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harm_script.py
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import matplotlib
import matplotlib.pyplot as plt
import matplotlib as mpl
import sys
from matplotlib import rc
from matplotlib.patches import Ellipse
from scipy.interpolate import interp1d
from matplotlib.gridspec import GridSpec
from matplotlib import cm,ticker
from numpy import sin, cos, tan, pi
#matplotlib.use('Agg') #so that it does ok with graphics in batch mode
#choose Computer Modern Roman fonts by default
mpl.rcParams['font.serif'] = 'cmr10'
mpl.rcParams['font.sans-serif'] = 'cmr10'
#font = { 'size' : 20}
#rc('font', **font)
rc('xtick', labelsize=20)
rc('ytick', labelsize=20)
#rc('xlabel', **font)
#rc('ylabel', **font)
# legend = {'fontsize': 20}
# rc('legend',**legend)
axes = {'labelsize': 20}
rc('axes', **axes)
rc('mathtext',fontset='cm')
#use this, but at the expense of slowdown of rendering
#rc('text', usetex=True)
# #add amsmath to the preamble
#matplotlib.rcParams['text.latex.preamble']=[r"\usepackage{amssymb,amsmath}"]
import pdb
import numpy as np
import glob
import os
from scipy.interpolate import griddata
from scipy.interpolate import interp1d
from numpy import ma
import matplotlib.colors as colors
#use_math_text = True
def mathify_axes_ticks(ax,fontsize=20,xticks=None,yticks=None):
if xticks is None:
xticks = ax.get_xticks()
if yticks is None:
yticks = ax.get_yticks()
if ax.get_xscale() != 'log': ax.set_xticklabels([(r'$%g$' % lab) for lab in xticks])
if ax.get_yscale() != 'log': ax.set_yticklabels([(r'$%g$' % lab) for lab in yticks])
if fontsize is not None:
if ax.get_xscale() != 'log':
for label in ax.get_xticklabels():
label.set_fontsize(fontsize)
if ax.get_yscale() != 'log':
for label in ax.get_yticklabels():
label.set_fontsize(fontsize)
def convert_to_single_file(startn=0,endn=-1,ln=10,whichi=0,whichn=1,**kwargs):
which = kwargs.pop("which","convert_file")
rg("gdump")
flist1 = np.sort(glob.glob( os.path.join("dumps/", "dump[0-9][0-9][0-9]_0000") ) )
flist2 = np.sort(glob.glob( os.path.join("dumps/", "dump[0-9][0-9][0-9][0-9]_0000") ) )
flist1.sort()
flist2.sort()
flist = np.concatenate((flist1,flist2))
firsttime = 1
for fldname in flist:
#find the index of the file
fldindex = np.int(fldname.split("_")[0].split("p")[-1])
if fldindex < startn:
continue
if endn>=0 and fldindex >= endn:
break
if fldindex % whichn != whichi:
#do every whichn'th snapshot starting with whichi'th snapshot
continue
#print( "Reading " + fldname + " ..." )
fname = "dump%03d" % fldindex
if os.path.isfile( fname ):
print("File %s exists, skipping..." % fname)
continue
if not os.path.isfile( fname ):
rd(fname)
def ellk(a,r):
ekval = ek(a,r)
lkval = lk(a,r)
return(lkval/ekval)
def ek(a,r):
#-u_t, I suspect
ek = (r**2-2*r+a*r**0.5)/(r*(r**2-3*r+2*a*r**0.5)**0.5)
return(ek)
def lk(a,r):
udphi = r**0.5*(r**2-2*a*r**0.5+a**2)/(r*(r**2-3*r+2*a*r**0.5)**0.5)
return( udphi )
def Risco(ain):
eps = np.finfo(np.float64).eps
a = np.minimum(ain,1.)
Z1 = 1 + (1. - a**2)**(1./3.) * ((1. + a)**(1./3.) + (1. - a)**(1./3.))
Z2 = (3*a**2 + Z1**2)**(1./2.)
risco = 3 + Z2 - np.sign(a)* ( (3 - Z1)*(3 + Z1 + 2*Z2) )**(1./2.)
return(risco)
def Ebind(r,a):
#1+u_t, I suspect
Eb = 1 - (r**2-2*r+a*r**0.5)/(r*(r**2-3*r+2*a*r**0.5)**0.5)
return( Eb )
def etaNT(a):
return( Ebindisco(a) )
def Ebindisco(a):
eps = np.finfo(np.float64).eps
a0 = 0.99999 #1.-1e8*eps
if a > a0:
a = a0
Eb = Ebind( Risco(a), a )
return((a-a0)/(1.-a0)*(1.-3.**(-0.5)) + (1.-a)/(1.-a0)*Eb)
Eb = Ebind( Risco(a), a)
#Eb = (1.-3.**(-0.5))*a**2
return( Eb )
def mkmov_simple(starti=0,endi=400):
for i in xrange(starti,endi+1):
rd("dump%03d" % i);
aphi=psicalc()
if i == starti: amax = aphi.max()
cs, cb = plco(np.log10(rho),levels=np.linspace(-8,0,100),isfilled=1,k=0,xy=1,xmax=10,ymax=5,dobh=1,cb=1,extend="both",pretty=1)
ax = plt.gca()
ax.set_xlabel(r"$R\ [r_g]$",fontsize=20,labelpad=-5)
ax.set_ylabel(r"$z\ [r_g]$",fontsize=20,labelpad=-5)
cb.ax.set_xlabel(r"$\log\rho$",fontsize=20,ha="left")
plc(aphi,levels=np.linspace(-amax,amax,10)[1:-1],colors="white",linewidths=2,xy=-1)
print(i);
plt.title("t=%.4g"%np.round(t));
plt.draw();
plt.savefig("frame%03d.png"%i)
def convert_wrapper(**kwargs):
if len(sys.argv[2:])==2 and sys.argv[2].isdigit() and sys.argv[3].isdigit():
whichi = int(sys.argv[2])
whichn = int(sys.argv[3])
else:
print( "Usage: %s %s <whichi> <whichn>" % (sys.argv[0], sys.argv[1]) )
return
convert_to_single_file(whichi = whichi, whichn = whichn, **kwargs)
def mkmov_wrapper(**kwargs):
if len(sys.argv[2:])==2 and sys.argv[2].isdigit() and sys.argv[3].isdigit():
whichi = int(sys.argv[2])
whichn = int(sys.argv[3])
else:
print( "Usage: %s %s <whichi> <whichn>" % (sys.argv[0], sys.argv[1]) )
return
mkmov(whichi = whichi, whichn = whichn, **kwargs)
def mkmov(startn=0,endn=-1,ln=10,whichi=0,whichn=1,**kwargs):
which = kwargs.pop("which","mkfrm8panel")
dosavefig = kwargs.pop("dosavefig",1)
print("Doing %s movie" % which)
rg("gdump")
#compute the total magnetic flux at t = 0
rd("dump000")
aphi=psicalc()
aphimax = aphi.max()
#construct file list
flist1 = np.sort(glob.glob( os.path.join("dumps/", "dump[0-9][0-9][0-9]") ) )
flist2 = np.sort(glob.glob( os.path.join("dumps/", "dump[0-9][0-9][0-9][0-9]") ) )
flist1.sort()
flist2.sort()
flist = np.concatenate((flist1,flist2))
if len(flist) == 0:
flist1 = np.sort(glob.glob( os.path.join("dumps/", "dump[0-9][0-9][0-9]_0000") ) )
flist2 = np.sort(glob.glob( os.path.join("dumps/", "dump[0-9][0-9][0-9][0-9]_0000") ) )
flist1.sort()
flist2.sort()
flist = np.concatenate((flist1,flist2))
firsttime = 1
dpi = 135
for fldname in flist:
#find the index of the file
fldindex = np.int(fldname.split("_")[0].split("p")[-1])
if fldindex < startn:
continue
if endn>=0 and fldindex >= endn:
break
if fldindex % whichn != whichi:
#do every whichn'th snapshot starting with whichi'th snapshot
continue
if dosavefig:
fname = "%s%04d.png" % (which,fldindex)
if os.path.isfile( fname ):
print("File %s exists, skipping..." % fname)
continue
#print( "Reading " + fldname + " ..." )
rd("dump%03d" % fldindex);
if which == "mkfrmsimple":
if firsttime:
firsttime = 0
fig = plt.figure(figsize=(12,8))
plt.clf()
mkfrmsimple(fig=fig,aphimax = aphimax)
else:
print("Unknown movie type: %s" % which)
return
print(fldindex)
plt.draw()
if dosavefig:
plt.savefig(fname,dpi = dpi)
#############
def mkfrmsimple(fig=None,aphimax=None,lnx=100,lny=100,vmin=-10,vmax=1,fntsize=20,asp=1.):
if fig is None: fig = plt.gcf();
aphi = psicalc() #vpot[3].mean(-1)
if aphimax is None: aphimax = aphi.max()
#ax.set_aspect(asp)
res,cb=plco(lrho,xy=1,xmax=lnx,ymax=lny,symmx=1,
isfilled=1,cb=1,pretty=1,
levels=np.linspace(vmin,vmax,100),
extend="both",cbxla=r"$\ \ \ \ \ \ \ \ \log_{10}\rho$")
plt.xlabel(r"$x\ [r_g]$",fontsize=fntsize)
plt.ylabel(r"$z\ [r_g]$",fontsize=fntsize,labelpad=-30)
ax = plt.gca()
#cmap = cm.jet
#label = r"$\log_{10}\rho$"
#cx1,cb1 = mkvertcolorbar(ax,fig,gap=0.02,width=0.05,vmin=vmin,vmax=vmax,loc="right",
# label=label,ticks=tcks,fntsize=fntsize,cmap=cmap,extend="both")
plc(aphi/aphimax,symmx=1,xy=-1,levels=np.linspace(0.,1.,20)[1:],colors="black",linewidths=1.)
plt.title(r"$t=%g$" % int(t+0.5), fontsize=fntsize)
plt.xlim(-lnx,lnx)
plt.ylim(-lny,lny)
mathify_axes_ticks(ax)
def mkvertcolorbar(ax,fig,vmin=0,vmax=1,label=None,ylabel=None,ticks=None,fntsize=20,cmap=mpl.cm.jet,gap=0.03,width=0.02,extend="neither",loc="right"):
box = ax.get_position()
#pdb.set_trace()
# cpos = [box.x0,box.y0+box.height+0.05,box.width,0.03]
locs = loc.split()
loc0 = locs[0]
if len(locs)>1:
loc1 = locs[1]
else:
loc1 = None
if loc0 == "left":
cpos = box.x0-gap-width,box.y0,width,box.height
elif loc0 == "right":
cpos = box.x0+box.width+gap,box.y0,width,box.height
elif loc0 == "top":
if loc1 == "right":
cpos = box.x0+box.width*0.55,box.y0+box.height+gap,box.width*0.45,width
elif loc1 == "left":
cpos = box.x0+box.width*0.0,box.y0+box.height+gap,box.width*0.45,width
else:
cpos = box.x0,box.y0+box.height+gap,box.width,width
ax1 = fig.add_axes(cpos)
#cmap = mpl.cm.jet
norm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
if loc0 == "left" or loc0 == "right":
ori = "vertical"
else:
ori = "horizontal"
if ticks is not None:
cb1 = mpl.colorbar.ColorbarBase(ax1, cmap=cmap,
norm=norm,
orientation=ori,
ticks=ticks,
extend=extend)
else:
cb1 = mpl.colorbar.ColorbarBase(ax1, cmap=cmap,
norm=norm,
orientation=ori,
extend=extend)
if loc0 == "top" or loc0 == "bottom":
cb1.ax.xaxis.set_ticks_position(loc0)
mathify_axes_ticks(cb1.ax,fontsize=fntsize,xticks=ticks)
elif loc0 == "left" or loc0 == "right":
cb1.ax.yaxis.set_ticks_position(loc0)
mathify_axes_ticks(cb1.ax,fontsize=fntsize,yticks=ticks)
if label is not None:
ax1.set_xlabel(label,fontsize=fntsize)
if ylabel is not None:
ax1.set_ylabel(ylabel,fontsize=fntsize)
for label in ax1.get_xticklabels() + ax1.get_yticklabels():
label.set_fontsize(fntsize)
return ax1,cb1
def Qmri(dir=2):
"""
APPROXIMATELY Computes number of theta cells resolving one MRI wavelength
"""
global bu,rho,uu,_dx2,_dx3
#cvel()
#corrected this expression to include both 2pi and dxdxp[3][3]
#also corrected defition of va^2 to contain bsq+gam*ug term
#need to figure out how to properly measure this in fluid frame
vaudir = np.abs(bu[dir])/np.sqrt(rho+bsq+gam*ug)
omega = dxdxp[3][3]*uu[3]/uu[0]+1e-15
lambdamriudir = 2*np.pi * vaudir / omega
if dir == 2:
res=lambdamriudir/_dx2
elif dir == 3:
res=lambdamriudir/_dx3
return(res)
def goodlabs(fntsize=20):
ax = plt.gca()
for label in ax.get_xticklabels() + ax.get_yticklabels():
label.set_fontsize(fntsize)
def iofr(rval):
rval = np.array(rval)
if np.max(rval) < r[0,0,0]:
return 0
res = interp1d(r[:,0,0], ti[:,0,0], kind='linear', bounds_error = False, fill_value = 0)(rval)
if len(res.shape)>0 and len(res)>0:
res[rval<r[0,0,0]]*=0
res[rval>r[nx-1,0,0]]=res[rval>r[nx-1,0,0]]*0+nx-1
else:
res = np.float64(res)
return(np.floor(res+0.5).astype(int))
#read in a dump file
def rd(dump):
read_file(dump,type="dump")
#read in a grid file
def rg(dump):
read_file(dump,type="gdump")
#read in a grid file
def rg2(dump):
read_file(dump,type="gdump2",noround=True)
#high-level function that reads either MPI or serial gdump's
def read_file(dump,type=None,savedump=True,saverdump=False,noround=False):
if type is None:
if dump.startswith("dump"):
type = "dump"
print("Reading a dump file %s ..." % dump)
elif dump.startswith("gdump2"):
type = "gdump2"
print("Reading a gdump2 file %s ..." % dump)
elif dump.startswith("gdump"):
type = "gdump"
print("Reading a gdump file %s ..." % dump)
elif dump.startswith("rdump"):
type = "rdump"
print("Reading a rdump file %s ..." % dump)
elif dump.startswith("fdump"):
type = "fdump"
print("Reading a fdump file %s ..." % dump)
else:
print("Couldn't guess dump type; assuming it is a data dump")
type = "dump"
#normal dump
if os.path.isfile( "dumps/" + dump ):
headerline = read_header("dumps/" + dump, returnheaderline = True)
gd = read_body("dumps/" + dump,nx=N1+2*N1G,ny=N2+2*N2G,nz=N3+2*N3G,noround=1)
if noround:
res = data_assign( gd,type=type,nx=N1+2*N1G,ny=N2+2*N2G,nz=N3+2*N3G)
else:
res = data_assign(myfloat(gd),type=type,nx=N1+2*N1G,ny=N2+2*N2G,nz=N3+2*N3G)
return res
#MPI-type dump that is spread over many files
else:
flist = np.sort(glob.glob( "dumps/" + dump + "_[0-9][0-9][0-9][0-9]" ))
if len(flist) == 0:
print( "Could not find %s or its MPI counterpart" % dump )
return
sys.stdout.write( "Reading %s (%d files)" % (dump, len(flist)) )
sys.stdout.flush()
ndots = 10
dndot = len(flist)/ndots
if dndot == 0: dndot = 1
for i,fname in enumerate(flist):
#print( "Reading file %d out of %d..." % (i,len(flist)) )
#header for each file might be different, so read each
header = read_header(fname,issilent=1)
if header is None:
print( "Error reading header of %s, aborting..." % fname )
return
lgd = read_body(fname,nx=N1+2*N1G,ny=N2+2*N2G,nz=N3+2*N3G)
#this gives an array of dimensions (-1,N1,N2,N3)+potentially ghost cells
if 0 == i:
#create full array: of dimensions, (-1,nx,ny,nz)
fgd = np.zeros( (lgd.shape[0], nx+2*N1G, ny+2*N2G, nz+2*N3G), dtype=np.float32)
if not type == "rdump":
#construct full indices: ti, tj, tk
#fti,ftj,ftk = mgrid[0:nx,0:ny,0:nz]
lti,ltj,ltk = lgd[0:3,:,:].view();
lti = np.int64(lti)
ltj = np.int64(ltj)
ltk = np.int64(ltk)
fgd[:,lti+N1G,ltj+N2G,ltk+N3G] = lgd[:,:,:,:]
else:
print(starti,startj,startk)
fgd[:,starti:starti+N1+2*N1G,startj:startj+N2+2*N2G,startk:startk+N3+2*N3G] = lgd[:,:,:,:]
del lgd
if i%dndot == 0:
sys.stdout.write(".")
sys.stdout.flush()
res = data_assign(fgd,type=type,nx=nx+2*N1G,ny=ny+2*N2G,nz=nz+2*N3G)
if savedump:
#if the full dump file does not exist, create it
dumpfullname = "dumps/" + dump
if (type == "dump" or type == "gdump") and not os.path.isfile(dumpfullname):
sys.stdout.write("Saving full dump to %s..." % dumpfullname)
sys.stdout.flush()
header[1] = header[4] #N1 = nx
header[2] = header[5] #N2 = ny
header[3] = header[6] #N3 = nz
fout = open( dumpfullname, "wb" )
#join header items with " " (space) as a glue
#see http://stackoverflow.com/questions/12377473/python-write-versus-writelines-and-concatenated-strings
#write it out with a new line char at the end
fout.write(" ".join(header) + "\n")
fout.flush()
os.fsync(fout.fileno())
#reshape the dump content
gd1 = fgd.transpose(1,2,3,0)
gd1.tofile(fout)
fout.close()
print( " done!" )
if res is not None:
return res
return res
#read in a header
def read_header(dump,issilent=True,returnheaderline=False):
global t,nx,ny,nz,N1,N2,N3,N1G,N2G,N3G,starti,startj,startk,_dx1,_dx2,_dx3,a,gam,Rin,Rout,hslope,R0,ti,tj,tk,x1,x2,x3,r,h,ph,gcov,gcon,gdet,drdx,gn3,gv3,guu,gdd,dxdxp, games, startx1, startx2, startx3, tf, NPR, DOKTOT, BL
global fractheta
global fracphi
global rbr
global npow2
global cpow2
#read image
fin = open( dump, "rb" )
headerline = fin.readline()
header = headerline.split()
nheadertot = len(header)
fin.close()
if not dump.startswith("dumps/rdump"):
if not issilent: print( "dump header: len(header) = %d" % len(header) )
nheader = 45
n = 0
t = myfloat(np.float64(header[n])); n+=1
#per tile resolution
N1 = int(header[n]); n+=1
N2 = int(header[n]); n+=1
N3 = int(header[n]); n+=1
#total resolution
nx = int(header[n]); n+=1
ny = int(header[n]); n+=1
nz = int(header[n]); n+=1
#numbers of ghost cells
N1G = int(header[n]); n+=1
N2G = int(header[n]); n+=1
N3G = int(header[n]); n+=1
startx1 = myfloat(float(header[n])); n+=1
startx2 = myfloat(float(header[n])); n+=1
startx3 = myfloat(float(header[n])); n+=1
_dx1=myfloat(float(header[n])); n+=1
_dx2=myfloat(float(header[n])); n+=1
_dx3=myfloat(float(header[n])); n+=1
tf=myfloat(float(header[n])); n+=1
nstep=myfloat(float(header[n])); n+=1
a=myfloat(float(header[n])); n+=1
gam=myfloat(float(header[n])); n+=1
cour=myfloat(float(header[n])); n+=1
DTd=myfloat(float(header[n])); n+=1
DTl=myfloat(float(header[n])); n+=1
DTi=myfloat(float(header[n])); n+=1
DTr=myfloat(float(header[n])); n+=1
DTr01=myfloat(float(header[n])); n+=1
dump_cnt=myfloat(float(header[n])); n+=1
image_cnt=myfloat(float(header[n])); n+=1
rdump_cnt=myfloat(float(header[n])); n+=1
rdump01_cnt=myfloat(float(header[n])); n+=1
dt=myfloat(float(header[n])); n+=1
lim=myfloat(float(header[n])); n+=1
failed=myfloat(float(header[n])); n+=1
Rin=myfloat(float(header[n])); n+=1
Rout=myfloat(float(header[n])); n+=1
hslope=myfloat(float(header[n])); n+=1
R0=myfloat(float(header[n])); n+=1
NPR=int(header[n]); n+=1
DOKTOT=int(header[n]); n+=1
fractheta = myfloat(header[n]); n+=1
fracphi = myfloat(header[n]); n+=1
rbr = myfloat(header[n]); n+=1
npow2 = myfloat(header[n]); n+=1
cpow2 = myfloat(header[n]); n+=1
BL = myfloat(header[n]); n+=1
else:
print("rdump header")
nheader = 46
n = 0
#per tile resolution
N1 = int(header[n]); n+=1
N2 = int(header[n]); n+=1
N3 = int(header[n]); n+=1
#total resolution
nx = int(header[n]); n+=1
ny = int(header[n]); n+=1
nz = int(header[n]); n+=1
#numbers of ghost cells
N1G = int(header[n]); n+=1
N2G = int(header[n]); n+=1
N3G = int(header[n]); n+=1
#starting indices
starti = int(header[n]); n+=1
startj = int(header[n]); n+=1
startk = int(header[n]); n+=1
t = myfloat(header[n]); n+=1
tf = myfloat(header[n]); n+=1
nstep = int(header[n]); n+=1
a = myfloat(header[n]); n+=1
gam = myfloat(header[n]); n+=1
game = myfloat(header[n]); n+=1
game4 = myfloat(header[n]); n+=1
game5 = myfloat(header[n]); n+=1
cour = myfloat(header[n]); n+=1
DTd = myfloat(header[n]); n+=1
DTl = myfloat(header[n]); n+=1
DTi = myfloat(header[n]); n+=1
DTr = myfloat(header[n]); n+=1
DTr01 = myfloat(header[n]); n+=1
dump_cnt = myfloat(header[n]); n+=1
image_cnt = myfloat(header[n]); n+=1
rdump_cnt = myfloat(header[n]); n+=1
rdump01_cnt=myfloat(float(header[n])); n+=1
dt = myfloat(header[n]); n+=1
lim = myfloat(header[n]); n+=1
failed = myfloat(header[n]); n+=1
Rin = myfloat(header[n]); n+=1
Rout = myfloat(header[n]); n+=1
hslope = myfloat(header[n]); n+=1
R0 = myfloat(header[n]); n+=1
fractheta = myfloat(header[n]); n+=1
fracphi = myfloat(header[n]); n+=1
rbr = myfloat(header[n]); n+=1
npow2 = myfloat(header[n]); n+=1
cpow2 = myfloat(header[n]); n+=1
tdump = myfloat(header[n]); n+=1
trdump = myfloat(header[n]); n+=1
timage = myfloat(header[n]); n+=1
tlog = myfloat(header[n]); n+=1
if n != nheader or n != nheadertot:
print("Wrong number of elements in header: nread = %d, nexpected = %d, nototal = %d: incorrect format?"
% (n, nheader, nheadertot) )
return headerline
if returnheaderline:
return headerline
else:
return header
def read_body(dump,nx=None,ny=None,nz=None,noround=False):
fin = open( dump, "rb" )
header = fin.readline()
if dump.startswith("dumps/rdump"):
dtype = np.float64
body = np.fromfile(fin,dtype=dtype,count=-1)
gd = body.view().reshape((nx,ny,nz,-1), order='C')
if noround:
gd=gd.transpose(3,0,1,2)
else:
gd=myfloat(gd.transpose(3,0,1,2))
elif dump.startswith("dumps/gdump2"):
dtype = np.float64
body = np.fromfile(fin,dtype=dtype,count=-1)
gd = body.view().reshape((nx,ny,nz,-1), order='C')
if noround:
gd=gd.transpose(3,0,1,2)
else:
gd=myfloat(gd.transpose(3,0,1,2))
elif dump.startswith("dumps/fdump"):
dtype = np.int64
body = np.fromfile(fin,dtype=dtype,count=-1)
gd = body.view().reshape((-1,nz,ny,nx), order='F')
gd=myfloat(gd.transpose(0,3,2,1))
else:
dtype = np.float32
body = np.fromfile(fin,dtype=dtype,count=-1)
gd = body.view().reshape((-1,nz,ny,nx), order='F')
gd=myfloat(gd.transpose(0,3,2,1))
return gd
def data_assign(gd,type=None,**kwargs):
if type is None:
print("Please specify data type")
return
if type == "gdump":
gdump_assign(gd,**kwargs)
return None
elif type == "gdump2":
gdump2_assign(gd,**kwargs)
return None
elif type == "dump":
dump_assign(gd,**kwargs)
return None
elif type == "rdump":
gd = rdump_assign(gd,**kwargs)
return gd
elif type == "fdump":
gd = fdump_assign(gd,**kwargs)
return gd
else:
print("Unknown data type: %s" % type)
return gd
def gdump_assign(gd,**kwargs):
global t,nx,ny,nz,N1,N2,N3,_dx1,_dx2,_dx3,a,gam,Rin,Rout,hslope,R0,ti,tj,tk,x1,x2,x3,r,h,ph,gcov,gcon,gdet,drdx,gn3,gv3,guu,gdd,dxdxp, games
nx = kwargs.pop("nx",nx)
ny = kwargs.pop("ny",ny)
nz = kwargs.pop("nz",nz)
ti,tj,tk,x1,x2,x3,r,h,ph = gd[0:9,:,:].view(); n = 9
gv3 = gd[n:n+16].view().reshape((4,4,nx,ny,nz),order='F').transpose(1,0,2,3,4); n+=16
gn3 = gd[n:n+16].view().reshape((4,4,nx,ny,nz),order='F').transpose(1,0,2,3,4); n+=16
gcov = gv3
gcon = gn3
guu = gn3
gdd = gv3
gdet = gd[n]; n+=1
drdx = gd[n:n+16].view().reshape((4,4,nx,ny,nz),order='F').transpose(1,0,2,3,4); n+=16
dxdxp = drdx
if n != gd.shape[0]:
print("rd: WARNING: nread = %d < ntot = %d: incorrect format?" % (n, gd.shape[0]) )
return 1
return 0
def gdump2_assign(gd,**kwargs):
global t,nx,ny,nz,N1,N2,N3,_dx1,_dx2,_dx3,a,gam,Rin,Rout,hslope,R0,ti,tj,tk,x1,x2,x3,gdet,games,rf1,hf1,phf1,rf2,hf2,phf2,rf3,hf3,phf3,rcorn,hcord,phcorn,re1,he1,phe1,re2,he2,phe2,re3,he3,phe3
nx = kwargs.pop("nx",nx)
ny = kwargs.pop("ny",ny)
nz = kwargs.pop("nz",nz)
ti,tj,tk,x1,x2,x3 = gd[0:6,:,:].view(); n = 6
rf1,hf1,phf1,rf2,hf2,phf2,rf3,hf3,phf3 = gd[0:9,:,:].view(); n += 9
rcorn,hcord,phcorn,rcent,hcent,phcen = gd[0:6,:,:].view(); n += 6
re1,he1,phe1,re2,he2,phe2,re3,he3,phe3 = gd[0:9,:,:].view(); n += 9
gdet = gd[n]; n+=1
if n != gd.shape[0]:
print("rd: WARNING: nread = %d < ntot = %d: incorrect format?" % (n, gd.shape[0]) )
return 1
return 0
#read in a dump file
def dump_assign(gd,**kwargs):
global t,nx,ny,nz,_dx1,_dx2,_dx3,gam,hslope,a,R0,Rin,Rout,ti,tj,tk,x1,x2,x3,r,h,ph,rho,ug,vu,B,pg,cs2,Sden,U,gdetB,divb,uu,ud,bu,bd,v1m,v1p,v2m,v2p,gdet,bsq,gdet,alpha,rhor, ktot, pg
nx = kwargs.pop("nx",nx)
ny = kwargs.pop("ny",ny)
nz = kwargs.pop("nz",nz)
ti,tj,tk,x1,x2,x3,r,h,ph,rho,ug = gd[0:11,:,:].view(); n = 11
pg = (gam-1)*ug
lrho=np.log10(rho)
vu=np.zeros_like(gd[0:4])
B=np.zeros_like(gd[0:4])
vu[1:4] = gd[n:n+3]; n+=3
B[1:4] = gd[n:n+3]; n+=3
#if total entropy equation is evolved (on by default)
if DOKTOT == 1:
ktot = gd[n]; n+=1
divb = gd[n]; n+=1
uu = gd[n:n+4]; n+=4
ud = gd[n:n+4]; n+=4
bu = gd[n:n+4]; n+=4
bd = gd[n:n+4]; n+=4
bsq = mdot(bu,bd)
v1m,v1p,v2m,v2p,v3m,v3p=gd[n:n+6]; n+=6
gdet=gd[n]; n+=1
rhor = 1+(1-a**2)**0.5
if "guu" in globals():
#lapse
alpha = (-guu[0,0])**(-0.5)
if n != gd.shape[0]:
print("rd: WARNING: nread = %d < ntot = %d: incorrect format?" % (n, gd.shape[0]) )
return 1
return 0
def rdump_assign(gd,**kwargs):
global t,nx,ny,nz,_dx1,_dx2,_dx3,gam,hslope,a,R0,Rin,Rout,ti,tj,tk,x1,x2,x3,r,h,ph,rho,ug,vu,B,pg,cs2,Sden,U,gdetB,divb,uu,ud,bu,bd,v1m,v1p,v2m,v2p,gdet,bsq,gdet,alpha,rhor, ktot, Ttot, game, qisosq, pflag, qisodotb, kel, uelvar, Tel4, Tel5,Teldis, Tels, kel4, kel5,ugel,ugeldis, ugcon, sel, ugscon, ugel4, ugel5,stot, uelvar, Telvar, Tsel, sel, ugels, games, phi, keldis, phihat,csphib,lrho
nx = kwargs.pop("nx",nx)
ny = kwargs.pop("ny",ny)
nz = kwargs.pop("nz",nz)
n = 0
rho = gd[n]; n+=1
ug = gd[n]; n+=1
vu=np.zeros_like(gd[0:4])
B=np.zeros_like(gd[0:4])
vu[1:4] = gd[n:n+3]; n+=3
B[1:4] = gd[n:n+3]; n+=3
# if n != gd.shape[0]:
# print("rd: WARNING: nread = %d < ntot = %d: incorrect format?" % (n, gd.shape[0]) )
# return 1
return gd
def fdump_assign(gd,**kwargs):
global t,nx,ny,nz,_dx1,_dx2,_dx3,gam,hslope,a,R0,Rin,Rout,ti,tj,tk,x1,x2,x3,r,h,ph,rho,ug,vu,B,pg,cs2,Sden,U,gdetB,divb,uu,ud,bu,bd,v1m,v1p,v2m,v2p,gdet,bsq,gdet,alpha,rhor, ktot, Ttot, game, qisosq, pflag, qisodotb, kel, uelvar, Tel4, Tel5,Teldis, Tels, kel4, kel5,ugel,ugeldis, ugcon, sel, ugscon, ugel4, ugel5,stot, uelvar, Telvar, Tsel, sel, ugels, games, phi, keldis, phihat,csphib,lrho,fail
nx = kwargs.pop("nx",nx)
ny = kwargs.pop("ny",ny)
nz = kwargs.pop("nz",nz)
fail = gd
return gd
def mdot(a,b):
"""
Computes a contraction of two tensors/vectors. Assumes
the following structure: tensor[m,n,i,j,k] OR vector[m,i,j,k],
where i,j,k are spatial indices and m,n are variable indices.
"""
if (a.ndim == 3 and b.ndim == 3) or (a.ndim == 4 and b.ndim == 4):
c = (a*b).sum(0)
elif a.ndim == 5 and b.ndim == 4:
c = np.empty(np.maximum(a[:,0,:,:,:].shape,b.shape),dtype=b.dtype)
for i in range(a.shape[0]):
c[i,:,:,:] = (a[i,:,:,:,:]*b).sum(0)
elif a.ndim == 4 and b.ndim == 5:
c = np.empty(np.maximum(b[0,:,:,:,:].shape,a.shape),dtype=a.dtype)
for i in range(b.shape[1]):
c[i,:,:,:] = (a*b[:,i,:,:,:]).sum(0)
elif a.ndim == 5 and b.ndim == 5:
c = np.empty((a.shape[0],b.shape[1],a.shape[2],a.shape[3],max(a.shape[4],b.shape[4])),dtype=a.dtype)
for i in range(c.shape[0]):
for j in range(c.shape[1]):
c[i,j,:,:,:] = (a[i,:,:,:,:]*b[:,j,:,:,:]).sum(0)
elif a.ndim == 5 and b.ndim == 6:
c = np.empty((a.shape[0],b.shape[1],b.shape[2],max(a.shape[2],b.shape[3]),max(a.shape[3],b.shape[4]),max(a.shape[4],b.shape[5])),dtype=a.dtype)
for mu in range(c.shape[0]):
for k in range(c.shape[1]):
for l in range(c.shape[2]):
c[mu,k,l,:,:,:] = (a[mu,:,:,:,:]*b[:,k,l,:,:,:]).sum(0)
else:
raise Exception('mdot', 'wrong dimensions')
return c
def psicalc(B1=None):
"""
Computes the field vector potential
"""
global B
if B1 is None: B1 = B[1]
daphi = -(gdet*B1).mean(-1)*_dx2
aphi=daphi[:,::-1].cumsum(axis=1)[:,::-1]
aphi-=0.5*daphi #correction for half-cell shift between face and center in theta
return(aphi)
def myfloat(f,acc=1):
""" acc=1 means np.float32, acc=2 means np.float64 """
if acc==1:
return( np.float32(f) )
else:
return( np.float64(f) )
def get_fracphi():
fracphi = dxdxp[3,3,0,0,0]*_dx3*nz/(2*np.pi)
return( fracphi )
def plco(myvar,**kwargs):
global r,h,ph
plt.clf()
return plc(myvar,**kwargs)
def plc(myvar,**kwargs): #plc
global r,h,ph
#xcoord = kwargs.pop('x1', None)
#ycoord = kwargs.pop('x2', None)
if(np.min(myvar)==np.max(myvar)):
print("The quantity you are trying to plot is a constant = %g." % np.min(myvar))
return
cb = kwargs.pop('cb', False)
nc = kwargs.pop('nc', 15)
k = kwargs.pop('k',0)
mirrorx = kwargs.pop('mirrorx',0)
mirrory = kwargs.pop('mirrory',0)
symmx = kwargs.pop('symmx',0)
#cmap = kwargs.pop('cmap',cm.jet)
isfilled = kwargs.pop('isfilled',False)
xy = kwargs.pop('xy',0)
xcoord = kwargs.pop("xcoord",None)
ycoord = kwargs.pop("ycoord",None)
lin = kwargs.pop('lin',0)
xmax = kwargs.pop('xmax',10)
ymax = kwargs.pop('ymax',5)
cbxlabel = kwargs.pop('cbxla',None)
cbylabel = kwargs.pop('cbyla',None)
fntsize = kwargs.pop("fntsize",20)
cbgoodticks = kwargs.pop("cbgoodticks",1)
xlabel = kwargs.pop("xla",None)
ylabel = kwargs.pop("yla",None)
dobh = kwargs.pop("dobh",1)
pretty = kwargs.pop("pretty",0)
ax = kwargs.pop("ax",None)
cbticks = kwargs.pop("cbticks",None)
domathify = kwargs.pop("domathify",0)
if np.abs(xy)==1:
if xcoord is None: xcoord = r * np.sin(h)
if ycoord is None: ycoord = r * np.cos(h)
if mirrory: ycoord *= -1
if mirrorx: xcoord *= -1
if xcoord is not None and ycoord is not None:
xcoord = xcoord[:,:,None] if xcoord.ndim == 2 else xcoord[:,:,k:k+1]
ycoord = ycoord[:,:,None] if ycoord.ndim == 2 else ycoord[:,:,k:k+1]
if np.abs(xy)==1 and symmx:
if myvar.ndim == 2:
myvar = myvar[:,:,None] if myvar.ndim == 2 else myvar[:,:,k:k+1]
myvar=np.concatenate((myvar[:,::-1],myvar),axis=1)
xcoord=np.concatenate((-xcoord[:,::-1],xcoord),axis=1)
ycoord=np.concatenate((ycoord[:,::-1],ycoord),axis=1)
else:
if myvar.shape[-1] > 1:
symmk = (k+nz/2)%nz
else:
symmk = k
myvar=np.concatenate((myvar[:,ny-1:ny,k:k+1],myvar[:,::-1,symmk:symmk+1],myvar[:,:,k:k+1]),axis=1)
xcoord=np.concatenate((xcoord[:,ny-1:ny,k:k+1],-xcoord[:,::-1],xcoord),axis=1)
ycoord=np.concatenate((ycoord[:,ny-1:ny,k:k+1],ycoord[:,::-1],ycoord),axis=1)
elif np.abs(xy) == 2 and symmx:
#if fracphi == 0.5 done in a robust way
if get_fracphi() < 0.75:
r1 = np.concatenate((r,r,r[...,0:1]),axis=2)
ph1 = np.concatenate((ph,ph+np.pi,ph[...,0:1]+2*np.pi),axis=2)
myvar = np.concatenate((myvar,myvar,myvar[...,0:1]),axis=2)
else:
r1 = np.concatenate((r,r[...,0:1]),axis=2)
ph1 = np.concatenate((ph,ph[...,0:1]+2*np.pi),axis=2)
myvar = np.concatenate((myvar,myvar[...,0:1]),axis=2)
xcoord=(r1*cos(ph1))[:,ny/2,:,None]
ycoord=(r1*sin(ph1))[:,ny/2,:,None]
myvar = myvar[:,ny/2,:,None]
else:
myvar = myvar[:,:,None] if myvar.ndim == 2 else myvar[:,:,k:k+1]
if lin:
xcoord = r
ycoord = h
if ax is None:
ax = plt.gca()
if xcoord is None or ycoord is None:
if isfilled:
res = ax.contourf(myvar[:,:,0].transpose(),nc,**kwargs)
else:
res = ax.contour(myvar[:,:,0].transpose(),nc,**kwargs)
else:
if isfilled:
res = ax.contourf(xcoord[:,:,0],ycoord[:,:,0],myvar[:,:,0],nc,**kwargs)
else:
res = ax.contour(xcoord[:,:,0],ycoord[:,:,0],myvar[:,:,0],nc,**kwargs)
if xy>0 and not symmx:
ax.set_xlim(0,xmax)
ax.set_ylim(-ymax,ymax)
if xy> 0 and symmx:
ax.set_xlim(-xmax,xmax)
ax.set_ylim(-ymax,ymax)
if xlabel is not None:
ax.set_xlabel(xlabel,fontsize=fntsize)
if ylabel is not None:
ax.set_ylabel(ylabel,fontsize=fntsize)
if pretty:
for label in ax.get_xticklabels() + ax.get_yticklabels():
label.set_fontsize(fntsize)
if domathify: mathify_axes_ticks(ax,fontsize=fntsize)
if cb: #use color bar
cb = plt.colorbar(res,ax=ax)
if pretty and cbgoodticks and cbticks is None:
vmin = cb.vmin
vmax = cb.vmax
#this returns incorrect ticks! so ignore it
#ticks = cb.ax.get_yticks()
#nticks = len(ticks)
#if not too many ticks, then pretty them up
rvmin = np.round(vmin)
rvmax = np.round(vmax)
if rvmin == vmin and rvmax == vmax and vmax-vmin <= 10:
ticks = np.arange(rvmin,rvmax+1)
cb.set_ticks(ticks)
mathify_axes_ticks(cb.ax,fontsize=fntsize,yticks=ticks)
elif rvmin == vmin and rvmax == vmax and vmax-vmin <= 20:
ticks = np.arange(rvmin,rvmax+1)[::2]
cb.set_ticks(ticks)
mathify_axes_ticks(cb.ax,fontsize=fntsize,yticks=ticks)
if cbticks is not None:
cb.set_ticks(cbticks)
mathify_axes_ticks(cb.ax,fontsize=fntsize,yticks=cbticks)
if cbxlabel is not None:
cb.ax.set_xlabel(cbxlabel,fontsize=fntsize)
if cbxlabel is not None:
cb.ax.set_xlabel(cbxlabel,fontsize=fntsize)
if cbylabel is not None:
cb.ax.set_ylabel(cbylabel,fontsize=fntsize)
if pretty:
for label in cb.ax.get_yticklabels():
label.set_fontsize(fntsize)
if xy and dobh and "rhor" in globals():
el = Ellipse((0,0), 2*rhor, 2*rhor, facecolor='k', alpha=1)
art=ax.add_artist(el)
art.set_zorder(20)
if cb:
return res, cb
else:
return res
def faraday():
global omegaf1, omegaf2
if 'omegaf1' in globals():
del omegaf1
if 'omemaf2' in globals():
del omegaf2
omegaf1=fFdd(0,1)/fFdd(1,3)
omegaf2=fFdd(0,2)/fFdd(2,3)
def Tcalcud():
global Tud, TudEM, TudMA
global mu, sigma
global enth
global unb, isunbound
pg = (gam-1)*ug
w=rho+ug+pg
eta=w+bsq
if 'Tud' in globals():
del Tud
if 'TudMA' in globals():
del TudMA
if 'TudEM' in globals():
del TudEM
if 'mu' in globals():
del mu
if 'sigma' in globals():
del sigma
if 'unb' in globals():
del unb
if 'isunbound' in globals():
del isunbound
Tud = np.zeros((4,4,nx,ny,nz),dtype=np.float32,order='F')
TudMA = np.zeros((4,4,nx,ny,nz),dtype=np.float32,order='F')
TudEM = np.zeros((4,4,nx,ny,nz),dtype=np.float32,order='F')
for kapa in np.arange(4):
for nu in np.arange(4):
if(kapa==nu): delta = 1
else: delta = 0
TudEM[kapa,nu] = bsq*uu[kapa]*ud[nu] + 0.5*bsq*delta - bu[kapa]*bd[nu]
TudMA[kapa,nu] = w*uu[kapa]*ud[nu]+pg*delta
#Tud[kapa,nu] = eta*uu[kapa]*ud[nu]+(pg+0.5*bsq)*delta-bu[kapa]*bd[nu]
Tud[kapa,nu] = TudEM[kapa,nu] + TudMA[kapa,nu]
mu = -Tud[1,0]/(rho*uu[1])
sigma = TudEM[1,0]/TudMA[1,0]
enth=1+ug*gam/rho
unb=enth*ud[0]
isunbound=(-unb>1.0)
def aux():
faraday()
Tcalcud()
if __name__ == "__main__":
if False:
#1D plot example
plt.clf()
rg("gdump")
rd("dump000")
plt.plot(r[:,ny/2,0],rho[:,ny/2,0])
plt.xscale("log")
plt.yscale("log")
plt.xlabel("r")
plt.ylabel("rho")
if False:
#2D plot example
plt.clf()
rg("gdump")
rd("dump000")
#R-z plot of the logarithm of density distribution
plc(r,np.log10(rho),cb=True,xy=1,xmax=100,ymax=50)
def bhole():
ax = plt.gca()
el = Ellipse((0,0), 2*rhor, 2*rhor, facecolor='k', alpha=1)
art=ax.add_artist(el)
art.set_zorder(20)
plt.draw()