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https://github.com/triqs/dft_tools
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plovasp: fixed some bugs for multiple ions per shell
This commit is contained in:
Malte Schüler
parent
d2263ae3d5
commit
2dda711aed
@ -81,6 +81,7 @@ def check_data_consistency(pars, el_struct):
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else:
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errmsg = "Projector for isite = %s, l = %s does not match PROJCAR"%(ion + 1, lshell)
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raise Exception(errmsg)
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################################################################################
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#
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@ -106,7 +107,8 @@ def generate_plo(conf_pars, el_struct):
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# eigvals(nktot, nband, ispin) are defined with respect to the Fermi level
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eigvals = el_struct.eigvals - efermi
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# check if at least one shell is correlated
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assert np.any([shell['corr'] for shell in conf_pars.shells]), 'at least one shell has be CORR = True'
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nshell = len(conf_pars.shells)
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print
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print " Generating %i shell%s..."%(nshell, '' if nshell == 1 else 's')
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@ -121,6 +123,7 @@ def generate_plo(conf_pars, el_struct):
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print " Correlated : %r"%(pshell.corr)
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pshells.append(pshell)
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pgroups = []
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for gr_par in conf_pars.groups:
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pgroup = ProjectorGroup(gr_par, pshells, eigvals)
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@ -436,20 +439,22 @@ def hk_output(conf_pars, el_struct, pgroups):
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shell = pgroup.shells[ish]
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sh_dict = {}
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sh_dict['shell_index'] = ish
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sh_dict['lorb'] = shell.lorb
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sh_dict['ndim'] = shell.ndim
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# Convert ion indices from the internal representation (starting from 0)
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# to conventional VASP representation (starting from 1)
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ion_output = [io + 1 for io in shell.ion_list]
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# Derive sorts from equivalence classes
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sh_dict['ion_list'] = ion_output
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sh_dict['ion_sort'] = shell.ion_sort
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for iion in ion_output:
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sh_dict = {}
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sh_dict['shell_index'] = ish
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sh_dict['lorb'] = shell.lorb
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sh_dict['ndim'] = shell.ndim
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# Convert ion indices from the internal representation (starting from 0)
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# to conventional VASP representation (starting from 1)
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# Derive sorts from equivalence classes
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sh_dict['ion_list'] = ion_output
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sh_dict['ion_sort'] = shell.ion_sort
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head_shells.append(sh_dict)
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head_shells.append(sh_dict)
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with open(hk_fname, 'wt') as f:
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# Eigenvalues within the window
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@ -192,12 +192,18 @@ class ProjectorGroup:
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H_ij(k) = sum_l P*_il eps_l P_lj
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"""
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# here we abuse the get_block_matrix_map(), however, it only works
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# if self.normion is false
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temp = self.normion
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self.normion = False
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block_maps, ndim = self.get_block_matrix_map()
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self.normion = temp
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_, ns, nk, _, _ = self.shells[0].proj_win.shape
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#print(p_mat.shape)
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print block_maps, ndim
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self.hk = np.zeros((ns,nk,ndim,ndim), dtype=np.complex128)
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# Note that 'ns' and 'nk' are the same for all shells
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for isp in xrange(ns):
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@ -218,8 +224,8 @@ class ProjectorGroup:
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shell = self.shells[ish]
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p_mat[i1:i2, :nb] = shell.proj_win[ion, isp, ik, :nlm, :nb]
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self.hk[isp,ik,:,:] = np.dot(p_mat.conjugate()*eigvals[ik,bmin:bmax,isp],
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p_mat.transpose())
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self.hk[isp,ik,:,:] = np.dot(p_mat*eigvals[ik,bmin:bmax,isp],
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p_mat.transpose().conjugate())
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################################################################################
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@ -145,7 +145,8 @@ class VaspConverter(ConverterTools):
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# TODO: think about multiple shell groups and how to map them on h5 structures
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assert ng == 1, "Only one group is allowed at the moment"
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try:
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#try:
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if True:
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for ig in xrange(ng):
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gr_file = self.basename + '.pg%i'%(ig + 1)
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jheader, rf = self.read_header_and_data(gr_file)
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@ -165,8 +166,9 @@ class VaspConverter(ConverterTools):
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shells = []
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corr_shells = []
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shion_to_shell = [[] for ish in xrange(len(p_shells))]
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cr_shion_to_shell = [[] for ish in xrange(len(p_shells))]
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shorbs_to_globalorbs = [[] for ish in xrange(len(p_shells))]
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shorbs_to_globalorbs[0] = [0,p_shells[0]['ndim'] ]
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last_dimension = 0
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crshorbs_to_globalorbs = []
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icsh = 0
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for ish, sh in enumerate(p_shells):
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@ -179,23 +181,22 @@ class VaspConverter(ConverterTools):
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pars['l'] = sh['lorb']
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#pars['corr'] = sh['corr']
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pars['dim'] = sh['ndim']
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pars['ion_list'] = sh['ion_list']
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#pars['ion_list'] = sh['ion_list']
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pars['SO'] = SO
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# TODO: check what 'irep' entry does (it seems to be very specific to dmftproj)
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pars['irep'] = 0
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shells.append(pars)
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shion_to_shell[ish].append(i)
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if ish > 0:
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shorbs_to_globalorbs[ish] = [shorbs_to_globalorbs[ish-1][1],
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shorbs_to_globalorbs[ish-1][1]+sh['ndim']]
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shorbs_to_globalorbs[ish].append([last_dimension,
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last_dimension+sh['ndim']])
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last_dimension = last_dimension+sh['ndim']
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if sh['corr']:
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corr_shells.append(pars)
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crshorbs_to_globalorbs.append(shorbs_to_globalorbs[ish])
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print shorbs_to_globalorbs
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# TODO: generalize this to the case of multiple shell groups
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n_corr_shells = len(corr_shells)
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#n_shells = n_corr_shells # No non-correlated shells at the moment
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#shells = corr_shells
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n_orbs = sum([sh['dim'] for sh in shells])
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# FIXME: atomic sorts in Wien2K are not the same as in VASP.
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# A symmetry analysis from OUTCAR or symmetry file should be used
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@ -260,18 +261,20 @@ class VaspConverter(ConverterTools):
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rf_hk = self.read_data(f_hk)
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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print ik
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for ib in xrange(n_orbs):
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for jb in xrange(n_orbs):
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hopping[ik, isp, ib, jb] = rf_hk.next()
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for ib in xrange(n_orbs):
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for jb in xrange(n_orbs):
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hopping[ik, isp, ib, jb] += 1j*rf_hk.next()
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rf_hk.close()
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# Projectors
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# print n_orbitals
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# print [crsh['dim'] for crsh in corr_shells]
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proj_mat_all = numpy.zeros([n_k, n_spin_blocs, n_corr_shells, sum([sh['dim'] for sh in shells]), numpy.max(n_orbitals)], numpy.complex_)
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proj_mat_csc = numpy.zeros([n_k, n_spin_blocs, sum([sh['dim'] for sh in shells]), numpy.max(n_orbitals)], numpy.complex_)
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print 'proj_mat_csc', proj_mat_csc.shape
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# TODO: implement reading from more than one projector group
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# In 'dmftproj' each ion represents a separate correlated shell.
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# In my interface a 'projected shell' includes sets of ions.
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@ -284,52 +287,51 @@ class VaspConverter(ConverterTools):
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#
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# At the moment I choose i.2 for its simplicity. But one should consider possible
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# use cases and decide which solution is to be made permanent.
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#
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#
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for ish, sh in enumerate(p_shells):
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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for ion in xrange(len(sh['ion_list'])):
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icsh = shion_to_shell[ish][ion]
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for ilm in xrange(shorbs_to_globalorbs[ish][0],shorbs_to_globalorbs[ish][1]):
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for ilm in xrange(shorbs_to_globalorbs[ish][ion][0],shorbs_to_globalorbs[ish][ion][1]):
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for ib in xrange(n_orbitals[ik, isp]):
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# This is to avoid confusion with the order of arguments
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pr = rf.next()
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pi = rf.next()
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proj_mat_all[ik, isp, icsh, ilm, ib] = complex(pr, pi)
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proj_mat_csc[ik, isp, ilm, ib] = complex(pr, pi)
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# now save only projectors with flag 'corr' to proj_mat
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proj_mat = numpy.zeros([n_k, n_spin_blocs, n_corr_shells, sum([crsh['dim'] for crsh in corr_shells]), numpy.max(n_orbitals)], numpy.complex_)
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proj_mat = numpy.zeros([n_k, n_spin_blocs, n_corr_shells, max([crsh['dim'] for crsh in corr_shells]), numpy.max(n_orbitals)], numpy.complex_)
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print 'proj_mat', proj_mat.shape
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if self.proj_or_hk == 'proj':
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addIndex = 0
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for ish, corr_shell in enumerate(corr_shells):
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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for ion in xrange(len(corr_shell['ion_list'])):
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icsh = shion_to_shell[ish][ion]
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for iclm,ilm in enumerate(xrange(crshorbs_to_globalorbs[ish][0],crshorbs_to_globalorbs[ish][1])):
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for ib in xrange(n_orbitals[ik, isp]):
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proj_mat[ik,isp,icsh,iclm+addIndex,ib] = proj_mat_all[ik,isp,icsh,ilm,ib]
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addIndex += corr_shell['dim']
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for ish, sh in enumerate(p_shells):
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if sh['corr']:
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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for ion in xrange(len(sh['ion_list'])):
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icsh = shion_to_shell[ish][ion]
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for iclm,ilm in enumerate(xrange(shorbs_to_globalorbs[ish][ion][0],shorbs_to_globalorbs[ish][ion][1])):
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for ib in xrange(n_orbitals[ik, isp]):
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proj_mat[ik,isp,icsh,iclm,ib] = proj_mat_csc[ik,isp,ilm,ib]
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elif self.proj_or_hk == 'hk':
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addIndex = 0
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for ish, corr_shell in enumerate(corr_shells):
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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for ion in xrange(len(corr_shell['ion_list'])):
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icsh = shion_to_shell[ish][ion]
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for iclm,ilm in enumerate(xrange(crshorbs_to_globalorbs[ish][0],crshorbs_to_globalorbs[ish][1])):
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proj_mat[ik,isp,icsh,iclm+addIndex,ilm] = 1.0
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addIndex += corr_shell['dim']
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corr_shell.pop('ion_list')
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print crshorbs_to_globalorbs, proj_mat.shape, shorbs_to_globalorbs
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for ish, sh in enumerate(p_shells):
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if sh['corr']:
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for ion in xrange(len(sh['ion_list'])):
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icsh = shion_to_shell[ish][ion]
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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for iclm,ilm in enumerate(xrange(shorbs_to_globalorbs[ish][ion][0],shorbs_to_globalorbs[ish][ion][1])):
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proj_mat[ik,isp,icsh,iclm,ilm] = 1.0
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print proj_mat[0,0,0,:,:].real
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print proj_mat[0,0,1,:,:].real
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#corr_shell.pop('ion_list')
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things_to_set = ['n_shells','shells','n_corr_shells','corr_shells','n_spin_blocs','n_orbitals','n_k','SO','SP','energy_unit']
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for it in things_to_set:
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# print "%s:"%(it), locals()[it]
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setattr(self,it,locals()[it])
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except StopIteration:
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raise "VaspConverter: error reading %s"%self.gr_file
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#except StopIteration:
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# raise "VaspConverter: error reading %s"%self.gr_file
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rf.close()
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@ -340,10 +342,12 @@ class VaspConverter(ConverterTools):
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# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!
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things_to_save = ['energy_unit','n_k','k_dep_projection','SP','SO','charge_below','density_required',
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'symm_op','n_shells','shells','n_corr_shells','corr_shells','use_rotations','rot_mat',
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'rot_mat_time_inv','n_reps','dim_reps','T','n_orbitals','proj_mat',
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# 'proj_mat_all',
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'bz_weights','hopping',
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'rot_mat_time_inv','n_reps','dim_reps','T','n_orbitals','proj_mat','bz_weights','hopping',
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'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr']
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if self.proj_or_hk == 'hk':
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proj_or_hk = self.proj_or_hk
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things_to_save.append('proj_mat_csc')
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things_to_save.append('proj_or_hk')
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for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it]
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# Store Fermi weights to 'dft_misc_input'
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