def get_children(self):
"""
Find all this children of all the elements and
and add them to l_ele_to_get
"""
cond = " ".join(cond_sql_or("name", self.l_ele_to_get))
c.execute("""SELECT name, formula
FROM id_tab
WHERE {where_cond}""".format(where_cond=cond))
# Uniquify the list
return list(set([a for _, f in c.fetchall() for a, _ in eval(f)]))
def get_children(self):
"""
Find all this children of all the elements and
and add them to l_ele_to_get
"""
cond = " ".join(cond_sql_or("name", self.l_ele_to_get))
c.execute("""SELECT name, formula
FROM id_tab
WHERE {where_cond}""".format(
where_cond=cond))
# Uniquify the list
return list(set([a for _, f in c.fetchall() for a, _ in eval(f)]))
def get_enr(cond_filter_ele):
"""
Return 1 dict:
* e_nr Dict of estimated exact no relativist energy (e_nr[name])
"""
# -#-#- #
# S Q L #
# -#-#- #
# Get Davidson est. atomics energies
try:
run_id_mol = e_nr_name_id_dict[config.get("estimated_exact",
"method")]
run_id_atom = e_nr_name_id_dict[config.get("estimated_exact",
"atomic")]
except KeyError:
print "WARNING bad method in cfg"
print "Will use by default Feller and Chakravorty"
run_id_mol = e_nr_name_id_dict["Feller"]
run_id_atom = e_nr_name_id_dict["Chakravorty"]
cmd_id = cond_sql_or("run_id", [run_id_atom, run_id_mol])
cmd_where = " AND ".join(cond_filter_ele + cmd_id)
c.execute("""SELECT name as name_atome,
energy as exact_energy
FROM simple_energy_tab
NATURAL JOIN id_tab
WHERE {cmd_where}""".format(cmd_where=cmd_where))
# -#-#-#- #
# I n i t #
# -#-#-#- #
e_nr = defaultdict()
# -#-#-#-#-#-#- #
# F i l l _ i n #
# -#-#-#-#-#-#- #
# Put exact energy non relativist for atom and molecule
for name, exact_energy in c.fetchall():
e_nr[name] = float(exact_energy)
return e_nr
def get_enr(cond_filter_ele):
"""
Return 1 dict:
* e_nr Dict of estimated exact no relativist energy (e_nr[name])
"""
# -#-#- #
# S Q L #
# -#-#- #
# Get Davidson est. atomics energies
try:
run_id_mol = e_nr_name_id_dict[config.get("estimated_exact", "method")]
run_id_atom = e_nr_name_id_dict[config.get("estimated_exact",
"atomic")]
except KeyError:
print "WARNING bad method in cfg"
print "Will use by default Feller and Chakravorty"
run_id_mol = e_nr_name_id_dict["Feller"]
run_id_atom = e_nr_name_id_dict["Chakravorty"]
cmd_id = cond_sql_or("run_id", [run_id_atom, run_id_mol])
cmd_where = " AND ".join(cond_filter_ele + cmd_id)
c.execute("""SELECT name as name_atome,
energy as exact_energy
FROM simple_energy_tab
NATURAL JOIN id_tab
WHERE {cmd_where}""".format(cmd_where=cmd_where))
# -#-#-#- #
# I n i t #
# -#-#-#- #
e_nr = defaultdict()
# -#-#-#-#-#-#- #
# F i l l _ i n #
# -#-#-#-#-#-#- #
# Put exact energy non relativist for atom and molecule
for name, exact_energy in c.fetchall():
e_nr[name] = float(exact_energy)
return e_nr
def get_cmd(arguments, l_ele_obj, need_all):
"""
Create the cmd string who will be executed by the db
"""
d = {"run_id": "--run_id",
"geo": "--geo",
"basis": "--basis",
"method": "--method",
"comments": "--comments"}
cond_filter = []
for k, v in d.items():
try:
cond_filter += cond_sql_or(k, arguments[v])
except KeyError:
pass
l_ele_to_get = l_ele_obj.l_ele_to_get
# We need to find the run_id who containt ALL the ele is needed
if l_ele_to_get:
cond_filter_ele = cond_sql_or("name",
l_ele_to_get) if need_all else ["(1)"]
else:
cond_filter_ele = []
# Maybe we dont need to filter
# Else just simplify the expresion :
# geo basis method -> run_id
if not any((cond_filter, cond_filter_ele)):
cmd_where = "(1)"
else:
cmd_where_tmp = " AND ".join(cond_filter + cond_filter_ele)
# Select all the run_id where all the condition is good
if l_ele_to_get and need_all:
cmd_having = "count(name) = {0}".format(len(l_ele_to_get))
else:
cmd_having = "(1)"
c.execute("""SELECT run_id
FROM (SELECT run_id,
name,
method_name method,
basis_name basis,
geo_name geo
FROM output_tab
WHERE {0})
GROUP BY run_id
HAVING {1}""".format(cmd_where_tmp, cmd_having))
l_run_id = [i[0] for i in c.fetchall()]
if not l_run_id:
print "Not run for you'r imput sorry"
sys.exit()
else:
# Now only the run_id count. It containt all the information
cond_filter = ["run_id in (" + ",".join(map(str, l_run_id)) + ")"]
cmd_where = " AND ".join(cond_filter + cond_filter_ele)
return [cond_filter_ele, cmd_where]
try:
from src.docopt import docopt
from src.SQL_util import cond_sql_or, list_geo, list_ele, dict_raw
from src.SQL_util import get_xyz, get_g09
except:
print "File in misc is corupted. Git reset may cure the disease."
sys.exit(1)
if __name__ == '__main__':
arguments = docopt(__doc__, version='G2 Api ' + version)
if arguments["list_geometries"]:
if arguments["--ele"]:
str_ = cond_sql_or("id_tab.name", arguments["--ele"])
str_ = "AND".join(str_)
else:
str_ = '(1)'
print ", ".join(list_geo(str_))
elif arguments["list_elements"]:
str_ = cond_sql_or("geo_tab.name", arguments["--geo"])
str_ = "AND".join(str_)
l = [x for x in list_ele(str_) if "-" not in x and "+" not in x]
print ", ".join(l)
try:
from src.docopt import docopt
from src.SQL_util import cond_sql_or, list_geo, list_ele, dict_raw
from src.SQL_util import get_xyz, get_g09
except:
print "File in misc is corupted. Git reset may cure the disease."
sys.exit(1)
if __name__ == '__main__':
arguments = docopt(__doc__, version='G2 Api ' + version)
if arguments["list_geometries"]:
if arguments["--ele"]:
str_ = cond_sql_or("id_tab.name", arguments["--ele"])
str_ = "AND".join(str_)
else:
str_ = '(1)'
print ", ".join(list_geo(str_))
elif arguments["list_elements"]:
str_ = cond_sql_or("geo_tab.name", arguments["--geo"])
str_ = "AND".join(str_)
l = [x for x in list_ele(str_) if "-" not in x and "+" not in x]
print ", ".join(l)
def get_cmd(arguments, l_ele_obj, need_all):
"""
Create the cmd string who will be executed by the db
"""
d = {
"run_id": "--run_id",
"geo": "--geo",
"basis": "--basis",
"method": "--method",
"comments": "--comments"
}
cond_filter = []
for k, v in d.items():
try:
cond_filter += cond_sql_or(k, arguments[v])
except KeyError:
pass
l_ele_to_get = l_ele_obj.l_ele_to_get
# We need to find the run_id who containt ALL the ele is needed
if l_ele_to_get:
cond_filter_ele = cond_sql_or("name",
l_ele_to_get) if need_all else ["(1)"]
else:
cond_filter_ele = []
# Maybe we dont need to filter
# Else just simplify the expresion :
# geo basis method -> run_id
if not any((cond_filter, cond_filter_ele)):
cmd_where = "(1)"
else:
cmd_where_tmp = " AND ".join(cond_filter + cond_filter_ele)
# Select all the run_id where all the condition is good
if l_ele_to_get and need_all:
cmd_having = "count(name) = {0}".format(len(l_ele_to_get))
else:
cmd_having = "(1)"
c.execute("""SELECT run_id
FROM (SELECT run_id,
name,
method_name method,
basis_name basis,
geo_name geo
FROM output_tab
WHERE {0})
GROUP BY run_id
HAVING {1}""".format(cmd_where_tmp, cmd_having))
l_run_id = [i[0] for i in c.fetchall()]
if not l_run_id:
print "Not run for you'r imput sorry"
sys.exit()
else:
# Now only the run_id count. It containt all the information
cond_filter = ["run_id in (" + ",".join(map(str, l_run_id)) + ")"]
cmd_where = " AND ".join(cond_filter + cond_filter_ele)
return [cond_filter_ele, cmd_where]