repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
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GraphLIME | GraphLIME-master/exp/noise_features/utils.py | import os
import numpy as np
from tqdm import tqdm
import seaborn as sns
import matplotlib.pyplot as plt
import torch
import torch.optim as optim
import torch.nn.functional as F
import torch_geometric.transforms as T
from torch_geometric.datasets import Planetoid
def prepare_data(args):
dataset = args.dataset.ti... | 5,089 | 28.766082 | 97 | py |
GraphLIME | GraphLIME-master/exp/noise_features/models.py | import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import GCNConv, GATConv
class GCN(nn.Module):
def __init__(self, input_dim, hidden_dim, output_dim, dropout=0.5):
super(GCN, self).__init__()
self.dropout = dropout
self.conv1 = GCNConv(input_dim, hidd... | 1,699 | 32.333333 | 116 | py |
arl-eegmodels | arl-eegmodels-master/EEGModels.py | """
ARL_EEGModels - A collection of Convolutional Neural Network models for EEG
Signal Processing and Classification, using Keras and Tensorflow
Requirements:
(1) tensorflow == 2.X (as of this writing, 2.0 - 2.3 have been verified
as working)
To run the EEG/MEG ERP classification sample script, you w... | 18,033 | 43.74938 | 96 | py |
arl-eegmodels | arl-eegmodels-master/examples/ERP.py | """
Sample script using EEGNet to classify Event-Related Potential (ERP) EEG data
from a four-class classification task, using the sample dataset provided in
the MNE [1, 2] package:
https://martinos.org/mne/stable/manual/sample_dataset.html#ch-sample-data
The four classes used from this dataset are:
L... | 10,178 | 40.717213 | 86 | py |
sampling_for_genomic_surveillance | sampling_for_genomic_surveillance-master/compare_distribution.py | #libraries to use
import pandas as pd
from scipy.stats import mannwhitneyu
from scipy.stats import ks_2samp
from scipy.stats import ttest_ind
def define_significance_value(p_value):
summary = ""
if p_value > 0.05:
summary = "NS"
elif p_value > 0.01 and p_value <= 0.05:
summary = "*"
el... | 2,285 | 37.1 | 269 | py |
amuse | amuse-main/setup.py | from setuptools import setup, find_packages
from support.setup_codes import setup_commands
from support.misc import find_data_files
name = 'amuse-devel'
author = 'The AMUSE team'
author_email = 'info@amusecode.org'
license_ = "Apache License 2.0"
url = 'http://www.amusecode.org/'
install_requires = [
'setuptools>=... | 2,853 | 26.980392 | 67 | py |
amuse | amuse-main/examples/examples_galaxia/orbit_one_star.py |
# ---------------------------------------------------------------------------
# Script that uses galaxia and the bridge in rotating coordinates |
# to integrate the orbit of a star. |
# For a complete explanation of the possible parameters and models |
# inclu... | 9,533 | 37.756098 | 103 | py |
amuse | amuse-main/examples/examples_galaxia/resonances.py | # ---------------------------------------------------------------------------
# This script generates the corrotation and Lindbland resonances |
# as a function of radius using galaxia. |
# For a complete explanation of the possible parameters and models |
# includ... | 2,479 | 36.014925 | 77 | py |
amuse | amuse-main/examples/examples_galaxia/evolution_cluster.py | # ---------------------------------------------------------------------------
# Script that uses galaxia and the bridge in rotating coordinates |
# to calculate the evolution of a star cluster in the Galaxy. |
# The physical processes involved are self gravity, stellar evolution |
# and th... | 13,348 | 40.200617 | 79 | py |
amuse | amuse-main/examples/examples_galaxia/rotation_curve_Milky_Way.py | # ---------------------------------------------------------------------------
# This script generates the rotation curve of the Milky Way using galaxia. |
# For a complete explanation of the possible parameters and models |
# included in galaxia, we refer the reader to the file: user_manual_galaxia.|
# ------... | 3,135 | 38.2 | 77 | py |
amuse | amuse-main/examples/examples_galaxia/utility_functions.py | # ---------------------------------------------------------------------------
# Script that shows the utility functions of galaxia. |
# These functions include: the computation of the components of the |
# tidal tensor at a given point, the eigen-values and the tidal radius |
# of a s... | 3,913 | 39.350515 | 78 | py |
amuse | amuse-main/examples/publications/2013MNRAS.429..895P/disk_script/boxedfi.py |
from amuse.units import nbody_system
from amuse.units import units
import amuse.datamodel as core
from amuse.community.fi.interface import Fi
from amuse.ext.gasplummer import MakePlummerGasModel
class BoxedFi(Fi):
def __init__(self, *args, **kargs):
Fi.__init__(self, *args, **kargs)
self.escapers=core.Pa... | 1,929 | 30.129032 | 69 | py |
amuse | amuse-main/examples/publications/2013MNRAS.429..895P/disk_script/fast.py | # issues:
# - for now, units in si
# - a common coordinate system is used for all systems
# - sync of systems should be checked
# - timestepping: adaptive dt?
from amuse.units import units
from amuse.units.quantities import zero
import threading
from amuse import datamodel
def radius_or_hsmooth(parts):
d=set(dir(pa... | 5,433 | 25.90099 | 100 | py |
amuse | amuse-main/examples/publications/2013MNRAS.429..895P/disk_script/run.py | from binary import circumbinary_disc_run
from amuse.units import units
# kepler 16
circumbinary_disc_run( tend=40. | units.yr, # simulation time
Ngas=100000, # number of gas particles
m1=0.6897 | units.MSun, # primary mass
... | 2,223 | 70.741935 | 119 | py |
amuse | amuse-main/examples/publications/2013MNRAS.429..895P/disk_script/binary.py | import os
from socket import gethostname
import numpy
import time
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot
from amuse.community.twobody.twobody import TwoBody
from amuse.units import units
from amuse.units import nbody_system
from amuse.units import constants
from amuse.datamodel import P... | 12,738 | 34.884507 | 123 | py |
amuse | amuse-main/examples/publications/2013MNRAS.429..895P/disk_script/directsum.py | from amuse.units import constants
from amuse.datamodel import Particles
from amuse.units.quantities import zero
from amuse.units.quantities import AdaptingVectorQuantity
class directsum(object):
def __init__(self, systems, G=constants.G):
self.systems=systems
self.G=G
def get_gravity_at_po... | 1,332 | 38.205882 | 81 | py |
amuse | amuse-main/examples/publications/2013MNRAS.429..895P/three_body_script/python_interface.py | from amuse.rfi.core import *
import cPickle as Pickle
from amuse.units import units
#from testmod import f
from bin_planet import binary_with_planet_run as f
def func(*arg,**kwarg):
return f(*arg,**kwarg)
class CodeImplementation(object):
def _func(self,argin,kwargin,argout):
try:
arg=Pickle.loads(a... | 1,540 | 30.44898 | 81 | py |
amuse | amuse-main/examples/publications/2013MNRAS.429..895P/three_body_script/kepler_16_three_body.py | from python_interface import CodeInterface
from amuse.units import units
from amuse.rfi.channel import AsyncRequestsPool
import numpy
from matplotlib import pyplot
ncpu=16
allhosts=[ ("paddegat",4),
("koppoel",4),
("gaasp",4),
("biesbosch",4),
]
hosts=reduce(lambda x,y: x+... | 2,111 | 21.709677 | 83 | py |
amuse | amuse-main/examples/publications/2013MNRAS.429..895P/three_body_script/bin_planet.py | import numpy
import time
from matplotlib import pyplot
from amuse.units import nbody_system,units,constants
from amuse.units.quantities import AdaptingVectorQuantity
from amuse.io import write_set_to_file,read_set_from_file
from amuse.community.huayno.interface import Huayno
from amuse.datamodel import Particles
d... | 7,935 | 26.651568 | 98 | py |
amuse | amuse-main/examples/simple/pre_main_sequence_evolution.py | # -*- coding: ascii -*-
"""
Calculated theoretical pre-main-sequance evolutionary tracks for stars of
various masses.
After Iben, ApJ 141, 993, 1965
"""
from __future__ import print_function
from matplotlib import pyplot
from amuse.units import units
from amuse.community.mesa.interface import MESA
from amuse import da... | 2,752 | 31.011628 | 76 | py |
amuse | amuse-main/examples/simple/helium_star.py | # -*- coding: ascii -*-
"""
Creates a helium burning star from the inner shells of a main sequence star.
"""
from __future__ import print_function
from amuse.units import units
from amuse.datamodel import Particle
from amuse.community.mesa.interface import MESA
from matplotlib import pyplot
from amuse.plot import logl... | 3,738 | 35.656863 | 76 | py |
amuse | amuse-main/examples/simple/stellar_lifetime_vs_mass.py | # -*- coding: ascii -*-
"""
Calculates the stellar lifetime in a range of masses between
Mmax and Mmin using SSE (or another stellar evolution code)
and an analytic expression.
"""
from __future__ import print_function
import numpy
from optparse import OptionParser
from amuse.units import units
from amuse.datamodel imp... | 2,332 | 29.697368 | 72 | py |
amuse | amuse-main/examples/simple/clump_finding.py | # -*- coding: ascii -*-
"""
Generates a random distribution of particles and uses Hop to determine clumps
in the particle set.
"""
from __future__ import print_function
# import numpy
from numpy import random
from matplotlib import pyplot
from amuse.units import units
from amuse.units import nbody_system
from amuse.co... | 2,734 | 25.553398 | 77 | py |
amuse | amuse-main/examples/simple/agb.py | # -*- coding: ascii -*-
"""
Evolves an the sun in it's AGB star phase using SSE
"""
from __future__ import print_function
import numpy
from matplotlib import pyplot
from amuse.community.sse.interface import SSE
from amuse.units import units
# from amuse.ext import solarsystem
from amuse import datamodel
def plottil... | 1,247 | 22.54717 | 74 | py |
amuse | amuse-main/examples/simple/cluster.py | # -*- coding: ascii -*-
"""
Evolves an equal mass stellar cluster.
"""
from __future__ import print_function
import numpy
from matplotlib import pyplot
from amuse.units import nbody_system
from amuse.community.hermite.interface import Hermite
# import logging
from amuse.ic.plummer import new_plummer_model
# logging.bas... | 4,118 | 28.847826 | 77 | py |
amuse | amuse-main/examples/simple/orbit_in_potential.py | # -*- coding: ascii -*-
"""
Integrates a stellar orbit in the galactic potential
This example illustrates the use of a simple external potential and simple
integrator, no
amuse community code is used.
"""
from __future__ import print_function
# import numpy
from amuse.units.optparse import OptionParser
from math impor... | 6,325 | 36.431953 | 77 | py |
amuse | amuse-main/examples/simple/stellar_mass_loss.py | # -*- coding: ascii -*-
"""
Set an artificial mass loss rate at a specific point
in the stellar evolution using MESA
and calculate the effect this has on the stellar radius.
"""
from __future__ import print_function
# import numpy
from amuse.units import units
from amuse.datamodel import Particle
from amus... | 2,442 | 30.727273 | 75 | py |
amuse | amuse-main/examples/simple/h2region.py | # -*- coding: ascii -*-
"""
Evolves the steady state solution of a star irridiating a H2 region.
"""
from __future__ import print_function
# import numpy
import os
from matplotlib import pyplot
from optparse import OptionParser
from amuse.community.mocassin.interface import Mocassin, mocassin_rydberg_unit
from amuse... | 5,925 | 31.382514 | 129 | py |
amuse | amuse-main/examples/simple/hydro_star.py | # -*- coding: ascii -*-
"""
Converts a 1d stellar model into a 3d spherical gas model for a star
"""
from __future__ import print_function
from amuse.units import units
from amuse.community.evtwin.interface import EVtwin
from amuse.ext.star_to_sph import convert_stellar_model_to_SPH
from amuse.plot import sph_particle... | 1,131 | 28.025641 | 73 | py |
amuse | amuse-main/examples/simple/unstable_binary.py | # -*- coding: ascii -*-
"""
Evolves two stars dynamically (hermit, nbody code) each star will
lose mass during the evolution (evtwin, stellar evolution code)
We start with two stars, one 10.0 and one 1.0 solar mass star. These
stars start orbiting with a stable kepler orbit.
After 2 orbital periods the stars will begi... | 6,092 | 31.935135 | 99 | py |
amuse | amuse-main/examples/simple/brunt.py | # -*- coding: ascii -*-
# -*-noplot-*-
from __future__ import print_function
from matplotlib import pyplot
from amuse.plot import semilogy, xlabel, ylabel
from amuse.units import units
from amuse.community.mesa.interface import MESA
from amuse.datamodel import Particle
def brunt_vaisala_frequency_squared_profile(mas... | 1,375 | 31.761905 | 81 | py |
amuse | amuse-main/examples/simple/supernova_in_binary_nbody.py | # -*- coding: ascii -*-
from __future__ import print_function
import numpy
from amuse.units import constants, units, nbody_system
from amuse.datamodel import Particles
from amuse.community.hermite.interface import Hermite
from amuse.ext.orbital_elements import orbital_elements_from_binary
def get_relative_velocity(to... | 3,242 | 32.091837 | 79 | py |
amuse | amuse-main/examples/simple/salpeter.py | # -*- coding: ascii -*-
"""
Generates a cluster using a plummer model with a salpeter Initial Mass
Function.
Compares the generated IMF against the expected line.
"""
from __future__ import print_function
import numpy
from matplotlib import pyplot
from amuse.units import units
from amuse.units import nbody_system
from ... | 2,175 | 26.544304 | 78 | py |
amuse | amuse-main/examples/simple/massloss.py | # -*- coding: ascii -*-
"""
Evolves the sun and earth where the sun will lose mass every 220th step.
"""
from __future__ import print_function
import numpy
from amuse.community.hermite.interface import Hermite
# from amuse.community.sse.interface import SSE
from amuse import datamodel
from amuse.units import units
from... | 2,003 | 27.225352 | 86 | py |
amuse | amuse-main/examples/simple/stellar_structure.py | # -*- coding: ascii -*-
"""
Make plots of the stellar structure of a star of given mass and age
"""
from __future__ import print_function
import numpy
from matplotlib import pyplot
from amuse.plot import semilogy, xlabel, ylabel
from amuse.units import units
from amuse.community.evtwin.interface import EVtwin
from amu... | 2,813 | 30.617978 | 72 | py |
amuse | amuse-main/examples/simple/boss_bodenheimer_test.py | # -*- coding: ascii -*-
"""
Fragmentation in a rotating protostar -- Boss & Bodenheimer (1979, BB79,
http://adsabs.harvard.edu/abs/1979ApJ...234..289B)
Calculate the collapse of an isothermal cloud with SPH code fi. The
cloud is initially spherical, with an uniform density with a
nonaxisymmetric perturbation o... | 5,467 | 30.976608 | 81 | py |
amuse | amuse-main/examples/simple/hrdiagram.py | # -*- coding: ascii -*-
"""
Generates a Hertzsprung-Russell diagram for a single star
"""
from __future__ import print_function
# import sys
# import numpy
from matplotlib import pyplot
from amuse.plot import loglog, xlabel, ylabel
from amuse.units import units
from amuse.community.sse.interface import SSE
from amus... | 1,860 | 27.630769 | 71 | py |
amuse | amuse-main/examples/simple/evolve_binary.py | # -*- coding: ascii -*-
"""
Evolves a stellar binary and reports the mass of each star during the
evolution.
Shows the type of each star as they change.
"""
from __future__ import print_function
from amuse.community.seba.interface import SeBa
from amuse.datamodel import Particles
from amuse.units import constants, uni... | 3,237 | 30.134615 | 78 | py |
amuse | amuse-main/examples/simple/protoplanetarydisk.py | # -*- coding: ascii -*-
"""
Creates a protoplanetary disk around a sun-like star
"""
from __future__ import print_function
import numpy
from matplotlib import pyplot
from amuse.community.fi.interface import Fi
from amuse.units import units
from amuse.units import nbody_system
from amuse.ext.protodisk import ProtoPla... | 2,223 | 23.711111 | 78 | py |
amuse | amuse-main/examples/simple/lagrange_points.py | # -*- coding: ascii -*-
"""
Make a contour plot of the effective potential of the Sun-Earth system (left)
and a system with a 10000 times more massive Earth with the Lagrangian points
visible.
"""
from __future__ import print_function
# import numpy
from matplotlib import pyplot
from amuse.plot import xlabel, ylabel, e... | 3,488 | 36.923913 | 77 | py |
amuse | amuse-main/examples/simple/stellar_mean_mass.py | # -*- coding: ascii -*-
"""
Calculates the mean mass of a stellar popultion as a function of time.
This routine was used to measure the <m> of a star cluster in order to
incorporate <m>(t) and d<m>/dt in a parametrized cluster evolution code.
"""
from __future__ import print_function
# import sys
# import numpy
# from ... | 2,863 | 38.232877 | 79 | py |
amuse | amuse-main/examples/simple/binary_population_synthesis.py | # -*- coding: ascii -*-
"""
Generates a grid of binaries with different, primary mass, mass ratio
and separation and evolves these over time.
"""
from __future__ import print_function
from amuse.units import units
from amuse.units import quantities
from amuse import datamodel
from amuse.community.seba.interface import... | 6,973 | 31.896226 | 79 | py |
amuse | amuse-main/examples/simple/molecular_cloud_chemistry.py | # -*- coding: ascii -*-
"""
Evolves a molecular cloud with chemical evolution
The dynamics is evolved in the sph code Fi, chemistry with Krome, assuming
an isothermal cloud (hence passive chemical evolution).
Initial condition is a smooth spherical cloud with random velocities as in
Bonnell et al. (2003)
"""
from __f... | 3,266 | 29.53271 | 97 | py |
amuse | amuse-main/examples/simple/isochrone.py | # -*- coding: ascii -*-
"""
Generates an isochrone of a cluster of stars in a Hertzsprung-Russell diagram
"""
from __future__ import print_function
from matplotlib import pyplot
from amuse.units import units
from amuse.datamodel import Particles
from amuse.ic.brokenimf import new_scalo_mass_distribution
from amuse.ext.... | 1,830 | 35.62 | 78 | py |
amuse | amuse-main/examples/simple/kelvin_helmholtz.py | # -*- coding: ascii -*-
"""
Runs the Kelvin-Helmholtz Instability problem in two dimensions with Athena.
"""
from __future__ import print_function
import numpy
from matplotlib import pyplot
from amuse.community.athena.interface import Athena
from amuse.units.generic_unit_system import (
length, mass, speed, time, d... | 3,526 | 25.125926 | 76 | py |
amuse | amuse-main/examples/simple/collision.py | """
Evolves a cluster until a collision is detected between two stars in the
cluster.
The stars in the cluster are distributed using a plummer sphere, the
masses are set according to a Salpeter initial mass function.
By default the radii of all stars are equal and very large.
All units are in nbody units.
"""
impo... | 2,959 | 27.737864 | 78 | py |
amuse | amuse-main/examples/simple/gas_in_cluster.py | # -*- coding: ascii -*-
"""
Simultaniously evolves gas and stars in a cluster.
The stars and gas particles evolve in their respective codes (Hermite and
Gadget2)
The force of the gas particles on the star particles is calculated by a
seperate code (BHTree)
The force of the star particles on the gas particles is calcul... | 7,737 | 31.107884 | 79 | py |
amuse | amuse-main/examples/simple/evolve_orbit_in_potential.py | # -*- coding: ascii -*-
"""
Evolve the orbital evolution in the galactic center potential
with different N-body codes.
All codes use default settings and are integrated using Bridge.
Since it is only a single particle being evolved, and the potential
is handled by bridge (externally) there should no... | 8,013 | 33.692641 | 78 | py |
amuse | amuse-main/examples/simple/plot_with_units.py | # -*- coding: ascii -*-
"""
Creates a number of plots using the AMUSE unit aware plot functions.
"""
from __future__ import print_function
from amuse.units import units, quantities
from amuse.plot import (
native_plot, plot, scatter, xlabel, ylabel, hist
)
import numpy as np
if __name__ == "__main__":
# late... | 1,688 | 28.12069 | 68 | py |
amuse | amuse-main/examples/simple/galactic_center.py | # -*- coding: ascii -*-
"""
Evolves a cluster in the potention of the galactic center
Uses the bridge integrator to couple different codes.
In this example a cluster is evolved circling the galactic center, represented
by a static potential.
"""
from __future__ import print_function
# import numpy
from amuse.units im... | 4,519 | 28.933775 | 79 | py |
amuse | amuse-main/examples/simple/molecular_cloud.py | # -*- coding: ascii -*-
"""
Evolves a molecular cloud with explictly split gravtiy evolution
The gas is evolved in a sph code, and it's gravity is determined by a tree
code.
Initial condition is a smooth spherical cloud with random velocities as in
Bonnell et al. (2003)
"""
from __future__ import print_function
impor... | 3,786 | 27.261194 | 77 | py |
amuse | amuse-main/examples/simple/save_and_load_particles.py | # -*- coding: ascii -*-
"""
Saves and loads a set of particles.
The 'write_set_to_file' and 'read_set_from_file' functionso can hadle
files in a variety of formats.
"""
from __future__ import print_function
# from amuse.units import nbody_system
from amuse.ic.plummer import new_plummer_model
from amuse.plot import plot... | 1,277 | 30.170732 | 78 | py |
amuse | amuse-main/examples/simple/pythagorean.py | # -*- coding: ascii -*-
"""
Calculates the Pythagorean 3-body problem using different values for
the smoothing length in the n-body code.
"""
from __future__ import print_function
# import numpy
# import time
# from amuse.community.phigrape.interface import PhiGRAPE
from amuse.community.hermite.interface import Hermit... | 2,491 | 30.15 | 79 | py |
amuse | amuse-main/examples/simple/__init__.py | 0 | 0 | 0 | py | |
amuse | amuse-main/examples/simple/grid_potential.py | # -*- coding: ascii -*-
from __future__ import print_function
from amuse.units import units, nbody_system
from amuse.datamodel import Particle
from amuse.community.athena.interface import Athena
from amuse.community.hermite.interface import Hermite
from matplotlib import pyplot
def hydro_grid_in_potential_well(mass=... | 3,310 | 32.444444 | 77 | py |
amuse | amuse-main/examples/simple/grav_stellar_simple.py | # -*- coding: ascii -*-
"""
simple coupling of a stellar evolution and a gravitational code to simulate
a cluster of stars.
"""
from __future__ import print_function
import os
from amuse.units.optparse import OptionParser
from amuse.units import units, nbody_system
from amuse.datamodel.particles import Channel... | 3,683 | 27.338462 | 79 | py |
amuse | amuse-main/examples/simple/orszag_tang.py | # -*- coding: ascii -*-
"""
Runs the Orszag-Tang Vortex problem described in the Athena test-suite
(http://www.astro.virginia.edu/VITA/ATHENA/ot.html):
'The Orszag-Tang Vortex is a well-known test for MHD codes. The intial
conditions lead to a system of supersonic MHD turbulence, making this problem a
good test of the... | 6,607 | 29.036364 | 79 | py |
amuse | amuse-main/examples/simple/galactic_center_in_code.py | # -*- coding: ascii -*-
"""
Evolves a cluster orbiting a massive central particle.
"""
from __future__ import print_function
# import numpy
from amuse.units import units
from amuse.units import constants
from amuse.units import nbody_system
from amuse.datamodel import particles
from amuse.community.phigrape.interface ... | 3,000 | 26.53211 | 76 | py |
amuse | amuse-main/examples/simple/sunandearth.py | # -*- coding: ascii -*-
"""
Evolves the dynamic evolution of the earth around the sun.
"""
from __future__ import print_function
from amuse.units import nbody_system
from amuse.units import units
from amuse.units import quantities
from amuse.community.hermite.interface import Hermite
from matplotlib import pyplot
fr... | 2,057 | 22.655172 | 60 | py |
amuse | amuse-main/examples/textbook/plot_hydro_disk_with_bump.py | """
Visualization for simple N-body integration.
Reads particle set from file (nbody.hdf5) and prints subsequent frames.
"""
import os
import sys
import numpy
import matplotlib
#matplotlib.use('Agg')
from matplotlib import pyplot
#from matplotlib import pyplot
from amuse.plot import scatter, xlabel, ylabel
from ... | 6,970 | 33.681592 | 126 | py |
amuse | amuse-main/examples/textbook/NonConservativeMassTransfer.py | #!/usr/bin/python
from numpy import *
from amuse.lab import *
#a XiTau = 263.973|units.RSun = 1.2272459225 AU
#HD a= 171.109773416 RSun = quantity<0.795511639712 AU>
def orbital_separation_after_mass_transfer(a, md, mdf, ma, maf, nj) :
mt = ma+md
mtf = maf+mdf
fa = ((mdf*maf)/(md*ma))**(-2.) * (mtf/mt)**... | 1,955 | 36.615385 | 74 | py |
amuse | amuse-main/examples/textbook/plot_supernova_IIp_and_disk_temperature.py | import numpy
from matplotlib import pyplot
from amuse.lab import *
from prepare_figure import single_frame, figure_frame, set_tickmarks
from distinct_colours import get_distinct
from supernova_IIp_Lightcurve import Supernova_IIp
def read_supernova_irradiation_file(filename):
t = []
Tmean = []
Tmax = []
... | 3,335 | 32.029703 | 100 | py |
amuse | amuse-main/examples/textbook/multiple_stellar_code.py | from amuse.lab import *
###BOOKLISTSTART###
def evolve_with_different_stellar_model():
times = [10, 100, 1000] | units.Myr
stars = Particles(mass=[1, 2, 4]|units.MSun)
stellars = [SeBa(), MESA(), SSE()]
channels = []
for star, stellar in zip(stars, stellars):
stellar.particles.add_particle(... | 1,350 | 31.95122 | 66 | py |
amuse | amuse-main/examples/textbook/merge_two_stars_sph_evolve.py | import numpy
from matplotlib import pyplot
from amuse.lab import *
from amuse.ext.star_to_sph import convert_stellar_model_to_SPH
from amuse.ext.sph_to_star import convert_SPH_to_stellar_model
from prepare_figure import single_frame
from distinct_colours import get_distinct
def plot_clumps(groups):
number_of_par... | 11,648 | 37.319079 | 79 | py |
amuse | amuse-main/examples/textbook/basic_multiples_nbody.py | import numpy
from amuse.units import nbody_system
from amuse.ic.plummer import new_plummer_model
from amuse.community.ph4.interface import ph4
from amuse.community.smalln.interface import SmallN
from amuse.community.kepler.interface import Kepler
from amuse.couple import multiples
# Awkward syntax here because multipl... | 3,322 | 27.895652 | 72 | py |
amuse | amuse-main/examples/textbook/gravity_gravity.py | #from __future__ import print_function
import numpy
from amuse.units import units
from amuse.units import quantities
from amuse.units import constants
from amuse.units import nbody_system
from amuse.ext.bridge import bridge
from amuse.community.phigrape.interface import PhiGRAPE
from amuse.community.ph4.interface impor... | 4,555 | 34.874016 | 106 | py |
amuse | amuse-main/examples/textbook/hydro_give_or_take.py | import numpy
from amuse.lab import *
from amuse import datamodel
from amuse.ext.evrard_test import uniform_unit_sphere
def hydro_sink_particles(sinks, gas):
removed_particles = Particles()
for s in sinks:
xs,ys,zs=s.x,s.y,s.z
radius_squared = s.sink_radius**2
#print "R=", s.key, numpy.s... | 6,603 | 37.847059 | 109 | py |
amuse | amuse-main/examples/textbook/merge_two_galaxies.py | import numpy
from matplotlib import pyplot
from amuse.lab import *
from amuse.ext.galactics_model import new_galactics_model
from prepare_figure import single_frame
def make_plot(disk1, disk2, filename):
x_label = "X [kpc]"
y_label = "Y [kpc]"
figure = single_frame(x_label, y_label, logy=False, xsize=14, y... | 3,708 | 41.632184 | 78 | py |
amuse | amuse-main/examples/textbook/helium_star.py | """
Creates a helium burning star from the inner shells of a main sequence star.
"""
from __future__ import print_function
from amuse.units import units
from amuse.datamodel import Particle
from amuse.community.mesa.interface import MESA
from matplotlib import pyplot
from amuse.plot import loglog, xlabel, ylabel, scat... | 4,261 | 38.831776 | 92 | py |
amuse | amuse-main/examples/textbook/hydro_sink_particles.py | from amuse.lab import *
def hydro_sink_particles(sinks, gas):
removed_particles = Particles()
for s in sinks:
xs,ys,zs=s.x,s.y,s.z
radius_squared = s.radius**2
insink=gas.select_array(lambda x,y,z: (x-xs)**2+(y-ys)**2+(z-zs)**2 < radius_squared,['x','y','z'])
if len(insink)==0... | 2,115 | 37.472727 | 109 | py |
amuse | amuse-main/examples/textbook/stellar_isochrone.py | """
Evolve a population of N stars.
Initial mass function between Mmin and Mmax with stellar evolution
for metallicity z.
"""
import sys
import numpy
from amuse.lab import *
from matplotlib import pyplot
from prepare_figure import single_frame, figure_frame, set_tickmarks
from distinct_colours import get_dist... | 5,316 | 35.170068 | 79 | py |
amuse | amuse-main/examples/textbook/plot_hydro_density_distributions.py | import numpy
from matplotlib import pyplot
from amuse.lab import *
from amuse.plot import sph_particles_plot
from prepare_figure import figure_frame
from distinct_colours import get_distinct
###BOOKLISTSTART1###
def stellar_model(N, M, t=0.0|units.Myr):
star = Particle(mass=M)
stellar_evolution = EVtwin()
... | 2,543 | 31.202532 | 78 | py |
amuse | amuse-main/examples/textbook/three_body_bridge_order4m4.py | import numpy
from amuse.lab import *
from amuse.ext.composition_methods import *
from amuse.couple import bridge
from amuse.ext.solarsystem import new_solar_system
def new_system_of_sun_and_earth():
stars = Particles(3)
sun = stars[0]
sun.mass = units.MSun(1.0)
sun.position = units.m(numpy.array((0.0... | 3,114 | 32.858696 | 103 | py |
amuse | amuse-main/examples/textbook/plot_solar_cluster.py | """
Visualization for simple N-body integration.
Reads particle set from file (nbody.hdf5) and prints subsequent frames.
"""
import sys
import numpy
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot
#from matplotlib import pyplot
from amuse.plot import scatter, xlabel, ylabel
from amuse.lab i... | 3,853 | 32.807018 | 111 | py |
amuse | amuse-main/examples/textbook/planetary_system.py | import math
import numpy
from amuse.lab import *
from amuse.ext.protodisk import ProtoPlanetaryDisk
from optparse import OptionParser
from amuse.couple import bridge
import make_planets_oligarch
from amuse.ext.orbital_elements import orbital_elements_from_binary
def calculate_orbital_elements(star, planet):
p = P... | 6,786 | 37.129213 | 100 | py |
amuse | amuse-main/examples/textbook/gravity_stellar_eventdriven.py | import numpy
from amuse.lab import *
from amuse.io import store
from amuse.community.seba.interface import SeBa
def merge_two_stars(bodies, particles_in_encounter):
com_pos = particles_in_encounter.center_of_mass()
com_vel = particles_in_encounter.center_of_mass_velocity()
new_particle=Particles(1)
new... | 7,592 | 41.183333 | 88 | py |
amuse | amuse-main/examples/textbook/plot_sstar_orbits.py | import os.path
import math
import numpy
from amuse.lab import *
from amuse.ext.protodisk import ProtoPlanetaryDisk
from amuse.ext.evrard_test import uniform_unit_sphere
import time
from initialize_sstars import *
from amuse.community.adaptb.interface import Adaptb
from gravity_class import Gravity
#from prepare_figur... | 3,020 | 32.566667 | 126 | py |
amuse | amuse-main/examples/textbook/merge_two_stars_sph_convergence.py | import sys
import numpy
from matplotlib import pyplot
from amuse.lab import *
from amuse.plot import plot
from amuse.ext.sph_to_star import convert_SPH_to_stellar_model
from prepare_figure import *
from distinct_colours import get_distinct
def return_evolved_star_hydro(mass, time, Nsph):
star = Particle(mass=mas... | 5,347 | 40.78125 | 109 | py |
amuse | amuse-main/examples/textbook/basic_multiples_si.py | import numpy
from amuse.units import nbody_system, units, constants
from amuse.ic.plummer import new_plummer_model
from amuse.community.ph4.interface import ph4
from amuse.community.smalln.interface import SmallN
from amuse.community.kepler.interface import Kepler
from amuse.couple import multiples
# Awkward syntax he... | 3,848 | 30.54918 | 72 | py |
amuse | amuse-main/examples/textbook/plot_accretion_from_windy_star.py | """
Visualization for simple N-body integration.
Reads particle set from file (nbody.hdf5) and prints subsequent frames.
"""
import sys
import numpy
from matplotlib import pyplot
from amuse.lab import *
from prepare_figure import single_frame
from distinct_colours import get_distinct
def Bondi_Hoyle_Littleton_a... | 3,325 | 28.433628 | 163 | py |
amuse | amuse-main/examples/textbook/gravity_stellar_collision.py | """
N-body integration of N particles with a Salpeter initial mass
function between Mmin and Mmax and with stellar evolution with
metallicity z.
"""
from amuse.lab import *
from amuse.io import store
from amuse.community.seba.interface import SeBa
###BOOKLISTSTART1###
def merge_two_stars(bodies, particles_in_... | 7,077 | 37.89011 | 93 | py |
amuse | amuse-main/examples/textbook/plot_M67Data.py | #!/usr/bin/python
from __future__ import division
from matplotlib import pyplot
import os
def logLuminosity(V):
VminMv = 9.7
MBolSun = 4.74
Mv = V - VminMv
L = (MBolSun - Mv)/2.5
return L
def logTeff(BminV):
logT = (14.551 - BminV)/3.684
if logT > 3.961:
a,b,c = [.344,-3.402,8.037... | 1,589 | 22.043478 | 64 | py |
amuse | amuse-main/examples/textbook/orbital_elements_to_cartesian.py | from amuse.lab import *
from math import pi, sin, cos, sqrt, atan2
import numpy
#Solve Kepler equation by iterating: M = E - e sin E
#Lit.: Sterne, T.E., 1960, An introduction to Celestial Mechanics, p. 13-14
def eccentric_anomaly(mean_anomaly, e) :
ecc_anomaly = mean_anomaly + 2*pi*(e * sin(mean_anomaly) + 0.5*e*... | 3,103 | 37.8 | 115 | py |
amuse | amuse-main/examples/textbook/molecular_cloud_collapse_with_sinks.py | import numpy
from matplotlib import pyplot
from amuse.lab import *
from amuse.ext.molecular_cloud import molecular_cloud
from amuse.ext.evrard_test import body_centered_grid_unit_cube
from cooling_class import SimplifiedThermalModel, SimplifiedThermalModelEvolver
from hydrodynamics_class import Hydro
def run_molecu... | 3,457 | 35.020833 | 79 | py |
amuse | amuse-main/examples/textbook/three_body_bridge.py | import numpy
from amuse.lab import *
from amuse.couple import bridge
def new_system_of_sun_and_earth():
stars = Particles(3)
sun = stars[0]
sun.mass = units.MSun(1.0)
sun.position = units.m(numpy.array((0.0,0.0,0.0)))
sun.velocity = units.ms(numpy.array((0.0,0.0,0.0)))
sun.radius = units.RSun(... | 2,739 | 30.860465 | 82 | py |
amuse | amuse-main/examples/textbook/hydro_wind_disk_interaction.py | from amuse.lab import *
from amuse.community.gadget2.interface import Gadget2 as Gadget2
from amuse.units import units, constants, nbody_system
from amuse.ext.sink import new_sink_particles
from amuse.ext.protodisk import ProtoPlanetaryDisk
from amuse.datamodel import Particles
import numpy
import time as timing
class... | 12,985 | 40.225397 | 175 | py |
amuse | amuse-main/examples/textbook/plot_projected_density_distributions_all.py | import numpy
from matplotlib import pyplot
from amuse.lab import *
from amuse.ext.molecular_cloud import molecular_cloud
from amuse.plot import sph_particles_plot, native_plot
from prepare_figure import figure_frame
from distinct_colours import get_distinct
def create_molecular_cloud(N, Mcloud, Rcloud, t_end):
... | 5,060 | 34.145833 | 119 | py |
amuse | amuse-main/examples/textbook/hydro_disk_with_bump.py | """
Simulate the radiative and hydrodynamial evolution of a disk with
a bump around a single star
"""
from time import time, localtime
from amuse.lab import *
from amuse.ext.molecular_cloud import ism_cube
from amuse.community.simplex.interface import SimpleXInterface, SimpleX, \
SimpleXSplitSet
from amuse.... | 10,086 | 38.402344 | 80 | py |
amuse | amuse-main/examples/textbook/plot_core_temperature_density.py | import math
from amuse.lab import *
from matplotlib import pyplot
from distinct_colours import get_distinct
Second_Asymptotic_Giant_Branch = 6 | units.stellar_type
HeWhiteDwarf = 10 | units.stellar_type
def stellar_remnant(stellar):
remnant = True
if stellar.particles[0].stellar_type < HeWhiteDwarf \
... | 2,649 | 26.894737 | 77 | py |
amuse | amuse-main/examples/textbook/gravity_stellar_minimal.py | from amuse.lab import *
from amuse.units.optparse import OptionParser
def main(N, t_end, W0, Rvir, Mmin, Mmax, z):
###BOOKLISTSTART1###
masses = new_salpeter_mass_distribution(N, Mmin, Mmax)
Mtot_init = masses.sum()
converter = nbody_system.nbody_to_si(Mtot_init, Rvir)
bodies = new_king_model(N, W... | 3,607 | 35.444444 | 78 | py |
amuse | amuse-main/examples/textbook/supernova_grid.py | import numpy
from amuse.lab import *
#from amuse import plot
from amuse.ext import cloud
from matplotlib import pyplot
from amuse import datamodel
from amuse.ext.sph_to_grid import convert_SPH_to_grid
from amuse.community.capreole.interface import Capreole
from amuse.units.generic_unit_converter import ConvertBetweenGe... | 7,421 | 37.65625 | 110 | py |
amuse | amuse-main/examples/textbook/plot_RLOF_triples.py | from matplotlib import pyplot
from amuse.lab import *
from prepare_figure import *
from distinct_colours import get_distinct
import numpy
set_printing_strategy("custom", #nbody_converter = converter,
preferred_units = [units.MSun, units.AU, units.Myr],
precision = 4, prefi... | 2,082 | 32.596774 | 75 | py |
amuse | amuse-main/examples/textbook/earthorbitvariation.py | from amuse.lab import *
from amuse.ext.solarsystem import solar_system_in_time
from prepare_figure import single_frame, figure_frame, \
set_tickmarks, get_distinct
def integrate_solar_system(particles, end_time):
convert_nbody = nbody_system.nbody_to_si(particles.mass.sum(),
... | 2,857 | 31.850575 | 80 | py |
amuse | amuse-main/examples/textbook/plot_stellar_massloss_response.py | """
Visualization for simple N-body integration.
Reads particle set from file (nbody.hdf5) and prints subsequent frames.
"""
import sys
import numpy
from matplotlib import pyplot
from prepare_figure import single_frame, figure_frame, set_tickmarks
from distinct_colours import get_distinct
#filenames = ["Zeta_M1... | 2,143 | 27.972973 | 87 | py |
amuse | amuse-main/examples/textbook/core_temperature_density.py | from amuse.lab import *
Second_Asymptotic_Giant_Branch = 6 | units.stellar_type
HeWhiteDwarf = 10 | units.stellar_type
def stellar_remnant(stellar):
remnant = True
if stellar.particles[0].stellar_type<HeWhiteDwarf or stellar.particles[0].stellar_type>11|units.stellar_type:
remnant = False
retu... | 1,554 | 36.02381 | 113 | py |
amuse | amuse-main/examples/textbook/plot_M67withBSS_tracks.py | """
Minimal routine for running a stellar evolution code.
"""
from amuse.lab import *
from matplotlib import pyplot
import plot_M67Data
from prepare_figure import single_frame, figure_frame, set_tickmarks
from distinct_colours import get_distinct
TBSS = [6170, 6820, 6675, 7050, 6650]
LBSS = [12.259, 11.078, 12.1... | 2,775 | 32.853659 | 72 | py |
amuse | amuse-main/examples/textbook/sun_venus_earth.py | ###BOOKLISTSTART1###
from amuse.lab import Particles, units
def sun_venus_and_earth():
particles = Particles(3)
sun = particles[0]
sun.mass = 1.0 | units.MSun
sun.radius = 1.0 | units.RSun
sun.position = (855251, -804836, -3186) |units.km
sun.velocity = (7.893, 11.894, 0.20642) | (units.m/unit... | 3,063 | 30.587629 | 76 | py |
amuse | amuse-main/examples/textbook/plot_Nbody_precision.py | from amuse.lab import *
import numpy
from distinct_colours import get_distinct
from matplotlib import pyplot
def energy_error_of_integrated_Nbody_system(code, particles,
end_time, precision):
gravity = code(number_of_workers=4)
gravity.parameters.timestep_parameter... | 2,236 | 28.434211 | 75 | py |
amuse | amuse-main/examples/textbook/gravity_class.py | import os.path
import math
import numpy
from amuse.lab import *
from amuse.ext.protodisk import ProtoPlanetaryDisk
from amuse.ext.evrard_test import uniform_unit_sphere
import time
from initialize_sstars import *
from calculate_orbital_parameters import calculate_orbital_parameters
from amuse.community.mercury.interf... | 3,827 | 37.666667 | 151 | py |
amuse | amuse-main/examples/textbook/prepare_figure.py | from matplotlib import pyplot
#import seaborn
# These are the "Tableau 20" colors as RGB.
tableau20 = [(31, 119, 180), (174, 199, 232), (255, 127, 14), (255, 187, 120),
(44, 160, 44), (152, 223, 138), (214, 39, 40), (255, 152, 150),
(148, 103, 189), (197, 176, 213), (140, 86, 75), (196,... | 6,734 | 29.613636 | 80 | py |
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