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https://github.com/triqs/dft_tools
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![Oleg Peil](/assets/img/avatar_default.png)
* 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).
631 lines
22 KiB
Python
631 lines
22 KiB
Python
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################################################################################
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#
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# TRIQS: a Toolbox for Research in Interacting Quantum Systems
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#
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# Copyright (C) 2011 by M. Ferrero, O. Parcollet
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#
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# DFT tools: Copyright (C) 2011 by M. Aichhorn, L. Pourovskii, V. Vildosola
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#
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# PLOVasp: Copyright (C) 2015 by O. E. Peil
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#
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# TRIQS is free software: you can redistribute it and/or modify it under the
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# terms of the GNU General Public License as published by the Free Software
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# Foundation, either version 3 of the License, or (at your option) any later
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# version.
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#
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# TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
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# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
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# details.
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#
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# You should have received a copy of the GNU General Public License along with
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# TRIQS. If not, see <http://www.gnu.org/licenses/>.
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#
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################################################################################
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r"""
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vasp.inpconfig
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==============
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Module for parsing and checking an input config-file.
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"""
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import ConfigParser
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import numpy as np
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import re
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import sys
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import itertools as it
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import vaspio
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def issue_warning(message):
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"""
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Issues a warning.
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"""
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print
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print " !!! WARNING !!!: " + message
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print
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################################################################################
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################################################################################
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#
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# class ConfigParameters
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#
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################################################################################
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################################################################################
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class ConfigParameters:
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r"""
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Class responsible for parsing of the input config-file.
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Parameters:
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- *sh_required*, *sh_optional* : required and optional parameters of shells
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- *gr_required*, *gr_optional* : required and optional parameters of groups
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The dictionary contains a mapping of conf-file keywords to
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a pair of objects:
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1. internal name of a parameter
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2. function used to convert an input string into data for a given parameter
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"""
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################################################################################
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#
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# __init__()
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#
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################################################################################
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def __init__(self, input_filename, verbosity=1):
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self.verbosity = verbosity
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self.cp = ConfigParser.SafeConfigParser()
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self.cp.readfp(open(input_filename, 'r'))
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self.parameters = {}
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self.sh_required = {
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'ions': ('ions', self.parse_string_ion_list),
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'lshell': ('lshell', int)}
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self.sh_optional = {
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'transform': ('tmatrix', lambda s: self.parse_string_tmatrix(s, real=True)),
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'transfile': ('tmatrices', self.parse_file_tmatrix)}
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self.gr_required = {
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'shells': ('shells', lambda s: map(int, s.split())),
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'ewindow': ('ewindow', self.parse_energy_window)}
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self.gr_optional = {
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'normalize' : ('normalize', self.parse_string_logical, True),
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'normion' : ('normion', self.parse_string_logical, True)}
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self.gen_optional = {
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'basename' : ('basename', str, 'vasp'),
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'efermi' : ('efermi', float),
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'dosmesh': ('dosmesh', self.parse_string_dosmesh)}
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#
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# Special parsers
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#
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################################################################################
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#
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# parse_string_ion_list()
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#
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################################################################################
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def parse_string_ion_list(self, par_str):
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"""
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The ion list accepts the following formats:
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1). A list of ion indices according to POSCAR.
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The list can be defined as a range '9..20'.
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2). A list of ion groups (e.g. '[1 4] [2 3]') in which
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case each group defines a set of equivalent sites.
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3). An element name, in which case all ions with
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this name are included. NOT YET IMPLEMENTED.
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The second option requires an input from POSCAR file.
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"""
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ion_info = {}
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# First check if a range is given
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patt = '([0-9]+)\.\.([0-9]+)'
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match = re.match(patt, par_str)
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if match:
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i1, i2 = tuple(map(int, match.groups()[:2]))
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mess = "First index of the range must be smaller or equal to the second"
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assert i1 <= i2, mess
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# Note that we need to subtract 1 from VASP indices
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ion_info['ion_list'] = [[ion - 1] for ion in range(i1, i2 + 1)]
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ion_info['nion'] = len(ion_info['ion_list'])
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else:
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# Check if a set of indices is given
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try:
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l_tmp = map(int, par_str.split())
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l_tmp.sort()
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# Subtract 1 so that VASP indices (starting with 1) are converted
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# to Python indices (starting with 0)
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ion_info['ion_list'] = [[ion - 1] for ion in l_tmp]
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ion_info['nion'] = len(ion_info['ion_list'])
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except ValueError:
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pass
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# Check if equivalence classes are given
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if not ion_info:
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try:
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patt = '[0-9][0-9,\s]*'
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patt2 = '[0-9]+'
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classes = re.findall(patt, par_str)
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ion_list = []
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nion = 0
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for cl in classes:
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ions = map(int, re.findall(patt2, cl))
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ion_list.append([ion - 1 for ion in ions])
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nion += len(ions)
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if not ion_list:
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raise ValueError
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ion_info['ion_list'] = ion_list
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ion_info['nion'] = nion
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except ValueError:
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err_msg = "Error parsing list of ions"
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raise NotImplementedError(err_msg)
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if 'ion_list' in ion_info:
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ion_list = ion_info['ion_list']
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assert all([all([ion >= 0 for ion in gr]) for gr in ion_list]), (
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"Lowest ion index is smaller than 1 in '%s'"%(par_str))
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return ion_info
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################################################################################
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#
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# parse_string_logical()
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#
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################################################################################
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def parse_string_logical(self, par_str):
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"""
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Logical parameters are given by string 'True' or 'False'
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(case does not matter). In fact, only the first symbol matters so that
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one can write 'T' or 'F'.
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"""
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first_char = par_str[0].lower()
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assert first_char in 'tf', "Logical parameters should be given by either 'True' or 'False'"
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return first_char == 't'
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################################################################################
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#
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# parse_energy_window()
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#
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################################################################################
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def parse_energy_window(self, par_str):
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"""
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Energy window is given by two floats, with the first one being smaller
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than the second one.
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"""
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ftmp = map(float, par_str.split())
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assert len(ftmp) == 2, "EWINDOW must be specified by exactly two floats"
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assert ftmp[0] < ftmp[1], "The first float in EWINDOW must be smaller than the second one"
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return tuple(ftmp)
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################################################################################
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#
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# parse_string_tmatrix()
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#
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################################################################################
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def parse_string_tmatrix(self, par_str, real):
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"""
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Transformation matrix is defined as a set of rows separated
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by a new line symbol.
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"""
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str_rows = par_str.split('\n')
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try:
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rows = [map(float, s.split()) for s in str_rows]
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except ValueError:
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err_mess = "Cannot parse a matrix string:\n%s"%(par_str)
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raise ValueError(err_mess)
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nr = len(rows)
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nm = len(rows[0])
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err_mess = "Number of columns must be the same:\n%s"%(par_str)
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for row in rows:
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assert len(row) == nm, err_mess
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if real:
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mat = np.array(rows)
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else:
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err_mess = "Complex matrix must contain 2*M values:\n%s"%(par_str)
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assert 2 * (nm / 2) == nm, err_mess
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tmp = np.array(rows, dtype=np.complex128)
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mat = tmp[:, 0::2] + 1.0j * tmp[:, 1::2]
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return mat
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################################################################################
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#
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# parse_file_tmatrix()
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#
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################################################################################
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def parse_file_tmatrix(self, filename):
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"""
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Parses a file 'filename' containing transformation matrices
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for each ion. The parser returns a raw matrix that will be
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interpreted elsewhere because the interpretation depends on
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shell parameters.
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"""
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tmatrices = np.loadtxt(filename)
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return tmatrices
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################################################################################
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#
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# parse_string_dosmesh()
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#
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################################################################################
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def parse_string_dosmesh(self, par_str):
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"""
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Two formats are accepted:
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1. Two floats (energy range) and an integer (number of energy points).
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2. One integer (number of energy points). In this case the energy
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range is taken to be equal to EMIN, EMAX of a shell.
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The parser returns a dictionary:
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{'n_points': int,
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'emin': float,
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'emax': float}
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If the second option is used, 'emin' and 'emax' are undefined
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and set to 'nan'.
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"""
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stmp = par_str.split()
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if len(stmp) == 3:
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emin, emax = float(stmp[0]), float(stmp[1])
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n_points = int(stmp[2])
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elif len(stmp) == 1:
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n_points = int(stmp[0])
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emin = emax = float('nan')
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else:
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err_mess = "DOSMESH must be either 'EMIN EMAX NPOINTS' or 'NPOINTS'"
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raise ValueError(err_mess)
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dos_pars = {
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'n_points': n_points,
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'emin': emin,
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'emax': emax}
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return dos_pars
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################################################################################
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#
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# parse_parameter_set()
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#
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################################################################################
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def parse_parameter_set(self, section, param_set, exception=False, defaults=True):
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"""
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Parses required or optional parameter set from a section.
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For required parameters `exception=True` must be set.
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"""
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parsed = {}
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for par in param_set.keys():
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key = param_set[par][0]
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try:
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par_str = self.cp.get(section, par)
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except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
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if exception:
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message = "Required parameter '%s' not found in section [%s]"%(par, section)
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raise Exception(message)
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else:
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# Use the default value if there is one
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if defaults and len(param_set[par]) > 2:
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parsed[key] = param_set[par][2]
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continue
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if self.verbosity > 0:
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print " %s = %s"%(par, par_str)
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parse_fun = param_set[par][1]
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parsed[key] = parse_fun(par_str)
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return parsed
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################################################################################
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#
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# parse_shells()
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#
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################################################################################
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def parse_shells(self):
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"""
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Parses all [Shell] sections.
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"""
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# Find all [Shell] sections
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# (note that ConfigParser transforms all names to lower case)
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sections = self.cp.sections()
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sh_patt1 = re.compile('shell +.*', re.IGNORECASE)
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sec_shells = filter(sh_patt1.match, sections)
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self.nshells = len(sec_shells)
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assert self.nshells > 0, "No projected shells found in the input file"
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if self.verbosity > 0:
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print
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if self.nshells > 1:
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print " Found %i projected shells"%(self.nshells)
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else:
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print " Found 1 projected shell"
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# Get shell indices
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sh_patt2 = re.compile('shell +([0-9]*)$', re.IGNORECASE)
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try:
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get_ind = lambda s: int(sh_patt2.match(s).groups()[0])
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sh_inds = map(get_ind, sec_shells)
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except (ValueError, AttributeError):
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raise ValueError("Failed to extract shell indices from a list: %s"%(sec_shells))
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self.sh_sections = {ind: sec for ind, sec in it.izip(sh_inds, sec_shells)}
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# Check that all indices are unique
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# In principle redundant because the list of sections will contain only unique names
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assert len(sh_inds) == len(set(sh_inds)), "There must be no shell with the same index!"
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# Ideally, indices should run from 1 to <nshells>
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# If it's not the case, issue a warning
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sh_inds.sort()
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if sh_inds != range(1, len(sh_inds) + 1):
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issue_warning("Shell indices are not uniform or not starting from 1. "
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"This might be an indication of a incorrect setup.")
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# Parse shell parameters and put them into a list sorted according to the original indices
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self.shells = []
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for ind in sh_inds:
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shell = {}
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# Store the original user-defined index
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shell['user_index'] = ind
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section = self.sh_sections[ind]
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if self.verbosity > 0:
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print
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print " Shell parameters:"
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# Shell required parameters
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parsed = self.parse_parameter_set(section, self.sh_required, exception=True)
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shell.update(parsed)
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# Shell optional parameters
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parsed = self.parse_parameter_set(section, self.sh_optional, exception=False)
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shell.update(parsed)
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# Group required parameters
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# Must be given if no group is explicitly specified
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# If in conflict with the [Group] section, the latter has a priority
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parsed = self.parse_parameter_set(section, self.gr_required, exception=False)
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shell.update(parsed)
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# Group optional parameters
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parsed = self.parse_parameter_set(section, self.gr_optional, exception=False, defaults=False)
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shell.update(parsed)
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self.shells.append(shell)
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################################################################################
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#
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# parse_groups()
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#
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################################################################################
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def parse_groups(self):
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"""
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Parses [Group] sections.
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"""
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# Find group sections
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sections = self.cp.sections()
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gr_patt = re.compile('group +(.*)', re.IGNORECASE)
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sec_groups = filter(gr_patt.match, sections)
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self.ngroups = len(sec_groups)
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self.groups = []
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# Parse group parameters
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for section in sec_groups:
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group = {}
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# Extract group index (FIXME: do we really need it?)
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gr_patt2 = re.compile('group +([0-9]*)$', re.IGNORECASE)
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try:
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gr_ind = int(gr_patt2.match(section).groups()[0])
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except (ValueError, AttributeError):
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raise ValueError("Failed to extract group index from a group name: %s"%(section))
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group['index'] = gr_ind
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if self.verbosity > 0:
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print
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print " Group parameters:"
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# Group required parameters
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parsed = self.parse_parameter_set(section, self.gr_required, exception=True)
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group.update(parsed)
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# Group optional parameters
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parsed = self.parse_parameter_set(section, self.gr_optional, exception=False)
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group.update(parsed)
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self.groups.append(group)
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# Sort groups according to indices defined in the config-file
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if self.ngroups > 0:
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self.groups.sort(key=lambda g: g['index'])
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|
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################################################################################
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#
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# groups_shells_consistency()
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#
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################################################################################
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def groups_shells_consistency(self):
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"""
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Ensures consistency between groups and shells.
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In particular:
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- if no groups are explicitly defined and only shell is defined create
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a group automatically
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- check the existance of all shells referenced in the groups
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- check that all shells are referenced in the groups
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"""
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# Special case: no groups is defined
|
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if self.ngroups == 0:
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# Check that 'nshells = 1'
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assert self.nshells == 1, "At least one group must be defined if there are more than one shells."
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# Otherwise create a single group taking group information from [Shell] section
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self.groups.append({})
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self.groups[0]['index'] = '1'
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# Check that the single '[Shell]' section contains enough information
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# (required group parameters except 'shells')
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# and move it to the `groups` dictionary
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sh_gr_required = dict(self.gr_required)
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sh_gr_required.pop('shells')
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try:
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for par in sh_gr_required.keys():
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key = sh_gr_required[par][0]
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value = self.shells[0].pop(key)
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self.groups[0][key] = value
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except KeyError:
|
|
message = "One [Shell] section is specified but no explicit [Group] section is provided."
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message += " In this case the [Shell] section must contain all required group information.\n"
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message += " Required parameters are: %s"%(sh_gr_required.keys())
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raise KeyError(message)
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|
|
# Do the same for optional group parameters, but do not raise an exception
|
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for par in self.gr_optional.keys():
|
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try:
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key = self.gr_optional[par][0]
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value = self.shells[0].pop(key)
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self.groups[0][key] = value
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except KeyError:
|
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if len(self.gr_optional[par]) > 2:
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self.groups[0][key] = self.gr_optional[par][2]
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continue
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# Add the index of the single shell into the group
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self.groups[0].update({'shells': [1]})
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|
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#
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|
# Consistency checks
|
|
#
|
|
# Check the existence of shells referenced in the groups
|
|
def find_shell_by_user_index(uindex):
|
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for ind, shell in enumerate(self.shells):
|
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if shell['user_index'] == uindex:
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return ind, shell
|
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raise KeyError
|
|
|
|
sh_all_inds = []
|
|
for group in self.groups:
|
|
gr_shells = group['shells']
|
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sh_inds = []
|
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for user_ind in gr_shells:
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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)
|
|
|