for zeff in zlist:
# Create the input file, setting Zeff
timestep = 5e3
if zeff < 128:
# reduce time-step. At large times these cases produce noise
timestep = 1e3
# Delete old output files
shell("rm data/BOUT.dmp.*.nc")
print("Running drift instability test, zeff = ", zeff)
# Run the case
s, out = launch_safe("./2fluid 2fluid:Zeff={} timestep={}".format(
zeff, timestep),
nproc=nproc,
mthread=nthreads,
pipe=True)
f = open("run.log." + str(zeff), "w")
f.write(out)
f.close()
# Collect data
Ni = collect("Ni", path="data", xind=2, yind=20, info=False)
phi = collect("phi", path="data", xind=2, yind=20, info=False)
zmax = collect("ZMAX", path="data", info=False)
rho_s = collect("rho_s", path="data", info=False)
wci = collect("wci", path="data", info=False)
t_array = collect("t_array", path="data", info=False)
# Create the input file, setting Zeff
# If we get passed Staggered or something like this, use staggered config file
inp='BOUT_stag.inp' if 'stag' in [i.lower()[:4] for i in argv] else 'BOUT.inp'
shell_safe("sed 's/Zeff = 128.0/Zeff = "+str(zeff)+"/g' "+inp+" > data/BOUT.inp")
timestep = 5e3
if zeff < 128:
# reduce time-step. At large times these cases produce noise
timestep = 1e3
# Delete old output files
shell("rm data/BOUT.dmp.*.nc")
print("Running drift instability test, zeff = ", zeff)
# Run the case
s, out = launch_safe("./2fluid timestep="+str(timestep), runcmd=MPIRUN, nproc=nproc, mthread=nthreads, pipe=True)
f = open("run.log."+str(zeff), "w")
f.write(out)
f.close()
# Collect data
Ni = collect("Ni", path="data", xind=2, yind=20, info=False)
phi = collect("phi", path="data", xind=2, yind=20, info=False)
zmax = collect("ZMAX", path="data", info=False)
rho_s = collect("rho_s", path="data", info=False)
wci = collect("wci", path="data", info=False)
t_array = collect("t_array", path="data", info=False)
dims = np.shape(Ni)
nt = dims[0]
beta_max_list = [5, 10, 20, 40]
colors = ['k','b','g','r']
ngroups_list = [20, 40, 80]
syms = ['x', 'o', 'D']
for beta_max, color in zip(beta_max_list, colors):
for ngroups, sym in zip(ngroups_list, syms):
flux_ratio = []
for Te in Telist:
cmd = "./conduction-snb \"Te={0}+0.01*sin(y)\" Ne={1} mesh:length={2} snb:beta_max={3} snb:ngroups={4}".format(Te, Ne, length, beta_max, ngroups)
# Run the case
s, out = launch_safe(cmd, nproc=1, mthread=1, pipe=True)
div_q = collect("Div_Q", path="data").ravel()
div_q_SH = collect("Div_Q_SH", path="data").ravel()
# Get the index of maximum S-H heat flux
ind = np.argmax(div_q_SH)
flux_ratio.append(div_q[ind] / div_q_SH[ind])
plt.plot(lambda_ee_T / length, flux_ratio, '-'+sym+color, label=r"$\beta_{{max}}={0}, N_g={1}$".format(beta_max,ngroups))
plt.legend()
plt.xlabel(r"$\lambda_{ee,T} / L$")
plt.ylabel(r"$q / q_{SH}$")
plt.xscale("log")
("boundary", "Model 2 (density, momentum)")
,("boundary-logn", "Model 3 (log density, momentum)")
#,("../fci-wave-logn/boundary", "Model 5 (log density, velocity)")
]
# Change this to select no boundary or boundary cases
data = data_noboundary
if run:
from boututils.run_wrapper import shell_safe, launch_safe, getmpirun
shell_safe("make > make.log")
MPIRUN=getmpirun()
for path,label in data:
launch_safe("./fci-wave -d "+path, runcmd=MPIRUN, nproc=nproc, pipe=False)
# Collect the results into a dictionary
sum_n_B = {}
for path,label in data:
n = collect("n", path=path)
Bxyz = collect("Bxyz", path=path)
time = collect("t_array", path=path)
nt, nx, ny, nz = n.shape
n_B = np.ndarray(nt)
for t in range(nt):
n_B[t] = np.sum(n[t,:,:,:] / Bxyz)
length = 6e-4 # Domain length in m
qe = 1.602176634e-19
import numpy as np
import matplotlib.pyplot as plt
from boututils.run_wrapper import build_and_log, launch_safe
from boutdata.collect import collect
path = "step"
build_and_log("Step SNB")
# Run the case
s, out = launch_safe("./conduction-snb -d " + path, nproc=1, mthread=1, pipe=True)
Te = collect("Te", path=path).ravel()
ny = len(Te)
dy = length / ny
position = (np.arange(ny) + 0.5) * length / ny
# Read divergence of heat flux
div_q = collect("Div_Q", path=path).ravel()
div_q_SH = collect("Div_Q_SH", path=path).ravel()
# Integrate the divergence of flux to get heat flux W/m^2
q = np.cumsum(div_q) * qe * dy
q_SH = np.cumsum(div_q_SH) * qe * dy
("boundary-logn", "Model 3 (log density, momentum)")
#,("../fci-wave-logn/boundary", "Model 5 (log density, velocity)")
]
# Change this to select no boundary or boundary cases
data = data_noboundary
if run:
from boututils.run_wrapper import shell_safe, launch_safe, getmpirun
shell_safe("make > make.log")
MPIRUN = getmpirun()
for path, label in data:
launch_safe("./fci-wave -d " + path,
runcmd=MPIRUN,
nproc=nproc,
pipe=False)
# Collect the results into a dictionary
sum_n_B = {}
for path, label in data:
n = collect("n", path=path)
Bxyz = collect("Bxyz", path=path)
time = collect("t_array", path=path)
nt, nx, ny, nz = n.shape
n_B = np.ndarray(nt)
for t in range(nt):
data_boundary = [
("boundary", "Model 2 (density, momentum)"),
("boundary-logn", "Model 3 (log density, momentum)")
#,("../fci-wave-logn/boundary", "Model 5 (log density, velocity)")
]
# Change this to select no boundary or boundary cases
data = data_noboundary
if run:
from boututils.run_wrapper import shell_safe, launch_safe
shell_safe("make > make.log")
for path, label in data:
launch_safe("./fci-wave -d " + path, nproc=nproc, pipe=False)
# Collect the results into a dictionary
sum_n_B = {}
for path, label in data:
n = collect("n", path=path)
Bxyz = collect("Bxyz", path=path)
time = collect("t_array", path=path)
nt, nx, ny, nz = n.shape
n_B = np.ndarray(nt)
for t in range(nt):
n_B[t] = np.sum(n[t, :, :, :] / Bxyz)