def get_data_TimeConv(time):
global folder
ls = os.listdir(folder)
condition_folder= lambda name: "l1x1" in name and gridsize in name
ls_selected=list(np.extract(map(condition_folder,ls),ls))
subfolders=sorted(ls_selected)
#print "subfolders:", subfolders
num_runs=len(subfolders)
print "No. of runs: ", num_runs
#get the spatial coordinates
x=exnode_reader.parse_file(folder+subfolders[0]+"/"+"Time_2_0.part0.exnode",[["Coordinate",1]]) #field_name and component_no
#print "x: ",x
Vm=[0.0 for i in range(num_runs)]
timesteps=[0.0 for i in range(num_runs)]
for i in range(num_runs):
#print "i: ",i
#print"subfolders: ", subfolders[i]
timesteps[i]=get_timestep(subfolders[i])
Indx=int(time/timesteps[i])
#print Indx
fileToread = folder+subfolders[i]+"/"+"Time_2_"+str(Indx)+".part0.exnode" #serial version
#print 'file',fileToread
Vm[i]=exnode_reader.parse_file(fileToread,[["Vm",1]])
#print Vm[i]
print "timesteps: ", timesteps
return x,Vm,timesteps
def animate(t, create_image=False):
global foldername, image_name
ax1.clear()
# get all exnode files sorted in that directory
files = exnode_reader.get_exnode_files(foldername)
if t >= len(files):
return
iron_filename = files[t]
iron_data = exnode_reader.parse_file(
foldername + iron_filename,
[["Vm", 1]]) # extract field Vm, component 1
n = len(iron_data)
nx = int(np.sqrt(n)) - 1
ny = int(np.sqrt(n)) - 1
print "t=", t, "/", len(files), ", n=", n, ", nx=", nx, ", ny=", ny
X = range(nx + 1)
Y = range(ny + 1)
X, Y = np.meshgrid(X, Y)
Z_iron = X.copy()
for x in range(nx + 1):
for y in range(ny + 1):
try:
Z_iron[x, y] = iron_data[x * (ny + 1) + y]
except: # fails for nans
Z_iron[x, y] = 0.0
ax1.plot_surface(X,
Y,
Z_iron,
cmap=cm.coolwarm,
linewidth=1,
antialiased=False,
rstride=1,
cstride=1)
ax1.set_zlim(-80, 30)
plt.title("t = " + str(t * 0.005))
if t % 100 == 0 or create_image:
filenamepng = image_name + "_t" + str(t) + ".png"
filenameeps = image_name + "_t" + str(t) + ".eps"
plt.savefig(filenamepng)
print "Image saved to {}".format(filenamepng)
os.system("convert " + filenamepng + " " + filenameeps)
input_filename_exelem += ".exelem"
if len(sys.argv) >= 3:
input_filename_exelem = sys.argv[2]
else:
print("usage: ./exfile_to_vtk.py <filename.exnode> [<filename.exelem>]")
sys.exit(0)
output_filename, _ = os.path.splitext(input_filename_exnode)
print("filename exnode: \"{}\"".format(input_filename_exnode))
print("filename exelem: \"{}\"".format(input_filename_exelem))
print("output filename: \"{}.vtu\"".format(output_filename))
nodal_values = exnode_reader.parse_file(
input_filename_exnode,
[["coordinates", 1], ["coordinates", 2], ["coordinates", 3]])
element_nodes = exnode_reader.parse_exelem_file(input_filename_exelem)
if True:
print("element_nodes:")
print(element_nodes)
print("result:")
print(nodal_values)
# create geometry for vtk unstructured grid
n_points = np.size(nodal_values, 0)
n_elements = len(list(element_nodes))
print "foldername: ", foldername
# creat image name
imagenamepng = "{}".format(foldername) + "image.png"
imagenameeps = "{}".format(foldername) + "image.eps"
# get all exnode files (sorted) from the folder
files = exnode_reader.get_exnode_files(foldername)
#print 'exnode files',files
n_timestep = len(files) - 1
#print "No. of time steps: ", n_timestep
#get the number of data in each file
x = exnode_reader.parse_file(foldername + files[0],
[["Coordinate", 1]]) #field_name and component_no
n_data = len(x)
#print "No. of data point: ",n_data
#print x
# get the data
Vm = [0.0 for i in range(n_timestep)]
for i_time in range(n_timestep):
Vm[i_time] = exnode_reader.parse_file(foldername + files[i_time + 1],
[["Vm", 1]])
#print "time step: ", i_time
#print Vm[i_time]
#print "Vm: ",Vm
def makeplot(x, y, z):
status = " matlab file: {}\n".format(foldername+matlab_filename)
matlab_data = None
if os.path.exists(foldername):
matlab_data = np.loadtxt(foldername+matlab_filename)
# read iron reference data
foldername = "reference/iron/l1x1_n"+str(nx)+"x"+str(ny)+"_i"+str(i)+"_s"+str(s)+"/"
pde_time_step = 0.005
filenumber = int(t / pde_time_step)
iron_reference_filename = "Time_2_"+str(filenumber)+".part0.exnode"
status += " iron reference file: {}\n".format(foldername+iron_reference_filename)
iron_reference_data = exnode_reader.parse_file(foldername+iron_reference_filename, [["Vm", 1]]) # extract field Vm, component 1
# read iron data of current run
foldername = "current_run/l1x1_n"+str(nx)+"x"+str(ny)+"_i"+str(i)+"_s"+str(s)+"_p"+str(p)+"/"
pde_time_step = 0.005
filenumber = int(t / pde_time_step)
iron_filename = "Time_2_"+str(filenumber)+".part0.exnode"
status += " iron file: {}\n".format(foldername+iron_filename)
iron_data = exnode_reader.parse_file(foldername+iron_filename, [["Vm", 1]]) # extract field Vm, component 1
if iron_data is None:
print "Warning! no data available for:\n"+status
continue
# determine which iron file would produce the least l2 error to the current matlab file