def allocate_drude_space( s, structure_groups, wrapbox_groups ): s.drude_space_list = [] for i, structure_list in enumerate( structure_groups ): c1 = wrapbox_groups[i][2] c2 = s.center_pt d1 = wrapbox_groups[i][3] d2 = s.length if is_overlap_3d( c1, c2, d1, d2 ) and structure_list[0].matter_type == 'drude': wb_pt1 = list( wrapbox_groups[i][0] ) wb_pt2 = list( wrapbox_groups[i][1] ) for i in xrange(3): if wb_pt1[i] < s.wrapbox_pt1[i]: wb_pt1[i] = s.wrapbox_pt1[i] if wb_pt2[i] > s.wrapbox_pt2[i]: wb_pt2[i] = s.wrapbox_pt2[i] local_wb_pt1 = [] local_wb_pt2 = [] for i in xrange(3): local_wb_pt1.append( wb_pt1[i] ) local_wb_pt2.append( wb_pt2[i] ) local_wb_pt1[0] -= s.wrapbox_pt1[0] local_wb_pt2[0] -= s.wrapbox_pt1[0] i1, j1, k1 = sc.int32( sc.array(local_wb_pt1,'f')/s.dx + 1e-5 ) + 1 i2, j2, k2 = sc.int32( sc.array(local_wb_pt2,'f')/s.dx + 1e-5 ) + 1 Nx = i2 - i1 Ny = j2 - j1 Nz = k2 - k1 s.drude_space_list.append( DrudeAde( s, Nx, Ny, Nz, i1, j1, k1 ) ) s.drude_space_list[-1].allocate() s.drude_space_list[-1].set_coeff( wb_pt1, wb_pt2, structure_list )
def allocate_drude_space(s, structure_groups, wrapbox_groups):
s.drude_space_list = []
for i, structure_list in enumerate(structure_groups):
c1 = wrapbox_groups[i][2]
c2 = s.center_pt
d1 = wrapbox_groups[i][3]
d2 = s.length
if is_overlap_3d(c1, c2, d1, d2) and structure_list[0].matter_type == "drude":
wb_pt1 = list(wrapbox_groups[i][0])
wb_pt2 = list(wrapbox_groups[i][1])
for i in xrange(3):
if wb_pt1[i] < s.wrapbox_pt1[i]:
wb_pt1[i] = s.wrapbox_pt1[i]
if wb_pt2[i] > s.wrapbox_pt2[i]:
wb_pt2[i] = s.wrapbox_pt2[i]
local_wb_pt1 = []
local_wb_pt2 = []
for i in xrange(3):
local_wb_pt1.append(wb_pt1[i])
local_wb_pt2.append(wb_pt2[i])
local_wb_pt1[0] -= s.wrapbox_pt1[0]
local_wb_pt2[0] -= s.wrapbox_pt1[0]
i1, j1, k1 = sc.int32(sc.array(local_wb_pt1, "f") / s.dx + 1e-5) + 1
i2, j2, k2 = sc.int32(sc.array(local_wb_pt2, "f") / s.dx + 1e-5) + 1
Nx = i2 - i1
Ny = j2 - j1
Nz = k2 - k1
s.drude_space_list.append(DrudeAde(s, Nx, Ny, Nz, i1, j1, k1))
s.drude_space_list[-1].allocate()
s.drude_space_list[-1].set_coeff(wb_pt1, wb_pt2, structure_list)
def set_coeff(s, structure_groups=[], wrapbox_groups=[]):
s.epr_x = sc.ones(s.shape, "f")
s.epr_y = sc.ones(s.shape, "f")
s.epr_z = sc.ones(s.shape, "f")
for i, structure_list in enumerate(structure_groups):
c1 = wrapbox_groups[i][2]
c2 = s.center_pt
d1 = wrapbox_groups[i][3]
d2 = s.length
if is_overlap_3d(c1, c2, d1, d2):
wb_pt1 = list(wrapbox_groups[i][0])
wb_pt2 = list(wrapbox_groups[i][1])
for i in xrange(3):
if wb_pt1[i] < s.wrapbox_pt1[i]:
wb_pt1[i] = s.wrapbox_pt1[i]
if wb_pt2[i] > s.wrapbox_pt2[i]:
wb_pt2[i] = s.wrapbox_pt2[i]
wb_pt1[0] -= s.wrapbox_pt1[0]
wb_pt2[0] -= s.wrapbox_pt1[0]
i1, j1, k1 = sc.int32(sc.array(wb_pt1, "f") / s.dx) + 1
i2, j2, k2 = sc.int32(sc.array(wb_pt2, "f") / s.dx) + 1
for st in structure_list:
for i in xrange(i1, i2 + 1):
for j in xrange(j1, j2 + 1):
for k in xrange(k1, k2 + 1):
pt_real_x = (s.wrapbox_pt1[0] + (i - 1) * s.dx, (j - 0.5) * s.dx, (k - 0.5) * s.dx)
pt_real_y = (s.wrapbox_pt1[0] + (i - 0.5) * s.dx, (j - 1) * s.dx, (k - 0.5) * s.dx)
pt_real_z = (s.wrapbox_pt1[0] + (i - 0.5) * s.dx, (j - 0.5) * s.dx, (k - 1) * s.dx)
if st.is_in(pt_real_x):
s.epr_x[i, j, k] = st.matter_parameter[0]
if st.is_in(pt_real_y):
s.epr_y[i, j, k] = st.matter_parameter[0]
if st.is_in(pt_real_z):
s.epr_z[i, j, k] = st.matter_parameter[0]
s.CEx[1:, 1:-1, 1:-1] = 0.5 / s.epr_x[1:, 1:-1, 1:-1]
s.CEy[1:-1, 1:, 1:-1] = 0.5 / s.epr_y[1:-1, 1:, 1:-1]
s.CEz[1:-1, 1:-1, 1:] = 0.5 / s.epr_z[1:-1, 1:-1, 1:]
del s.epr_x, s.epr_y, s.epr_z
def set_coeff( s, structure_groups=[], wrapbox_groups=[] ): s.epr_x = sc.ones( s.shape, 'f' ) s.epr_y = sc.ones( s.shape, 'f' ) s.epr_z = sc.ones( s.shape, 'f' ) for i, structure_list in enumerate( structure_groups ): c1 = wrapbox_groups[i][2] c2 = s.center_pt d1 = wrapbox_groups[i][3] d2 = s.length if is_overlap_3d( c1, c2, d1, d2 ): wb_pt1 = list( wrapbox_groups[i][0] ) wb_pt2 = list( wrapbox_groups[i][1] ) for i in xrange(3): if wb_pt1[i] < s.wrapbox_pt1[i]: wb_pt1[i] = s.wrapbox_pt1[i] if wb_pt2[i] > s.wrapbox_pt2[i]: wb_pt2[i] = s.wrapbox_pt2[i] wb_pt1[0] -= s.wrapbox_pt1[0] wb_pt2[0] -= s.wrapbox_pt1[0] i1, j1, k1 = sc.int32( sc.array(wb_pt1,'f')/s.dx ) + 1 i2, j2, k2 = sc.int32( sc.array(wb_pt2,'f')/s.dx ) + 1 for st in structure_list: for i in xrange( i1, i2+1 ): for j in xrange( j1, j2+1 ): for k in xrange( k1, k2+1 ): pt_real_x = ( s.wrapbox_pt1[0] + (i-1)*s.dx, (j-0.5)*s.dx, (k-0.5)*s.dx ) pt_real_y = ( s.wrapbox_pt1[0] + (i-0.5)*s.dx, (j-1)*s.dx, (k-0.5)*s.dx ) pt_real_z = ( s.wrapbox_pt1[0] + (i-0.5)*s.dx, (j-0.5)*s.dx, (k-1)*s.dx ) if st.is_in( pt_real_x ): s.epr_x[i,j,k] = st.matter_parameter[0] if st.is_in( pt_real_y ): s.epr_y[i,j,k] = st.matter_parameter[0] if st.is_in( pt_real_z ): s.epr_z[i,j,k] = st.matter_parameter[0] s.CEx[1:,1:-1,1:-1] = 0.5/s.epr_x[1:,1:-1,1:-1] s.CEy[1:-1,1:,1:-1] = 0.5/s.epr_y[1:-1,1:,1:-1] s.CEz[1:-1,1:-1,1:] = 0.5/s.epr_z[1:-1,1:-1,1:] del s.epr_x, s.epr_y, s.epr_z
def set_coeff( s, structure_groups, wrapbox_groups ): s.epr_x = sc.ones( s.shape, 'f' ) s.epr_y = sc.ones( s.shape, 'f' ) s.epr_z = sc.ones( s.shape, 'f' ) s.pfreq_x = sc.zeros( s.shape, 'f' ) s.pfreq_y = sc.zeros( s.shape, 'f' ) s.pfreq_z = sc.zeros( s.shape, 'f' ) s.gamma_x = sc.zeros( s.shape, 'f' ) s.gamma_y = sc.zeros( s.shape, 'f' ) s.gamma_z = sc.zeros( s.shape, 'f' ) for i, structure_list in enumerate( structure_groups ): c1 = wrapbox_groups[i][2] c2 = s.center_pt d1 = wrapbox_groups[i][3] d2 = s.length if is_overlap_3d( c1, c2, d1, d2 ): wb_pt1 = list( wrapbox_groups[i][0] ) wb_pt2 = list( wrapbox_groups[i][1] ) for i in xrange(3): if wb_pt1[i] < s.wrapbox_pt1[i]: wb_pt1[i] = s.wrapbox_pt1[i] if wb_pt2[i] > s.wrapbox_pt2[i]: wb_pt2[i] = s.wrapbox_pt2[i] wb_pt1[0] -= s.wrapbox_pt1[0] wb_pt2[0] -= s.wrapbox_pt1[0] i1, j1, k1 = sc.int32( sc.array(wb_pt1,'f')/s.dx ) + 1 i2, j2, k2 = sc.int32( sc.array(wb_pt2,'f')/s.dx ) + 1 for st in structure_list: for i in xrange( i1, i2+1 ): for j in xrange( j1, j2+1 ): for k in xrange( k1, k2+1 ): pt_real_x = ( s.wrapbox_pt1[0] + (i-1)*s.dx, (j-0.5)*s.dx, (k-0.5)*s.dx ) pt_real_y = ( s.wrapbox_pt1[0] + (i-0.5)*s.dx, (j-1)*s.dx, (k-0.5)*s.dx ) pt_real_z = ( s.wrapbox_pt1[0] + (i-0.5)*s.dx, (j-0.5)*s.dx, (k-1)*s.dx ) if st.is_in( pt_real_x ): s.epr_x[i,j,k] = st.matter_parameter[0] s.pfreq_x[i,j,k] = st.matter_parameter[1] s.gamma_x[i,j,k] = st.matter_parameter[2] if st.is_in( pt_real_y ): s.epr_y[i,j,k] = st.matter_parameter[0] s.pfreq_y[i,j,k] = st.matter_parameter[1] s.gamma_y[i,j,k] = st.matter_parameter[2] if st.is_in( pt_real_z ): s.epr_z[i,j,k] = st.matter_parameter[0] s.pfreq_z[i,j,k] = st.matter_parameter[1] s.gamma_z[i,j,k] = st.matter_parameter[2] s.CEx[1:,1:-1,1:-1] = 0.5/s.epr_x[1:,1:-1,1:-1] s.CEy[1:-1,1:,1:-1] = 0.5/s.epr_y[1:-1,1:,1:-1] s.CEz[1:-1,1:-1,1:] = 0.5/s.epr_z[1:-1,1:-1,1:] tmp = sc.zeros( s.shape, 'f' ) tmp[:,:,:] = (2+s.gamma_x[:,:,:]*s.dt) s.CJAx[:,:,:] = (2-s.gamma_x[:,:,:]*s.dt)/tmp[:,:,:] s.CJBx[:,:,:] = 4*(s.dt*s.pfreq_x[:,:,:])**2/tmp[:,:,:] tmp[:,:,:] = (2+s.gamma_y[:,:,:]*s.dt) s.CJAy[:,:,:] = (2-s.gamma_y[:,:,:]*s.dt)/tmp[:,:,:] s.CJBy[:,:,:] = 4*(s.dt*s.pfreq_y[:,:,:])**2/tmp[:,:,:] tmp[:,:,:] = (2+s.gamma_z[:,:,:]*s.dt) s.CJAz[:,:,:] = (2-s.gamma_z[:,:,:]*s.dt)/tmp[:,:,:] s.CJBz[:,:,:] = 4*(s.dt*s.pfreq_z[:,:,:])**2/tmp[:,:,:] del s.epr_x, s.epr_y, s.epr_z del tmp del s.pfreq_x, s.pfreq_y, s.pfreq_z del s.gamma_x, s.gamma_y, s.gamma_z