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plovasp: documentation and cleaning

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This commit is contained in:
Malte Schüler 2019-06-27 16:26:22 +02:00
parent 96a6891f64
commit 29cfe8f711
3 changed files with 48 additions and 85 deletions
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78
python/converters/plovasp/plotools.py
View File

@ -205,7 +205,7 @@ def output_as_text(pars, el_struct, pshells, pgroups):
ctrl_output(pars, el_struct, len(pgroups))
plo_output(pars, el_struct, pshells, pgroups)
if pars.general['hk']:
hk_output(pars, el_struct, pshells, pgroups)
hk_output(pars, el_struct, pgroups)
# TODO: k-points with weights should be stored once and for all
@ -384,7 +384,6 @@ def plo_output(conf_pars, el_struct, pshells, pgroups):
f.write("# Shell %i\n"%(ish))
nion, ns, nk, nlm, nb = shell.proj_win.shape
print(nlm)
for isp in xrange(ns):
f.write("# is = %i\n"%(isp + 1))
for ik in xrange(nk):
@ -403,47 +402,36 @@ def plo_output(conf_pars, el_struct, pshells, pgroups):
# plo_output
#
################################################################################
def hk_output(conf_pars, el_struct, pshells, pgroups):
def hk_output(conf_pars, el_struct, pgroups):
"""
Outputs HK into text file.
Filename is defined by <basename> that is passed from config-file.
The Hk for all groups is stored in a '<basename>.hk' file. The format is as
defined in the Hk dft_tools format
# Energy window: emin, emax
ib_min, ib_max
nelect
# Eigenvalues
isp, ik1, kx, ky, kz, kweight
ib1, ib2
eig1
eig2
...
eigN
ik2, kx, ky, kz, kweight
...
# Projected shells
Nshells
# Shells: <shell indices>
# Shell <1>
Shell 1
ndim
# complex arrays: plo(ns, nion, ndim, nb)
...
# Shells: <shell indices>
# Shell <2>
Shell 2
...
The Hk for each groups is stored in a '<basename>.hk<Ng>' file. The format is
as defined in the Hk dft_tools format
nk # number of k-points
n_el # electron density
n_sh # number of total atomic shells
at sort l dim # atom, sort, l, dim
at sort l dim # atom, sort, l, dim
n_cr_sh # number of correlated shells
at sort l dim SO irep # atom, sort, l, dim, SO, irep
n_irrep dim_irrep # number of ireps, dim of irep
After these header lines, the file has to contain the Hamiltonian matrix
in orbital space. The standard convention is that you give for each k-point
first the matrix of the real part, then the matrix of the imaginary part,
and then move on to the next k-point.
"""
print 'writing hk'
for ig, pgroup in enumerate(pgroups):
hk_fname = conf_pars.general['basename'] + '.hk%i'%(ig + 1)
for ig, pgroup in enumerate(pgroups):
hk_fname = conf_pars.general['basename'] + '.hk%i'%(ig + 1)
print " Storing HK-group file '%s'..."%(hk_fname)
head_corr_shells = []
head_shells = []
@ -462,32 +450,26 @@ def hk_output(conf_pars, el_struct, pshells, pgroups):
sh_dict['ion_list'] = ion_output
sh_dict['ion_sort'] = shell.ion_sort
# TODO: add the output of transformation matrices
head_shells.append(sh_dict)
if shell.corr:
head_corr_shells.append(sh_dict)
#head_dict['shells'] = head_shells
#header = json.dumps(head_dict, indent=4, separators=(',', ': '))
with open(hk_fname, 'wt') as f:
# Eigenvalues within the window
# Eigenvalues within the window
nk, nband, ns_band = el_struct.eigvals.shape
f.write('%i # number of kpoints\n'%nk)
f.write('%f # electron density\n'%1.0)
f.write('%i # number of shells\n'%len(head_shells))
f.write('%i # number of kpoints\n'%nk)
f.write('{0:0.4f} # electron density\n'.format(pgroup.nelect_window(el_struct)))
f.write('%i # number of shells\n'%len(head_shells))
for head in head_shells:
f.write('%i %i %i %i # atom sort l dim\n'%(head['ion_list'][0],head['ion_sort'][0],head['lorb'],head['ndim']))
f.write('%i # number of correlated shells\n'%len(head_corr_shells))
f.write('%i %i %i %i # atom sort l dim\n'%(head['ion_list'][0],head['ion_sort'][0],head['lorb'],head['ndim']))
f.write('%i # number of correlated shells\n'%len(head_corr_shells))
for head in head_corr_shells:
f.write('%i %i %i %i 0 0 # atom sort l dim SO irrep\n'%(head['ion_list'][0],head['ion_sort'][0],head['lorb'],head['ndim']))
f.write('1 5 # number of ireps, dim of irep\n')
f.write('%i %i %i %i 0 0 # atom sort l dim SO irrep\n'%(head['ion_list'][0],head['ion_sort'][0],head['lorb'],head['ndim']))
f.write('1 5 # number of ireps, dim of irep\n')
norbs = pgroup.hk.shape[2]
for isp in xrange(ns_band):
#f.write("# is = %i\n"%(isp + 1))
for ik in xrange(nk):
for io in xrange(norbs):
for iop in xrange(norbs):

18
python/converters/plovasp/proj_group.py
View File

@ -81,6 +81,19 @@ class ProjectorGroup:
self.ib_min = ib_min
self.ib_max = ib_max
self.nb_max = ib_max - ib_min + 1
if gr_pars['complement']:
n_bands = self.ib_win[:,:,1] - self.ib_win[:,:,0]
n_orbs = sum([x.ndim for x in self.shells])
assert np.all( n_bands == n_bands[0,0] ), "At each band the same number of bands has to be selected for calculating the complement (to end up with an equal number of orbitals at each k-point)."
if n_orbs == n_bands[0,0]+1:
gr_pars['complement'] = False
print "\nWARNING: The total number of orbitals in this group is "
print "equal to the number of bands. Setting COMPLEMENT to FALSE!\n"
# Select projectors within the energy window
for ish in self.ishells:
@ -222,7 +235,7 @@ class ProjectorGroup:
"""
print 'claculating complemet'
print '\nCalculating complement\n'
block_maps, ndim = self.get_block_matrix_map()
_, ns, nk, _, _ = self.shells[0].proj_win.shape
@ -267,9 +280,6 @@ class ProjectorGroup:
sh_pars['corr'] = False
self.shells.append(ComplementShell(sh_pars,p_full[:,:,:,ndim:,:],False))
self.ishells.append(self.ishells[-1]+1)
print(self.shells)
print(self.ishells)
#p_full -= p_mat
################################################################################

37
python/converters/plovasp/proj_shell.py
View File

@ -493,43 +493,14 @@ class ComplementShell(ProjectorShell):
self.proj_win = proj_compl
def extract_tmatrices(self, sh_pars):
pass
raise Exception('not implemented')
def local_hamiltonian(self, el_struct, site_diag=True, spin_diag=True):
"""
Returns occupation matrix/matrices for the shell.
"""
nion, ns, nk, nlm, nbtot = self.proj_win.shape
assert site_diag, "site_diag = False is not implemented"
assert spin_diag, "spin_diag = False is not implemented"
loc_ham = np.zeros((ns, nion, nlm, nlm), dtype=np.float64)
return loc_ham
raise Exception('not implemented')
def density_matrix(self, el_struct, site_diag=True, spin_diag=True):
"""
Returns occupation matrix/matrices for the shell.
"""
nion, ns, nk, nlm, nbtot = self.proj_win.shape
# assert site_diag, "site_diag = False is not implemented"
assert spin_diag, "spin_diag = False is not implemented"
if site_diag:
occ_mats = np.zeros((ns, nion, nlm, nlm), dtype=np.float64)
overlaps = np.zeros((ns, nion, nlm, nlm), dtype=np.float64)
else:
ndim = nion * nlm
occ_mats = np.zeros((ns, 1, ndim, ndim), dtype=np.float64)
overlaps = np.zeros((ns, 1, ndim, ndim), dtype=np.float64)
return occ_mats, overlaps
raise Exception('not implemented')
def density_of_states(self, el_struct, emesh):
nion, ns, nk, nlm, nbtot = self.proj_win.shape
ne = len(emesh)
dos = np.zeros((ne, ns, nion, nlm))
return dos
raise Exception('not implemented')