basis.append(tmp_basis)
print (basis)
####################
# 3.0. Now, for each timestep, we compute the energies of the SDs and sort them by energy. This prevents the state energies from crossing in this basis. However, note that the St_ks files (time-overlaps in the KS basis) have no knowledge of the reordering of the SDs by energies
nSDs = len(basis)
E_sd_sorted = []
basis_sorted = []
SD_energy_corr = [0.0]*nSDs
for step in range(finish_time-start_time):
E = mapping.energy_mat_arb( basis, E_ks[0][step], SD_energy_corr )
nstates = E.num_of_cols
e = np.zeros( nstates )
for state in range(nstates):
e[state] = E.get(state,state).real
reindex = np.argsort(e)
E_sd_sorted.append( CMATRIX(nstates,nstates) )
basis_sorted.append( [] )
for i in range(len(reindex)):
E_sd_sorted[step].set( i, i, E.get( int(reindex[i]), int(reindex[i]) ) )
basis_sorted[step].append( basis[ int(reindex[i]) ] )
1. Reindexing the SD bases from the native ES format to what Libra expects
2. Sorting the SD bases at each timestep by their energies
"""
# 3.1. Reindex the SDs into the format expected by Libra
sd_states_reindexed = step2_many_body.reindex_cp2k_sd_states( ks_orbital_homo_index, ks_orbital_indicies, sd_basis_states_unique, sd_format=1 )
#print("The reindexed Slater determinants = \n", sd_states_reindexed)
# 3.2. Sort the SDs at each timestep
E_sd_job = []
sd_states_reindexed_sorted = []
sd_states_unique_sorted = []
SD_energy_corr = [0.0]*len(sd_states_reindexed)
for step in range( finish_time-start_time ):
# At this step, compute the energy of the SD
E_this_sd = mapping.energy_mat_arb( sd_states_reindexed, E_ks_job[0][step], SD_energy_corr )
nstates_sd = len(sd_states_reindexed)
# Make an array of zeros, these will be overwritten with the energy of each SD
e = np.zeros( nstates_sd )
for state in range(nstates_sd):
e[state] = E_this_sd.get(state,state).real
# Obtain the indexing fo the SDs by their energies
reindex = np.argsort(e)
# We need to write the energies into matrix form
E_sd_job.append( CMATRIX(nstates_sd,nstates_sd) )
sd_states_reindexed_sorted.append( [] )
# For each SD basis, make the energy matrix and reindex the list of basis according to their energies
for i in range(len(reindex)):
# This is making the energy matrix
E_sd_job[step].set( i,i, E_this_sd.get( int(reindex[i]), int(reindex[i])) )
# This is reindexing the list of SD bases at this time step according to their energies