def get_available_modules( self ): """Get all available modules: modules that are found but not loaded""" modules = [ key for key in self.modules.keys() if key not in self.loaded_modules ] modules.sort() return modules
def main_routine(wf_total,
wf_per_pl,
cells_per_pl,
cond_dir,
second_dir,
wannier_functions,
atom_number,
atomic_coordinates,
matrix,
angle,
delta):
# first we separate the left-most principal layer, the conductor region
# and the right-most principal layer
PL1 = wannier_functions[:wf_per_pl]
conductor = wannier_functions[wf_per_pl:-wf_per_pl]
PL4 = wannier_functions[-wf_per_pl:]
# now we compute the unit vector for the axis of rotation
point_A = barycenter(PL1)
point_B = barycenter(PL4)
unit_vector = (1.0/numpy.linalg.norm(point_B-point_A))*(point_B-point_A)
if cond_dir=='x':
reference = numpy.array([1.0,0.0,0.0])
elif cond_dir=='y':
reference = numpy.array([0.0,1.0,0.0])
else:
reference = numpy.array([0.0,0.0,1.0])
if numpy.dot(unit_vector,reference)<=0.95:
print ""
print " Warning in rotate_conductor :"
print " The computed unit vector for the axis of"
print " rotation seems to be off from the reference"
print " unit vector : %s" %(cond_dir)
print " The dot product of unit vector with %s is : %3.2f" %(cond_dir,numpy.dot(unit_vector,reference))
print ""
user_answer = ""
while user_answer not in ["yes", "no"]:
user_answer = str(raw_input(" is this OK ? ('yes' or 'no') "))
if user_answer=='no':
print " Exiting the program..."
print ""
sys.exit(1)
# we search the groups of WF with similar centres. To do this
# a group is identified by the index of the first WF in the group
# and the group size
gp_dict = {}
gp_bool = numpy.zeros(len(conductor),dtype='bool')
for i in xrange(len(conductor)):
if gp_bool[i]==False:
gp_bool[i] = True
gp_size = 1
# for each wf we search for similar centres just around that wf
for j in xrange(max(i-10,0),min(i+11,len(conductor))):
if gp_bool[j]==False:
if same_center(conductor[i],conductor[j]):
gp_bool[j] = True
gp_size += 1
# if gp_size is at least 2 we add this group to the dictionnary
if gp_size >= 2:
gp_dict[conductor[i].index] = gp_size
# now we need to remove the redondant WF from the conductor
not_to_add = []
for wf in conductor:
if wf.index in gp_dict.keys():
for j in xrange(1,gp_dict[wf.index]):
not_to_add.append(wf.index+j)
reduced_conductor = []
for wf in conductor:
if wf.index not in not_to_add:
reduced_conductor.append(wf)
# with the reduced_conductor list, we can rotate the centers
reduced_rotated_conductor = rotate_wf(reduced_conductor,angle,unit_vector,point_A)
# we then sort the rotated Wannier Functions
sorted_reduced_conductor = sort(reduced_rotated_conductor,
cond_dir,
second_dir,
delta)
# we re-insert the WF with similar centers
sorted_conductor = []
for wf in sorted_reduced_conductor:
if wf.index not in gp_dict.keys():
sorted_conductor.append(wf)
else:
sorted_conductor.append(wf)
for j in xrange(1,gp_dict[wf.index]):
new_wf = wannier_function()
pos_in_list = wf.index+j-conductor[0].index
new_wf.setindex(conductor[pos_in_list].index)
new_wf.setx(wf.x)
new_wf.sety(wf.y)
new_wf.setz(wf.z)
new_wf.setonsite(conductor[pos_in_list].onsite)
sorted_conductor.append(new_wf)
# we now find the mapping between the original order of WF
# and the final order after sorting
final_order = []
reference = conductor[0].index
for wf in sorted_conductor:
final_order.append(wf.index-reference)
# now we can reconstruct the matrix
final_matrix = numpy.zeros((matrix.shape[0],matrix.shape[1]),dtype='float')
for i in xrange(matrix.shape[0]):
for j in xrange(matrix.shape[1]):
final_matrix[i,j] = matrix[final_order[i],final_order[j]]
write_htC('rotated_matrix_htC.dat',final_matrix)
# at last we re-generate the *_tran_info.dat file
final_wf_list = PL1 + sorted_conductor + PL4
final_atomic_coordinates = rotate_atoms(atomic_coordinates,angle,unit_vector,point_A)
write_tran_info(wf_total,
wf_per_pl,
cells_per_pl,
cond_dir,
second_dir,
final_wf_list,
atom_number,
final_atomic_coordinates)
return
