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(self, ax=None):
if ax == None:
ax=self.ax
sm = ax.imshow(self.u.T,aspect='auto',origin='lower',
extent=[self.xmin,self.xmax,
self.ymin,self.ymax],
interpolation="none",vmin=-1.,vmax=1.,
alpha=0.5, cmap=plt.cm.RdYlBu_r)
# sm = ax.pcolormesh(self.X,self.Y,self.u.T,vmin=-1.,vmax=1.,alpha=0.5,
# cmap=plt.cm.RdYlBu_r)
draw_grid(ax, nx=self.x.size,ny=self.y.size, nz=1,
xmin=self.xmin,xmax=self.xmax,
ymin=self.ymin,ymax=self.ymax)
#Plot velocity profile offset to the left
axisloc = self.xmax+1.
ax.arrow(axisloc, 0., self.ymin, self.ymax, width=0.0015, color="k",
clip_on=False, head_width=0.12, head_length=0.12)
mid = .5*(self.ymin+self.ymax)
ax.arrow(axisloc-1., mid, 2.0, 0., width=0.0015, color="k",
clip_on=False, head_width=0.12, head_length=0.12)
yp = np.linspace(self.ymin+.5*self.dy, self.ymax - 0.5*self.dy, self.y.size)
ax.plot(np.mean(self.u,0)+axisloc,yp,'g-x')
#ax.set_xlim((0.,2.))
if self.first_time:
plt.colorbar(sm)
self.first_time=False
plt.pause(0.001)
ax.cla()
def plot(self, ax=None, showarrows=False):
if ax == None:
ax=self.ax
for i in range(self.N):
if (self.tag[i] == 0):
ax.plot(self.r[i,0],self.r[i,1],'ko',alpha=0.5)
else:
ax.plot(self.r[i,0],self.r[i,1],'ro', ms=7.)
#Overlay grid
draw_grid(ax, nx=self.xbin, ny=self.ybin, nz=1,
xmin=-self.halfdomain[0], xmax=self.halfdomain[0],
ymin=-self.halfdomain[1], ymax=self.halfdomain[1])
#Get velocity field
u = self.get_velfield([self.xbin,self.ybin])
#Plot velocity profile offset to the left
axisloc = self.halfdomain[0]+1
ax.arrow(axisloc,-self.halfdomain[1], 0.,self.domain[1],
width=0.015, color="k", clip_on=False, head_width=0.12, head_length=0.12)
ax.arrow(axisloc-1,0., 2.,0., width=0.015,
color="k", clip_on=False, head_width=0.12, head_length=0.12)
yp = np.linspace(-self.halfdomain[1]+.5*self.dy, self.halfdomain[1] - 0.5*self.dy, self.ybin)
ax.plot(np.mean(u[0,:,:],1)+axisloc,yp,'g-x')
sm = ax.imshow(u[0,:,:].T,aspect='auto',origin='lower',
extent=[-self.halfdomain[0], self.halfdomain[0],
-self.halfdomain[1], self.halfdomain[1]],
interpolation="none",vmin=-1.,vmax=1.,
alpha=0.5, cmap=plt.cm.RdYlBu_r)
# sm = ax.pcolormesh(self.Xb,self.Yb,u[0,:,:].T,vmin=-1.,vmax=1.,alpha=0.5,
# cmap=plt.cm.RdYlBu_r)
# cb=ax.imshow(u[0,:,:],interpolation="none",
# extent=[-self.halfdomain[0],self.halfdomain[0],
# -self.halfdomain[1],self.halfdomain[1]],
# cmap=plt.cm.RdYlBu_r,vmin=-3.,vmax=3.)
if self.first_time:
plt.colorbar(sm)
self.first_time=False
if showarrows:
#Show velocity of molecules
Q = ax.quiver(self.r[:,0], self.r[:,1],
self.v[:,0], self.v[:,1], color='k')
#Set limits and plot
ax.set_xlim((-self.halfdomain[0], self.halfdomain[0]+2.))
ax.set_ylim((-self.halfdomain[1], self.halfdomain[1]))
plt.pause(0.001)
plt.cla()
print("Temperature =", np.sum(self.v[:,0]**2+self.v[:,1]**2)/(2.*self.N))
def main():
display_surface = timer('Initialisation', initialise_pygame)
draw_grid(display_surface)
ProgramVariables.game_state = GameState.RUNNING
running_loop(display_surface)
pygame.quit()
sys.exit()
def plot(self, ax=None):
if ax == None:
ax = self.ax
if type(ax) is list:
ax = ax[0]
sm = ax.imshow(self.u.T,
aspect='auto',
origin='lower',
extent=[self.xmin, self.xmax, self.ymin, self.ymax],
interpolation="none",
vmin=-1.,
vmax=1.,
alpha=0.5,
cmap=plt.cm.RdYlBu_r)
# sm = ax.pcolormesh(self.X,self.Y,self.u.T,vmin=-1.,vmax=1.,alpha=0.5,
# cmap=plt.cm.RdYlBu_r)
draw_grid(ax,
nx=self.x.size,
ny=self.y.size,
nz=1,
xmin=self.xmin,
xmax=self.xmax,
ymin=self.ymin,
ymax=self.ymax)
#Plot velocity profile offset to the left
axisloc = self.xmax + 1.
ax.arrow(axisloc,
0.,
self.ymin,
self.ymax,
width=0.0015,
color="k",
clip_on=False,
head_width=0.12,
head_length=0.12)
mid = .5 * (self.ymin + self.ymax)
ax.arrow(axisloc - 1.,
mid,
2.0,
0.,
width=0.0015,
color="k",
clip_on=False,
head_width=0.12,
head_length=0.12)
yp = np.linspace(self.ymin + .5 * self.dy, self.ymax - 0.5 * self.dy,
self.y.size)
ax.plot(np.mean(self.u, 0) + axisloc, yp, 'g-x')
#ax.set_xlim((0.,2.))
if self.first_time:
plt.colorbar(sm)
self.first_time = False
plt.pause(0.001)
ax.cla()
koverlap = (CPL.get("kcmax_olap")-CPL.get("kcmin_olap")+1)
xoverlap = ioverlap*dx
yoverlap = joverlap*dy
zoverlap = koverlap*dz
print(CPL.get("xl_cfd"))
#Plot CFD and coupler Grid
draw_grid(ax,
nx=CPL.get("ncx"),
ny=CPL.get("ncy"),
nz=CPL.get("ncz"),
px=CPL.get("npx_cfd"),
py=CPL.get("npy_cfd"),
pz=CPL.get("npz_cfd"),
xmin=CPL.get("x_orig_cfd"),
ymin=CPL.get("y_orig_cfd"),
zmin=CPL.get("z_orig_cfd"),
xmax=(CPL.get("icmax_olap")+1)*dx,
ymax=CPL.get("yl_cfd"),
zmax=(CPL.get("kcmax_olap")+1)*dz,
lc = 'r',
label='CFD')
#Plot MD domain
draw_grid(ax, nx=1, ny=1, nz=1,
px=CPL.get("npx_md"),
py=CPL.get("npy_md"),
pz=CPL.get("npz_md"),
xmin=CPL.get("x_orig_md"),
ymin=-CPL.get("yl_md")+yoverlap,
def plot(self, ax=None, showarrows=False):
if ax == None:
ax = self.ax
for i in range(self.N):
if (self.tag[i] == 0):
ax.plot(self.r[i, 0], self.r[i, 1], 'ko', alpha=0.5)
else:
ax.plot(self.r[i, 0], self.r[i, 1], 'ro', ms=7.)
#Overlay grid
draw_grid(ax,
nx=self.xbin,
ny=self.ybin,
nz=1,
xmin=-self.halfdomain[0],
xmax=self.halfdomain[0],
ymin=-self.halfdomain[1],
ymax=self.halfdomain[1])
#Get velocity field
u = self.get_velfield([self.xbin, self.ybin])
#Plot velocity profile offset to the left
axisloc = self.halfdomain[0] + 1
ax.arrow(axisloc,
-self.halfdomain[1],
0.,
self.domain[1],
width=0.015,
color="k",
clip_on=False,
head_width=0.12,
head_length=0.12)
ax.arrow(axisloc - 1,
0.,
2.,
0.,
width=0.015,
color="k",
clip_on=False,
head_width=0.12,
head_length=0.12)
yp = np.linspace(-self.halfdomain[1] + .5 * self.dy,
self.halfdomain[1] - 0.5 * self.dy, self.ybin)
ax.plot(np.mean(u[0, :, :], 1) + axisloc, yp, 'g-x')
sm = ax.imshow(u[0, :, :].T,
aspect='auto',
origin='lower',
extent=[
-self.halfdomain[0], self.halfdomain[0],
-self.halfdomain[1], self.halfdomain[1]
],
interpolation="none",
vmin=-1.,
vmax=1.,
alpha=0.5,
cmap=plt.cm.RdYlBu_r)
# sm = ax.pcolormesh(self.Xb,self.Yb,u[0,:,:].T,vmin=-1.,vmax=1.,alpha=0.5,
# cmap=plt.cm.RdYlBu_r)
# cb=ax.imshow(u[0,:,:],interpolation="none",
# extent=[-self.halfdomain[0],self.halfdomain[0],
# -self.halfdomain[1],self.halfdomain[1]],
# cmap=plt.cm.RdYlBu_r,vmin=-3.,vmax=3.)
if self.first_time:
plt.colorbar(sm)
self.first_time = False
if showarrows:
#Show velocity of molecules
Q = ax.quiver(self.r[:, 0],
self.r[:, 1],
self.v[:, 0],
self.v[:, 1],
color='k')
#Set limits and plot
ax.set_xlim((-self.halfdomain[0], self.halfdomain[0] + 2.))
ax.set_ylim((-self.halfdomain[1], self.halfdomain[1]))
plt.pause(0.001)
plt.cla()
print("Temperature =",
np.sum(self.v[:, 0]**2 + self.v[:, 1]**2) / (2. * self.N))
# === Plot both grids ===
#Get overlap region
comm = cfd_socket.topology._topo_comm
rank = comm.Get_rank()
COMM_size = comm.Get_size()
pcoords=comm.Get_coords(rank)
if rank == root:
#Plot
fig, ax = plt.subplots(1,1)
draw_grid(ax, nx=ncx,
ny=ncy,
nz=ncz,
px=npx_cfd,
py=npy_cfd,
pz=npz_cfd,
xmin=0.,ymin=0.,zmin=0.,
xmax=xl_cfd,
ymax=yl_cfd,
zmax=zl_cfd,
lc = 'r',
label='CFD')
draw_grid(ax, nx=1, ny=1, nz=1,
px=npx_md,
py=npy_md,
pz=npz_md,
xmin=-xl_md+xoverlap,
ymin=-yl_md+yoverlap,
zmin=-zl_md+zoverlap,
xmax=xoverlap,
ymax=yoverlap,
# recv data to plot
olap_limits = CPL.get_olap_limits()
portion = CPL.my_proc_portion(olap_limits)
[ncxl, ncyl, nczl] = CPL.get_no_cells(portion)
recv_array = np.zeros((1, ncxl, ncyl, nczl), order='F', dtype=np.float64)
recv_array, ierr = CPL.recv(recv_array, olap_limits)
#Plot CFD and coupler Grid
draw_grid(ax,
nx=CPL.get("ncx"),
ny=CPL.get("ncy"),
nz=CPL.get("ncz"),
px=CPL.get("npx_cfd"),
py=CPL.get("npy_cfd"),
pz=CPL.get("npz_cfd"),
xmin=CPL.get("x_orig_cfd"),
ymin=CPL.get("y_orig_cfd"),
zmin=CPL.get("z_orig_cfd"),
xmax=(CPL.get("icmax_olap") + 1) * dx,
ymax=CPL.get("yl_cfd"),
zmax=(CPL.get("kcmax_olap") + 1) * dz,
lc='r',
label='CFD')
#Plot MD domain
draw_grid(ax,
nx=1,
ny=1,
nz=1,
px=CPL.get("npx_md"),
py=CPL.get("npy_md"),
def redraw_grid(display_surface):
draw_grid(display_surface)
for drawable_object in drawn_objects:
drawable_object.draw_self(display_surface)
def update_grid(self, e):
#Reset the figure ready for plot
self.pyplotp.reset_fig()
#CPL setup
minnx = self.cntrp.CPLpanel.nx.GetValue()
minny = self.cntrp.CPLpanel.ny.GetValue()
minnz = self.cntrp.CPLpanel.nz.GetValue()
maxnx = self.cntrp.CPLpanel.px.GetValue()
maxny = self.cntrp.CPLpanel.py.GetValue()
maxnz = self.cntrp.CPLpanel.pz.GetValue()
print("CPL", minnx, minny, minnz, maxnx, maxny, maxnz)
#MD
px_MD = self.cntrp.MDpanel.px.GetValue()
py_MD = self.cntrp.MDpanel.py.GetValue()
pz_MD = self.cntrp.MDpanel.pz.GetValue()
xmin_MD = self.cntrp.MDpanel.xmin.GetValue()
ymin_MD = self.cntrp.MDpanel.ymin.GetValue()
zmin_MD = self.cntrp.MDpanel.zmin.GetValue()
xmax_MD = self.cntrp.MDpanel.xmax.GetValue()
ymax_MD = self.cntrp.MDpanel.ymax.GetValue()
zmax_MD = self.cntrp.MDpanel.zmax.GetValue()
print("MD", 1, 1, 1, xmin_MD, ymin_MD, zmin_MD, xmax_MD, ymax_MD,
zmax_MD)
draw_grid(self.pyplotp.ax,
1,
1,
1,
px=px_MD,
py=py_MD,
pz=pz_MD,
xmin=xmin_MD,
ymin=ymin_MD,
zmin=zmin_MD,
xmax=xmax_MD,
ymax=ymax_MD,
zmax=zmax_MD,
fc='b',
lc='g',
label="MD",
XKCD_plots=self.XKCD_plots)
#CFD
nx_CFD = self.cntrp.CFDpanel.nx.GetValue()
ny_CFD = self.cntrp.CFDpanel.ny.GetValue()
nz_CFD = self.cntrp.CFDpanel.nz.GetValue()
px_CFD = self.cntrp.CFDpanel.px.GetValue()
py_CFD = self.cntrp.CFDpanel.py.GetValue()
pz_CFD = self.cntrp.CFDpanel.pz.GetValue()
xmin_CFD = self.cntrp.CFDpanel.xmin.GetValue()
ymin_CFD = self.cntrp.CFDpanel.ymin.GetValue()
zmin_CFD = self.cntrp.CFDpanel.zmin.GetValue()
xmax_CFD = self.cntrp.CFDpanel.xmax.GetValue()
ymax_CFD = self.cntrp.CFDpanel.ymax.GetValue()
zmax_CFD = self.cntrp.CFDpanel.zmax.GetValue()
dx = (xmax_CFD - xmin_CFD) / float(nx_CFD)
dy = (ymax_CFD - ymin_CFD) / float(ny_CFD)
dz = (zmax_CFD - zmin_CFD) / float(nz_CFD)
ymin_CPL = ymax_MD - maxny * dy
ymax_CPL = ymin_CPL + ny_CFD * dy
print("CFD", nx_CFD, ny_CFD, nz_CFD, xmin_CFD, ymin_CFD, zmin_CFD,
xmax_CFD, ymax_CFD, zmax_CFD, dx, dy, dz)
draw_grid(self.pyplotp.ax,
nx_CFD,
ny_CFD,
nz_CFD,
px=px_CFD,
py=py_CFD,
pz=pz_CFD,
xmin=xmin_CFD,
ymin=ymin_CPL,
zmin=zmin_CFD,
xmax=xmax_CFD,
ymax=ymax_CPL,
zmax=zmax_CFD,
lc='r',
fc='k',
label="CFD",
XKCD_plots=self.XKCD_plots)
pnl = self.cntrp.TextPanel
pnl.text["dx"].SetLabel(latex2utf("\Delta x=") + str(np.round(dx, 5)))
pnl.text["dy"].SetLabel(latex2utf("\Delta y=") + str(np.round(dy, 5)))
pnl.text["dz"].SetLabel(latex2utf("\Delta z=") + str(np.round(dz, 5)))
pnl.Layout()
pnl.Update()
#pnl.vbox.Layout()
#Redraw
self.pyplotp.redraw()
def update_grid(self, e):
#Reset the figure ready for plot
self.pyplotp.reset_fig()
#CFD
nx = self.cntrp.CFDpanel.nx.GetValue()
ny = self.cntrp.CFDpanel.ny.GetValue()
nz = self.cntrp.CFDpanel.nz.GetValue()
px = self.cntrp.CFDpanel.px.GetValue()
py = self.cntrp.CFDpanel.py.GetValue()
pz = self.cntrp.CFDpanel.pz.GetValue()
xmin = self.cntrp.CFDpanel.xmin.GetValue()
ymin = self.cntrp.CFDpanel.ymin.GetValue()
zmin = self.cntrp.CFDpanel.zmin.GetValue()
xmax = self.cntrp.CFDpanel.xmax.GetValue()
ymax = self.cntrp.CFDpanel.ymax.GetValue()
zmax = self.cntrp.CFDpanel.zmax.GetValue()
print("CFD", nx, ny, nz, xmin, ymin, zmin, xmax, ymax, zmax)
draw_grid(self.pyplotp.ax,
nx,
ny,
nz,
px=px,
py=py,
pz=pz,
xmin=xmin,
ymin=ymin,
zmin=zmin,
xmax=xmax,
ymax=ymax,
zmax=zmax,
lc='r',
fc='k',
label="CFD",
XKCD_plots=self.XKCD_plots)
#MD
nx = self.cntrp.MDpanel.nx.GetValue()
ny = self.cntrp.MDpanel.ny.GetValue()
nz = self.cntrp.MDpanel.nz.GetValue()
px = self.cntrp.MDpanel.px.GetValue()
py = self.cntrp.MDpanel.py.GetValue()
pz = self.cntrp.MDpanel.pz.GetValue()
xmin = self.cntrp.MDpanel.xmin.GetValue()
ymin = self.cntrp.MDpanel.ymin.GetValue()
zmin = self.cntrp.MDpanel.zmin.GetValue()
xmax = self.cntrp.MDpanel.xmax.GetValue()
ymax = self.cntrp.MDpanel.ymax.GetValue()
zmax = self.cntrp.MDpanel.zmax.GetValue()
print("MD", nx, ny, nz, xmin, ymin, zmin, xmax, ymax, zmax)
draw_grid(self.pyplotp.ax,
nx,
ny,
nz,
px=px,
py=py,
pz=pz,
xmin=xmin,
ymin=ymin,
zmin=zmin,
xmax=xmax,
ymax=ymax,
zmax=zmax,
fc='b',
lc='g',
label="MD",
XKCD_plots=self.XKCD_plots)
self.pyplotp.redraw()
comm = md_socket.topology._topo_comm
rank = comm.Get_rank()
COMM_size = comm.Get_size()
pcoords = comm.Get_coords(rank)
if rank == root:
#Plot
fig, ax = plt.subplots(1, 1)
draw_grid(ax,
nx=ncx,
ny=ncy,
nz=ncz,
px=npx_cfd,
py=npy_cfd,
pz=npz_cfd,
xmin=0.,
ymin=0.,
zmin=0.,
xmax=xl_cfd,
ymax=yl_cfd,
zmax=zl_cfd,
lc='r',
label='CFD')
draw_grid(ax,
nx=1,
ny=1,
nz=1,
px=npx_md,
py=npy_md,
pz=npz_md,
