mirror of
https://github.com/triqs/dft_tools
synced 2025-01-03 01:55:56 +01:00
SumK generated output in new group 'lda_output', cleaning up.
* updated update_archive.py script to move output elements out * added clear_lda_output.py script to restore state of converter generated h5
This commit is contained in:
Priyanka Seth
parent
8bbbe81c7d
commit
8d44e5ce91
@ -8,6 +8,7 @@ Changed the following:
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* retval -> read_value
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* Gupf -> G_upfold
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* read_symmetry_input -> convert_symmetry_input
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* Symm_corr -> symmcorr
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**********
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* changed default h5 subgroup names
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24
python/clear_lda_output.py
Normal file
24
python/clear_lda_output.py
Normal file
@ -0,0 +1,24 @@
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import h5py
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import sys
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import subprocess
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if len(sys.argv) < 2:
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print "Usage: python clear_lda_output.py archive"
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sys.exit()
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print """
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This script is to remove any SumkLDA generated output from the h5 archive
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and to restore it to the original post-converter state.
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"""
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filename = sys.argv[1]
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A = h5py.File(filename)
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del(A["lda_output"])
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A.close()
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# Repack to reclaim disk space
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retcode = subprocess.call(["h5repack","-i%s"%filename, "-otemphgfrt.h5"])
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if retcode != 0:
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print "h5repack failed!"
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else:
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subprocess.call(["mv","-f","temphgfrt.h5","%s"%filename])
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@ -32,8 +32,9 @@ class SumkLDA:
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"""This class provides a general SumK method for combining ab-initio code and pytriqs."""
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def __init__(self, hdf_file, mu = 0.0, h_field = 0.0, use_lda_blocks = False, lda_data = 'lda_input', symmcorr_data = 'lda_symmcorr_input',
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parproj_data = 'lda_parproj_input', symmpar_data = 'lda_symmpar_input', bands_data = 'lda_bands_input'):
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def __init__(self, hdf_file, mu = 0.0, h_field = 0.0, use_lda_blocks = False,
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lda_data = 'lda_input', symmcorr_data = 'lda_symmcorr_input', parproj_data = 'lda_parproj_input',
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symmpar_data = 'lda_symmpar_input', bands_data = 'lda_bands_input', lda_output = 'lda_output'):
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"""
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Initialises the class from data previously stored into an HDF5
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"""
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@ -47,6 +48,7 @@ class SumkLDA:
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self.parproj_data = parproj_data
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self.symmpar_data = symmpar_data
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self.bands_data = bands_data
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self.lda_output = lda_output
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self.block_names = [ ['up','down'], ['ud'] ]
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self.n_spin_blocks_gf = [2,1]
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self.G_upfold = None
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@ -56,15 +58,12 @@ class SumkLDA:
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things_to_read = ['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','bz_weights','hopping']
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optional_things = ['gf_struct_solver','map_inv','map','chemical_potential','dc_imp','dc_energ','deg_shells']
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self.read_value = self.read_input_from_hdf(subgrp=self.lda_data,things_to_read=things_to_read,optional_things=optional_things)
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self.subgroup_present, self.value_read = self.read_input_from_hdf(subgrp = self.lda_data, things_to_read = things_to_read)
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if (self.SO) and (abs(self.h_field)>0.000001):
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self.h_field=0.0
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mpi.report("For SO, the external magnetic field is not implemented, setting it to 0!")
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# determine the number of inequivalent correlated shells (self.n_inequiv_corr_shells)
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# and related maps (self.shellmap, self.invshellmap)
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self.inequiv_shells(self.corr_shells)
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@ -73,14 +72,19 @@ class SumkLDA:
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self.names_to_ind = [{}, {}]
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for ibl in range(2):
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for inm in range(self.n_spin_blocks_gf[ibl]):
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self.names_to_ind[ibl][self.block_names[ibl][inm]] = inm * self.SP #(self.Nspinblocs-1)
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self.names_to_ind[ibl][self.block_names[ibl][inm]] = inm * self.SP
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# GF structure used for the local things in the k sums
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# Most general form allowing for all hybridisation, i.e. largest blocks possible
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self.gf_struct_corr = [ [ (al, range( self.corr_shells[i][3])) for al in self.block_names[self.corr_shells[i][4]] ]
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for i in xrange(self.n_corr_shells) ]
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if not (self.read_value['gf_struct_solver']):
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#-----
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# If these quantities are not in HDF, set them up and save into HDF
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optional_things = ['gf_struct_solver','map_inv','map','chemical_potential','dc_imp','dc_energ','deg_shells']
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self.subgroup_present, self.value_read = self.read_input_from_hdf(subgrp = self.lda_output, things_to_read = [],
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optional_things = optional_things)
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if (not self.subgroup_present) or (not self.value_read['gf_struct_solver']):
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# No gf_struct was stored in HDF, so first set a standard one:
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self.gf_struct_solver = [ dict([ (al, range(self.corr_shells[self.invshellmap[i]][3]) )
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for al in self.block_names[self.corr_shells[self.invshellmap[i]][4]] ])
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@ -93,100 +97,91 @@ class SumkLDA:
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self.map[i][al] = [al for j in range( self.corr_shells[self.invshellmap[i]][3] ) ]
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self.map_inv[i][al] = al
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if not (self.read_value['dc_imp']):
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if (not self.subgroup_present) or (not self.value_read['dc_imp']):
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# init the double counting:
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self.__init_dc()
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if not (self.read_value['chemical_potential']):
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if (not self.subgroup_present) or (not self.value_read['chemical_potential']):
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self.chemical_potential = mu
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if not (self.read_value['deg_shells']):
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if (not self.subgroup_present) or (not self.value_read['deg_shells']):
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self.deg_shells = [ [] for i in range(self.n_inequiv_corr_shells)]
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#-----
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if self.symm_op:
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#mpi.report("Do the init for symm:")
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self.Symm_corr = Symmetry(hdf_file,subgroup=self.symmcorr_data)
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self.symmcorr = Symmetry(hdf_file,subgroup=self.symmcorr_data)
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# Analyse the block structure and determine the smallest blocs, if desired
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if (use_lda_blocks): dm=self.analyse_BS()
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# now save things again to HDF5:
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if (mpi.is_master_node()):
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ar=HDFArchive(self.hdf_file,'a')
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ar[self.lda_data]['h_field'] = self.h_field
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del ar
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self.save()
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# Now save things again to HDF5:
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# FIXME WHAT HAPPENS TO h_field? INPUT TO __INIT__? ADD TO OPTIONAL_THINGS?
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things_to_save=['chemical_potential','dc_imp','dc_energ','h_field']
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self.save(things_to_save)
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def read_input_from_hdf(self, subgrp, things_to_read, optional_things=[]):
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def read_input_from_hdf(self, subgrp, things_to_read=[], optional_things=[]):
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"""
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Reads data from the HDF file
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"""
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read_value = True
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value_read = True
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# init variables on all nodes to ensure mpi broadcast works at the end
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for it in things_to_read: setattr(self,it,0)
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for it in optional_things: setattr(self,it,0)
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if (mpi.is_master_node()):
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if mpi.is_master_node():
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ar=HDFArchive(self.hdf_file,'a')
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if (subgrp in ar):
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if subgrp in ar:
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subgroup_present = True
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# first read the necessary things:
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for it in things_to_read:
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if (it in ar[subgrp]):
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if it in ar[subgrp]:
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setattr(self,it,ar[subgrp][it])
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else:
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mpi.report("Loading %s failed!"%it)
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read_value = False
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value_read = False
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if ((read_value) and (len(optional_things)>0)):
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if (value_read and (len(optional_things)>0)):
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# if necessary things worked, now read optional things:
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read_value = {}
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value_read = {}
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for it in optional_things:
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if (it in ar[subgrp]):
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if it in ar[subgrp]:
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setattr(self,it,ar[subgrp][it])
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read_value['%s'%it] = True
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value_read['%s'%it] = True
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else:
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read_value['%s'%it] = False
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value_read['%s'%it] = False
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else:
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mpi.report("Loading failed: No %s subgroup in HDF5!"%subgrp)
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read_value = False
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subgroup_present = False
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value_read = False
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del ar
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# now do the broadcasting:
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for it in things_to_read: setattr(self,it,mpi.bcast(getattr(self,it)))
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for it in optional_things: setattr(self,it,mpi.bcast(getattr(self,it)))
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subgroup_present = mpi.bcast(subgroup_present)
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value_read = mpi.bcast(value_read)
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read_value = mpi.bcast(read_value)
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return read_value
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return (subgroup_present, value_read)
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def save(self):
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def save(self,things_to_save):
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"""Saves some quantities into an HDF5 arxiv"""
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if not (mpi.is_master_node()): return # do nothing on nodes
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ar=HDFArchive(self.hdf_file,'a')
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things_to_save=['chemical_potential','dc_imp','dc_energ']
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for it in things_to_save: ar[self.lda_data][it] = getattr(self,it)
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ar = HDFArchive(self.hdf_file,'a')
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if not (self.lda_output in ar): ar.create_group(self.lda_output)
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for it in things_to_save:
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try:
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ar[self.lda_output][it] = getattr(self,it)
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except:
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mpi.report("%s not found, and so not stored."%it)
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del ar
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def load(self):
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"""Loads some quantities from an HDF5 arxiv"""
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things_to_read=['chemical_potential','dc_imp','dc_energ']
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read_value = self.read_input_from_hdf(subgrp=self.lda_data,things_to_read=things_to_read)
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return read_value
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def downfold(self,ik,icrsh,sig,gf_to_downfold,gf_inp):
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"""Downfolding a block of the Greens function"""
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@ -344,7 +339,7 @@ class SumkLDA:
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mpi.barrier()
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if (self.symm_op!=0): dens_mat = self.Symm_corr.symmetrize(dens_mat)
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if (self.symm_op!=0): dens_mat = self.symmcorr.symmetrize(dens_mat)
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# Rotate to local coordinate system:
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if (self.use_rotations):
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@ -391,7 +386,7 @@ class SumkLDA:
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mpi.barrier()
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if (self.symm_op!=0): dens_mat = self.Symm_corr.symmetrize(dens_mat)
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if (self.symm_op!=0): dens_mat = self.symmcorr.symmetrize(dens_mat)
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# Rotate to local coordinate system:
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if (self.use_rotations):
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@ -486,16 +481,8 @@ class SumkLDA:
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elif ((ind1<0)and(ind2<0)):
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self.deg_shells[ish].append([bl[0],bl2[0]])
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if (mpi.is_master_node()):
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ar=HDFArchive(self.hdf_file,'a')
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ar[self.lda_data]['gf_struct_solver'] = self.gf_struct_solver
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ar[self.lda_data]['map'] = self.map
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ar[self.lda_data]['map_inv'] = self.map_inv
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try:
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ar[self.lda_data]['deg_shells'] = self.deg_shells
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except:
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mpi.report("deg_shells not stored, degeneracies not found")
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del ar
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things_to_save=['gf_struct_solver','map','map_inv','deg_shells']
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self.save(things_to_save)
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return dens_mat
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@ -552,7 +539,7 @@ class SumkLDA:
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self.proj_mat[ik,isp,icrsh,0:dim,0:n_orb].conjugate().transpose() )
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# symmetrisation:
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if (self.symm_op!=0): self.Hsumk = self.Symm_corr.symmetrize(self.Hsumk)
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if (self.symm_op!=0): self.Hsumk = self.symmcorr.symmetrize(self.Hsumk)
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# Rotate to local coordinate system:
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if (self.use_rotations):
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@ -743,9 +730,8 @@ class SumkLDA:
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def set_mu(self,mu):
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"""Sets a new chemical potential"""
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self.chemical_potential = mu
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#print "Chemical potential in SumK set to ",mu
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self.chemical_potential = mu
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def inequiv_shells(self,lst):
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@ -810,13 +796,13 @@ class SumkLDA:
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F = lambda mu : self.total_density(mu = mu)
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Dens_rel = self.density_required - self.charge_below
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density = self.density_required - self.charge_below
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self.chemical_potential = dichotomy.dichotomy(function = F,
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x_init = self.chemical_potential, y_value = Dens_rel,
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precision_on_y = precision, delta_x=0.5,
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max_loops = 100, x_name="chemical_potential", y_name= "Total Density",
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x_init = self.chemical_potential, y_value = density,
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precision_on_y = precision, delta_x = 0.5, max_loops = 100,
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x_name = "Chemical Potential", y_name = "Total Density",
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verbosity = 3)[0]
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return self.chemical_potential
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@ -856,7 +842,7 @@ class SumkLDA:
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# Gloc[:] is now the sum over k projected to the local orbitals.
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# here comes the symmetrisation, if needed:
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if (self.symm_op!=0): Gloc = self.Symm_corr.symmetrize(Gloc)
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if (self.symm_op!=0): Gloc = self.symmcorr.symmetrize(Gloc)
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# Gloc is rotated to the local coordinate system:
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if (self.use_rotations):
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@ -1003,7 +989,6 @@ class SumkLDA:
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def find_mu_nonint(self, dens_req, orb = None, beta = 40, precision = 0.01):
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def F(mu):
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#gnonint = self.nonint_G(beta=beta,mu=mu)
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gnonint = self.extract_G_loc(mu=mu,with_Sigma=False)
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if (orb is None):
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@ -1018,8 +1003,8 @@ class SumkLDA:
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self.chemical_potential = dichotomy.dichotomy(function = F,
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x_init = self.chemical_potential, y_value = dens_req,
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precision_on_y = precision, delta_x=0.5,
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max_loops = 100, x_name="chemical_potential", y_name= "Local Density",
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precision_on_y = precision, delta_x = 0.5, max_loops = 100,
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x_name = "Chemical Potential", y_name = "Total Density",
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verbosity = 3)[0]
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return self.chemical_potential
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@ -1042,12 +1027,12 @@ class SumkLDA:
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if (dens_req is None):
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Dens_rel = self.density_required - self.charge_below
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density = self.density_required - self.charge_below
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else:
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Dens_rel = dens_req
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density = dens_req
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dcnew = dichotomy.dichotomy(function = F,
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x_init = guess, y_value = Dens_rel,
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x_init = guess, y_value = density,
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precision_on_y = precision, delta_x=0.5,
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max_loops = 100, x_name="Double-Counting", y_name= "Total Density",
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verbosity = 3)[0]
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@ -1068,7 +1053,7 @@ class SumkLDA:
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n_orb = self.n_orbitals[ik,0]
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dens_mat[ish][:,:] += numpy.dot(self.proj_mat[ik,0,ish,0:dim,0:n_orb],self.proj_mat[ik,0,ish,0:dim,0:n_orb].transpose().conjugate()) * self.bz_weights[ik]
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if (self.symm_op!=0): dens_mat = self.Symm_corr.symmetrize(dens_mat)
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if (self.symm_op!=0): dens_mat = self.symmcorr.symmetrize(dens_mat)
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# Rotate to local coordinate system:
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if (self.use_rotations):
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@ -202,7 +202,7 @@ class SumkLDATools(SumkLDA):
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if (self.symm_op!=0): Gloc = self.Symm_corr.symmetrize(Gloc)
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if (self.symm_op!=0): Gloc = self.symmcorr.symmetrize(Gloc)
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if (self.use_rotations):
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for icrsh in xrange(self.n_corr_shells):
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@ -243,8 +243,8 @@ class SumkLDATools(SumkLDA):
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"""
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things_to_read = ['dens_mat_below','n_parproj','proj_mat_pc','rot_mat_all','rot_mat_all_time_inv']
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read_value = self.read_input_from_hdf(subgrp=self.parproj_data,things_to_read = things_to_read)
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return read_value
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value_read = self.read_input_from_hdf(subgrp=self.parproj_data,things_to_read = things_to_read)
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return value_read
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@ -254,9 +254,9 @@ class SumkLDATools(SumkLDA):
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assert hasattr(self,"Sigma_imp"), "Set Sigma First!!"
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#things_to_read = ['Dens_Mat_below','N_parproj','Proj_Mat_pc','rotmat_all']
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#read_value = self.read_input_from_HDF(SubGrp=self.parproj_data, things_to_read=things_to_read)
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read_value = self.read_parproj_input_from_hdf()
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if not read_value: return read_value
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#value_read = self.read_input_from_HDF(SubGrp=self.parproj_data, things_to_read=things_to_read)
|
||||
value_read = self.read_parproj_input_from_hdf()
|
||||
if not value_read: return value_read
|
||||
if self.symm_op: self.Symm_par = Symmetry(self.hdf_file,subgroup=self.symmpar_data)
|
||||
|
||||
mu = self.chemical_potential
|
||||
@ -348,8 +348,8 @@ class SumkLDATools(SumkLDA):
|
||||
|
||||
assert hasattr(self,"Sigma_imp"), "Set Sigma First!!"
|
||||
things_to_read = ['n_k','n_orbitals','proj_mat','hopping','n_parproj','proj_mat_pc']
|
||||
read_value = self.read_input_from_hdf(subgrp=self.bands_data,things_to_read=things_to_read)
|
||||
if not read_value: return read_value
|
||||
value_read = self.read_input_from_hdf(subgrp=self.bands_data,things_to_read=things_to_read)
|
||||
if not value_read: return value_read
|
||||
|
||||
if fermi_surface: ishell=None
|
||||
|
||||
@ -515,9 +515,9 @@ class SumkLDATools(SumkLDA):
|
||||
|
||||
|
||||
#things_to_read = ['Dens_Mat_below','N_parproj','Proj_Mat_pc','rotmat_all']
|
||||
#read_value = self.read_input_from_HDF(SubGrp=self.parproj_data,things_to_read=things_to_read)
|
||||
read_value = self.read_parproj_input_from_hdf()
|
||||
if not read_value: return read_value
|
||||
#value_read = self.read_input_from_HDF(SubGrp=self.parproj_data,things_to_read=things_to_read)
|
||||
value_read = self.read_parproj_input_from_hdf()
|
||||
if not value_read: return value_read
|
||||
if self.symm_op: self.Symm_par = Symmetry(self.hdf_file,subgroup=self.symmpar_data)
|
||||
|
||||
# Density matrix in the window
|
||||
|
||||
@ -25,6 +25,16 @@ for old, new in old_to_new.iteritems():
|
||||
print "Changing %s to %s ..."%(old, new)
|
||||
A.copy(old,new)
|
||||
del(A[old])
|
||||
|
||||
move_to_output = ['gf_struct_solver','map_inv','map',
|
||||
'chemical_potential','dc_imp','dc_energ','deg_shells',
|
||||
'h_field']
|
||||
for obj in move_to_output:
|
||||
if (obj in A['lda_input'].keys()) and (not 'lda_output' in A): A.create_group('lda_output')
|
||||
print "Moving %s to lda_output ..."%obj
|
||||
A.copy('lda_input/'+obj,'lda_output/'+obj)
|
||||
del(A['lda_input'][obj])
|
||||
|
||||
A.close()
|
||||
|
||||
# Repack to reclaim disk space
|
||||
|
||||
Loading…
Reference in New Issue
Block a user