mirror of https://github.com/triqs/dft_tools
Added possibility to specify equivalent groups of ions
* 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
Manuel
parent
3539ffd336
commit
7471691219
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@ -54,7 +54,7 @@ def issue_warning(message):
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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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@ -79,7 +79,7 @@ class ConfigParameters:
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self.parameters = {}
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self.sh_required = {
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'ions': ('ion_list', self.parse_string_ion_list),
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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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@ -109,14 +109,20 @@ class ConfigParameters:
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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 two formats:
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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). An element name, in which case all ions with
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this name are included.
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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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@ -125,7 +131,8 @@ class ConfigParameters:
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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_list = np.array(range(i1 - 1, i2))
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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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@ -133,15 +140,40 @@ class ConfigParameters:
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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_list = np.array(l_tmp) - 1
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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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err_msg = "Only an option with a list of ion indices is implemented"
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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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err_mess = "Lowest ion index is smaller than 1 in '%s'"%(par_str)
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assert np.all(ion_list >= 0), err_mess
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if 'ion_list' in ion_info:
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ion_list = ion_info['ion_list']
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return 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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@ -225,7 +257,7 @@ class ConfigParameters:
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################################################################################
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#
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# parse_string_ion_list()
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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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@ -470,13 +502,13 @@ class ConfigParameters:
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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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# 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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# Consistency checks
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#
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# Check the existance of shells referenced in the groups
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# Check the existence of shells referenced in the groups
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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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@ -529,7 +561,7 @@ class ConfigParameters:
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# Check that all shells are referenced in the groups
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assert sh_refs_used == range(self.nshells), "Some shells are not inside any of the groups"
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################################################################################
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#
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# parse_general()
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