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dft_tools/python/vasp/inpconf.py
Oleg E. Peil 819fc987f0 Reshuffled files after repository merge 
The files from the original vasp-interface repository are reshuffled in
accord with the directory structure of dft_tools. Some of the directories,
such as 'test' (unit tests for the interface), 'examples' (simple examples for
the development purposes) are temporarily placed into 'python/vasp' directory
to avoid confusion with integral tests and examples of dft_tools.
2015-10-13 11:27:55 +02:00

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r"""
Module for parsing and checking an input config-file.
"""
import ConfigParser
import numpy as np
import re
import sys
import itertools as it
import vaspio
def issue_warning(message):
"""
Issues a warning.
"""
print
print " !!! WARNING !!!: " + message
print
################################################################################
################################################################################
#
# class ConfigParameters
#
################################################################################
################################################################################
class ConfigParameters:
r"""
Class responsible for parsing of the input config-file.
Parameters:
- *sh_required*, *sh_optional* : required and optional parameters of shells
- *gr_required*, *gr_optional* : required and optional parameters of groups
The dictionary contains a mapping of conf-file keywords to
a pair of objects:
1. internal name of a parameter
2. function used to convert an input string into data for a given parameter
"""
################################################################################
#
# __init__()
#
################################################################################
def __init__(self, input_filename, verbosity=1):
self.verbosity = verbosity
self.cp = ConfigParser.SafeConfigParser()
self.cp.readfp(open(input_filename, 'r'))
self.parameters = {}
self.sh_required = {
'ions': ('ion_list', self.parse_string_ion_list),
'lshell': ('lshell', int)}
self.sh_optional = {
'rtransform': ('tmatrix', lambda s: self.parse_string_tmatrix(s, real=True)),
'ctransform': ('tmatrix', lambda s: self.parse_string_tmatrix(s, real=False))}
self.gr_required = {
'shells': ('shells', lambda s: map(int, s.split())),
'emin': ('emin', float),
'emax': ('emax', float)}
self.gr_optional = {
'normalize' : ('normalize', self.parse_string_logical, True),
'normion' : ('normion', self.parse_string_logical, False)}
self.gen_optional = {
'basename' : ('basename', str, 'vasp'),
'efermi' : ('efermi', float)}
#
# Special parsers
#
################################################################################
#
# parse_string_ion_list()
#
################################################################################
def parse_string_ion_list(self, par_str):
"""
The ion list accepts two 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.
The second option requires an input from POSCAR file.
"""
# First check if a range is given
patt = '([0-9]+)\.\.([0-9]+)'
match = re.match(patt, par_str)
if match:
i1, i2 = tuple(map(int, match.groups()[:2]))
mess = "First index of the range must be smaller or equal to the second"
assert i1 <= i2, mess
ion_list = np.array(range(i1 - 1, i2))
else:
# Check if a set of indices is given
try:
l_tmp = map(int, par_str.split())
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
except ValueError:
err_msg = "Only an option with a list of ion indices is implemented"
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
return ion_list
################################################################################
#
# parse_string_logical()
#
################################################################################
def parse_string_logical(self, par_str):
"""
Logical parameters are given by string 'True' or 'False'
(case does not matter). In fact, only the first symbol matters so that
one can write 'T' or 'F'.
"""
first_char = par_str[0].lower()
assert first_char in 'tf', "Logical parameters should be given by either 'True' or 'False'"
return first_char == 't'
################################################################################
#
# parse_string_tmatrix()
#
################################################################################
def parse_string_tmatrix(self, par_str, real):
"""
Transformation matrix is defined as a set of rows separated
by a new line symbol.
"""
str_rows = par_str.split('\n')
try:
rows = [map(float, s.split()) for s in str_rows]
except ValueError:
err_mess = "Cannot parse a matrix string:\n%s"%(par_str)
raise ValueError(err_mess)
nr = len(rows)
nm = len(rows[0])
err_mess = "Number of columns must be the same:\n%s"%(par_str)
for row in rows:
assert len(row) == nm, err_mess
if real:
mat = np.array(rows)
else:
err_mess = "Complex matrix must contain 2*M values:\n%s"%(par_str)
assert 2 * (nm / 2) == nm, err_mess
tmp = np.array(rows, dtype=np.complex128)
mat = tmp[:, 0::2] + 1.0j * tmp[:, 1::2]
return mat
################################################################################
#
# parse_parameter_set()
#
################################################################################
def parse_parameter_set(self, section, param_set, exception=False, defaults=True):
"""
Parses required or optional parameter set from a section.
For required parameters `exception=True` must be set.
"""
parsed = {}
for par in param_set.keys():
key = param_set[par][0]
try:
par_str = self.cp.get(section, par)
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
if exception:
message = "Required parameter '%s' not found in section [%s]"%(par, section)
raise Exception(message)
else:
# Use the default value if there is one
if defaults and len(param_set[par]) > 2:
parsed[key] = param_set[par][2]
continue
if self.verbosity > 0:
print " %s = %s"%(par, par_str)
parse_fun = param_set[par][1]
parsed[key] = parse_fun(par_str)
return parsed
################################################################################
#
# parse_shells()
#
################################################################################
def parse_shells(self):
"""
Parses all [Shell] sections.
"""
# Find all [Shell] sections
# (note that ConfigParser transforms all names to lower case)
sections = self.cp.sections()
sh_patt1 = re.compile('shell +.*', re.IGNORECASE)
sec_shells = filter(sh_patt1.match, sections)
self.nshells = len(sec_shells)
assert self.nshells > 0, "No projected shells found in the input file"
if self.verbosity > 0:
print
if self.nshells > 1:
print " Found %i projected shells"%(self.nshells)
else:
print " Found 1 projected shell"
# Get shell indices
sh_patt2 = re.compile('shell +([0-9]*)$', re.IGNORECASE)
try:
get_ind = lambda s: int(sh_patt2.match(s).groups()[0])
sh_inds = map(get_ind, sec_shells)
except (ValueError, AttributeError):
raise ValueError("Failed to extract shell indices from a list: %s"%(sec_shells))
self.sh_sections = {ind: sec for ind, sec in it.izip(sh_inds, sec_shells)}
# Check that all indices are unique
# In principle redundant because the list of sections will contain only unique names
assert len(sh_inds) == len(set(sh_inds)), "There must be no shell with the same index!"
# Ideally, indices should run from 1 to <nshells>
# If it's not the case, issue a warning
sh_inds.sort()
if sh_inds != range(1, len(sh_inds) + 1):
issue_warning("Shell indices are not uniform or not starting from 1. "
"This might be an indication of a incorrect setup.")
# Parse shell parameters and put them into a list sorted according to the original indices
self.shells = []
for ind in sh_inds:
shell = {}
# Store the original user-defined index
shell['user_index'] = ind
section = self.sh_sections[ind]
if self.verbosity > 0:
print
print " Shell parameters:"
# Shell required parameters
parsed = self.parse_parameter_set(section, self.sh_required, exception=True)
shell.update(parsed)
# Shell optional parameters
parsed = self.parse_parameter_set(section, self.sh_optional, exception=False)
shell.update(parsed)
# Group required parameters
# Must be given if no group is explicitly specified
# If in conflict with the [Group] section, the latter has a priority
parsed = self.parse_parameter_set(section, self.gr_required, exception=False)
shell.update(parsed)
# Group optional parameters
parsed = self.parse_parameter_set(section, self.gr_optional, exception=False, defaults=False)
shell.update(parsed)
self.shells.append(shell)
################################################################################
#
# parse_groups()
#
################################################################################
def parse_groups(self):
"""
Parses [Group] sections.
"""
# Find group sections
sections = self.cp.sections()
gr_patt = re.compile('group +(.*)', re.IGNORECASE)
sec_groups = filter(gr_patt.match, sections)
self.ngroups = len(sec_groups)
self.groups = []
# Parse group parameters
for section in sec_groups:
group = {}
# Extract group index (FIXME: do we really need it?)
gr_patt2 = re.compile('group +([0-9]*)$', re.IGNORECASE)
try:
gr_ind = int(gr_patt2.match(section).groups()[0])
except (ValueError, AttributeError):
raise ValueError("Failed to extract group index from a group name: %s"%(section))
group['index'] = gr_ind
if self.verbosity > 0:
print
print " Group parameters:"
# Group required parameters
parsed = self.parse_parameter_set(section, self.gr_required, exception=True)
group.update(parsed)
# Group optional parameters
parsed = self.parse_parameter_set(section, self.gr_optional, exception=False)
group.update(parsed)
self.groups.append(group)
# Sort groups according to indices defined in the config-file
if self.ngroups > 0:
self.groups.sort(key=lambda g: g['index'])
################################################################################
#
# groups_shells_consistency()
#
################################################################################
def groups_shells_consistency(self):
"""
Ensures consistency between groups and shells.
In particular:
- if no groups are explicitly defined and only shell is defined create
a group automatically
- check the existance of all shells referenced in the groups
- check that all shells are referenced in the groups
"""
# Special case: no groups is defined
if self.ngroups == 0:
# Check that 'nshells = 1'
assert self.nshells == 1, "At least one group must be defined if there are more than one shells."
# Otherwise create a single group taking group information from [Shell] section
self.groups.append({})
self.groups[0]['index'] = '1'
# Check that the single '[Shell]' section contains enough information
# (required group parameters except 'shells')
# and move it to the `groups` dictionary
sh_gr_required = dict(self.gr_required)
sh_gr_required.pop('shells')
try:
for par in sh_gr_required.keys():
key = sh_gr_required[par][0]
value = self.shells[0].pop(key)
self.groups[0][key] = value
except KeyError:
message = "One [Shell] section is specified but no explicit [Group] section is provided."
message += " In this case the [Shell] section must contain all required group information.\n"
message += " Required parameters are: %s"%(sh_gr_required.keys())
raise KeyError(message)
# Do the same for optional group parameters, but do not raise an exception
for par in self.gr_optional.keys():
try:
key = self.gr_optional[par][0]
value = self.shells[0].pop(key)
self.groups[0][key] = value
except KeyError:
if len(self.gr_optional[par]) > 2:
self.groups[0][key] = self.gr_optional[par][2]
continue
# Add the index of the single shell into the group
self.groups[0].update({'shells': [1]})
#
# Consistency checks
#
# Check the existance 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:
return ind, shell
raise KeyError
sh_all_inds = []
for group in self.groups:
gr_shells = group['shells']
sh_inds = []
for user_ind in gr_shells:
try:
ind, shell = find_shell_by_user_index(user_ind)
except KeyError:
raise Exception("Shell %i referenced in group '%s' does not exist"%(user_ind, group['index']))
sh_inds.append(ind)
# If [Shell] section contains (potentially conflicting) group parameters
# remove them and issue a warning.
#
# First, required group parameters
for par in self.gr_required.keys():
try:
key = self.gr_required[par][0]
value = shell.pop(key)
mess = (" Redundant group parameter '%s' in [Shell] section"
" %i is discarded"%(par, user_ind))
issue_warning(mess)
except KeyError:
continue
# Second, optional group parameters
for par in self.gr_optional.keys():
try:
key = self.gr_optional[par][0]
value = shell.pop(key)
mess = (" Redundant group parameter '%s' in [Shell] section"
" %i is discarded"%(par, user_ind))
issue_warning(mess)
except KeyError:
continue
sh_all_inds += sh_inds
# Replace user shell indices with internal ones
group['shells'] = sh_inds
sh_refs_used = list(set(sh_all_inds))
sh_refs_used.sort()
# Check that all shells are referenced in the groups
assert sh_refs_used == range(self.nshells), "Some shells are not inside any of the groups"
################################################################################
#
# parse_general()
#
################################################################################
def parse_general(self):
"""
Parses [General] section.
"""
self.general = {}
sections = self.cp.sections()
gen_section = filter(lambda s: s.lower() == 'general', sections)
# If no [General] section is found parse a dummy section name to the parser
# to reset parameters to their default values
if len(gen_section) > 1:
raise Exception("More than one section [General] is found")
if len(gen_section) == 0:
gen_section = 'general'
gen_section = gen_section[0]
parsed = self.parse_parameter_set(gen_section, self.gen_optional, exception=False)
self.general.update(parsed)
################################################################################
#
# Main parser function
#
################################################################################
def parse_input(self):
"""
Parses input conf-file.
"""
self.parse_general()
self.parse_shells()
self.parse_groups()
self.groups_shells_consistency()
#
# Obsolete part
#
if __name__ == '__main__':
narg = len(sys.argv)
if narg < 2:
raise SystemExit(" Usage: python pyconf.py <conf-file> [<path-to-vasp-calcultaion>]")
else:
filename = sys.argv[1]
if narg > 2:
vasp_dir = sys.argv[2]
if vasp_dir[-1] != '/':
vasp_dir += '/'
else:
vasp_dir = './'
# plocar = vaspio.Plocar()
# plocar.from_file(vasp_dir)
# poscar = vaspio.Poscar()
# poscar.from_file(vasp_dir)
# kpoints = vaspio.Kpoints()
# kpoints.from_file(vasp_dir)
eigenval = vaspio.Eigenval()
eigenval.from_file(vasp_dir)
doscar = vaspio.Doscar()
doscar.from_file(vasp_dir)
# pars = parse_input(filename)
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