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EMSL_Basis_Set_Exchange_Local
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Merge pull request #4 from TApplencourt/master 

Restor many ele ; and Case Insentivity for basis in get_basis_data
This commit is contained in:
Anthony Scemama 2015-03-25 21:07:10 +01:00
parent 839391ffe7 a313b3e243
commit b6432b4eff
8 changed files with 115 additions and 120 deletions
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12
EMSL_api.py
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@ -44,7 +44,7 @@ import os
from src.misc.docopt import docopt
from src.EMSL_dump import EMSL_dump
from src.EMSL_local import EMSL_local, checkSQLite3
from src.EMSL_local import EMSL_local
if __name__ == '__main__':
@ -63,6 +63,7 @@ if __name__ == '__main__':
# Check the db
try:
if not(arguments['create_db']):
from src.EMSL_local import checkSQLite3
db_path, db_path_changed = checkSQLite3(db_path)
except:
raise
@ -83,10 +84,12 @@ if __name__ == '__main__':
if arguments["--average_mo_number"]:
for name, des, avg in l:
print "- '{}' ({}) || {:<50}".format(name, avg, des)
des_str = "{:<50}".format(des)
print "- '{0}' ({1}) || {2}".format(name, avg, des_str)
else:
for name, des in l:
print "- '{}' || {:<50}".format(name, des)
des_str = "{:<50}".format(des)
print "- '{0}' || {1}".format(name, des_str)
# _ _ _ _____ _ _
# | | (_) | | | ___| | | |
@ -140,8 +143,7 @@ if __name__ == '__main__':
# | |___| \__ \ |_ | || (_) | | | | | | | | (_| | |_\__ \
# \_____/_|___/\__| |_| \___/|_| |_| |_| |_|\__,_|\__|___/
elif arguments["list_formats"]:
e = EMSL_dump()
for i in e.get_list_format():
for i in EMSL_dump.get_list_format():
print i
# _____ _ _ _

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db/Pseudo.db Normal file
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66
src/EMSL_dump.py
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@ -2,7 +2,13 @@ import os
import sys
import re
import time
import sqlite3
try:
import sqlite3
except ImportError:
print "you maybe need libsqlite3-dev from the package manager"
print "and the recompile Python"
raise
from collections import OrderedDict
@ -32,9 +38,8 @@ def install_with_pip(name):
class EMSL_dump:
"""
This call implement all you need for download the EMSL and save it localy
This class implement all you need for download the EMSL and save it localy
"""
def __init__(self, db_path=None, format="GAMESS-US", contraction="True"):
@ -45,14 +50,16 @@ class EMSL_dump:
self.format = check_format(format)
self.parser = get_parser_function(self.format)
"""Define the database path"""
if db_path:
self.db_path = db_path
else:
head_path = os.path.dirname(__file__)
self.db_path = "{0}/../db/{1}.db".format(head_path, self.format)
db_path = "{0}/../db/{1}.db".format(head_path, self.format)
self.db_path = os.path.abspath(db_path)
self.contraction = str(contraction)
self.debug = False
self.debug = True
try:
import requests
@ -62,15 +69,12 @@ class EMSL_dump:
finally:
self.requests = requests
def get_list_format(self):
@staticmethod
def get_list_format():
"""List all the format available in EMSL"""
from src.parser_handler import parser_dict
return parser_dict.keys()
def set_db_path(self, path):
"""Define the database path"""
self.db_path = path
def dwl_basis_list_raw(self):
"""Return the source code of the iframe
who contains the list of the basis set available"""
@ -85,13 +89,9 @@ class EMSL_dump:
dbcache = 'db/cache'
if not os.path.isfile(dbcache):
page = self.requests.get(url).text
file = open(dbcache, 'w')
pickle.dump(page, file)
pickle.dump(page, open(dbcache, 'wb'))
else:
file = open(dbcache, 'r')
page = pickle.load(file)
file.close()
page = pickle.load(open(dbcache, 'rb'))
else:
page = self.requests.get(url).text
@ -142,6 +142,7 @@ class EMSL_dump:
name = tup[1]
elts = re.sub('[["\ \]]', '', tup[3]).split(',')
des = re.sub('\s+', ' ', tup[-1])
d[name] = [name, xml_path, des, elts]
@ -155,7 +156,7 @@ class EMSL_dump:
# | \__/\ | | __/ (_| | || __/
# \____/_| \___|\__,_|\__\___|
#
def create_sql(self, dict_basis_list):
def create_and_populate_sql(self, dict_basis_list):
"""Create the sql from strach.
Take the list of basis available data,
download her, put her in sql"""
@ -204,7 +205,14 @@ class EMSL_dump:
num_worker_threads = 7
attemps_max = 20
q_in = Queue.Queue(num_worker_threads)
# All the task need to be executed
nb_basis = len(dict_basis_list)
q_in = Queue.Queue(nb_basis)
# Populate the q_in list
for [name, path_xml, des, elts] in dict_basis_list.itervalues():
q_in.put([name, path_xml, des, elts])
# All the queue who have been executed
q_out = Queue.Queue(num_worker_threads)
def worker():
@ -216,7 +224,8 @@ class EMSL_dump:
url = "https://bse.pnl.gov:443/bse/portal/user/anon/js_peid/11535052407933/action/portlets.BasisSetAction/template/courier_content/panel/Main/"
url += "/eventSubmit_doDownload/true"
params = {'bsurl': path_xml, 'bsname': name,
params = {'bsurl': path_xml,
'bsname': name,
'elts': " ".join(elts),
'format': self.format,
'minimize': self.contraction}
@ -239,26 +248,15 @@ class EMSL_dump:
if self.debug:
print "Fail on q_out.put", basis_data
raise
else:
q_in.task_done()
def enqueue():
for [name, path_xml, des, elts] in dict_basis_list.itervalues():
q_in.put([name, path_xml, des, elts])
return 0
t = threading.Thread(target=enqueue)
t.daemon = True
t.start()
# Create all the worker (q_in |> worker |> q_out)
for i in range(num_worker_threads):
t = threading.Thread(target=worker)
t.daemon = True
t.start()
nb_basis = len(dict_basis_list)
# Take the result from the out queue (populate by the worker)
# and put in in the SQL database
for i in range(nb_basis):
name, des, basis_data = q_out.get()
q_out.task_done()
@ -300,4 +298,4 @@ class EMSL_dump:
_data = self.dwl_basis_list_raw()
array_basis = self.basis_list_raw_to_array(_data)
self.create_sql(array_basis)
self.create_and_populate_sql(array_basis)

44
src/EMSL_local.py Executable file → Normal file
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@ -63,13 +63,14 @@ def checkSQLite3(db_path):
def cond_sql_or(table_name, l_value, glob=False):
"""Take a table_name, a list of value and create the sql or combande"""
"""Take a table_name, a list of value and create the sql 'or' commande
for example : (elt = "Na" OR elt = "Mg"')"""
opr = "GLOB" if glob else "="
return [" OR ".join(['{} {} "{}"'.format(table_name,
opr,
val) for val in l_value])]
l_cmd = ['{} {} "{}"'.format(table_name, opr, val) for val in l_value]
return "({0})".format(" OR ".join(l_cmd))
def string_to_nb_mo(str_type):
@ -93,7 +94,7 @@ def string_to_nb_mo(str_type):
# |_ |\/| (_ | | _ _ _. |
# |_ | | __) |_ |_ (_) (_ (_| |
#
class EMSL_local:
class EMSL_local(object):
"""
All the method for using the EMSL db localy
@ -128,7 +129,7 @@ class EMSL_local:
# ~#~#~#~#~#~ #
if basis:
cmd_filter_basis = " ".join(cond_sql_or("name", basis, glob=True))
cmd_filter_basis = cond_sql_or("name", basis, glob=True)
else:
cmd_filter_basis = "(1)"
@ -164,8 +165,8 @@ class EMSL_local:
# C r e a t e _ t h e _ c m d #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
cmd_filter_basis = " ".join(cond_sql_or("basis_id", l_basis_id))
cmd_filter_ele = " ".join(cond_sql_or("elt", elts))
cmd_filter_basis = cond_sql_or("basis_id", l_basis_id)
cmd_filter_ele = cond_sql_or("elt", elts)
column_to_fech = "name, description"
if average_mo_number:
@ -251,17 +252,23 @@ class EMSL_local:
handle_l_format=False, check_format=None):
"""
Return the data from the basis set
basis_name : The value of 'name'raw from output_tab in the SQL database
elts : List of element avalaible in 'elt'raw
handle_l_format : If you want to use special treatement for SP function
(see src.parser_handler.get_handle_l_function)
check_format : If you want to verify some condition for special program
(see src.parser.check_validity)
"""
# ~#~#~#~#~#~ #
# F i l t e r #
# ~#~#~#~#~#~ #
cmd_filter_ele = " ".join(cond_sql_or("elt", elts)) if elts else "(1)"
cmd_filter_ele = cond_sql_or("elt", elts) if elts else "(1)"
self.c.execute('''SELECT DISTINCT data from output_tab
WHERE name="{0}"
AND {1}'''.format(basis_name, cmd_filter_ele))
WHERE name LIKE "{0}"
AND ({1})'''.format(basis_name, cmd_filter_ele))
# We need to take i[0] because fetchall return a tuple [(value),...]
l_atom_basis = [i[0].strip() for i in self.c.fetchall()]
@ -281,7 +288,7 @@ class EMSL_local:
if check_format:
from src.parser_handler import get_symmetry_function
from src.parser.check_validity import get_check_function
from src.parser_handler import get_check_function
f = get_check_function(check_format)
f_symmetry = get_symmetry_function(self.format)
@ -302,16 +309,3 @@ class EMSL_local:
# R e t u r n #
# ~#~#~#~#~#~ #
return l_atom_basis
if __name__ == "__main__":
e = EMSL_local(db_path="EMSL.db")
l = e.get_list_basis_available()
for i in l:
print i
l = e.get_list_element_available("pc-0")
print l
l = e.get_basis("cc-pVTZ", ["H", "He"])
for i in l:
print i

52
src/parser/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

13
src/parser/gamess_us.py
View File

@ -136,3 +136,16 @@ def handle_l_gamess_us(l_atom_basis):
l_data.append("\n".join(l_line))
return l_data
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

13
src/parser/nwchem.py
View File

@ -226,3 +226,16 @@ def parse_basis_data_nwchem(data, name, description, elements, debug=True):
serialized = json.dumps(chunk)
pairs.append([symbol, serialized])
return [name, description, pairs]
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

35
src/parser_handler.py
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@ -1,6 +1,5 @@
import sys
import os
import re
def get_dict_ele():
@ -129,10 +128,38 @@ def get_handle_l_function(format):
into S and P
"""
try:
f = handle_l_dict[format]
return 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)
else:
return f
# _ _ _ _ _ _ _
# | | | | | (_) | | | | (_)
# | | | | __ _| |_ __| | __ _| |_ _ ___ _ __
# | | | |/ _` | | |/ _` |/ _` | __| |/ _ \| '_ \
# \ \_/ / (_| | | | (_| | (_| | |_| | (_) | | | |
# \___/ \__,_|_|_|\__,_|\__,_|\__|_|\___/|_| |_|
#
from src.parser.gamess_us import check_gamess
from src.parser.nwchem import check_NWChem
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:
return 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)