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()
velBCRegion = np.copy(olap_limits)
velBCRegion[3] = velBCRegion[2]
velBCPortion = cpllib.my_proc_portion(velBCRegion)
[velBCncx, velBCncy, velBCncz] = cpllib.get_no_cells(velBCPortion)
# Send dummy random stress distribution (constant value of stress = 0) to MD
np.random.seed(1000)
send_array = 5 * np.array(np.random.rand(9, cnstncx, cnstncy, cnstncz), order='F', dtype=np.float64)
# Receive averaged velocities from LAMMPS socket
recv_array = np.zeros((4, velBCncx, velBCncy, velBCncz), order='F',
dtype=np.float64)
cpllib.send(send_array, cnstFRegion)
cpllib.recv(recv_array, velBCRegion)
for step in xrange(nsteps):
print("CFD step: ", step)
cpllib.send(send_array, cnstFRegion)
cpllib.recv(recv_array, velBCRegion)
dx, dy, dz = (Lx / NCx, Ly / NCy, Lz / NCz)
dA = dx * dz
# Dump 1, 4 an 7 components of the stress tensor multiplied by the area of the cell
func = lambda x: x*dA
cpllib.dump_region(cnstFRegion, send_array, "cfd_forces.dat", realm_comm,
components={1:func, 4:func, 7:func}, coords="other")
cpllib.finalize()
print("After CPL init")
## Parameters of the cpu topology (cartesian grid)
npxyz = [1, 1, 1]
xyzL = [1.5E-003, 1.5E-003, 2.5E-003]
xyz_orig = [0.0, 0.0, 0.0]
ncxyz = [8, 8, 8]
#Setup coupled simulation
cart_comm = MD_COMM.Create_cart([npxyz[0], npxyz[1], npxyz[2]])
CPL.setup_cfd(cart_comm, xyzL, xyz_orig, ncxyz)
recv_array, send_array = CPL.get_arrays(recv_size=4, send_size=3)
print("After CPL setup")
ft = True
for time in range(100):
# send data to update
send_array[2, :, :, :] = mi * g
CPL.send(send_array)
# recv data and plot
recv_array, ierr = CPL.recv(recv_array)
print("CFD time = ", time)
comm.Barrier()
CPL.finalize()
MPI.Finalize()
py=CPL.get("npy_md"),
pz=CPL.get("npz_md"),
xmin=CPL.get("x_orig_md"),
ymin=-CPL.get("yl_md")+yoverlap,
zmin=CPL.get("z_orig_md"),
xmax=(CPL.get("icmax_olap")+1)*dx,
ymax=yoverlap,
zmax=(CPL.get("kcmax_olap")+1)*dz,
label='MD')
#Plot some random molecules
#ax.plot(np.random.random(100)*(CPL.get("xl_md")),
# np.random.random(100)*(CPL.get("yl_md"))-CPL.get("yl_md")+yoverlap,
# 'ob',alpha=0.5)
#Plot x component on grid
x = np.linspace(CPL.get("x_orig_cfd")+.5*dx,xoverlap-.5*dx,ioverlap)
z = np.linspace(CPL.get("z_orig_cfd")+.5*dz,zoverlap-.5*dz,koverlap)
for j in range(joverlap):
ax.plot(x, 0.5*dy*(recv_array[0,:,j,0]+1.+2*j), 's-')
ax.set_xlabel('$x$')
ax.set_ylabel('$y$')
plt.show()
CPL.finalize()
MPI.Finalize()
class CFD():
def __init__(self, npxyz, xyzL, xyz_orig, ncxyz):
#initialise MPI and CPL
self.comm = MPI.COMM_WORLD
self.CPL = CPL()
self.CFD_COMM = self.CPL.init(CPL.CFD_REALM)
self.nprocs_realm = self.CFD_COMM.Get_size()
# Parameters of the cpu topology (cartesian grid)
self.npxyz = np.array(npxyz, order='F', dtype=np.int32)
self.NProcs = np.product(npxyz)
self.xyzL = np.array(xyzL, order='F', dtype=np.float64)
self.xyz_orig = np.array(xyz_orig, order='F', dtype=np.float64)
self.ncxyz = np.array(ncxyz, order='F', dtype=np.int32)
if (self.nprocs_realm != self.NProcs):
print("Non-coherent number of processes in CFD ",
self.nprocs_realm, " no equal to ", self.npxyz[0], " X ",
self.npxyz[1], " X ", self.npxyz[2])
MPI.Abort(errorcode=1)
#Setup coupled simulation
self.cart_comm = self.CFD_COMM.Create_cart(
[self.npxyz[0], self.npxyz[1], self.npxyz[2]])
self.CPL.setup_cfd(self.cart_comm, self.xyzL, self.xyz_orig,
self.ncxyz)
#Get limits of overlap region
self.olap_limits = self.CPL.get_olap_limits()
self.portion = self.CPL.my_proc_portion(self.olap_limits)
[self.ncxl, self.ncyl, self.nczl] = self.CPL.get_no_cells(self.portion)
self.dx = self.CPL.get("xl_cfd") / float(self.CPL.get("ncx"))
self.dy = self.CPL.get("yl_cfd") / float(self.CPL.get("ncy"))
self.dz = self.CPL.get("zl_cfd") / float(self.CPL.get("ncz"))
self.ioverlap = (self.CPL.get("icmax_olap") -
self.CPL.get("icmin_olap") + 1)
self.joverlap = (self.CPL.get("jcmax_olap") -
self.CPL.get("jcmin_olap") + 1)
self.koverlap = (self.CPL.get("kcmax_olap") -
self.CPL.get("kcmin_olap") + 1)
self.xoverlap = self.ioverlap * self.dx
self.yoverlap = self.joverlap * self.dy
self.zoverlap = self.koverlap * self.dz
def recv_CPL_data(self):
# recv data to plot
self.recv_array = np.zeros((1, self.ncxl, self.ncyl, self.nczl),
order='F',
dtype=np.float64)
self.recv_array, ierr = self.CPL.recv(self.recv_array,
self.olap_limits)
def plot_grid(self, ax):
#Plot CFD and coupler Grid
draw_grid(ax,
nx=self.CPL.get("ncx"),
ny=self.CPL.get("ncy"),
nz=self.CPL.get("ncz"),
px=self.CPL.get("npx_cfd"),
py=self.CPL.get("npy_cfd"),
pz=self.CPL.get("npz_cfd"),
xmin=self.CPL.get("x_orig_cfd"),
ymin=self.CPL.get("y_orig_cfd"),
zmin=self.CPL.get("z_orig_cfd"),
xmax=(self.CPL.get("icmax_olap") + 1) * self.dx,
ymax=self.CPL.get("yl_cfd"),
zmax=(self.CPL.get("kcmax_olap") + 1) * self.dz,
lc='r',
label='CFD')
#Plot MD domain
draw_grid(ax,
nx=1,
ny=1,
nz=1,
px=self.CPL.get("npx_md"),
py=self.CPL.get("npy_md"),
pz=self.CPL.get("npz_md"),
xmin=self.CPL.get("x_orig_md"),
ymin=-self.CPL.get("yl_md") + self.yoverlap,
zmin=self.CPL.get("z_orig_md"),
xmax=(self.CPL.get("icmax_olap") + 1) * self.dx,
ymax=self.yoverlap,
zmax=(self.CPL.get("kcmax_olap") + 1) * self.dz,
label='MD')
def plot_data(self, ax):
# === Plot both grids ===
#Plot x component on grid
x = np.linspace(
self.CPL.get("x_orig_cfd") + .5 * self.dx,
self.xoverlap - .5 * self.dx, self.ioverlap)
z = np.linspace(
self.CPL.get("z_orig_cfd") + .5 * self.dz,
self.zoverlap - .5 * self.dz, self.koverlap)
try:
for j in range(self.joverlap):
ax.plot(
x,
0.5 * self.dy * (self.recv_array[0, :, j, 0] + 1. + 2 * j),
's-')
except ValueError:
print("Arrays not equal:", x.shape, z.shape, self.recv_array.shape)
def finalise(self):
self.CPL.finalize()
MPI.Finalize()
def CFD(xyzL=[1.5E-003, 1.5E-003, 2.50E-003],
g=9.81,
ncxyz=[8, 8, 8],
npxyz=[1, 1, 1],
Nsteps=101):
#initialise MPI and CPL
comm = MPI.COMM_WORLD
CPL = CPL()
MD_COMM = CPL.init(CPL.CFD_REALM)
nprocs_realm = MD_COMM.Get_size()
## Parameters of the cpu topology (cartesian grid)
npxyz = np.array(npxyz, order='F', dtype=np.int32)
NProcs = np.product(npxyz)
xyzL = np.array(xyz, order='F', dtype=np.float64)
xyz_orig = np.array([0.0, 0.0, 0.0], order='F', dtype=np.float64)
ncxyz = np.array(ncxyz, order='F', dtype=np.int32)
if (nprocs_realm != NProcs):
print("Non-coherent number of processes in MD ", nprocs_realm,
" no equal to ", npxyz[0], " X ", npxyz[1], " X ", npxyz[2])
MPI.Abort(errorcode=1)
#Setup coupled simulation
cart_comm = MD_COMM.Create_cart([npxyz[0], npxyz[1], npxyz[2]])
CPL.setup_cfd(cart_comm, xyzL, xyz_orig, ncxyz)
#Get constraint region
cnst_limits = CPL.get_cnst_limits()
cnst_portion = CPL.my_proc_portion(cnst_limits)
[cnst_ncxl, cnst_ncyl, cnst_nczl] = CPL.get_no_cells(cnst_portion)
#Get overlap region
olap_limits = CPL.get_olap_limits()
BC_limits = np.array([
olap_limits[0], olap_limits[1], olap_limits[2], olap_limits[3],
olap_limits[4], olap_limits[5]
],
dtype=np.int32)
BC_portion = CPL.my_proc_portion(BC_limits)
[BC_ncxl, BC_ncyl, BC_nczl] = CPL.get_no_cells(BC_portion)
#Allocate send and recv arrays
recv_array = np.zeros((4, BC_ncxl, BC_ncyl, BC_nczl),
order='F',
dtype=np.float64)
send_array = np.zeros((9, cnst_ncxl, cnst_ncyl, cnst_nczl),
order='F',
dtype=np.float64)
for time in range(Nsteps):
# send data to update
send_array[2, :, :, :] = -5.9490638385009208e-08 * g # * mi
CPL.send(send_array, cnst_portion)
# recv data and plot
recv_array, ierr = CPL.recv(recv_array, BC_portion)
print(time)
CPL.finalize()
MPI.Finalize()
