def init_pos(natom):
from qharv.inspect import crystal
from ase import Atoms
from ase.build import make_supercell
rho = 2.2e22 * 1e6 / 1e30 # atoms/A^3
lbox = (natom / rho)**(1. / 3)
nxf = (natom / 4.)**(1. / 3)
nx = int(round(nxf))
if not np.isclose(nx, nxf):
raise RuntimeError('natom=%d nxf=%3.2f!=%d' % (natom, nxf, nx))
# create FCC crystal
alat = lbox / nx
axes0 = alat / 2 * (np.ones(3) - np.eye(3))
tmat = nx * (np.ones(3) - 2 * np.eye(3))
s0 = Atoms('H', cell=axes0, positions=[[0, 0, 0]], pbc=[1, 1, 1])
s1 = make_supercell(s0, tmat)
pos = s1.get_positions()
axes = s1.get_cell()
# check density
rho1 = natom / axes_pos.volume(axes)
if not np.isclose(rho, rho1):
raise RuntimeError('supercell density is wrong')
# save/view crystal
fig, ax = volumetric.figax3d()
crystal.draw_cell(ax, axes)
crystal.draw_atoms(ax, pos)
plt.show()
return pos
def show_moR(moR):
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # enable 3D projection
from qharv.inspect import volumetric,crystal
fig = plt.figure()
iplot = 0
for iorb in mo_to_plot:
iplot += 1
val = moR[:,iorb].reshape(2*dgs+1)
fval= volumetric.spline_volumetric(val)
grid= volumetric.axes_func_on_grid3d(axes,fval,grid_shape)
myup = default_up
mydn = default_dn
if iorb in up_dn_map.keys():
myup = up_dn_map[iorb]['up']
mydn = up_dn_map[iorb]['dn']
# end if
ax = fig.add_subplot(2,2,iplot,projection='3d')
crystal.draw_cell(ax,axes*grid_shape/alat0,pos*grid_shape/alat0,'y')
ax.set_title('orb %d' % iorb)
if myup >0:
meshm = volumetric.isosurf(ax,grid,level_frac=myup)
meshm.set_facecolor('#3498db')
meshm.set_edgecolor('#34495e')
if mydn >0:
meshp = volumetric.isosurf(ax,grid,level_frac=mydn)
meshp.set_facecolor('#fb9a99')
meshp.set_edgecolor('#e11a1c')
# end for
plt.show()
def make_mhcpc(s1, rb=0.74, iax=2, check=False):
# copied from f16b1/prim.py
axes = s1.get_cell()
pos = s1.get_positions()
box = np.diag(axes)
# make sure cell is diagonal
assert np.allclose(np.diag(box), axes)
posl = []
for center in pos:
p1 = center.copy()
p1[iax] += rb/2.
posl.append(p1.copy())
p1[iax] -= rb
posl.append(p1)
pos1 = np.array(posl)
if check: # check pos1
from qharv.inspect import box_pos
from qharv.inspect import crystal, volumetric
pos1 = box_pos.pos_in_box(pos1, box)
fig, ax = volumetric.figax3d()
crystal.draw_cell(ax, axes)
crystal.draw_atoms(ax, pos, c='k', ms=2)
crystal.draw_atoms(ax, pos1)
plt.show()
s2 = make_atoms(axes, pos1)
s2.wrap()
return s2
val_arr = df.loc[:, ['x']].values.flatten()
k1, v1 = unfold(pos, val_arr)
pos = k1
val_arr = v1
vmin, vmax = val_arr.min(), val_arr.max()
fig = plt.figure()
from mpl_toolkits.mplot3d import Axes3D
ax = fig.add_subplot(1, 1, 1, projection="3d")
ax.set_xlabel("k1")
ax.set_ylabel("k2")
ax.set_zlabel("k3")
from qharv.inspect import crystal
crystal.draw_cell(ax, axes)
uValpts = []
cmap = plt.get_cmap('rainbow')
for ipos in range(len(pos)):
val = val_arr[ipos]
if abs(val) < 2e-5:
continue
uval = (val - vmin) / (vmax - vmin)
rgb = cmap(uval)
cs = crystal.draw_atoms(ax, np.array([pos[ipos]]),
c=rgb) #,ms=5,alpha=0.5)
uValpts.append(uval)
# end for
fig1 = plt.figure()
ax1 = fig1.gca()
else:
from pyscf.pbc.gto.cell import gen_uniform_grids
from pyscf.pbc.dft.numint import eval_ao
coords = gen_uniform_grids(cell,gs=dgs)
aoR = eval_ao(cell,coords)
dm = mf.make_rdm1(mf.mo_coeff, mf.mo_occ)
rho = np.dot(aoR, np.diag(dm) )
np.savetxt(rho_fname,rho)
# end if
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # enable 3D projection
from qharv.inspect import volumetric,crystal
fig = plt.figure()
fval= volumetric.spline_volumetric(rho.reshape(2*dgs+1) )
grid= volumetric.axes_func_on_grid3d(axes,fval,grid_shape)
ax = fig.add_subplot(1,1,1,projection='3d')
crystal.draw_cell(ax,axes*grid_shape/alat0,pos*grid_shape/alat0,'y')
meshm = volumetric.isosurf(ax,grid,level_frac=0.3)
meshm.set_facecolor('#3498db')
meshm.set_edgecolor('#34495e')
meshp = volumetric.isosurf(ax,grid,level_frac=0.75)
meshp.set_facecolor('#fb9a99')
meshp.set_edgecolor('#e11a1c')
plt.show()
# end __main__