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plovasp: added documentation and tests

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This commit is contained in:
Malte Schüler 2019-06-28 14:47:15 +02:00
parent 29cfe8f711
commit 1dd7552529
12 changed files with 180 additions and 55 deletions
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4
python/converters/plovasp/inpconf.py
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@ -221,8 +221,8 @@ class ConfigParameters:
than the second one.
"""
ftmp = map(int, par_str.split())
assert len(ftmp) == 2, "BWINDOW must be specified by exactly two ints"
assert ftmp[0] < ftmp[1], "The first int in BWINDOW must be smaller than the second one"
assert len(ftmp) == 2, "BANDS must be specified by exactly two ints"
assert ftmp[0] < ftmp[1], "The first int in BANDS must be smaller than the second one"
return tuple(ftmp)
################################################################################

2
python/converters/plovasp/plotools.py
View File

@ -180,7 +180,7 @@ def generate_plo(conf_pars, el_struct):
emesh = np.linspace(dos_emin, dos_emax, n_points)
for ish in pgroup.ishells:
if not isinstance(pshells[pgroup.ishells[ish]],ComplementShell):
if not isinstance(pshells[pgroup.ishells[ish]],ComplementShell) or True:
print " Shell %i"%(ish + 1)
dos = pshells[pgroup.ishells[ish]].density_of_states(el_struct, emesh)
de = emesh[1] - emesh[0]

90
python/converters/plovasp/proj_group.py
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@ -70,8 +70,8 @@ class ProjectorGroup:
if 'bands' in gr_pars:
nk, nband, ns_band = eigvals.shape
ib_win = np.zeros((nk, ns_band, 2), dtype=np.int32)
ib_win[:,:,0] = gr_pars['bands'][0]
ib_win[:,:,1] = gr_pars['bands'][1]
ib_win[:,:,0] = gr_pars['bands'][0]-1
ib_win[:,:,1] = gr_pars['bands'][1]-1
ib_min = gr_pars['bands'][0]
ib_max = gr_pars['bands'][1]
@ -85,11 +85,10 @@ class ProjectorGroup:
if gr_pars['complement']:
n_bands = self.ib_win[:,:,1] - self.ib_win[:,:,0]
n_bands = self.ib_win[:,:,1] - self.ib_win[:,:,0]+1
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:
if n_orbs == n_bands[0,0]:
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"
@ -187,14 +186,17 @@ class ProjectorGroup:
################################################################################
def calc_hk(self, eigvals):
"""
Calculate H(k) for a group by applying the projectors to the eigenvalues.
Calculate H(k) for a group by applying the projectors P
to the eigenvalues eps.
H_ij(k) = sum_l P*_il eps_l P_lj
"""
block_maps, ndim = self.get_block_matrix_map()
_, ns, nk, _, _ = self.shells[0].proj_win.shape
p_mat = np.zeros((ndim, self.nb_max), dtype=np.complex128)
#print(p_mat.shape)
self.hk = np.zeros((ns,nk,ndim,ndim), dtype=np.complex128)
# Note that 'ns' and 'nk' are the same for all shells
@ -204,6 +206,7 @@ class ProjectorGroup:
bmax = self.ib_win[ik, isp, 1]+1
nb = bmax - bmin
p_mat = np.zeros((ndim, nb), dtype=np.complex128)
#print(bmin,bmax,nb)
# Combine all projectors of the group to one block projector
for bl_map in block_maps:
@ -214,14 +217,9 @@ class ProjectorGroup:
nlm = i2 - i1 + 1
shell = self.shells[ish]
p_mat[i1:i2, :nb] = shell.proj_win[ion, isp, ik, :nlm, :nb]
#print(p_mat.shape, eigvals[ik,:,isp].shape)
self.hk[isp,ik,:,:] = np.einsum('ij,jk->ik',p_mat*eigvals[ik,bmin:bmax,isp],
p_mat.transpose().conjugate())
#print(np.linalg.eigvals(self.hk[isp,ik,...]))
#print(eigvals[ik,bmin:bmax,isp])
#print(self.hk.shape)
#self.hk[isp,ik,:,:] = np.dot(p_mat.conjugate()*eigvals[ik,bmin:bmax,isp],
# p_mat.transpose())
self.hk[isp,ik,:,:] = np.dot(p_mat.conjugate()*eigvals[ik,bmin:bmax,isp],
p_mat.transpose())
################################################################################
@ -232,6 +230,17 @@ class ProjectorGroup:
def complement(self,eigvals):
"""
Calculate the complement for a group of projectors.
This leads to quadtratic projectors P = <l|n> by using a Gram-Schmidt.
The projector on the orthogonal complement of the existing projectors
{|l>} is P^u = 1 - sum_l |l><l|
We get candidates for complement projectors by applying P^u to a Bloch
state |n>: |l*> = P^u |n>. For numerical stability we select that Bloch
state which leads to the |l*> with the largest norm (that corresponds to
that Bloch state with the smallest overlap with the space spanned by {|l>})
We normalize |l*> and add it to {|l>}. We do so untill we have as many
|l> states as we have {|n>} states.
"""
@ -242,42 +251,47 @@ class ProjectorGroup:
p_mat = np.zeros((ndim, self.nb_max), dtype=np.complex128)
p_full = np.zeros((1,ns,nk,self.nb_max, self.nb_max), dtype=np.complex128)
#print(p_mat.shape)
self.hk = np.zeros((ns,nk,ndim,ndim), dtype=np.complex128)
# Note that 'ns' and 'nk' are the same for all shells
orbs_done = 1*ndim
while orbs_done < self.nb_max:
for isp in xrange(ns):
for ik in xrange(nk):
bmin = self.ib_win[ik, isp, 0]
bmax = self.ib_win[ik, isp, 1]+1
nb = bmax - bmin
#print(bmin,bmax,nb)
# Combine all projectors of the group to one block projector
for bl_map in block_maps:
p_mat[:, :] = 0.0j # !!! Clean-up from the last k-point and block!
for ibl, block in enumerate(bl_map):
i1, i2 = block['bmat_range']
ish, ion = block['shell_ion']
nlm = i2 - i1 + 1
shell = self.shells[ish]
p_mat[i1:i2, :nb] = shell.proj_win[ion, isp, ik, :nlm, :nb]
p_full[0,isp,ik,:ndim,:] = p_mat
for isp in xrange(ns):
for ik in xrange(nk):
bmin = self.ib_win[ik, isp, 0]
bmax = self.ib_win[ik, isp, 1]+1
nb = bmax - bmin
# Combine all projectors of the group to one block projector
for bl_map in block_maps:
p_mat[:, :] = 0.0j # !!! Clean-up from the last k-point and block!
for ibl, block in enumerate(bl_map):
i1, i2 = block['bmat_range']
ish, ion = block['shell_ion']
nlm = i2 - i1 + 1
shell = self.shells[ish]
p_mat[i1:i2, :nb] = shell.proj_win[ion, isp, ik, :nlm, :nb]
orbs_done = 1*ndim
p_full[0,isp,ik,:ndim,:] = p_mat
while orbs_done < self.nb_max:
proj_work = p_full[0,isp,ik,:,:]
#We calculate the overlap of all bloch states: sum_l <n|l><l|m>
overlap = np.dot(proj_work.transpose().conjugate(),proj_work)
# work is the projector onto the orthogonal complment <n| ( 1 - sum_l |l><l| ) |m>
work = np.eye(self.nb_max) - overlap
# calculate the norm of the projected bloch function
norm = np.sqrt(np.sum(work*work.transpose().conjugate(),axis=1))
# select the bloch function leading to the largest norm
max_ind = np.argmax(norm)
# normalize and put it to the projectors
p_full[0,isp,ik,orbs_done,:] = work[max_ind]/norm[max_ind]
orbs_done += 1
orbs_done += 1
sh_pars = {}
sh_pars['lshell'] = -1
sh_pars['ions'] = {'nion':1,'ion_list':[[1]]}
sh_pars['user_index'] = 'complement'
sh_pars['corr'] = False
sh_pars['ib_min'] = bmin
sh_pars['ib_max'] = bmax
sh_pars['ib_win'] = self.ib_win
self.shells.append(ComplementShell(sh_pars,p_full[:,:,:,ndim:,:],False))
self.ishells.append(self.ishells[-1]+1)

10
python/converters/plovasp/proj_shell.py
View File

@ -473,7 +473,11 @@ class ComplementShell(ProjectorShell):
self.ions = sh_pars['ions']
self.user_index = sh_pars['user_index']
self.corr = sh_pars['corr']
self.nc_flag = nc_flag
self.nc_flag = nc_flag
self.ib_min = sh_pars['ib_min']
self.ib_max = sh_pars['ib_max']
self.ib_win = sh_pars['ib_win']
#self.lm1 = self.lorb**2
@ -501,6 +505,6 @@ class ComplementShell(ProjectorShell):
def density_matrix(self, el_struct, site_diag=True, spin_diag=True):
raise Exception('not implemented')
def density_of_states(self, el_struct, emesh):
raise Exception('not implemented')
#def density_of_states(self, el_struct, emesh):
# raise Exception('not implemented')

13
test/plovasp/inpconf/parse_shells_5.cfg Normal file
View File

@ -0,0 +1,13 @@
[General]
[Group 1]
SHELLS = 1 2
[Shell 1]
LSHELL = 2
IONS = 5..8
[Shell 2]
LSHELL = 1
IONS = 1..4
CORR = False

18
test/plovasp/inpconf/parse_shells_5.cfg~ Normal file
View File

@ -0,0 +1,18 @@
[General]
[Group 1]
SHELLS = 1 2
[Shell 1]
LSHELL = 2
IONS = 5..8
[Shell 2]
LSHELL = 1
IONS = 1..4
TRANSFORM = 0.0 1.0 0.0
1.0 0.0 0.0
0.0 0.0 1.0
CORR = False

3
test/plovasp/inpconf/test_general.py
View File

@ -30,7 +30,8 @@ class TestParseGeneral(arraytest.ArrayTestCase):
conf_pars.parse_general()
res = conf_pars.general
expected = {'basename': 'test_base', 'efermi': 0.1,
'dosmesh': {'n_points': 101, 'emin': -8.0, 'emax': 4.0}}
'dosmesh': {'n_points': 101, 'emin': -8.0, 'emax': 4.0},
'hk' : False}
self.assertDictEqual(res, expected)

6
test/plovasp/inpconf/test_groups.py
View File

@ -39,9 +39,11 @@ class TestParseGroups(arraytest.ArrayTestCase):
conf_pars.parse_groups()
res = conf_pars.groups
expected = [{'index': 1, 'shells': [1, 2], 'ewindow': (-7.6, 3.0),
'normalize': True, 'normion': True},
'normalize': True, 'normion': True,'complement': False},
{'index': 2, 'shells': [3], 'ewindow': (-1.6, 2.0),
'normalize': True, 'normion': True}]
'normalize': True, 'normion': True,'complement': False}]
print res
print expected
self.assertListEqual(res, expected)

10
test/plovasp/inpconf/test_input.py
View File

@ -78,12 +78,12 @@ class TestParseInput(arraytest.ArrayTestCase):
res = res.replace(" ","") # Remove spaces for comparison
expected = r"""Shells:
[{'ions':{'nion':4,'ion_list':[[4],[5],[6],[7]]},'user_index':1,'lshell':2},{'tmatrix':array([[0.,1.,0.],
[{'ions':{'nion':4,'ion_list':[[4],[5],[6],[7]]},'user_index':1,'lshell':2,'corr':True},{'tmatrix':array([[0.,1.,0.],
[1.,0.,0.],
[0.,0.,1.]]),'ions':{'nion':4,'ion_list':[[0],[1],[2],[3]]},'user_index':2,'lshell':1},{'ions':{'nion':4,'ion_list':[[0],[1],[2],[3]]},'user_index':3,'lshell':3}]
[0.,0.,1.]]),'ions':{'nion':4,'ion_list':[[0],[1],[2],[3]]},'user_index':2,'lshell':1,'corr':True},{'ions':{'nion':4,'ion_list':[[0],[1],[2],[3]]},'user_index':3,'lshell':3,'corr':True}]
Groups:
[{'normalize':True,'index':1,'ewindow':(-7.6,3.0),'normion':True,'shells':[0,1]},{'normalize':True,'index':2,'ewindow':(-1.6,2.0),'normion':True,'shells':[2]}]"""
[{'normalize':True,'index':1,'ewindow':(-7.6,3.0),'shells':[0,1],'complement':False,'normion':True},{'normalize':True,'index':2,'ewindow':(-1.6,2.0),'shells':[2],'complement':False,'normion':True}]"""
self.assertEqual(res, expected)
@ -103,10 +103,10 @@ Groups:
res = res.replace(" ","") # Remove spaces for comparison
expected = r"""Shells:
[{'ions':{'nion':4,'ion_list':[[4],[5],[6],[7]]},'user_index':1,'lshell':2}]
[{'ions':{'nion':4,'ion_list':[[4],[5],[6],[7]]},'user_index':1,'lshell':2,'corr':True}]
Groups:
[{'normalize':True,'index':'1','ewindow':(-7.6,3.0),'shells':[0],'normion':True}]"""
[{'normalize':True,'index':'1','ewindow':(-7.6,3.0),'normion':True,'complement':False,'shells':[0]}]"""
self.assertEqual(res, expected)

24
test/plovasp/inpconf/test_shells.py
View File

@ -30,6 +30,8 @@ class TestParseShells(arraytest.ArrayTestCase):
**raise** Exception
- **if** two correct [Shell] sections are defined
**return** a dictionary of shell parameters
- **if** two correct [Shell] sections (one has CORR=False are defined
**return** a dictionary of shell parameters
"""
# Scenario 1
def test_no_shell(self):
@ -57,9 +59,9 @@ class TestParseShells(arraytest.ArrayTestCase):
conf_pars = ConfigParameters(_rpath + 'parse_shells_4.cfg')
conf_pars.parse_shells()
res = conf_pars.shells
expected = [{'user_index': 1, 'lshell': 2, 'ions': {'nion': 4, 'ion_list': [[4],[5],[6],[7]]}},
expected = [{'user_index': 1, 'lshell': 2, 'ions': {'nion': 4, 'ion_list': [[4],[5],[6],[7]]},'corr': True},
{'user_index': 2, 'lshell': 1, 'ions': {'nion': 4, 'ion_list': [[0],[1],[2],[3]]},
'tmatrix': np.array([[ 0., 1., 0.], [ 1., 0., 0.], [ 0., 0., 1.]])}]
'tmatrix': np.array([[ 0., 1., 0.], [ 1., 0., 0.], [ 0., 0., 1.]]),'corr': True}]
# ...lousy way to test equality of two dictionaries containing numpy arrays
self.assertEqual(len(res), len(expected))
@ -77,6 +79,24 @@ class TestParseShells(arraytest.ArrayTestCase):
self.assertListEqual(res, expected)
# Scenario 5
def test_two_shells_with_corr_false(self):
conf_pars = ConfigParameters(_rpath + 'parse_shells_5.cfg')
conf_pars.parse_shells()
res = conf_pars.shells
expected = [{'user_index': 1, 'lshell': 2, 'ions': {'nion': 4, 'ion_list': [[4],[5],[6],[7]]},'corr': True},
{'user_index': 2, 'lshell': 1, 'ions': {'nion': 4, 'ion_list': [[0],[1],[2],[3]]},'corr': False}]
self.assertEqual(len(res), len(expected))
arr = res[0].pop('ions')
arr_exp = expected[0].pop('ions')
self.assertDictEqual(arr, arr_exp)
arr = res[1].pop('ions')
arr_exp = expected[1].pop('ions')
self.assertDictEqual(arr, arr_exp)
self.assertListEqual(res, expected)
if __name__ == '__main__':
import unittest

53
test/plovasp/inpconf/test_special_parsers.py
View File

@ -212,6 +212,59 @@ class TestParseEnergyWindow(arraytest.ArrayTestCase):
with self.assertRaisesRegexp(AssertionError, err_mess):
self.cpars.parse_energy_window('1.5 3.0 2.0')
################################################################################
#
# TestParseBandWindow
#
################################################################################
class TestParseBandWindow(arraytest.ArrayTestCase):
"""
Function:
def parse_band_window(self, par_str)
Scenarios:
- **if** par_str == '1 10' **return** (1, 10)
- **if** par_str == '3.0 -1.5' **raise** AssertionError
- **if** par_str == '1.0' **raise** AssertionError
- **if** par_str == 'aaa' **raise** ValueError
- **if** par_str == '1.5 3.0 2.0' **raise** AssertionError
"""
def setUp(self):
"""
"""
# Dummy ConfigParameters object
self.cpars = ConfigParameters(_rpath + 'test1.cfg')
# Scenario 1
def test_correct_range(self):
expected = (1, 10)
res = self.cpars.parse_band_window('1 10')
self.assertEqual(res, expected)
# Scenario 2
def test_wrong_range(self):
err_mess = "The first int in BANDS"
with self.assertRaisesRegexp(AssertionError, err_mess):
self.cpars.parse_band_window('10 1')
# Scenario 3
def test_one_float(self):
err_mess = "BANDS must be specified"
with self.assertRaisesRegexp(AssertionError, err_mess):
self.cpars.parse_band_window('1')
# Scenario 4
def test_wrong_string(self):
with self.assertRaises(ValueError):
self.cpars.parse_band_window('aaa')
# Scenario 5
def test_three_ints(self):
err_mess = "BANDS must be specified"
with self.assertRaisesRegexp(AssertionError, err_mess):
self.cpars.parse_band_window('1 2 3')
################################################################################
#

2
test/plovasp/proj_shell/projshells.out
View File

@ -1,4 +1,4 @@
pars: {'ions': {'nion': 1, 'ion_list': [[1]]}, 'user_index': 1, 'lshell': 2}
pars: {'ions': {'nion': 1, 'ion_list': [[1]]}, 'user_index': 1, 'lshell': 2, 'corr': True}
10 25
1 0.000000 -0.000000
2 0.000000 0.000000