cwpearson/astaroth
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General purpose Python tool improvements.

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This commit is contained in:
Miikka Vaisala
2020-01-14 14:23:24 +08:00
parent 185b33980f
commit d947bdccb8
3 changed files with 162 additions and 36 deletions
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115
analysis/python/astar/data/read.py
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@@ -21,6 +21,12 @@
import numpy as np
#Optional YT interface
try:
import yt
yt_present = True
except ImportError:
yt_present = False
def set_dtype(endian, AcRealSize):
if endian == 0:
@@ -55,7 +61,8 @@ def read_bin(fname, fdir, fnum, minfo, numtype=np.longdouble):
return array, timestamp, read_ok
def read_meshtxt(fdir, fname):
def read_meshtxt(fdir, fname, dbg_output):
with open(fdir+fname) as f:
filetext = f.read().splitlines()
@@ -65,30 +72,33 @@ def read_meshtxt(fdir, fname):
line = line.split()
if line[0] == 'int':
contents[line[1]] = np.int(line[2])
print(line[1], contents[line[1]])
if dbg_output:
print(line[1], contents[line[1]])
elif line[0] == 'size_t':
contents[line[1]] = np.int(line[2])
print(line[1], contents[line[1]])
if dbg_output:
print(line[1], contents[line[1]])
elif line[0] == 'int3':
contents[line[1]] = [np.int(line[2]), np.int(line[3]), np.int(line[4])]
print(line[1], contents[line[1]])
if dbg_output:
print(line[1], contents[line[1]])
elif line[0] == 'real':
contents[line[1]] = np.float(line[2])
print(line[1], contents[line[1]])
if dbg_output:
print(line[1], contents[line[1]])
elif line[0] == 'real3':
contents[line[1]] = [np.float(line[2]), np.float(line[3]), np.float(line[4])]
print(line[1], contents[line[1]])
if dbg_output:
print(line[1], contents[line[1]])
else:
print(line)
print('ERROR: ' + line[0] +' not recognized!')
return contents
#Now just 2nd order
def DERX(array, dx):
output = np.zeros_like(array)
for i in range(3, array.shape[0]-3): #Keep boundary poits as 0
#output[i,:,:] = (- array[i-1,:,:] + array[i+1,:,:])/(2.0*dx)
output[i,:,:] =( -45.0*array[i-1,:,:] + 45.0*array[i+1,:,:]
+ 9.0*array[i-2,:,:] - 9.0*array[i+2,:,:]
- array[i-3,:,:] + array[i+3,:,:] )/(60.0*dx)
@@ -97,7 +107,6 @@ def DERX(array, dx):
def DERY(array, dy):
output = np.zeros_like(array)
for i in range(3,array.shape[1]-3):
#output[:,i,:] = (- array[:,i-1,:] + array[:,i+1,:])/(2.0*dy)
output[:,i,:] =( -45.0*array[:,i-1,:] + 45.0*array[:,i+1,:]
+ 9.0*array[:,i-2,:] - 9.0*array[:,i+2,:]
- array[:,i-3,:] + array[:,i+3,:] )/(60.0*dy)
@@ -106,7 +115,6 @@ def DERY(array, dy):
def DERZ(array, dz):
output = np.zeros_like(array)
for i in range(3, array.shape[2]-3):
#output[:,:,i] = (- array[:,:,i-1] + array[:,:,i+1])/(2.0*dz)
output[:,:,i] =( -45.0*array[:,:,i-1] + 45.0*array[:,:,i+1]
+ 9.0*array[:,:,i-2] - 9.0*array[:,:,i+2]
- array[:,:,i-3] + array[:,:,i+3] )/(60.0*dz)
@@ -124,8 +132,8 @@ def curl(aa, minfo):
class MeshInfo():
'''Object that contains all mesh info'''
def __init__(self, fdir):
self.contents = read_meshtxt(fdir, 'mesh_info.list')
def __init__(self, fdir, dbg_output=False):
self.contents = read_meshtxt(fdir, 'mesh_info.list', dbg_output)
class Mesh:
'''Class tha contains all 3d mesh data'''
@@ -176,9 +184,88 @@ class Mesh:
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 Bfield(self):
def Bfield(self, get_jj = False):
self.bb = curl(self.aa, self.minfo)
print(self.bb[2])
if get_jj:
self.jj = curl(self.bb, self.minfo)
def yt_conversion(self):
if yt_present:
self.ytdict = dict(density = (np.exp(self.lnrho)*self.minfo.contents['AC_unit_density'], "g/cm**3"),
uux = (self.uu[0]*self.minfo.contents['AC_unit_velocity'], "cm/s"),
uuy = (self.uu[1]*self.minfo.contents['AC_unit_velocity'], "cm/s"),
uuz = (self.uu[2]*self.minfo.contents['AC_unit_velocity'], "cm/s"),
bbx = (self.bb[0]*self.minfo.contents['AC_unit_magnetic'], "gauss"),
bby = (self.bb[1]*self.minfo.contents['AC_unit_magnetic'], "gauss"),
bbz = (self.bb[2]*self.minfo.contents['AC_unit_magnetic'], "gauss"),
)
bbox = self.minfo.contents['AC_unit_length'] \
*np.array([[self.xx.min(), self.xx.max()], [self.yy.min(), self.yy.max()], [self.zz.min(), self.zz.max()]])
self.ytdata = yt.load_uniform_grid(self.ytdict, self.lnrho.shape, length_unit="cm", bbox=bbox)
else:
print("ERROR. No YT support found!")
def export_csv(self):
csvfile = open("grid.csv.%s" % self.framenum, "w")
csvfile.write("xx, yy, zz, rho, uux, uuy, uuz, bbx, bby, bbz\n")
ul = self.minfo.contents['AC_unit_length']
uv = self.minfo.contents['AC_unit_velocity']
ud = self.minfo.contents['AC_unit_density']
um = self.minfo.contents['AC_unit_magnetic']
for kk in np.arange(3, self.zz.size-3):
for jj in np.arange(3, self.yy.size-3):
for ii in np.arange(3, self.xx.size-3):
#print(self.xx.size, self.yy.size, self.zz.size)
linestring = "%e, %e, %e, %e, %e, %e, %e, %e, %e, %e\n"% (self.xx[ii]*ul, self.yy[jj]*ul, self.zz[kk]*ul,
np.exp(self.lnrho[ii, jj, kk])*ud,
self.uu[0][ii, jj, kk]*uv, self.uu[1][ii, jj, kk]*uv,
self.uu[2][ii, jj, kk]*uv,
self.bb[0][ii, jj, kk]*um, self.bb[1][ii, jj, kk]*um,
self.bb[2][ii, jj, kk]*um)
csvfile.write(linestring)
csvfile.close()
def export_raw(self):
uv = self.minfo.contents['AC_unit_velocity']
ud = self.minfo.contents['AC_unit_density']
um = self.minfo.contents['AC_unit_magnetic']
print(self.lnrho.shape, set_dtype(self.minfo.contents['endian'], self.minfo.contents['AcRealSize']))
f = open("rho%s.raw" % self.framenum, 'w+b')
binary_format =(np.exp(self.lnrho)*ud).tobytes()
f.write(binary_format)
f.close()
f = open("uux%s.raw" % self.framenum, 'w+b')
binary_format =(self.uu[0]*uv).tobytes()
f.write(binary_format)
f.close()
f = open("uuy%s.raw" % self.framenum, 'w+b')
binary_format =(self.uu[1]*uv).tobytes()
f.write(binary_format)
f.close()
f = open("uuz%s.raw" % self.framenum, 'w+b')
binary_format =(self.uu[2]*uv).tobytes()
f.write(binary_format)
f.close()
f = open("bbx%s.raw" % self.framenum, 'w+b')
binary_format =(self.bb[0]*um).tobytes()
f.write(binary_format)
f.close()
f = open("bby%s.raw" % self.framenum, 'w+b')
binary_format =(self.bb[1]*um).tobytes()
f.write(binary_format)
f.close()
f = open("bbz%s.raw" % self.framenum, 'w+b')
binary_format =(self.bb[2]*um).tobytes()
f.write(binary_format)
f.close()
def parse_ts(fdir, fname):