def density(chain,chem,grid,scft_obj):
nx=len(grid.x)
ny=len(grid.y)
nz=len(grid.z)
ds=1.0/chain.Ns
if grid.dim==1:
Mv=nx*grid.x[1]
if grid.dim==2:
Mv=nx*grid.x[1]*ny*grid.y[1]
if grid.dim==3:
Mv=nx*grid.x[1]*ny*grid.y[1]*nz*grid.z[1]
if np.abs(Mv)<EPS:
raise ValueError('Unkonwn Mv.')
ar=np.zeros((nx,ny,nz))
ar[:,:,:]=chain.qf[chain.Ns,:,:,:]
chain.Q=simposon_int_pbc(ar,grid)/Mv
scft_obj.logQ=np.log(chain.Q)
R_s=np.zeros(chain.Ns+1)
for x in np.arange(nx) :
for y in np.arange(ny) :
for z in np.arange(nz) :
ar[x,y,z]=0.0
chem.R[:,x,y,z]=0.0
for blk in np.arange(chain.n_blk):
sum_blk=0.0
sta=chain.blk_sta[blk]
end=chain.blk_end[blk]
for s in np.arange(sta,end+1): # this is a trick to make sure we have odd number when doing simps
R_s[s]=chain.qf[s,x,y,z]*chain.qb[s,x,y,z]
if blk!=chain.n_blk-1:
end=end+1
R_s[end]=chain.qf[end,x,y,z]*chain.qb[end,x,y,z]
sum_blk=simps(R_s[sta:end+1:1],dx=ds)
ar[x,y,z]=ar[x,y,z]+sum_blk
nch=chain.blk_sp[blk]
chem.R[nch,x,y,z]=chem.R[nch,x,y,z]+sum_blk
totden=simposon_int_pbc(ar,grid)/Mv
chem.R[:,:,:,:]=chem.R[:,:,:,:]/totden
def free_energy_abmelt(chain,chem,grid,scft_obj):
nx=len(grid.x)
ny=len(grid.y)
nz=len(grid.z)
if grid.dim==1:
Mv=nx*grid.x[1]
if grid.dim==2:
Mv=nx*grid.x[1]*ny*grid.y[1]
if grid.dim==3:
Mv=nx*grid.x[1]*ny*grid.y[1]*nz*grid.z[1]
if np.abs(Mv)<EPS:
raise ValueError('Unkonwn Mv.')
ar=np.zeros((nx,ny,nz))
ar[:,:,:]=chem.XN*chem.R[0,:,:,:]*chem.R[1,:,:,:]
ar[:,:,:]=ar[:,:,:]-chem.W[0,:,:,:]*chem.R[0,:,:,:]-chem.W[1,:,:,:]*chem.R[1,:,:,:]
ar[:,:,:]=ar[:,:,:]+0.5*(chem.W[0,:,:,:]+chem.W[1,:,:,:])*(chem.R[0,:,:,:]+chem.R[1,:,:,:]-1.0)
scft_obj.f_FH=simposon_int_pbc(ar,grid)/Mv
scft_obj.f_tot=scft_obj.f_FH-scft_obj.logQ
