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Added Astaroth 2.0

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jpekkila
2019-06-14 14:18:35 +03:00
parent 4e4f84c8ff
commit 0e48766a68
87 changed files with 18058 additions and 1 deletions
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analysis/python/astar/__init__.py Normal file
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'''
Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
This file is part of Astaroth.
Astaroth is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Astaroth is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Astaroth. If not, see <http://www.gnu.org/licenses/>.
'''
# Developers note. We require Python 3 approach to have
# compatibility towards the future.
import numpy as np
import pylab as plt

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analysis/python/astar/data/__init__.py Normal file
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'''
Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
This file is part of Astaroth.
Astaroth is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Astaroth is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Astaroth. If not, see <http://www.gnu.org/licenses/>.
'''
from . import read

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analysis/python/astar/data/read.py Normal file
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'''
Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
This file is part of Astaroth.
Astaroth is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Astaroth is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Astaroth. If not, see <http://www.gnu.org/licenses/>.
'''
# This module is for reading data.
import numpy as np
def read_bin(fname, fdir, fnum, minfo, numtype=np.longdouble):
'''Read in a floating point array'''
filename = fdir + fname + '_' + fnum + '.mesh'
datas = np.DataSource()
read_ok = datas.exists(filename)
if read_ok:
print(filename)
array = np.fromfile(filename, dtype=numtype)
timestamp = array[0]
array = np.reshape(array[1:], (minfo.contents['AC_mx'],
minfo.contents['AC_my'],
minfo.contents['AC_mz']), order='F')
else:
array = None
timestamp = None
return array, timestamp, read_ok
def read_meshtxt(fdir, fname):
with open(fdir+fname) as f:
filetext = f.read().splitlines()
contents = {}
for line in filetext:
line = line.split()
if line[0] == 'int':
contents[line[1]] = np.int(line[2])
elif line[0] == 'real':
contents[line[1]] = np.float(line[2])
else:
print('ERROR: ' + line[0] +' no recognized!')
return contents
class MeshInfo():
'''Object that contains all mesh info'''
def __init__(self, fdir):
self.contents = read_meshtxt(fdir, 'mesh_info.list')
class Mesh:
'''Class tha contains all 3d mesh data'''
def __init__(self, fnum, fdir=""):
fnum = str(fnum)
self.framenum = fnum.zfill(10)
self.minfo = MeshInfo(fdir)
self.lnrho, self.timestamp, self.ok = read_bin('VTXBUF_LNRHO', fdir, fnum, self.minfo)
if self.ok:
self.ss, timestamp, ok = read_bin('VTXBUF_ENTROPY', fdir, fnum, self.minfo)
#TODO Generalize is a dict. Do not hardcode!
uux, timestamp, ok = read_bin('VTXBUF_UUX', fdir, fnum, self.minfo)
uuy, timestamp, ok = read_bin('VTXBUF_UUY', fdir, fnum, self.minfo)
uuz, timestamp, ok = read_bin('VTXBUF_UUZ', fdir, fnum, self.minfo)
self.uu = (uux, uuy, uuz)
uux = []
uuy = []
uuz = []
aax, timestamp, ok = read_bin('VTXBUF_AX', fdir, fnum, self.minfo)
aay, timestamp, ok = read_bin('VTXBUF_AY', fdir, fnum, self.minfo)
aaz, timestamp, ok = read_bin('VTXBUF_AZ', fdir, fnum, self.minfo)
self.aa = (aax, aay, aaz)
aax = []
aay = []
aaz = []
self.xx = self.minfo.contents['AC_inv_dsx']*np.arange(self.minfo.contents['AC_mx'])
self.yy = self.minfo.contents['AC_inv_dsy']*np.arange(self.minfo.contents['AC_my'])
self.zz = self.minfo.contents['AC_inv_dsz']*np.arange(self.minfo.contents['AC_mz'])
self.xmid = int(self.minfo.contents['AC_mx']/2)
self.ymid = int(self.minfo.contents['AC_my']/2)
self.zmid = int(self.minfo.contents['AC_mz']/2)
def parse_ts(fdir, fname):
with open(fdir+fname) as f:
filetext = f.read().splitlines()
var = {}
line = filetext[0].split()
for i in range(len(line)):
line[i] = line[i].replace('VTXBUF_', "")
line[i] = line[i].replace('UU', "uu")
line[i] = line[i].replace('_total', "tot")
line[i] = line[i].replace('A', "aa")
line[i] = line[i].replace('LNRHO', "lnrho")
line[i] = line[i].replace('X', "x")
line[i] = line[i].replace('Y', "y")
line[i] = line[i].replace('Z', "z")
tsdata = np.loadtxt(fdir+fname,skiprows=1)
for i in range(len(line)):
var[line[i]] = tsdata[:,i]
var['step'] = np.int64(var['step'])
print("HERE ARE ALL KEYS FOR TS DATA:")
print(var.keys())
return var
class TimeSeries:
'''Class for time series data'''
def __init__(self, fdir="", fname="timeseries.ts"):
self.var = parse_ts(fdir, fname)

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analysis/python/astar/visual/__init__.py Normal file
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'''
Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
This file is part of Astaroth.
Astaroth is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Astaroth is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Astaroth. If not, see <http://www.gnu.org/licenses/>.
'''
from . import slices

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analysis/python/astar/visual/slices.py Normal file
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'''
Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
This file is part of Astaroth.
Astaroth is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Astaroth is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Astaroth. If not, see <http://www.gnu.org/licenses/>.
'''
import pylab as plt
import numpy as np
import matplotlib.gridspec as gridspec
import matplotlib.colors as colors
CM_INFERNO = plt.get_cmap('inferno')
def plot_3(mesh, input_grid, title = '', fname = 'default', bitmap=False, slicetype = 'middle', colrange=None, colormap=CM_INFERNO , contourplot=False):
fig = plt.figure(figsize=(8, 8))
grid = gridspec.GridSpec(2, 3, wspace=0.4, hspace=0.4, width_ratios=[1,1, 0.15])
ax00 = fig.add_subplot( grid[0,0] )
ax10 = fig.add_subplot( grid[0,1] )
ax11 = fig.add_subplot( grid[1,1] )
axcbar = fig.add_subplot( grid[:,2] )
print(mesh.minfo.contents.keys())
if slicetype == 'middle':
yz_slice = input_grid[mesh.xmid, :, :]
xz_slice = input_grid[:, mesh.ymid, :]
xy_slice = input_grid[:, :, mesh.zmid]
if colrange==None:
plotnorm = colors.Normalize(vmin=input_grid.min(),vmax=input_grid.max())
else:
plotnorm = colors.Normalize(vmin=colrange[0],vmax=colrange[1])
elif slicetype == 'sum':
yz_slice = np.sum(input_grid, axis=0)
xz_slice = np.sum(input_grid, axis=1)
xy_slice = np.sum(input_grid, axis=2)
cmin = np.amin([yz_slice.min(), xz_slice.min(), xy_slice.min()])
cmax = np.amax([yz_slice.max(), xz_slice.max(), xy_slice.max()])
if colrange==None:
plotnorm = colors.Normalize(vmin=cmin,vmax=cmax)
else:
plotnorm = colors.Normalize(vmin=colrange[0],vmax=colrange[1])
yy, zz = np.meshgrid(mesh.yy, mesh.zz, indexing='ij')
if contourplot:
map1 = ax00.contourf(yy, zz, yz_slice, norm=plotnorm, cmap=colormap, nlev=10)
else:
map1 = ax00.pcolormesh(yy, zz, yz_slice, norm=plotnorm, cmap=colormap)
ax00.set_xlabel('y')
ax00.set_ylabel('z')
ax00.set_title('%s t = %.4e' % (title, mesh.timestamp) )
ax00.set_aspect('equal')
xx, zz = np.meshgrid(mesh.xx, mesh.zz, indexing='ij')
if contourplot:
ax10.contourf(xx, zz, xz_slice, norm=plotnorm, cmap=colormap, nlev=10)
else:
ax10.pcolormesh(xx, zz, xz_slice, norm=plotnorm, cmap=colormap)
ax10.set_xlabel('x')
ax10.set_ylabel('z')
ax10.set_aspect('equal')
xx, yy = np.meshgrid(mesh.xx, mesh.yy, indexing='ij')
if contourplot:
ax11.contourf(xx, yy, xy_slice, norm=plotnorm, cmap=colormap, nlev=10)
else:
ax11.pcolormesh(xx, yy, xy_slice, norm=plotnorm, cmap=colormap)
ax11.set_xlabel('x')
ax11.set_ylabel('y')
ax11.set_aspect('equal')
cbar = plt.colorbar(map1, cax=axcbar)
if bitmap:
plt.savefig('%s_%s.png' % (fname, mesh.framenum))
print('Saved %s_%s.png' % (fname, mesh.framenum))
plt.close(fig)