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utils.py
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utils.py
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"""
UTILITIES
This file contains miscellaneous functions, which are used for small tasks such
as printing errors, messages and checking input validity.
Author details:
Muhammad Arslan Ahmed
maa8g09@soton.ac.uk
Aerodynamics and Flight Mechanics Research Group
Faculty of Engineering and the Environment
University of Southampton
"""
import os
import sys
import math
import numpy as np
from scipy.interpolate import interp1d
verbose = False
def printEdgeStatesStart():
print('=============================================================')
print(' ______ __ _____ __ __ ')
print(' / ____/___/ /___ ____ / ___// /_____ _/ /____ _____ ')
print(' / __/ / __ / __ `/ _ \ \__ \/ __/ __ `/ __/ _ \/ ___/ ')
print(' / /___/ /_/ / /_/ / __/ ___/ / /_/ /_/ / /_/ __(__ ) ')
print(' /_____/\__,_/\__, /\___/ /____/\__/\__,_/\__/\___/____/ ')
print(' /____/ ')
print('')
print(' Muhammad Arslan Ahmed')
print(' University of Southampton')
print('=============================================================')
return
def printStart():
if verbose:
print('##################################################################')
print('_________ .__ .__ ')
print('\_ ___ \| |__ _____ ____ ____ ____ | | ')
print('/ \ \/| | \\__ \ / \ / \_/ __ \| | ')
print('\ \___| Y \/ __ \| | \ | \ ___/| |__ ')
print(' \______ /___| (____ /___| /___| /\___ >____/ ')
print(' \/ \/ \/ \/ \/ \/ ')
print(' __________ .__ __ ')
print(' \______ \ ____ __________ | |___ __ ____ _____/ |_ ')
print(' | _// __ \ / ___/ _ \| |\ \/ // __ \ / \ __\.')
print(' | | \ ___/ \___ ( <_> ) |_\ /\ ___/| | \ | ')
print(' |____|_ /\___ >____ >____/|____/\_/ \___ >___| /__| ')
print(' \/ \/ \/ \/ \/ ')
print('Muhammad Arslan Ahmed')
print('University of Southampton')
print('##################################################################')
return
def printSectionHeader():
if verbose:
print('__________________________________________________________________\n')
return
def printSectionTitle(str):
# Print the section headers for each main section of the code output.
if verbose:
print(' **', str, '\n')
return
def error(str):
# Print the error and then exit from the program entirely
print('!!!!====!!!!====!!!!====!!!!====!!!!====')
print('ERROR:', str)
print('!!!!====!!!!====!!!!====!!!!====!!!!====')
print('\n')
print(' ______ ______ __ __ ________ ')
print(' / \ / \ | \ / \| \ ')
print('| $$$$$$\| $$$$$$\| $$\ / $$| $$$$$$$$ ')
print('| $$ __\$$| $$__| $$| $$$\ / $$$| $$__ ')
print('| $$| \| $$ $$| $$$$\ $$$$| $$ \ ')
print('| $$ \$$$$| $$$$$$$$| $$\$$ $$ $$| $$$$$ ')
print('| $$__| $$| $$ | $$| $$ \$$$| $$| $$_____ ')
print(' \$$ $$| $$ | $$| $$ \$ | $$| $$ \ ')
print(' \$$$$$$ \$$ \$$ \$$ \$$ \$$$$$$$$ ')
print(' ')
print(' ______ __ __ ________ _______ ')
print(' / \ | \ | \| \| \ ')
print('| $$$$$$\| $$ | $$| $$$$$$$$| $$$$$$$\ ')
print('| $$ | $$| $$ | $$| $$__ | $$__| $$ ')
print('| $$ | $$ \$$\ / $$| $$ \ | $$ $$ ')
print('| $$ | $$ \$$\ $$ | $$$$$ | $$$$$$$\ ')
print('| $$__/ $$ \$$ $$ | $$_____ | $$ | $$ ')
print(' \$$ $$ \$$$ | $$ \| $$ | $$ ')
print(' \$$$$$$ \$ \$$$$$$$$ \$$ \$$ ')
print('\n')
print('!!!!====!!!!====!!!!====!!!!====!!!!====')
print('ERROR:', str)
print('!!!!====!!!!====!!!!====!!!!====!!!!====')
print('\n\n')
sys.exit('')
return
def message(str):
if verbose:
print(' ', str, '\n')
return
def openFile(str):
"""
INPUTS:
str: string of the directory where the file exists.
OUTPUTS:
f: file object
"""
f = open(str, 'r')
if verbose:
message('Opened the file: ' + str)
return f
def printGeoVars(geom_variables):
"""
This function prints out the grid dimensions of the channelflow solution.
"""
print('\n The geometry variables are:')
print(' Nx:', geom_variables['Nx'])
print(' Ny:', geom_variables['Ny'])
print(' Nz:', geom_variables['Nz'])
return
def checkInputValidity(fourdarray, geom_variables):
"""
This function checks that the values in the fourdarray are valid to allow
the plotting of the slice specified. If it is valid the function executes
as normal and a message is output in the shell to let the user know all's
well.
If, however, the values in the fourdarray are invalid, the whole routine
is stopped and an error message is output which specifies the invalidity
of the input.
INPUTS:
fourdarray: the plane co-ordinates of data you want to plot, indexed
as (i, nx, ny, nz)
geom_variables: a dictionary contianing all the geometrical values
OUTPUTS:
"""
printSectionHeader()
printSectionTitle('Checking validity of 4D array input')
for i in range(1,4):
if fourdarray[i] != 'all':
if i == 1:
if fourdarray[i] >= geom_variables['Nx']:
print('\n ! The 4D array input is invalid')
printGeoVars(geom_variables)
error('X point given exceeds the maximum grid points available')
elif i == 2:
if fourdarray[i] >= geom_variables['Ny']:
print('\n ! The 4D array input is invalid')
printGeoVars(geom_variables)
error('Y point given exceeds the maximum grid points available')
else:
if fourdarray[i] >= geom_variables['Nz']:
print('\n ! The 4D array input is invalid')
printGeoVars(geom_variables)
error('Z point given exceeds the maximum grid points available')
if fourdarray[0] < 0 or fourdarray[0] >= 3:
message('Invalid velocity component given, velocity component must be in range 0 to 2.')
error('Invalid velocity component given!')
message('The 4D array input is valid.')
return
def write_ASCII_file(data, directory):
"""
The data variable is a dictionary which has the generated flowField and
geometry information. The dictionary can be unpacked and an ASCII file with
the flowfield can be written. It should be written with the following indices:
u(nx, ny, nz, i)
The file us written with the title:
wave_packet_kx_kz_c_A.asc
The wave number triplet followed by the amplitude.
The way that I store the flow field is in the following indexing
U[i, nx, ny, nz]. Just be weary of this when unpacking the matrix to file.
"""
# kx = data['kx']
# kz = data['kz']
# c = data['c']
# A = data['A']
flowField = data['resolvent_flowField']
# fileName = "/wave_packet_" + str(kx) + "_+-" + str(kz) + "_" + str(c) + "_" + str(A) + ".asc"
fileName = "/u0.asc"
file = open(directory + fileName, "w")
for nx in range(0, data['Nx']):
for ny in range(0, data['Ny']):
for nz in range(0, data['Nz']):
for nd in range(0, data['Nd']):
tmp = flowField[nd, nx, ny, nz]
tmp = format(tmp, '.16f')
file.write(tmp + "\n")
file.close()
print('Boom, the ASCII is done.')
return 0
def write_GEOM_file(data, directory):
kx = data['kx']
kz = data['kz']
c = data['c']
A = data['A']
# fileName = "/wave_packet_" + str(kx) + "_+-" + str(kz) + "_" + str(c) + "_" + str(A) + ".geom"
fileName = "/u0.geom"
file = open(directory + fileName, "w")
file.write(str( int(data['Nx']) ) + '\t\t\t\t\t\t%Nx' + "\n")
file.write(str( int(data['Ny']) ) + '\t\t\t\t\t\t%Ny' + "\n")
file.write(str( int(data['Nz']) ) + '\t\t\t\t\t\t%Nz' + "\n")
file.write(str( int(data['Nd']) ) + '\t\t\t\t\t\t%Nd' + "\n")
Lx = format( data['Lx'], '.16f')
Lz = format( data['Lz'], '.16f')
file.write(Lx + '\t\t%Lx' + "\n")
file.write(Lz + '\t\t%Lz' + "\n")
lx = data['Lx'] / (2. * math.pi)
lz = data['Lz'] / (2. * math.pi)
file.write(str( lx ) + '\t\t\t\t\t\t%lx=Lx/(2pi)' + "\n")
file.write(str( lz ) + '\t\t\t\t\t\t%lz=Lz/(2pi)' + "\n")
alpha = (2.* math.pi) / data['Lx']
file.write(str( alpha ) + '\t\t\t\t\t\t%alpha=2pi/Lx' + "\n")
gamma = (2.* math.pi) / data['Lz']
file.write(str( gamma ) + '\t\t\t\t\t\t%gamma=2pi/Lz' + "\n")
file.close()
return 0
def write_DAT_file(data, directory):
# Write a '.dat' file for the geometry info for Paraview
flowField = data['resolvent_flowField']
fileName = "/u0.dat"
file = open(directory + fileName, "w")
title = 'TITLE= "Initial flow field at Re = 1200"\n'
columns = 'VARIABLES = "X", "Y", "Z", "U", "V", "W"\n'
zones = 'ZONE I=' + str( int(data['Nx'])) + ', J=' + str( int(data['Ny']) ) + ', K=' + str( int(data['Nz']) ) + ', F=POINT\n'
file.write(title)
file.write(columns)
file.write(zones)
for nx in range(0, data['Nx']):
for ny in range(0, data['Ny']):
for nz in range(0, data['Nz']):
string = format(data['X'][nx], '.8f') + ' '
string += format(data['Y'][ny], '.8f') + ' '
string += format(data['Z'][nz], '.8f') + ' '
string += format(flowField[0, nx, ny, nz], '.16f') + ' '
string += format(flowField[1, nx, ny, nz], '.16f') + ' '
string += format(flowField[2, nx, ny, nz], '.16f') + ' '
file.write(string+'\n')
file.close()
return 0
def write_DAT_file_from_ff(data, directory, t, fileName):
# Write a '.dat' file for the geometry info for Paraview
flowField = data['flowField']['physical']
fileName = '/u'+fileName+'.dat'
file = open(directory + fileName, "w")
Nx = data['geometry']['physical']['Nx']
Ny = data['geometry']['physical']['Ny']
Nz = data['geometry']['physical']['Nz']
Lx = data['geometry']['physical']['Lx']
Lz = data['geometry']['physical']['Lz']
x = np.linspace(0.0, Lx, Nx)
z = np.linspace(-Lz/2.0, Lz/2.0, Nz)
y = np.linspace(-1.0,1.0,Ny)
for ny in range(0, Ny):
y[ny] = math.cos(ny*math.pi/(Ny-1))
title = 'TITLE= "Flow field at t = ' + str(t) + '"\n'
columns = 'VARIABLES = "X", "Y", "Z", "U", "V", "W"\n'
zones = 'ZONE I=' + str( int(Nx)) + ', J=' + str( int(Ny) ) + ', K=' + str( int(Nz) ) + ', F=POINT\n'
file.write(title)
file.write(columns)
file.write(zones)
for nx in range(0, Nx):
for ny in range(0, Ny):
for nz in range(0, Nz):
string = format(x[nx], '.8f') + ' '
string += format(y[ny], '.8f') + ' '
string += format(z[nz], '.8f') + ' '
string += format(flowField[0, nx, ny, nz], '.16f') + ' '
string += format(flowField[1, nx, ny, nz], '.16f') + ' '
string += format(flowField[2, nx, ny, nz], '.16f') + ' '
file.write(string+'\n')
file.close()
return 0
def writeMeanASCIIfile(flowField, directory):
fileName = "/umean.asc"
file = open(directory + fileName, "w")
for nx in range(0, flowField.shape[1]):
for ny in range(0, flowField.shape[2]):
for nz in range(0, flowField.shape[3]):
for nd in range(0, flowField.shape[0]):
tmp = flowField[nd, nx, ny, nz]
tmp = format(tmp, '.16f')
string = str(nx) + '\t'
string+= str(ny) + '\t'
string+= str(nz) + '\t'
string+= str(nd) + '\t'
string+= tmp + '\n'
file.write(string)
file.close()
print('Boom, the Mean ASCII is done.')
return 0
def makeSolutionDirectory(data, directory, n, re, kx, kz, c, amplitudes, i):
i = i+1
kxstr = data['kx']
if kx.shape[0] > 1:
i = str(i).zfill(3)
folderName = "/wavepacket_" + str(i) + "_" + str(kx.shape[0]) + "modes_" + str(amplitudes[0])
else:
kxstr = data['kx']
kz = data['kz']
c = data['c']
A = data['A']
i = str(i).zfill(3)
if kx[0][0] < 0:
folderName = "/triplet_case_"+ str(i) +"_+-" + str(kxstr) + "_+-" + str(kz) + "_" + str(c) + "_" + str(A)
else:
folderName = "/triplet_case_"+ str(i) +"_" + str(kxstr) + "_+-" + str(kz) + "_" + str(c) + "_" + str(A)
directory = directory + folderName
if not os.path.exists(directory):
os.makedirs(directory)
fileName = '/details.txt'
file = open(directory + fileName, "w")
file.write('n (Ny - 2)'+ "\n")
file.write(str(n)+ "\n"+ "\n")
file.write('Re'+ "\n")
file.write(str(re)+ "\n"+ "\n")
file.write('kx'+ "\n")
file.write(str(kx)+ "\n"+ "\n")
file.write('kz'+ "\n")
file.write(str(kz)+ "\n"+ "\n")
file.write('c'+ "\n")
file.write(str(c)+ "\n"+ "\n")
file.write('amplitudes'+ "\n")
file.write(str(amplitudes)+ "\n"+ "\n")
file.close()
return directory
def perturbFlowField(data):
if data['read']:
u = data['flowField']['physical'][0, :, :, :]
# perturb u vel
u[:, 1, :] = 0.01
u[:, 2, :] = 0.02
u[:, 3, :] = 0.01
data['flowField']['physical'] = u
else:
u = data['resolvent_flowField'][0, :, :, :]
# perturb u vel
u[:, 1, :] = 0.4
u[:, 2, :] = 0.7
u[:, 3, :] = 0.6
u[:, 4, :] = 0.3
data['resolvent_flowField'][0, :, :, :] = u
data['U'] = u
return data
def writeASCIIfile_general(data, directory):
flowField = data['flowField']['physical']
fileName = "/wave_packet_" + str(kx) + "_+-" + str(kz) + "_" + str(c) + "_" + str(A) + ".asc"
file = open(directory + fileName, "w")
for nx in range(0, data['Nx']):
for ny in range(0, data['Ny']):
for nz in range(0, data['Nz']):
for nd in range(0, data['Nd']):
tmp = flowField[nd, nx, ny, nz]
tmp = format(tmp, '.16f')
file.write(tmp + "\n")
file.close()
print('Boom, the ASCII is done.')
return 0
def writeSpectralASCIIfile(data, directory):
flowField = data['spectral_ff']
fileName = "/u0_spec_rank-"+str(data['Rank'])+".asc"
file = open(directory + fileName, "w")
for mx in range(0, data['Mx']):
for ny in range(0, data['Ny']):
for mz in range(0, data['Mz']):
for nd in range(0, data['Nd']):
tmpReal = flowField[nd, mx, ny, mz].real
tmpImag = flowField[nd, mx, ny, mz].imag
# tmpReal = format(tmpReal, '.8f')
# tmpImag = format(tmpImag, '.8f')
output = '(' + str(tmpReal) + ', ' + str(tmpImag) + ')'
# if tmpImag >= 0.0:
# output = str(tmpReal) +'+'+ str(tmpImag)+'j'
# elif tmpImag < 0.0:
# output = str(tmpReal) + str(tmpImag)+'j'
file.write(output + "\n")
file.close()
print('Boom, the SPECTRAL ASCII is done.')
return 0
def writeSpectralGEOMfile(data, directory):
kx = data['kx']
kz = data['kz']
c = data['c']
A = data['A']
# fileName = "/wave_packet_" + str(kx) + "_+-" + str(kz) + "_" + str(c) + "_" + str(A) + ".geom"
fileName = "/u0_spec_rank-"+str(data['Rank'])+".geom"
file = open(directory + fileName, "w")
# file.write(str( int(len(data['Mx'])) ) + '\t\t\t\t\t\t%Mx' + "\n")
# file.write(str( int(len(data['Mz'])) ) + '\t\t\t\t\t\t%Mz' + "\n")
file.write(str( int(data['Nx']) ) + '\t\t\t\t\t\t%Nx' + "\n")
file.write(str( int(data['Ny']) ) + '\t\t\t\t\t\t%Ny' + "\n")
file.write(str( int(data['Nz']) ) + '\t\t\t\t\t\t%Nz' + "\n")
file.write(str( int(data['Nd']) ) + '\t\t\t\t\t\t%Nd' + "\n")
Lx = format( data['Lx'], '.16f')
Lz = format( data['Lz'], '.16f')
file.write(Lx + '\t\t%Lx' + "\n")
file.write(Lz + '\t\t%Lz' + "\n")
lx = data['Lx'] / (2. * math.pi)
lz = data['Lz'] / (2. * math.pi)
file.write(str( lx ) + '\t\t%lx=Lx/(2pi)' + "\n")
file.write(str( lz ) + '\t\t%lz=Lz/(2pi)' + "\n")
alpha = str(data['fund_alpha'])
file.write(str( alpha ) + '\t\t%alpha=2pi/Lx' + "\n")
gamma = str(data['fund_beta'])
file.write(str( gamma ) + '\t\t%gamma=2pi/Lz' + "\n")
file.close()
return 0
def makeOutputDictionary(generated_ff, geom, y_cheb, uniform, string_kx, string_kz, string_c, string_A):
outputDic = {}
U = np.zeros((geom['Nd'], geom['Nx'], 3*geom['m'], geom['Nz']))
U_u = generated_ff.real[:, 0:geom['m'] , :]
U_v = generated_ff.real[:, geom['m']:2*geom['m'], :]
U_w = generated_ff.real[:, 2*geom['m']:3*geom['m'], :]
for i in range(0, geom['Nd']):
for nx in range(0, geom['Nx']):
for ny in range(0, geom['m']):
for nz in range(0, geom['Nz']):
if i == 0: # u direction
U[i, nx, ny, nz] = U_u[nx, ny, nz]
elif i == 1: # v direction
U[i, nx, ny, nz] = U_v[nx, ny, nz]
elif i == 2: # w direction
U[i, nx, ny, nz] = U_w[nx, ny, nz]
# L2Norm = np.linalg.norm(U)
# print(np.allclose(L2Norm, np.sqrt(np.sum(np.square(U[:,:,:,:])))))
# magn = 10.0
# U *= magn / L2Norm
# Interpolation to go from y_cheb toy_uniform
Ny = geom['m']
y_uniform = np.linspace(1.0, -1.0, Ny*1.0)
y_cheb = np.asarray(y_cheb)
y_cheb = np.squeeze(y_cheb)
U_u_uniform = np.zeros((geom['Nx'], geom['m'], geom['Nz']))
U_v_uniform = np.zeros((geom['Nx'], geom['m'], geom['Nz']))
U_w_uniform = np.zeros((geom['Nx'], geom['m'], geom['Nz']))
for nx in range(0, geom['Nx']):
for nz in range(0, geom['Nz']):
uprofile = U_u[nx, :, nz] # 1-d vector
# fill value is the no-slip boundary condition
fu = interp1d(y_cheb, uprofile, bounds_error=False, fill_value=0.0, kind='cubic')
fu = fu(y_uniform)
U_u_uniform[nx, :, nz] = fu
vprofile=U_v[nx, :, nz] # 1-d vector
fv = interp1d(y_cheb, vprofile, bounds_error=False, fill_value=0.0, kind='cubic')
fv = fv(y_uniform)
U_v_uniform[nx, :, nz] = fv
wprofile=U_w[nx, :, nz] # 1-d vector
fw = interp1d(y_cheb, wprofile, bounds_error=False, fill_value=0.0, kind='cubic')
fw = fw(y_uniform)
U_w_uniform[nx, :, nz] = fw
# plt.plot(y_cheb, uprofile, 'r-', y_uniform, fu, 'g--')
# plt.legend(['data', 'cubic'], loc='best')
# plt.grid(True)
# plt.show()
outputDic['resolvent_flowField'] = U
if uniform:
outputDic['U'] = U_u_uniform
outputDic['V'] = U_v_uniform
outputDic['W'] = U_w_uniform
outputDic['Y'] = y_uniform
else:
outputDic['U'] = U_u
outputDic['V'] = U_v
outputDic['W'] = U_w
outputDic['Y'] = y_cheb
outputDic['X'] = geom['x']
outputDic['Z'] = geom['z']
outputDic['Nx'] = geom['Nx']
outputDic['Ny'] = geom['m']
outputDic['Nz'] = geom['Nz']
outputDic['Nd'] = geom['Nd']
outputDic['Lx'] = geom['Lx']
outputDic['Lz'] = geom['Lz']
outputDic['kx'] = string_kx
outputDic['kz'] = string_kz
outputDic['c'] = string_c
outputDic['A'] = string_A
return outputDic
def convert2ff(direc):
os.chdir(direc)
os.system('ascii2field -p false -ge u0.geom u0.asc u0.ff')
return 0
def writeSymmsFile(directory, fileName, N, symStrAry):
"""
The FieldSymmetry uses ASCII input-output. The storage format is
s sx sy sz ax az
"""
file = open(directory + '/' + fileName, "w")
if N == 1:
# simply write the sigma file
file.write(symStrAry[0])
elif N > 1:
# Change format of file
header = '% ' + str(N) + '\n'
file.write(header)
for i in range(0, N):
string = symStrAry[i] + '\n'
file.write(string)
file.close()
return 0