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Added possibility to specify equivalent groups of ions

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* Added a new input format for the list of ions. It is now possible
  to group ions (like this [1  2]  [5  6]) that are considered
  equivalent in the solver. This has required changing the internal
  variable 'ion_list' to a dictionary 'ions' which can later be
  enhanced by other features (such as specifying ions by element name).
This commit is contained in:
Oleg Peil 2018-05-04 16:03:23 +02:00 committed by Manuel
parent 3539ffd336
commit 7471691219
1 changed files with 47 additions and 15 deletions
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56
python/converters/plovasp/inpconf.py
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@ -79,7 +79,7 @@ class ConfigParameters:
self.parameters = {}
self.sh_required = {
'ions': ('ion_list', self.parse_string_ion_list),
'ions': ('ions', self.parse_string_ion_list),
'lshell': ('lshell', int)}
self.sh_optional = {
@ -109,14 +109,20 @@ class ConfigParameters:
################################################################################
def parse_string_ion_list(self, par_str):
"""
The ion list accepts two formats:
The ion list accepts the following formats:
1). A list of ion indices according to POSCAR.
The list can be defined as a range '9..20'.
2). An element name, in which case all ions with
this name are included.
2). A list of ion groups (e.g. '[1 4] [2 3]') in which
case each group defines a set of equivalent sites.
3). An element name, in which case all ions with
this name are included. NOT YET IMPLEMENTED.
The second option requires an input from POSCAR file.
"""
ion_info = {}
# First check if a range is given
patt = '([0-9]+)\.\.([0-9]+)'
match = re.match(patt, par_str)
@ -125,7 +131,8 @@ class ConfigParameters:
mess = "First index of the range must be smaller or equal to the second"
assert i1 <= i2, mess
# Note that we need to subtract 1 from VASP indices
ion_list = np.array(range(i1 - 1, i2))
ion_info['ion_list'] = [[ion - 1] for ion in range(i1, i2 + 1)]
ion_info['nion'] = len(ion_info['ion_list'])
else:
# Check if a set of indices is given
try:
@ -133,15 +140,40 @@ class ConfigParameters:
l_tmp.sort()
# Subtract 1 so that VASP indices (starting with 1) are converted
# to Python indices (starting with 0)
ion_list = np.array(l_tmp) - 1
ion_info['ion_list'] = [[ion - 1] for ion in l_tmp]
ion_info['nion'] = len(ion_info['ion_list'])
except ValueError:
err_msg = "Only an option with a list of ion indices is implemented"
pass
# Check if equivalence classes are given
if not ion_info:
try:
patt = '[0-9][0-9,\s]*'
patt2 = '[0-9]+'
classes = re.findall(patt, par_str)
ion_list = []
nion = 0
for cl in classes:
ions = map(int, re.findall(patt2, cl))
ion_list.append([ion - 1 for ion in ions])
nion += len(ions)
if not ion_list:
raise ValueError
ion_info['ion_list'] = ion_list
ion_info['nion'] = nion
except ValueError:
err_msg = "Error parsing list of ions"
raise NotImplementedError(err_msg)
err_mess = "Lowest ion index is smaller than 1 in '%s'"%(par_str)
assert np.all(ion_list >= 0), err_mess
if 'ion_list' in ion_info:
ion_list = ion_info['ion_list']
return ion_list
assert all([all([ion >= 0 for ion in gr]) for gr in ion_list]), (
"Lowest ion index is smaller than 1 in '%s'"%(par_str))
return ion_info
################################################################################
#
@ -225,7 +257,7 @@ class ConfigParameters:
################################################################################
#
# parse_string_ion_list()
# parse_string_dosmesh()
#
################################################################################
def parse_string_dosmesh(self, par_str):
@ -476,7 +508,7 @@ class ConfigParameters:
#
# Consistency checks
#
# Check the existance of shells referenced in the groups
# Check the existence of shells referenced in the groups
def find_shell_by_user_index(uindex):
for ind, shell in enumerate(self.shells):
if shell['user_index'] == uindex: