.
import numpy as np
Nx = 500 # Grid points
Ny = Nx
dt = 0.001 # Evolution s... | Python |
2D | pyNLSE/bpm | examples1D/Sech2_Pot_1D.py | .py | 1,372 | 37 | # File: ./examples1D/Sech2_Pot_1D.py
# Run as python3 bpm.py Sech2_Pot_1D 1D
# A Gaussian wave packet traverses a reflectionless potential. The simulation
# non-trivially shows that there is no reflected energy. Try changing the value
# of s to different (integer and non-integer) values
import numpy as np
Nx = 2... | Python |
2D | pyNLSE/bpm | examples1D/Soliton_Emission_A_1D.py | .py | 1,300 | 38 | # File: ./examples1D/Soliton_Emission_A_1D.py
# Run as python3 bpm.py Soliton_Emission_A_1D 1D
# Initially, there is a Gaussian wavefunction within a shallow trap.
# Due to a space-dependent attractive nonlineary, the energy moves rightwards
# and it turns out that a train of solitons is emitted.
import numpy as ... | Python |
2D | pyNLSE/bpm | examples1D/Rectangular_Barrier_1D.py | .py | 1,234 | 36 | # File: ./examples1D/Rectangular_Barrier_1D.py
# Run as python3 bpm.py Rectangular_Barrier_1D 1D
# A Gaussian wave packet impinges on a rectangular barrier. Part of the wave
# is reflected, part of the wave is transmitted.
import numpy as np
Nx = 1600 # Grid points
Ny = Nx
dt = 0.0001 # Evolution step
t... | Python |
2D | pillowlab/GLMspiketools | setpaths_GLMspiketools.m | .m | 600 | 19 | % SETPATHS.m - GLMspiketools code repository
%
% This simple script sets the path to include relevant directories for the
% GLMspiketools code package. You must 'cd' into this directory in order
% to evaluate it.
%
% More info: http://pillowlab.princeton.edu/code_GLM.html
% Github page: https://github.com/pillowlab/GL... | MATLAB |
2D | pillowlab/GLMspiketools | glmtools_spline/mksplineDesignMat.m | .m | 2,179 | 71 | function [Xdesign,Ysrt,Mspline] = mksplineDesignMat(X,Y,ss,sortflag,dcflag)
% [Xdesign,Ysrt,Mspline] = mksplineDesignMat(X,Y,ss,sortflag)
%
% Computes design matrix for least-squares fitting cubic splines, so that
% the problem can be written:
% argmin_w ||Ysrt - Xdesign*w||^2
%
% "Standard" spline coefficients ... | MATLAB |
2D | pillowlab/GLMspiketools | glmtools_spline/mksplineParamMtx.m | .m | 3,300 | 85 | function Mspline = mksplineParamMtx(ss,dcflag)
% Mspline = mksplineParamMtx(ss,dcflag)
%
% Computes matrix parametrizing a cubic spline (3rd order piecewise
% polynomial) with given smoothness and end-point conditions
%
% Inputs:
% ss - spline struct with fields "breaks", "smoothness", and "extrapDeg"
% field... | MATLAB |
2D | pillowlab/GLMspiketools | glmtools_spline/ppfun.m | .m | 1,481 | 59 | function [f,df,ddf]=ppfun(pp,xx)
% [f,df,ddf]=ppfun(pp,xx)
%
% Evaluate piecewise polynomial 'pp' at values 'xx'. Optionally returns first and
% second derivs at these points.
%
% Inputs:
% pp = piecewise polynomial structure, given (eg) by makepp or spline
% xx = vector of values at which to ev... | MATLAB |
2D | pillowlab/GLMspiketools | glmtools_spline/MLfit_GLMwithspline.m | .m | 1,684 | 55 | function [gg,neglogli,H] = MLfit_GLMwithspline(gg,Stim,optimargs,npasses)
% [gg,neglogli,H] = MLfit_GLMwithspline(gg,Stim,optimargs,npasses)
%
% Fit GLM filters and spline nonlinearity using alternating
% ascent of filter and spline parameters
%
% Inputs:
% gg = glm param structure
% Stim = stimulus
% optima... | MATLAB |
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