LCPQ/EMSL_Basis_Set_Exchange_Local
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This commit is contained in:
Thomas Applencourt 2015-03-17 15:39:51 +01:00
parent 0af5cb6fa1
commit baebe0de19
8 changed files with 117 additions and 1093 deletions
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4
EMSL_api.py
View File

@ -38,11 +38,11 @@ Example of use:
./EMSL_api.py get_basis_data --basis 3-21++G* ./EMSL_api.py get_basis_data --basis 3-21++G*
""" """
version = "0.3.0" version = "0.8.1"
import os import os
from src.docopt import docopt from src.misc.docopt import docopt
from src.EMSL_dump import EMSL_dump from src.EMSL_dump import EMSL_dump
from src.EMSL_local import EMSL_local, checkSQLite3 from src.EMSL_local import EMSL_local, checkSQLite3

3
src/EMSL_dump.py
View File

@ -5,7 +5,7 @@ import time
import sqlite3 import sqlite3
from collections import OrderedDict from collections import OrderedDict
from src.parser import format_dict from src.parser_handler import format_dict
def install_with_pip(name): def install_with_pip(name):
@ -233,6 +233,7 @@ class EMSL_dump:
basis_data = self.parser(text, name, des, elts, basis_data = self.parser(text, name, des, elts,
self.debug) self.debug)
except: except:
raise
time.sleep(0.1) time.sleep(0.1)
attemps += 1 attemps += 1
else: else:

8
src/EMSL_local.py
View File

@ -192,7 +192,7 @@ class EMSL_local:
dict_info = OrderedDict() dict_info = OrderedDict()
# Description : dict_info[name] = [description, nb_mo, nb_ele] # Description : dict_info[name] = [description, nb_mo, nb_ele]
from src.parser import get_symmetry_function from src.parser_handler import get_symmetry_function
if average_mo_number: if average_mo_number:
f_symmetry = get_symmetry_function(self.format) f_symmetry = get_symmetry_function(self.format)
@ -267,7 +267,7 @@ class EMSL_local:
# h a n d l e _ f # # h a n d l e _ f #
# ~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~ #
if handle_l_format: if handle_l_format:
from src.parser import get_handle_l_function from src.parser_handler import get_handle_l_function
f = get_handle_l_function(self.format) f = get_handle_l_function(self.format)
l_atom_basis = f(l_atom_basis) l_atom_basis = f(l_atom_basis)
@ -277,8 +277,8 @@ class EMSL_local:
if check_format: if check_format:
from src.parser import get_symmetry_function from src.parser_handler import get_symmetry_function
from src.check_validity import get_check_function from src.parser.check_validity import get_check_function
f = get_check_function(check_format) f = get_check_function(check_format)
f_symmetry = get_symmetry_function(self.format) f_symmetry = get_symmetry_function(self.format)

52
src/check_validity.py
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@ -1,52 +0,0 @@
# _
# / |_ _ _ | _. | o _| o _|_
# \_ | | (/_ (_ |< \/ (_| | | (_| | |_ \/
# /
# Do this After the L special case traitement.
import sys
def check_gamess(str_type):
"""Check is the orbital type is handle by gamess"""
assert len(str_type) == 1
if str_type in "S P D".split():
return True
elif str_type == "SP":
raise BaseException
else:
return True
def check_NWChem(str_type):
"""Check is the orbital type is handle by gamess"""
assert len(str_type) == 1
if str_type in "S P D".split():
return True
elif str_type > "I" or str_type in "K L M".split():
raise BaseException
else:
return True
d_check = {"GAMESS-US": check_gamess,
"NWChem": check_NWChem}
def get_check_function(name_program):
"""
Tranforme SP special function (create using get_symmetry_function)
into S and P
"""
try:
f = d_check[name_program]
except KeyError:
str_ = "You need to add a check funtion for your program {0}"
print >> sys.stderr, str_.format(name_program)
print >> sys.stderr, "This one are avalaible {0}".format(d_check.keys())
sys.exit(1)
return f

590
src/docopt.py
View File

@ -1,590 +0,0 @@
"""Pythonic command-line interface parser that will make you smile.
* http://docopt.org
* Repository and issue-tracker: https://github.com/docopt/docopt
* Licensed under terms of MIT license (see LICENSE-MIT)
* Copyright (c) 2013 Vladimir Keleshev, vladimir@keleshev.com
"""
import sys
import re
__all__ = ['docopt']
__version__ = '0.6.1'
class DocoptLanguageError(Exception):
"""Error in construction of usage-message by developer."""
class DocoptExit(SystemExit):
"""Exit in case user invoked program with incorrect arguments."""
usage = ''
def __init__(self, message=''):
SystemExit.__init__(self, (message + '\n' + self.usage).strip())
class Pattern(object):
def __eq__(self, other):
return repr(self) == repr(other)
def __hash__(self):
return hash(repr(self))
def fix(self):
self.fix_identities()
self.fix_repeating_arguments()
return self
def fix_identities(self, uniq=None):
"""Make pattern-tree tips point to same object if they are equal."""
if not hasattr(self, 'children'):
return self
uniq = list(set(self.flat())) if uniq is None else uniq
for i, child in enumerate(self.children):
if not hasattr(child, 'children'):
assert child in uniq
self.children[i] = uniq[uniq.index(child)]
else:
child.fix_identities(uniq)
def fix_repeating_arguments(self):
"""Fix elements that should accumulate/increment values."""
either = [list(child.children) for child in transform(self).children]
for case in either:
for e in [child for child in case if case.count(child) > 1]:
if isinstance(
e,
Argument) or isinstance(
e,
Option) and e.argcount:
if e.value is None:
e.value = []
elif not isinstance(e.value, list):
e.value = e.value.split()
if isinstance(
e,
Command) or isinstance(
e,
Option) and e.argcount == 0:
e.value = 0
return self
def transform(pattern):
"""Expand pattern into an (almost) equivalent one, but with single Either.
Example: ((-a | -b) (-c | -d)) => (-a -c | -a -d | -b -c | -b -d)
Quirks: [-a] => (-a), (-a...) => (-a -a)
"""
result = []
groups = [[pattern]]
while groups:
children = groups.pop(0)
parents = [Required, Optional, OptionsShortcut, Either, OneOrMore]
if any(t in map(type, children) for t in parents):
child = [c for c in children if type(c) in parents][0]
children.remove(child)
if isinstance(child, Either):
for c in child.children:
groups.append([c] + children)
elif isinstance(child, OneOrMore):
groups.append(child.children * 2 + children)
else:
groups.append(child.children + children)
else:
result.append(children)
return Either(*[Required(*e) for e in result])
class LeafPattern(Pattern):
"""Leaf/terminal node of a pattern tree."""
def __init__(self, name, value=None):
self.name, self.value = name, value
def __repr__(self):
return '%s(%r, %r)' % (self.__class__.__name__, self.name, self.value)
def flat(self, *types):
return [self] if not types or type(self) in types else []
def match(self, left, collected=None):
collected = [] if collected is None else collected
pos, match = self.single_match(left)
if match is None:
return False, left, collected
left_ = left[:pos] + left[pos + 1:]
same_name = [a for a in collected if a.name == self.name]
if type(self.value) in (int, list):
if isinstance(self.value, int):
increment = 1
else:
increment = ([match.value] if isinstance(match.value, str)
else match.value)
if not same_name:
match.value = increment
return True, left_, collected + [match]
same_name[0].value += increment
return True, left_, collected
return True, left_, collected + [match]
class BranchPattern(Pattern):
"""Branch/inner node of a pattern tree."""
def __init__(self, *children):
self.children = list(children)
def __repr__(self):
return '%s(%s)' % (self.__class__.__name__,
', '.join(repr(a) for a in self.children))
def flat(self, *types):
if type(self) in types:
return [self]
return sum([child.flat(*types) for child in self.children], [])
class Argument(LeafPattern):
def single_match(self, left):
for n, pattern in enumerate(left):
if isinstance(pattern, Argument):
return n, Argument(self.name, pattern.value)
return None, None
@classmethod
def parse(class_, source):
name = re.findall('(<\S*?>)', source)[0]
value = re.findall('\[default: (.*)\]', source, flags=re.I)
return class_(name, value[0] if value else None)
class Command(Argument):
def __init__(self, name, value=False):
self.name, self.value = name, value
def single_match(self, left):
for n, pattern in enumerate(left):
if isinstance(pattern, Argument):
if pattern.value == self.name:
return n, Command(self.name, True)
else:
break
return None, None
class Option(LeafPattern):
def __init__(self, short=None, long=None, argcount=0, value=False):
assert argcount in (0, 1)
self.short, self.long, self.argcount = short, long, argcount
self.value = None if value is False and argcount else value
@classmethod
def parse(class_, option_description):
short, long, argcount, value = None, None, 0, False
options, _, description = option_description.strip().partition(' ')
options = options.replace(',', ' ').replace('=', ' ')
for s in options.split():
if s.startswith('--'):
long = s
elif s.startswith('-'):
short = s
else:
argcount = 1
if argcount:
matched = re.findall('\[default: (.*)\]', description, flags=re.I)
value = matched[0] if matched else None
return class_(short, long, argcount, value)
def single_match(self, left):
for n, pattern in enumerate(left):
if self.name == pattern.name:
return n, pattern
return None, None
@property
def name(self):
return self.long or self.short
def __repr__(self):
return 'Option(%r, %r, %r, %r)' % (self.short, self.long,
self.argcount, self.value)
class Required(BranchPattern):
def match(self, left, collected=None):
collected = [] if collected is None else collected
l = left
c = collected
for pattern in self.children:
matched, l, c = pattern.match(l, c)
if not matched:
return False, left, collected
return True, l, c
class Optional(BranchPattern):
def match(self, left, collected=None):
collected = [] if collected is None else collected
for pattern in self.children:
m, left, collected = pattern.match(left, collected)
return True, left, collected
class OptionsShortcut(Optional):
"""Marker/placeholder for [options] shortcut."""
class OneOrMore(BranchPattern):
def match(self, left, collected=None):
assert len(self.children) == 1
collected = [] if collected is None else collected
l = left
c = collected
l_ = None
matched = True
times = 0
while matched:
# could it be that something didn't match but changed l or c?
matched, l, c = self.children[0].match(l, c)
times += 1 if matched else 0
if l_ == l:
break
l_ = l
if times >= 1:
return True, l, c
return False, left, collected
class Either(BranchPattern):
def match(self, left, collected=None):
collected = [] if collected is None else collected
outcomes = []
for pattern in self.children:
matched, _, _ = outcome = pattern.match(left, collected)
if matched:
outcomes.append(outcome)
if outcomes:
return min(outcomes, key=lambda outcome: len(outcome[1]))
return False, left, collected
class Tokens(list):
def __init__(self, source, error=DocoptExit):
self += source.split() if hasattr(source, 'split') else source
self.error = error
@staticmethod
def from_pattern(source):
source = re.sub(r'([\[\]\(\)\|]|\.\.\.)', r' \1 ', source)
source = [s for s in re.split('\s+|(\S*<.*?>)', source) if s]
return Tokens(source, error=DocoptLanguageError)
def move(self):
return self.pop(0) if len(self) else None
def current(self):
return self[0] if len(self) else None
def parse_long(tokens, options):
"""long ::= '--' chars [ ( ' ' | '=' ) chars ] ;"""
long, eq, value = tokens.move().partition('=')
assert long.startswith('--')
value = None if eq == value == '' else value
similar = [o for o in options if o.long == long]
if tokens.error is DocoptExit and similar == []: # if no exact match
similar = [o for o in options if o.long and o.long.startswith(long)]
if len(similar) > 1: # might be simply specified ambiguously 2+ times?
raise tokens.error('%s is not a unique prefix: %s?' %
(long, ', '.join(o.long for o in similar)))
elif len(similar) < 1:
argcount = 1 if eq == '=' else 0
o = Option(None, long, argcount)
options.append(o)
if tokens.error is DocoptExit:
o = Option(None, long, argcount, value if argcount else True)
else:
o = Option(similar[0].short, similar[0].long,
similar[0].argcount, similar[0].value)
if o.argcount == 0:
if value is not None:
raise tokens.error('%s must not have an argument' % o.long)
else:
if value is None:
if tokens.current() in [None, '--']:
raise tokens.error('%s requires argument' % o.long)
value = tokens.move()
if tokens.error is DocoptExit:
o.value = value if value is not None else True
return [o]
def parse_shorts(tokens, options):
"""shorts ::= '-' ( chars )* [ [ ' ' ] chars ] ;"""
token = tokens.move()
assert token.startswith('-') and not token.startswith('--')
left = token.lstrip('-')
parsed = []
while left != '':
short, left = '-' + left[0], left[1:]
similar = [o for o in options if o.short == short]
if len(similar) > 1:
raise tokens.error('%s is specified ambiguously %d times' %
(short, len(similar)))
elif len(similar) < 1:
o = Option(short, None, 0)
options.append(o)
if tokens.error is DocoptExit:
o = Option(short, None, 0, True)
else: # why copying is necessary here?
o = Option(short, similar[0].long,
similar[0].argcount, similar[0].value)
value = None
if o.argcount != 0:
if left == '':
if tokens.current() in [None, '--']:
raise tokens.error('%s requires argument' % short)
value = tokens.move()
else:
value = left
left = ''
if tokens.error is DocoptExit:
o.value = value if value is not None else True
parsed.append(o)
return parsed
def parse_pattern(source, options):
tokens = Tokens.from_pattern(source)
result = parse_expr(tokens, options)
if tokens.current() is not None:
raise tokens.error('unexpected ending: %r' % ' '.join(tokens))
return Required(*result)
def parse_expr(tokens, options):
"""expr ::= seq ( '|' seq )* ;"""
seq = parse_seq(tokens, options)
if tokens.current() != '|':
return seq
result = [Required(*seq)] if len(seq) > 1 else seq
while tokens.current() == '|':
tokens.move()
seq = parse_seq(tokens, options)
result += [Required(*seq)] if len(seq) > 1 else seq
return [Either(*result)] if len(result) > 1 else result
def parse_seq(tokens, options):
"""seq ::= ( atom [ '...' ] )* ;"""
result = []
while tokens.current() not in [None, ']', ')', '|']:
atom = parse_atom(tokens, options)
if tokens.current() == '...':
atom = [OneOrMore(*atom)]
tokens.move()
result += atom
return result
def parse_atom(tokens, options):
"""atom ::= '(' expr ')' | '[' expr ']' | 'options'
| long | shorts | argument | command ;
"""
token = tokens.current()
result = []
if token in '([':
tokens.move()
matching, pattern = {'(': [')', Required], '[': [']', Optional]}[token]
result = pattern(*parse_expr(tokens, options))
if tokens.move() != matching:
raise tokens.error("unmatched '%s'" % token)
return [result]
elif token == 'options':
tokens.move()
return [OptionsShortcut()]
elif token.startswith('--') and token != '--':
return parse_long(tokens, options)
elif token.startswith('-') and token not in ('-', '--'):
return parse_shorts(tokens, options)
elif token.startswith('<') and token.endswith('>') or token.isupper():
return [Argument(tokens.move())]
else:
return [Command(tokens.move())]
def parse_argv(tokens, options, options_first=False):
"""Parse command-line argument vector.
If options_first:
argv ::= [ long | shorts ]* [ argument ]* [ '--' [ argument ]* ] ;
else:
argv ::= [ long | shorts | argument ]* [ '--' [ argument ]* ] ;
"""
parsed = []
while tokens.current() is not None:
if tokens.current() == '--':
return parsed + [Argument(None, v) for v in tokens]
elif tokens.current().startswith('--'):
parsed += parse_long(tokens, options)
elif tokens.current().startswith('-') and tokens.current() != '-':
parsed += parse_shorts(tokens, options)
elif options_first:
return parsed + [Argument(None, v) for v in tokens]
else:
parsed.append(Argument(None, tokens.move()))
return parsed
def parse_defaults(doc):
defaults = []
for s in parse_section('options:', doc):
# FIXME corner case "bla: options: --foo"
_, _, s = s.partition(':') # get rid of "options:"
split = re.split('\n[ \t]*(-\S+?)', '\n' + s)[1:]
split = [s1 + s2 for s1, s2 in zip(split[::2], split[1::2])]
options = [Option.parse(s) for s in split if s.startswith('-')]
defaults += options
return defaults
def parse_section(name, source):
pattern = re.compile('^([^\n]*' + name + '[^\n]*\n?(?:[ \t].*?(?:\n|$))*)',
re.IGNORECASE | re.MULTILINE)
return [s.strip() for s in pattern.findall(source)]
def formal_usage(section):
_, _, section = section.partition(':') # drop "usage:"
pu = section.split()
return '( ' + ' '.join(') | (' if s == pu[0] else s for s in pu[1:]) + ' )'
def extras(help, version, options, doc):
if help and any((o.name in ('-h', '--help')) and o.value for o in options):
print(doc.strip("\n"))
sys.exit()
if version and any(o.name == '--version' and o.value for o in options):
print(version)
sys.exit()
class Dict(dict):
def __repr__(self):
return '{%s}' % ',\n '.join('%r: %r' % i for i in sorted(self.items()))
def docopt(doc, argv=None, help=True, version=None, options_first=False):
"""Parse `argv` based on command-line interface described in `doc`.
`docopt` creates your command-line interface based on its
description that you pass as `doc`. Such description can contain
--options, <positional-argument>, commands, which could be
[optional], (required), (mutually | exclusive) or repeated...
Parameters
----------
doc : str
Description of your command-line interface.
argv : list of str, optional
Argument vector to be parsed. sys.argv[1:] is used if not
provided.
help : bool (default: True)
Set to False to disable automatic help on -h or --help
options.
version : any object
If passed, the object will be printed if --version is in
`argv`.
options_first : bool (default: False)
Set to True to require options precede positional arguments,
i.e. to forbid options and positional arguments intermix.
Returns
-------
args : dict
A dictionary, where keys are names of command-line elements
such as e.g. "--verbose" and "<path>", and values are the
parsed values of those elements.
Example
-------
>>> from docopt import docopt
>>> doc = '''
... Usage:
... my_program tcp <host> <port> [--timeout=<seconds>]
... my_program serial <port> [--baud=<n>] [--timeout=<seconds>]
... my_program (-h | --help | --version)
...
... Options:
... -h, --help Show this screen and exit.
... --baud=<n> Baudrate [default: 9600]
... '''
>>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30']
>>> docopt(doc, argv)
{'--baud': '9600',
'--help': False,
'--timeout': '30',
'--version': False,
'<host>': '127.0.0.1',
'<port>': '80',
'serial': False,
'tcp': True}
See also
--------
* For video introduction see http://docopt.org
* Full documentation is available in README.rst as well as online
at https://github.com/docopt/docopt#readme
"""
argv = sys.argv[1:] if argv is None else argv
usage_sections = parse_section('usage:', doc)
if len(usage_sections) == 0:
raise DocoptLanguageError('"usage:" (case-insensitive) not found.')
if len(usage_sections) > 1:
raise DocoptLanguageError('More than one "usage:" (case-insensitive).')
DocoptExit.usage = usage_sections[0]
options = parse_defaults(doc)
pattern = parse_pattern(formal_usage(DocoptExit.usage), options)
# [default] syntax for argument is disabled
# for a in pattern.flat(Argument):
# same_name = [d for d in arguments if d.name == a.name]
# if same_name:
# a.value = same_name[0].value
argv = parse_argv(Tokens(argv), list(options), options_first)
pattern_options = set(pattern.flat(Option))
for options_shortcut in pattern.flat(OptionsShortcut):
doc_options = parse_defaults(doc)
options_shortcut.children = list(set(doc_options) - pattern_options)
# if any_options:
# options_shortcut.children += [Option(o.short, o.long, o.argcount)
# for o in argv if type(o) is Option]
extras(help, version, argv, doc)
matched, left, collected = pattern.fix().match(argv)
if matched and left == []: # better error message if left?
return Dict((a.name, a.value) for a in (pattern.flat() + collected))
raise DocoptExit()

118
src/elts_abrev.dat
View File

@ -1,118 +0,0 @@
1 - H - Hydrogen
2 - He - Helium
3 - Li - Lithium
4 - Be - Beryllium
5 - B - Boron
6 - C - Carbon
7 - N - Nitrogen
8 - O - Oxygen
9 - F - Fluorine
10 - Ne - Neon
11 - Na - Sodium
12 - Mg - Magnesium
13 - Al - Aluminum
14 - Si - Silicon
15 - P - Phosphorus
16 - S - Sulfur
17 - Cl - Chlorine
18 - Ar - Argon
19 - K - Potassium
20 - Ca - Calcium
21 - Sc - Scandium
22 - Ti - Titanium
23 - V - Vanadium
24 - Cr - Chromium
25 - Mn - Manganese
26 - Fe - Iron
27 - Co - Cobalt
28 - Ni - Nickel
29 - Cu - Copper
30 - Zn - Zinc
31 - Ga - Gallium
32 - Ge - Germanium
33 - As - Arsenic
34 - Se - Selenium
35 - Br - Bromine
36 - Kr - Krypton
37 - Rb - Rubidium
38 - Sr - Strontium
39 - Y - Yttrium
40 - Zr - Zirconium
41 - Nb - Niobium
42 - Mo - Molybdenum
43 - Tc - Technetium
44 - Ru - Ruthenium
45 - Rh - Rhodium
46 - Pd - Palladium
47 - Ag - Silver
48 - Cd - Cadmium
49 - In - Indium
50 - Sn - Tin
51 - Sb - Antimony
52 - Te - Tellurium
53 - I - Iodine
54 - Xe - Xenon
55 - Cs - Cesium
56 - Ba - Barium
57 - La - Lanthanum
58 - Ce - Cerium
59 - Pr - Praseodymium
60 - Nd - Neodymium
61 - Pm - Promethium
62 - Sm - Samarium
63 - Eu - Europium
64 - Gd - Gadolinium
65 - Tb - Terbium
66 - Dy - Dysprosium
67 - Ho - Holmium
68 - Er - Erbium
69 - Tm - Thulium
70 - Yb - Ytterbium
71 - Lu - Lutetium
72 - Hf - Hafnium
73 - Ta - Tantalum
74 - W - Tungsten
75 - Re - Rhenium
76 - Os - Osmium
77 - Ir - Iridium
78 - Pt - Platinum
79 - Au - Gold
80 - Hg - Mercury
81 - Tl - Thallium
82 - Pb - Lead
83 - Bi - Bismuth
84 - Po - Polonium
85 - At - Astatine
86 - Rn - Radon
87 - Fr - Francium
88 - Ra - Radium
89 - Ac - Actinium
90 - Th - Thorium
91 - Pa - Protactinium
92 - U - Uranium
93 - Np - Neptunium
94 - Pu - Plutonium
95 - Am - Americium
96 - Cm - Curium
97 - Bk - Berkelium
98 - Cf - Californium
99 - Es - Einsteinium
100 - Fm - Fermium
101 - Md - Mendelevium
102 - No - Nobelium
103 - Lr - Lawrencium
104 - Rf - Rutherfordium
105 - Db - Dubnium
106 - Sg - Seaborgium
107 - Bh - Bohrium
108 - Hs - Hassium
109 - Mt - Meitnerium
110 - Ds - Darmstadtium
111 - Rg - Roentgenium
112 - Cn - Copernicium
113 - Uut - Ununtrium
114 - Fl - Flerovium
115 - Uup - Ununpentium
116 - Lv - Livermorium
117 - Uus - Ununseptium
118 - Uuo - Ununoctium

326
src/parser.py
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@ -1,326 +0,0 @@
import sys
import os
import re
def get_dict_ele():
"""Return dict[atom]=[abreviation]"""
elt_path = os.path.dirname(sys.argv[0]) + "/src/elts_abrev.dat"
with open(elt_path, "r") as f:
data = f.readlines()
dict_ele = dict()
for i in data:
l = i.split("-")
dict_ele[l[1].strip().lower()] = l[2].strip().lower()
return dict_ele
# ______
# | ___ \
# | |_/ /_ _ _ __ ___ ___ _ __
# | __/ _` | '__/ __|/ _ \ '__|
# | | | (_| | | \__ \ __/ |
# \_| \__,_|_| |___/\___|_|
#
# __
# /__ _. ._ _ _ _ _ _
# \_| (_| | | | (/_ _> _> |_| _>
#
def parse_basis_data_gamess_us(data, name, des, elts, debug=False):
"""Parse the basis data raw html of gamess-us to get a nice tuple
Return [name, description, [[ele, data_ele],...]]"""
basis_data = []
b = data.find("$DATA")
e = data.find("$END")
if (b == -1 or data.find("$DATA$END") != -1):
if debug:
print data
raise Exception("WARNING not DATA")
else:
dict_replace = {"PHOSPHOROUS": "PHOSPHORUS",
"D+": "E+",
"D-": "E-"}
for k, v in dict_replace.iteritems():
data = data.replace(k, v)
data = data[b + 5:e - 1].split('\n\n')
dict_ele = get_dict_ele()
for (elt, data_elt) in zip(elts, data):
elt_long_th = dict_ele[elt.lower()]
elt_long_exp = data_elt.split()[0].lower()
if "$" in data_elt:
if debug:
print "Eror",
raise Exception("WARNING bad split")
if elt_long_th == elt_long_exp:
basis_data.append([elt, data_elt.strip()])
else:
if debug:
print "th", elt_long_th
print "exp", elt_long_exp
print "abv", elt
raise Exception("WARNING not a good ELEMENT")
return [name, des, basis_data]
symmetry_regex = re.compile(ur'^(\w)\s+\d+\b')
def l_symmetry_gamess_us(atom_basis):
"""
Return the begin and the end of all the type of orbital
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
output: [ [type, begin, end], ...]
"""
# Example
# [[u'S', 1, 5], [u'L', 5, 9], [u'L', 9, 12], [u'D', 16, 18]]"
l = []
for i, line in enumerate(atom_basis):
m = re.search(symmetry_regex, line)
if m:
# Cause of L !
read_symmetry = m.group(1)
# L is real L or special SP
# Just check the number of exponant
if read_symmetry == "L" and len(atom_basis[i + 1].split()) == 4:
real_symmetry = "SP"
else:
real_symmetry = read_symmetry
l.append([real_symmetry, i])
try:
l[-2].append(i)
except IndexError:
pass
l[-1].append(i + 1)
return l
def handle_l_gamess_us(l_atom_basis):
"""
Read l_atom_basis and change the SP in L and P
"""
l_data = []
for atom_basis in l_atom_basis:
# Split the data in line
l_line_raw = atom_basis.split("\n")
l_line = [l_line_raw[0]]
# l_line_raw[0] containt the name of the Atom
for symmetry, begin, end in l_symmetry_gamess_us(l_line_raw):
if symmetry == "SP":
body_s = []
body_p = []
for i_l in l_line_raw[begin + 1:end]:
# one L => S & P
a = i_l.split()
common = "{:>3}".format(a[0])
common += "{:>15.7f}".format(float(a[1]))
tail_s = common + "{:>23.7f}".format(float(a[2]))
body_s.append(tail_s)
tail_p = common + "{:>23.7f}".format(float(a[3]))
body_p.append(tail_p)
l_line += [l_line_raw[begin].replace("L", "S")]
l_line += body_s
l_line += [l_line_raw[begin].replace("L", "P")]
l_line += body_p
else:
l_line += l_line_raw[begin:end]
l_data.append("\n".join(l_line))
return l_data
# __ _
# /__ _. _ _ o _. ._ (_| |_|_
# \_| (_| |_| _> _> | (_| | | | |
#
def parse_basis_data_gaussian94(data, name, description, elements, debug=True):
"""Parse the Gaussian94 basis data raw html to get a nice tuple.
The data-pairs item is actually expected to be a 2 item list:
[symbol, data]
e.g. ["Ca", "#BASIS SET..."]
N.B.: Currently ignores ECP data!
@param data: raw HTML from BSE
@type data : unicode
@param name: basis set name
@type name : str
@param des: basis set description
@type des : str
@param elements: element symbols e.g. ['H', 'C', 'N', 'O', 'Cl']
@type elements : list
@return: (name, description, data-pairs)
@rtype : tuple
"""
d = []
# Each basis set block starts and ends with ****. Find the region
# containing all the basis blocks using the first and last ****.
mark = "****"
begin = data.find(mark)
end = data.rfind(mark)
if begin == -1 or end == -1:
if debug:
print(data)
str_ = " No basis set data found while attempting to process {0} ({1})"
raise ValueError(str_.format(name, description))
trimmed = data[begin + len(mark): end - len(mark)].strip()
chunks = []
lines = []
# group lines of data delimited by mark into per-element chunks
for line in trimmed.split("\n"):
if line.startswith(mark):
if lines:
chunks.append(lines)
lines = [line]
else:
lines.append(line)
# handle trailing chunk that is not followed by another basis set block
# also remove the marker lines from the chunk itself
if lines and (not chunks or lines != chunks[-1]):
chunks.append(lines)
# join lines back into solid text blocks
chunks = ["\n".join([L for L in c if mark not in L]) for c in chunks]
# check each block for element and assign symbols to final pairs
pairs = []
unused_elements = set([e.upper() for e in elements])
for chunk in chunks:
# get first 3 chars of first line in block
symbol = chunk.split("\n")[0][:3].strip()
try:
unused_elements.remove(symbol.upper())
except KeyError:
if debug:
msg = "Warning: already processed {0}\n".format(symbol)
sys.stderr.write(msg)
pairs.append([symbol, chunk])
if unused_elements:
msg = "Warning: elements {0} left over for {1}".format(
list(unused_elements),
name)
print(msg)
return [name, description, pairs]
# ______ _ _ _ _
# | ___| | | | (_) | |
# | |_ _ __ ___ _ __ ___ __ _| |_ __| |_ ___| |_
# | _| '__/ _ \| '_ ` _ \ / _` | __| / _` | |/ __| __|
# | | | | | (_) | | | | | | (_| | |_ | (_| | | (__| |_
# \_| |_| \___/|_| |_| |_|\__,_|\__| \__,_|_|\___|\__|
#
format_dict = {"Gaussian94": parse_basis_data_gaussian94,
"GAMESS-US": parse_basis_data_gamess_us,
"GAMESS-UK": None,
"Turbomole": None,
"TX93": None,
"Molpro": None,
"MolproInt": None,
"Hondo": None,
"SuperMolecule": None,
"Molcas": None,
"HyperChem": None,
"Dalton": None,
"deMon-KS": None,
"deMon2k": None,
"AcesII": None}
# _____ _ _ _ _
# / ___| | | | (_) | |
# \ `--. _ _ _ __ ___ _ __ ___ ___| |_ _ __ _ _ __| |_ ___| |_
# `--. \ | | | '_ ` _ \| '_ ` _ \ / _ \ __| '__| | | | / _` | |/ __| __|
# /\__/ / |_| | | | | | | | | | | | __/ |_| | | |_| | | (_| | | (__| |_
# \____/ \__, |_| |_| |_|_| |_| |_|\___|\__|_| \__, | \__,_|_|\___|\__|
# __/ | __/ |
# |___/ |___/
"""
Return the begin and the end of all the type of orbital
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
output: [ [type, begin, end], ...]
"""
symmetry_dict = {"GAMESS-US": l_symmetry_gamess_us}
def get_symmetry_function(format):
"""
Return the begin and the end of all the type of orbital
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
output: [ [type, begin, end], ...]
"""
try:
f = symmetry_dict[format]
except KeyError:
print >> sys.stderr, "You need to add a function in symmetry_dict"
print >> sys.stderr, "for your format ({0})".format(format)
sys.exit(1)
return f
# _ _ _ _ _ _ _ _ _ ______ _ _
# | | | | | | | ( | ) | ( | ) | _ (_) | |
# | |_| | __ _ _ __ __| | | ___ V V| | V V | | | |_ ___| |_
# | _ |/ _` | '_ \ / _` | |/ _ \ | | | | | | |/ __| __|
# | | | | (_| | | | | (_| | | __/ | |____ | |/ /| | (__| |_
# \_| |_/\__,_|_| |_|\__,_|_|\___| \_____/ |___/ |_|\___|\__|
"""
Tranforme SP special function (create using get_symmetry_function) into S and P
"""
handle_l_dict = {"GAMESS-US": handle_l_gamess_us}
def get_handle_l_function(format):
"""
Tranforme SP special function (create using get_symmetry_function)
into S and P
"""
try:
f = handle_l_dict[format]
except KeyError:
print >> sys.stderr, "You need to add a function in handle_l_dict"
print >> sys.stderr, "for your format ({0})".format(format)
sys.exit(1)
return f

109
src/parser_handler.py Normal file
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@ -0,0 +1,109 @@
import sys
import os
import re
def get_dict_ele():
"""Return dict[atom]=[abreviation]"""
elt_path = os.path.dirname(sys.argv[0]) + "/src/misc/elts_abrev.dat"
with open(elt_path, "r") as f:
data = f.readlines()
dict_ele = dict()
for i in data:
l = i.split("-")
dict_ele[l[1].strip().lower()] = l[2].strip().lower()
return dict_ele
# ______ _ _ _ _
# | ___| | | | (_) | |
# | |_ _ __ ___ _ __ ___ __ _| |_ __| |_ ___| |_
# | _| '__/ _ \| '_ ` _ \ / _` | __| / _` | |/ __| __|
# | | | | | (_) | | | | | | (_| | |_ | (_| | | (__| |_
# \_| |_| \___/|_| |_| |_|\__,_|\__| \__,_|_|\___|\__|
#
from src.parser.gamess_us import parse_basis_data_gamess_us
from src.parser.gaussian94 import parse_basis_data_gaussian94
from src.parser.nwchem import parse_basis_data_nwchem
format_dict = {"Gaussian94": parse_basis_data_gaussian94,
"GAMESS-US": parse_basis_data_gamess_us,
"GAMESS-UK": None,
"Turbomole": None,
"TX93": None,
"Molpro": None,
"MolproInt": None,
"Hondo": None,
"SuperMolecule": None,
"Molcas": None,
"HyperChem": None,
"Dalton": None,
"deMon-KS": None,
"deMon2k": None,
"AcesII": None,
"NWChem": parse_basis_data_nwchem}
# _____ _ _ _ _
# / ___| | | | (_) | |
# \ `--. _ _ _ __ ___ _ __ ___ ___| |_ _ __ _ _ __| |_ ___| |_
# `--. \ | | | '_ ` _ \| '_ ` _ \ / _ \ __| '__| | | | / _` | |/ __| __|
# /\__/ / |_| | | | | | | | | | | | __/ |_| | | |_| | | (_| | | (__| |_
# \____/ \__, |_| |_| |_|_| |_| |_|\___|\__|_| \__, | \__,_|_|\___|\__|
# __/ | __/ |
# |___/ |___/
"""
Return the begin and the end of all the type of orbital
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
output: [ [type, begin, end], ...]
"""
from src.parser.gamess_us import l_symmetry_gamess_us
symmetry_dict = {"GAMESS-US": l_symmetry_gamess_us}
def get_symmetry_function(format):
"""
Return the begin and the end of all the type of orbital
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
output: [ [type, begin, end], ...]
"""
try:
f = symmetry_dict[format]
except KeyError:
print >> sys.stderr, "You need to add a function in symmetry_dict"
print >> sys.stderr, "for your format ({0})".format(format)
sys.exit(1)
return f
# _ _ _ _ _ _ _ _ _ ______ _ _
# | | | | | | | ( | ) | ( | ) | _ (_) | |
# | |_| | __ _ _ __ __| | | ___ V V| | V V | | | |_ ___| |_
# | _ |/ _` | '_ \ / _` | |/ _ \ | | | | | | |/ __| __|
# | | | | (_| | | | | (_| | | __/ | |____ | |/ /| | (__| |_
# \_| |_/\__,_|_| |_|\__,_|_|\___| \_____/ |___/ |_|\___|\__|
"""
Tranforme SP special function (create using get_symmetry_function) into S and P
"""
from src.parser.gamess_us import handle_l_gamess_us
handle_l_dict = {"GAMESS-US": handle_l_gamess_us}
def get_handle_l_function(format):
"""
Tranforme SP special function (create using get_symmetry_function)
into S and P
"""
try:
f = handle_l_dict[format]
except KeyError:
print >> sys.stderr, "You need to add a function in handle_l_dict"
print >> sys.stderr, "for your format ({0})".format(format)
sys.exit(1)
return f