def main():
"""Converts PETSc output to .vtk format."""
# parse command-line
args = read_inputs()
print('[case-directory] {}'.format(args.case_directory))
print('[variables] {}'.format(args.variables))
# list of time-steps to post-process
time_steps = ioPetIBM.get_time_steps(args.case_directory, args.time_steps)
# read mesh grid
grid = ioPetIBM.read_grid(args.case_directory)
for time_step in time_steps:
if 'velocity' in args.variables:
velocity = ioPetIBM.read_velocity(args.case_directory, time_step, grid,
periodic=args.periodic)
# need to get velocity at cell-centers, not staggered arrangement
velocity = interpolate_cell_centers(velocity)
ioPetIBM.write_vtk(velocity, args.case_directory, time_step,
name='velocity',
view=[args.bottom_left, args.top_right],
stride=args.stride)
if 'pressure' in args.variables:
pressure = ioPetIBM.read_pressure(args.case_directory, time_step, grid)
ioPetIBM.write_vtk(pressure, args.case_directory, time_step,
name='pressure',
view=[args.bottom_left, args.top_right],
stride=args.stride)
def compare_velocity(self):
"""Compares the velocity field node by node with a reference."""
time_step = ioPetIBM.get_time_steps(self.directory)[-1]
grid = ioPetIBM.read_grid(self.directory)
velocity = ioPetIBM.read_velocity(self.directory,
time_step,
grid,
periodic=self.periodic)
grid = ioPetIBM.read_grid(self.reference)
velocity_reference = ioPetIBM.read_velocity(self.reference,
time_step,
grid,
periodic=self.periodic)
for i, component in enumerate(velocity):
self.compare_arrays(component.x,
velocity_reference[i].x,
tag='velocity[{}]: x-nodes'.format(i))
self.compare_arrays(component.y,
velocity_reference[i].y,
tag='velocity[{}]: y-nodes'.format(i))
try:
self.compare_arrays(component.z,
velocity_reference[i].z,
tag='velocity[{}]: z-nodes'.format(i))
except:
pass
self.compare_arrays(component.values,
velocity_reference[i].values,
tag='velocity[{}]: values'.format(i))
def main(args):
"""
Generates .vtk files out of the saved PETSc solutions.
Parameters
----------
args: namespace
Databased with arguments parsed from the command-line.
"""
print('[directory] {}'.format(args.directory))
print('[variables] {}'.format(args.variables))
# list of time-steps to post-process
time_steps = ioPetIBM.get_time_steps(args.directory, args.time_steps)
# read mesh grid
grid = ioPetIBM.read_grid(args.directory)
for time_step in time_steps:
if 'velocity' in args.variables:
velocity = ioPetIBM.read_velocity(args.directory, time_step, grid,
periodic=args.periodic)
# need to get velocity at cell-centers, not staggered arrangement
velocity = interpolate_cell_centers(velocity)
ioPetIBM.write_vtk(velocity, args.directory, time_step,
name='velocity',
view=[args.bottom_left, args.top_right],
stride=args.stride)
if 'pressure' in args.variables:
pressure = ioPetIBM.read_pressure(args.directory, time_step, grid)
ioPetIBM.write_vtk(pressure, args.directory, time_step,
name='pressure',
view=[args.bottom_left, args.top_right],
stride=args.stride)
def compare_pressure(self):
"""
Compares the pressure field node by node with a reference.
"""
time_step = ioPetIBM.get_time_steps(directory=self.directory)[-1]
grid = ioPetIBM.read_grid(directory=self.directory)
pressure = ioPetIBM.read_pressure(time_step,
grid,
directory=self.directory)
grid = ioPetIBM.read_grid(directory=self.reference)
pressure_reference = ioPetIBM.read_pressure(time_step,
grid,
directory=self.reference)
self.compare_arrays(pressure.x,
pressure_reference.x,
tag='pressure: x-nodes')
self.compare_arrays(pressure.y,
pressure_reference.y,
tag='pressure: y-nodes')
try:
self.compare_arrays(pressure.z,
pressure_reference.z,
tag='pressure: z-nodes')
except:
pass
self.compare_arrays(pressure.values,
pressure_reference.values,
tag='pressure: values')
def main():
"""Plots the the velocity, pressure and vorticity fields at saved time-steps
for a two-dimensional simulation.
"""
# parse command-line
args = read_inputs()
print('[case directory] {}'.format(args.case_directory))
time_steps = ioPetIBM.get_time_steps(args.case_directory, args.time_steps)
# create directory where images will be saved
images_directory = '{}/images'.format(args.case_directory)
print('[images directory] {}'.format(images_directory))
if not os.path.isdir(images_directory):
os.makedirs(images_directory)
# read the grid nodes
coords = ioPetIBM.read_grid(args.case_directory)
# load default style of matplotlib figures
pyplot.style.use('{}/scripts/python/style/'
'style_PetIBM.mplstyle'.format(os.environ['PETIBM_DIR']))
for time_step in time_steps:
if args.velocity or args.vorticity:
# get velocity fields
u, v = ioPetIBM.read_velocity(args.case_directory, time_step, coords,
periodic=args.periodic)
if args.velocity:
# plot u-velocity field
u.label = 'u-velocity'
image_path = '{}/uVelocity{:0>7}.png'.format(images_directory, time_step)
plot_contour(u, args.u_range, image_path,
view=args.bottom_left+args.top_right,
size=args.size, dpi=args.dpi)
# plot v-velocity field
v.label = 'v-velocity'
image_path = '{}/vVelocity{:0>7}.png'.format(images_directory, time_step)
plot_contour(v, args.v_range, image_path,
view=args.bottom_left+args.top_right,
size=args.size, dpi=args.dpi)
if args.vorticity:
# compute vorticity field
w = vorticity(u, v)
# plot vorticity field
w.label = 'vorticity'
image_path = '{}/vorticity{:0>7}.png'.format(images_directory, time_step)
plot_contour(w, args.vorticity_range, image_path,
view=args.bottom_left+args.top_right,
size=args.size, dpi=args.dpi)
if args.pressure:
# get pressure field
p = ioPetIBM.read_pressure(args.case_directory, time_step, coords)
# plot pressure field
p.label = 'pressure'
image_path = '{}/pressure{:0>7}.png'.format(images_directory, time_step)
plot_contour(p, args.pressure_range, image_path,
view=args.bottom_left+args.top_right,
size=args.size, dpi=args.dpi)
def compare_pressure(self):
"""Compares the pressure field node by node with a reference."""
time_step = ioPetIBM.get_time_steps(self.directory)[-1]
grid = ioPetIBM.read_grid(self.directory)
pressure = ioPetIBM.read_pressure(self.directory, time_step, grid)
grid = ioPetIBM.read_grid(self.reference)
pressure_reference = ioPetIBM.read_pressure(self.reference, time_step, grid)
self.compare_arrays(pressure.x, pressure_reference.x,
tag='pressure: x-nodes')
self.compare_arrays(pressure.y, pressure_reference.y,
tag='pressure: y-nodes')
try:
self.compare_arrays(pressure.z, pressure_reference.z,
tag='pressure: z-nodes')
except:
pass
self.compare_arrays(pressure.values, pressure_reference.values,
tag='pressure: values')
def compare_velocity(self):
"""Compares the velocity field node by node with a reference."""
time_step = ioPetIBM.get_time_steps(self.directory)[-1]
grid = ioPetIBM.read_grid(self.directory)
velocity = ioPetIBM.read_velocity(self.directory, time_step, grid,
periodic=self.periodic)
grid = ioPetIBM.read_grid(self.reference)
velocity_reference = ioPetIBM.read_velocity(self.reference, time_step, grid,
periodic=self.periodic)
for i, component in enumerate(velocity):
self.compare_arrays(component.x, velocity_reference[i].x,
tag='velocity[{}]: x-nodes'.format(i))
self.compare_arrays(component.y, velocity_reference[i].y,
tag='velocity[{}]: y-nodes'.format(i))
try:
self.compare_arrays(component.z, velocity_reference[i].z,
tag='velocity[{}]: z-nodes'.format(i))
except:
pass
self.compare_arrays(component.values, velocity_reference[i].values,
tag='velocity[{}]: values'.format(i))
def main():
"""Converts PETSc output to .vtk format."""
# parse command-line
args = read_inputs()
print('[case-directory] {}'.format(args.case_directory))
print('[variables] {}'.format(args.variables))
# list of time-steps to post-process
time_steps = ioPetIBM.get_time_steps(args.case_directory, args.time_steps)
# read mesh grid
grid = ioPetIBM.read_grid(args.case_directory)
for time_step in time_steps:
if 'velocity' in args.variables:
velocity = ioPetIBM.read_velocity(args.case_directory,
time_step,
grid,
periodic=args.periodic)
# need to get velocity at cell-centers, not staggered arrangement
velocity = interpolate_cell_centers(velocity)
ioPetIBM.write_vtk(velocity,
args.case_directory,
time_step,
name='velocity',
view=[args.bottom_left, args.top_right],
stride=args.stride)
if 'pressure' in args.variables:
pressure = ioPetIBM.read_pressure(args.case_directory, time_step,
grid)
ioPetIBM.write_vtk(pressure,
args.case_directory,
time_step,
name='pressure',
view=[args.bottom_left, args.top_right],
stride=args.stride)
def main(args):
"""
Plots and writes the velocity components at the centerline of the cavity
and compares with experimental results form Ghia et al. (1982).
Parameters
----------
args: namespace
Database with arguments parsed from the command-line.
"""
# column indices in file with experimental results
cols = {
'100': {
'u': 1,
'v': 7
},
'1000': {
'u': 2,
'v': 8
},
'3200': {
'u': 3,
'v': 9
},
'5000': {
'u': 4,
'v': 10
},
'10000': {
'u': 5,
'v': 11
}
}
experimental_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'cavity-GGS82.txt')
print('[case directory] {}'.format(args.directory))
Re = args.Re
if not args.time_step:
args.time_step = ioPetIBM.get_time_steps(directory=args.directory)[-1]
# read mesh grid
grid = ioPetIBM.read_grid(directory=args.directory)
nx, ny = grid[0].size - 1, grid[1].size - 1
# create directory where images will be saved
images_directory = os.path.join(args.directory, 'images')
print('[images directory] {}'.format(images_directory))
if not os.path.isdir(images_directory):
os.makedirs(images_directory)
# create directory where data will be saved
data_directory = os.path.join(args.directory, 'data')
print('[data directory] {}'.format(data_directory))
if not os.path.isdir(data_directory):
os.makedirs(data_directory)
# get velocity field
u, v = ioPetIBM.read_velocity(args.time_step,
grid,
directory=args.directory)
# load default style for figures
pyplot.style.use(
os.path.join(os.environ['PETIBM_DIR'], 'scripts', 'python', 'style',
'style_PetIBM.mplstyle'))
# plot and write u-velocity along y-centerline
print('\nPlot u-velocity along vertical centerline ...')
pyplot.grid(True)
pyplot.xlabel('y', )
pyplot.ylabel('u-velocity along vertical centerline')
if nx % 2 == 0:
u_centerline = u.values[:, nx / 2 - 1]
else:
u_centerline = 0.5 * (u.values[:, nx / 2 - 1] + u.values[:, nx / 2])
pyplot.plot(u.y,
u_centerline,
label='PetIBM',
color='k',
linestyle='-',
linewidth=1)
if Re in list(cols.keys()):
print('\nComparison with Ghia et al. (1982)')
with open(experimental_file, 'r') as infile:
y_exp, u_exp = numpy.loadtxt(infile,
dtype=float,
usecols=(0, cols[Re]['u']),
unpack=True)
pyplot.plot(y_exp,
u_exp,
label='Ghia et al. (1982)',
linewidth=0,
marker='o')
pyplot.legend()
pyplot.title('Lid-driven cavity flow at Re={} (mesh: {}x{})'
''.format(Re, nx, ny))
pyplot.savefig(
os.path.join(images_directory,
'uVelocityCenterlineRe{}_{}x{}.png'.format(Re, nx, ny)))
pyplot.close()
print('\nWrite u-velocity along vertical centerline ...')
data_path = os.path.join(
data_directory, 'uVelocityCenterlineRe{}_{}x{}.txt'.format(Re, nx, ny))
with open(data_path, 'w') as outfile:
numpy.savetxt(outfile,
numpy.c_[u.y, u_centerline],
fmt='%.6f',
delimiter='\t',
header='u-velocity along vertical centerline\n'
'Re={}, mesh: {}x{}\n[y]\t[u]'.format(Re, nx, ny))
# plot and write v-velocity along x-centerline
print('\nPlot v-velocity along horizontal centerline ...')
pyplot.grid(True)
pyplot.xlabel('x')
pyplot.ylabel('v-velocity along horizontal centerline')
if ny % 2 == 0:
v_centerline = v.values[ny / 2 - 1, :]
else:
v_centerline = 0.5 * (v.values[ny / 2 - 1, :] + v.values[ny / 2, :])
pyplot.plot(v.x,
v_centerline,
label='PetIBM',
color='k',
linestyle='-',
linewidth=1)
if Re in list(cols.keys()):
print('Comparison with Ghia et al. (1982)')
with open(experimental_file, 'r') as infile:
x_exp, u_exp = numpy.loadtxt(infile,
dtype=float,
usecols=(6, cols[Re]['v']),
unpack=True)
pyplot.plot(x_exp,
u_exp,
label='Ghia et al. (1982)',
linewidth=0,
marker='o')
pyplot.legend()
pyplot.title('Lid-driven cavity flow at Re={} (mesh: {}x{})'
''.format(Re, nx, ny))
pyplot.savefig(
os.path.join(images_directory,
'vVelocityCenterlineRe{}_{}x{}.png'.format(Re, nx, ny)))
pyplot.close()
print('\nwrite v-velocity along horizontal centerline ...')
data_path = os.path.join(
data_directory, 'vVelocityCenterlineRe{}_{}x{}.txt'.format(Re, nx, ny))
with open(data_path, 'w') as outfile:
numpy.savetxt(outfile,
numpy.c_[v.x, v_centerline],
fmt='%.6f',
delimiter='\t',
header='v-velocity along horizontal centerline\n'
'Re={}, mesh: {}x{}\n[x]\t[v]'.format(Re, nx, ny))
def main():
"""Plots and writes the velocity components at the centerline of the cavity
and compares with experimental results form Ghia et al. (1982).
"""
# column indices in file with experimental results
cols = {'100': {'u': 1, 'v': 7},
'1000': {'u':2, 'v': 8},
'3200': {'u':3, 'v': 9},
'5000': {'u':4, 'v': 10},
'10000': {'u': 5, 'v': 11}}
experimental_file = ('{}/validation_data/'
'cavity-GGS82.txt'.format(os.environ['PETIBM_DIR']))
# parse command-line
args = read_inputs()
print('[case directory] {}'.format(args.case_directory))
Re = args.Re
if not args.time_step:
args.time_step = ioPetIBM.get_time_steps(args.case_directory)[-1]
# read mesh grid
grid = ioPetIBM.read_grid(args.case_directory)
nx, ny = grid[0].size-1, grid[1].size-1
# create directory where images will be saved
images_directory = '{}/images'.format(args.case_directory)
print('[images directory] {}'.format(images_directory))
if not os.path.isdir(images_directory):
os.makedirs(images_directory)
# create directory where data will be saved
data_directory = '{}/data'.format(args.case_directory)
print('[data directory] {}'.format(data_directory))
if not os.path.isdir(data_directory):
os.makedirs(data_directory)
# get velocity field
u, v = ioPetIBM.read_velocity(args.case_directory, args.time_step, grid)
# load default style for figures
pyplot.style.use('{}/scripts/python/style/'
'style_PetIBM.mplstyle'.format(os.environ['PETIBM_DIR']))
# plot and write u-velocity along y-centerline
print('\nPlot u-velocity along vertical centerline ...')
pyplot.xlabel('y',)
pyplot.ylabel('u-velocity along vertical centerline')
if nx%2 == 0:
u_centerline = u.values[:, nx/2-1]
else:
u_centerline = 0.5*(u.values[:, nx/2-1]+u.values[:, nx/2])
pyplot.plot(u.y, u_centerline, label='PetIBM',
color='k', linestyle='-', linewidth=1)
if Re in list(cols.keys()):
print('\nComparison with Ghia et al. (1982)')
with open(experimental_file, 'r') as infile:
y_exp, u_exp = numpy.loadtxt(infile, dtype=float,
usecols= (0, cols[Re]['u']), unpack=True)
pyplot.plot(y_exp, u_exp, label='Ghia et al. (1982)',
linewidth=0, marker='o')
pyplot.legend()
pyplot.title('Lid-driven cavity flow at Re={} (mesh: {}x{})'.format(Re, nx, ny))
pyplot.savefig('{}/uVelocityCenterlineRe{}_{}x{}.png'.format(images_directory,
Re, nx, ny))
pyplot.close()
print('\nWrite u-velocity along vertical centerline ...')
data_path = '{}/uVelocityCenterlineRe{}_{}x{}.txt'.format(data_directory,
Re, nx, ny)
with open(data_path, 'w') as outfile:
numpy.savetxt(outfile, numpy.c_[u.y, u_centerline],
fmt='%.6f', delimiter='\t',
header='u-velocity along vertical centerline\n'
'Re={}, mesh: {}x{}\n[y]\t[u]'.format(Re, nx, ny))
# plot and write v-velocity along x-centerline
print('\nPlot v-velocity along horizontal centerline ...')
pyplot.xlabel('x')
pyplot.ylabel('v-velocity along horizontal centerline')
if ny%2 == 0:
v_centerline = v.values[ny/2-1, :]
else:
v_centerline = 0.5*(v.values[ny/2-1, :]+v.values[ny/2, :])
pyplot.plot(v.x, v_centerline, label='PetIBM',
color='k', linestyle='-', linewidth=1)
if Re in list(cols.keys()):
print('Comparison with Ghia et al. (1982)')
with open(experimental_file, 'r') as infile:
x_exp, u_exp = numpy.loadtxt(infile, dtype=float,
usecols= (6, cols[Re]['v']), unpack=True)
pyplot.plot(x_exp, u_exp, label='Ghia et al. (1982)',
linewidth=0, marker='o')
pyplot.legend()
pyplot.title('Lid-driven cavity flow at Re={} (mesh: {}x{})'.format(Re, nx, ny))
pyplot.savefig('{}/vVelocityCenterlineRe{}_{}x{}.png'.format(images_directory,
Re, nx, ny))
pyplot.close()
print('\nwrite v-velocity along horizontal centerline ...')
data_path = '{}/vVelocityCenterlineRe{}_{}x{}.txt'.format(data_directory,
Re, nx, ny)
with open(data_path, 'w') as outfile:
numpy.savetxt(outfile, numpy.c_[v.x, v_centerline],
fmt='%.6f', delimiter='\t',
header='v-velocity along horizontal centerline\n'
'Re={}, mesh: {}x{}\n[x]\t[v]'.format(Re, nx, ny))
def main():
"""Plots the the velocity, pressure and vorticity fields at saved time-steps
for a two-dimensional simulation.
"""
# parse command-line
args = read_inputs()
print('[case directory] {}'.format(args.case_directory))
time_steps = ioPetIBM.get_time_steps(args.case_directory, args.time_steps)
# create directory where images will be saved
images_directory = '{}/images'.format(args.case_directory)
print('[images directory] {}'.format(images_directory))
if not os.path.isdir(images_directory):
os.makedirs(images_directory)
# read the grid nodes
coords = ioPetIBM.read_grid(args.case_directory)
# load default style of matplotlib figures
pyplot.style.use('{}/scripts/python/style/'
'style_PetIBM.mplstyle'.format(os.environ['PETIBM_DIR']))
for time_step in time_steps:
if args.velocity or args.vorticity:
# get velocity fields
u, v = ioPetIBM.read_velocity(args.case_directory,
time_step,
coords,
periodic=args.periodic)
if args.velocity:
# plot u-velocity field
u.label = 'u-velocity'
image_path = '{}/uVelocity{:0>7}.png'.format(
images_directory, time_step)
plot_contour(u,
args.u_range,
image_path,
view=args.bottom_left + args.top_right,
size=args.size,
dpi=args.dpi)
# plot v-velocity field
v.label = 'v-velocity'
image_path = '{}/vVelocity{:0>7}.png'.format(
images_directory, time_step)
plot_contour(v,
args.v_range,
image_path,
view=args.bottom_left + args.top_right,
size=args.size,
dpi=args.dpi)
if args.vorticity:
# compute vorticity field
w = vorticity(u, v)
# plot vorticity field
w.label = 'vorticity'
image_path = '{}/vorticity{:0>7}.png'.format(
images_directory, time_step)
plot_contour(w,
args.vorticity_range,
image_path,
view=args.bottom_left + args.top_right,
size=args.size,
dpi=args.dpi)
if args.pressure:
# get pressure field
p = ioPetIBM.read_pressure(args.case_directory, time_step, coords)
# plot pressure field
p.label = 'pressure'
image_path = '{}/pressure{:0>7}.png'.format(
images_directory, time_step)
plot_contour(p,
args.pressure_range,
image_path,
view=args.bottom_left + args.top_right,
size=args.size,
dpi=args.dpi)
def main(args):
"""
Plots the the velocity, pressure and vorticity fields at saved time-steps
for a two-dimensional simulation.
Parameters
----------
args: namespace
Database with arguments parsed from the command-line.
"""
print('[case directory] {}'.format(args.directory))
time_steps = ioPetIBM.get_time_steps(args.time_steps,
directory=args.directory)
# create directory where images will be saved
images_directory = os.path.join(args.directory, 'images')
print('[images directory] {}'.format(images_directory))
if not os.path.isdir(images_directory):
os.makedirs(images_directory)
# read the grid nodes
coords = ioPetIBM.read_grid(directory=args.directory)
# load default style of matplotlib figures
pyplot.style.use(
os.path.join(os.environ['PETIBM_DIR'], 'scripts', 'python', 'style',
'style_PetIBM.mplstyle'))
for time_step in time_steps:
if args.velocity or args.vorticity:
# get velocity fields
u, v = ioPetIBM.read_velocity(time_step,
coords,
directory=args.directory,
periodic=args.periodic)
if args.velocity:
# plot u-velocity field
u.label = 'u-velocity'
image_path = os.path.join(
images_directory, 'uVelocity{:0>7}.png'.format(time_step))
plot_contour(u,
args.u_range,
image_path,
view=args.bottom_left + args.top_right,
size=args.size,
dpi=args.dpi)
# plot v-velocity field
v.label = 'v-velocity'
image_path = os.path.join(
images_directory, 'vVelocity{:0>7}.png'.format(time_step))
plot_contour(v,
args.v_range,
image_path,
view=args.bottom_left + args.top_right,
size=args.size,
dpi=args.dpi)
if args.vorticity:
# compute vorticity field
w = vorticity(u, v)
# plot vorticity field
w.label = 'vorticity'
image_path = os.path.join(
images_directory, 'vorticity{:0>7}.png'.format(time_step))
plot_contour(w,
args.vorticity_range,
image_path,
view=args.bottom_left + args.top_right,
size=args.size,
dpi=args.dpi)
if args.pressure:
# get pressure field
p = ioPetIBM.read_pressure(time_step,
coords,
directory=args.directory)
# plot pressure field
p.label = 'pressure'
image_path = os.path.join(images_directory,
'pressure{:0>7}.png'.format(time_step))
plot_contour(p,
args.pressure_range,
image_path,
view=args.bottom_left + args.top_right,
size=args.size,
dpi=args.dpi)