def setup():
#Import CPL library
from cplpy import CPL
#initialise MPI
from mpi4py import MPI
comm = MPI.COMM_WORLD
#Check run as part of a coupled run
comm.rank
# Parameters of the cpu topology (cartesian grid)
npxyz = np.array([1, 1, 1], order='F', dtype=np.int32)
xyzL = np.array([1., 1., 1.], order='F', dtype=np.float64)
xyz_orig = np.array([0.0, 0.0, 0.0], order='F', dtype=np.float64)
#initialise CPL
CPL = CPL()
MD_COMM = CPL.init(CPL.MD_REALM)
CPL.setup_md(MD_COMM.Create_cart([npxyz[0], npxyz[1], npxyz[2]]), xyzL, xyz_orig)
recvbuf, sendbuf = CPL.get_arrays(recv_size=9, send_size=8)
#Analytical solution
dt = 0.05
U = 1.0
nu = 1.004e-2
Re = xyzL[1]/nu #Note Reynolds in independent of velocity in analytical fn
ncx = CPL.get("ncx")
ncy = CPL.get("ncy")
ncz = CPL.get("ncz")
CAObj = CA(Re=Re, U=U, Lmin=0., Lmax=xyzL[1], npoints=2*ncy+1, nmodes=100*ncy)
#Yield statement delineates end of setup and start of teardown
yield [CPL, MD_COMM, recvbuf, sendbuf, CAObj, dt, U, nu]
CPL.finalize()
MPI.Finalize()
#Get values from CPL library
ncy = CPL.get("ncy")
yL_md = CPL.get("yl_md")
yL_cfd = CPL.get("yl_cfd")
dy = CPL.get("dy")
jcmax_olap = CPL.get("jcmax_olap")
#Setup Coupled domain details
yL_cpl = yL_md + yL_cfd - dy * jcmax_olap
ncy_cpl = int(yL_cpl / dy)
#Create analytical solution object
nu = 1.7
Re = yL_cpl / nu
CAObj = CA(Re=Re, U=1., Lmin=0.0, Lmax=yL_cpl, npoints=2 * ncy_cpl + 2)
#Setup send and recv buffers
recv_array, send_array = CPL.get_arrays(recv_size=3, send_size=4)
#Set velocity
U = 0.5
N = 10
n = 0
for time in range(-2, 199):
# recv data
recv_array, ierr = CPL.recv(recv_array)
# send data
def check_OpenFOAM_vs_Analytical(fdir, plotstuff=False):
OpenFOAMfdir = fdir + "/cfd_data/openfoam_ico/"
print("Openfoam dir = ", OpenFOAMfdir)
OpenFOAMuObj = ppl.OpenFOAM_vField(OpenFOAMfdir, parallel_run=True)
dt = float(OpenFOAMuObj.Raw.delta_t)
tplot = float(
OpenFOAMuObj.Raw.header.headerDict['controlDict']['writeInterval'])
endtime = float(
OpenFOAMuObj.Raw.header.headerDict['controlDict']['endTime'])
enditer = int(endtime / dt)
OpenFOAMwriteinterval = int(tplot / dt)
# Parameters of the cpu topology (cartesian grid)
xyzL = [OpenFOAMuObj.Raw.xL, OpenFOAMuObj.Raw.yL, OpenFOAMuObj.Raw.zL]
dx = OpenFOAMuObj.Raw.dx
dy = OpenFOAMuObj.Raw.dy
dz = OpenFOAMuObj.Raw.dz
ncx = OpenFOAMuObj.Raw.ncx
ncy = OpenFOAMuObj.Raw.ncy
ncz = OpenFOAMuObj.Raw.ncz
#Analytical solution
scriptdir = fdir + "/md_data/python_dummy/"
with open(scriptdir + "MD_sendrecv.py", 'r') as f:
for l in f:
if "U =" in l:
d = l.split("=")
U = float(d[1].replace("\n", "").replace(" ", ""))
nu = OpenFOAMuObj.Raw.nu[0]
Re = (xyzL[1] + dy / 2.) / nu
CAObj = CA(Re=Re,
U=U,
Lmin=0. - dy / 2.,
Lmax=xyzL[1],
npoints=2 * ncy + 2)
if plotstuff:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1, 1)
if "dynamic" in plotstuff or plotstuff == True:
plotstuff = "dynamic"
recds = range(enditer)
elif "summary" in plotstuff:
recds = [5, int(0.1 * enditer), int(0.25 * enditer), enditer - 1]
else:
plotstuff = "False"
n = 0
for time in range(enditer):
#Plot data
if time % OpenFOAMwriteinterval == 0:
rec = int(time / float(OpenFOAMwriteinterval))
try:
OpenFOAMuObj = ppl.OpenFOAM_vField(OpenFOAMfdir,
parallel_run=True)
y, u = OpenFOAMuObj.profile(1, startrec=rec, endrec=rec)
halou = OpenFOAMuObj.read_halo(startrec=rec,
endrec=rec,
haloname="CPLReceiveMD")
print(halou.shape, halou[..., 0].min(), halou[..., 0].max())
halout = OpenFOAMuObj.read_halo(startrec=rec,
endrec=rec,
haloname="movingWall")
y_anal, u_anal = CAObj.get_vprofile(time * dt, flip=True)
error = (u_anal[2:-1:2] - u[:, 0]) / U #/u_anal[2:-1:2]
#error[u_anal[2:-1:2] < 0.005] = 0.
if plotstuff != "False":
if time in recds:
l, = ax.plot(u[:, 0],
y,
'ro-',
label="OpenFOAM domain from file")
ax.plot(np.mean(halou[:, :, :, :, 0], (0, 2)),
y[0] - 0.5 * dy,
'bs',
ms=10,
label="OpenFOAM halo from file")
ax.plot(np.mean(halout[:, :, :, :, 0], (0, 2)),
y[-1] + 0.5 * dy,
'bs',
ms=10,
label="OpenFOAM halo fixed")
ax.plot(u_anal,
y_anal,
'k.-',
label="Analytical Solution")
ax.plot(-error,
y_anal[2:-1:2],
'g--',
label="Analytical Solution")
#ax.plot(10.*(u[:,0]-u_anal[-2:0:-2]),y,'y--')
if "dynamic" in plotstuff:
ax.set_xlim([-0.1, U * 1.1])
ax.set_xlabel("$u$", fontsize=24)
ax.set_ylabel("$y$", fontsize=24)
plt.legend(loc=1)
plt.pause(0.001)
plt.savefig('out{:05}.png'.format(n))
n += 1
ax.cla()
l2 = np.sqrt(np.sum(error[1:]**2))
if not np.isnan(l2):
print(time, "L2 norm error =", l2)
test_error(l2, time)
except AssertionError as e:
print("AssertionError ", e)
raise
except ppl.field.OutsideRecRange:
print("Error result missing", time, OpenFOAMuObj.maxrec, rec)
raise
if "summary" in plotstuff:
ax.set_xlim([-0.1, U * 1.1])
ax.set_xlabel("$u$", fontsize=24)
ax.set_ylabel("$y$", fontsize=24)
#plt.legend(loc=1)
plt.savefig('summary.png')
order='F',
dtype=np.int32)
BC_portion = CPL.my_proc_portion(BC_limits)
[BC_ncxl, BC_ncyl, BC_nczl] = CPL.get_no_cells(BC_portion)
#Plot output
fig, ax = plt.subplots(1, 1)
plt.ion()
plt.show()
#Analytical solution
U = 1.
nu = 1e-02
Re = U / nu
ncy = CPL.get("ncy")
CAObj = CA(Re=Re, U=U, Lmin=0., Lmax=xyzL[1], npoints=ncy)
#Porous region solution
pcell = 7
dy = CPL.get("dy")
yl_cfd = CPL.get("yl_cfd")
CApObj = CA(Re=Re,
U=U,
Lmin=yl_cfd - (pcell + 2.5) * dy,
Lmax=xyzL[1],
npoints=ncy)
#y_p = np.linspace(yl_cfd-(pcell+2)*dy,yl_cfd, ncy)
# Coupling parameters
eps = 0.0001
MD_COMM = CPL.init(CPL.MD_REALM)
CPL.setup_md(MD_COMM.Create_cart([npxyz[0], npxyz[1], npxyz[2]]), xyzL,
xyz_orig)
recvbuf, sendbuf = CPL.get_arrays(recv_size=9, send_size=8)
#Analytical solution
dt = 0.05
U = 1.
nu = 1e-02
Re = xyzL[1] * U / nu
ncx = CPL.get("ncx")
ncy = CPL.get("ncy")
ncz = CPL.get("ncz")
CAObj = CA(Re=Re,
U=U,
Lmin=0.,
Lmax=xyzL[1],
npoints=2 * ncy + 1,
nmodes=100 * ncy)
dx = xyzL[0] / float(ncx)
dy = xyzL[1] / float(ncy)
dz = xyzL[2] / float(ncz)
dV = dx * dy * dz
y = np.linspace(dy / 2., xyzL[1] - dy / 2., num=ncy)
#Main time loop
pcount = 0
for time in range(10000):
print(time, recvbuf.shape)
# Recv data:
# [Ux, Uy, Uz, gradPx, gradPy, gradPz, divTaux, divTauy, divTauz]
ymin = yMD[3]
# ax.plot(uMD[:-12,0], yMD[:-12]-4.33021, 'ro')
# ax.plot(uCFD[:,0], yCFD-9.296, 'bx')
# CAObj = CA(Re=Re, U=U, Lmin=0.0, Lmax=yCFD[-1]-9.296+5.66/2., npoints=2*nxyz[1]+2)
# y_anal, u_anal = CAObj.get_vprofile(rec*rec_dt)
# ax.plot(u_anal, y_anal, 'k-')
#yMD = np.linspace(-4, 50, uMD.shape[0])
ax.plot(uMD[:,0], yMD[:], 'bo')
ax.plot(uCFD[:,0], yCFD, 'gx')
haloCFD = CFDObj.read_halo(startrec=rec,endrec=rec,
haloname="movingWall")
haloCPL = CFDObj.read_halo(startrec=rec, endrec=rec,
haloname="CPLReceiveMD")
ax.plot(np.mean(haloCPL[...,0],(0,2,3)), yCFD[0 ]-dy/2., 'gs')
ax.plot(np.mean(haloCFD[...,0],(0,2,3)), yCFD[-1]+dy/2., 'gs')
#Get analytical solns
CAObj = CA(Re=Re, U=U, Lmin=ymin, Lmax=yCFD[-1]+dy/2., npoints=2*nxyz[1]+2)
y_anal, u_anal = CAObj.get_vprofile(rec*rec_dt)
ax.plot(u_anal, y_anal, 'k-')
#plt.pause(0.001)
#plt.cla()
plt.show()
#Get values from CPL library
ncy = CPL.get("ncy")
yL_md = CPL.get("yl_md")
yL_cfd = CPL.get("yl_cfd")
dy = CPL.get("dy")
jcmax_olap = CPL.get("jcmax_olap")
#Setup Coupled domain details
yL_cpl = yL_md + yL_cfd - dy*jcmax_olap
ncy_cpl = int(yL_cpl/dy)
#Create analytical solution object
Uwall = 1.0
nu = 1.7
Re = yL_cpl/nu
CAObj = CA(Re=Re, U=Uwall, Lmin=0.0, Lmax=yL_cpl, npoints=ncy_cpl+2)
for time in range(500):
y_anal, u_anal = CAObj.get_vprofile(time)
# send data to update
send_array[...] = 0.0
send_array[0,:,:,:] = Uwall # u_anal[-ncy]
CPL.send(send_array)
# recv data and plot
recv_array, ierr = CPL.recv(recv_array)
Ux = np.mean(recv_array[0,:,:,:])/np.mean(recv_array[3,:,:,:])
def check_OpenFOAM_vs_Analytical(fdir, plotstuff=False):
OpenFOAMfdir = fdir + "/cfd_data/openfoam/"
print("Openfoam dir = ", OpenFOAMfdir)
OpenFOAMuObj = ppl.OpenFOAM_vField(OpenFOAMfdir, parallel_run=True)
dt = float(OpenFOAMuObj.Raw.delta_t)
tplot = float(
OpenFOAMuObj.Raw.header.headerDict['controlDict']['writeInterval'])
endtime = float(
OpenFOAMuObj.Raw.header.headerDict['controlDict']['endTime'])
enditer = int(endtime / dt)
OpenFOAMwriteinterval = int(tplot / dt)
# Parameters of the cpu topology (cartesian grid)
xyzL = [OpenFOAMuObj.Raw.xL, OpenFOAMuObj.Raw.yL, OpenFOAMuObj.Raw.zL]
dx = OpenFOAMuObj.Raw.dx
dy = OpenFOAMuObj.Raw.dy
dz = OpenFOAMuObj.Raw.dz
ncx = OpenFOAMuObj.Raw.ncx
ncy = OpenFOAMuObj.Raw.ncy
ncz = OpenFOAMuObj.Raw.ncz
#Analytical solution
scriptdir = fdir + "/md_data/python_dummy/"
with open(scriptdir + "test_vs_couette_analytical.py", 'r') as f:
for l in f:
if "U =" in l:
d = l.split("=")
U = float(d[1].replace("\n", "").replace(" ", ""))
nu = OpenFOAMuObj.Raw.nu[0]
Re = (xyzL[1] + dy / 2.) / nu
CAObj = CA(Re=Re, U=U, Lmin=0., Lmax=xyzL[1], npoints=2 * ncy + 1)
if plotstuff:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1, 1)
n = 0
for time in range(enditer):
#Plot data
if time % OpenFOAMwriteinterval == 0:
rec = int(time / float(OpenFOAMwriteinterval))
try:
OpenFOAMpp = ppl.OpenFOAM_PostProc(OpenFOAMfdir)
OpenFOAMuObj = OpenFOAMpp.plotlist[
'Ub'] #ppl.OpenFOAM_vField(OpenFOAMfdir, parallel_run=True)
y, u = OpenFOAMuObj.profile(1, startrec=rec, endrec=rec)
y_anal, u_anal = CAObj.get_vprofile(time * dt, flip=False)
error = (u_anal[1:-1:2] - u[:, 0]) / u_anal[1:-1:2]
if plotstuff:
l, = ax.plot(u[:, 0],
y,
'ro-',
label="OpenFOAM domain from file")
ax.plot(u_anal[1:-1:2],
y_anal[1:-1:2],
'k.-',
label="Analytical Solution")
#ax.plot(10.*(u[:,0]-u_anal[-2:0:-2]),y,'y--')
ax.set_xlim([-0.1, U * 1.1])
ax.set_xlabel("$u$", fontsize=24)
ax.set_ylabel("$y$", fontsize=24)
plt.legend(loc=1)
plt.pause(0.001)
plt.savefig('out{:05}.png'.format(n))
n += 1
ax.cla()
l2 = np.sqrt(np.sum(error[1:]**2))
if not np.isnan(l2):
print("Time = ", time, "Error= ", l2)
test_error(l2, time)
except AssertionError as e:
print("AssertionError ", e)
raise
except: # ppl.field.OutsideRecRange:
print("Error result missing", time, OpenFOAMuObj.maxrec, rec)
raise
def check_LAMMPS_vs_Analytical(fdir, uwall=1., plotevolve=False):
with open(fdir + "/profile.wall.2d", "r") as f:
filestr = f.read()
header = filestr.split("\n")[:3]
body = filestr.split("\n")[3:]
u = read_rec(body, 0)
y = u[:,1]
nsteps = 25
dt = 0.005
nu = 1.7
Ly = 40.3103
liquidstart = 0.13*Ly
liquidend = 0.82*Ly
liquidregion = liquidend-liquidstart
liquidbins = y.shape[0]
Re = liquidregion/nu
CAObj = CA(Re=Re, U=uwall, Lmin=liquidstart, Lmax=liquidend,
npoints=10*liquidbins, nmodes=100*liquidbins)
if "dynamic" is plotevolve or plotevolve == True:
plotevolve = "dynamic"
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1,1)
plt.ion()
plt.show()
recds = range(nsteps)
elif "summary" is plotevolve:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1,1)
recds = [1, 3, 7, 24]
elif plotevolve == False or plotevolve == None:
plotevolve = "False"
else:
raise IOError("plotevolve="+str(plotevolve)+
" which is unknown, should be dynamic or summary")
ft = True
timeerror = []
for rec in range(nsteps):
try:
u = read_rec(body, rec)
except IndexError:
print("Last value read, exiting loop")
break
if plotevolve != "False":
# 0=Chunk 1=Coord1 2=Ncount 3=density/mass
# 4=vx 5=vy 6=vz 7=temperature
if rec in recds:
ax.plot(u[:,4], u[:,1]*Ly, 'o', label="vx")
y_anal, u_anal = CAObj.get_vprofile(1000*(rec+0.5)*dt)
indxs = []
mn = 1
mx = -2
for i in range(mn, u.shape[0]+mx):
indxs.append(find_nearest_indx(y_anal, u[i,1]*Ly))
if plotevolve != "False":
if rec in recds:
ax.plot(u_anal[indxs], y_anal[indxs], 'k-x', label="vx Analytical")
error = (u_anal[indxs] - u[mn:mx,4])/uwall
if "dynamic" is plotevolve:
ax.plot(error, y_anal[indxs], 'r-', label="Error")
assert np.max(np.abs(error[:-1])) < 0.2
timeerror.append(error)
#print("Error = ", np.sum(error))
if "dynamic" is plotevolve:
if ft:
plt.legend()
ft = False
#plt.xlim([-0.1, 1.2])
plt.pause(.2)
plt.cla()
elif "summary" in plotevolve:
pass
timeerror = np.array(timeerror)
if "dynamic" is plotevolve:
plt.ioff()
plt.pcolormesh(timeerror[:,:-1].T, cmap=plt.cm.RdYlBu_r)
plt.colorbar()
plt.show()
elif "summary" is plotevolve:
ax.set_xlabel("$u$")
ax.set_ylabel("$y$")
plt.savefig("LAMMPS_Validation_uwall" + str(uwall) + ".png", bbox_inches="tight")
#Check average error less than 4%
#print(np.mean(np.abs(timeerror),0))
assert np.all(np.mean(np.abs(timeerror[:,:-1]),0) < 0.04)