def get_dict_element():
c.execute('''SELECT id,name,charge,multiplicity,
num_atoms,num_elec,symmetry FROM ele_tab''')
d = defaultdict(dict)
for i in c.fetchall():
d[str(i[1])] = {
"id": str(i[0]),
"charge": int(i[2]),
"multiplicity": int(i[3]),
"num_atoms": int(i[4]),
"symmetry": str(i[6])
}
for ele in d:
f = get_formula(ele)
d[ele]["formula"] = f
for geo in list_geo():
l = [get_coord(ele, a, geo) for a in f]
d[ele][geo] = l
return d
def get_l_ele(arguments):
"""
Return the good list of element needed using arguments dict.
arguments need to have all this key:
--ele ; --like_toulouse ; --like_applencourt ; --like_run_id
"""
if "--ele" in arguments and arguments["--ele"]:
l_ele = "--ele" in arguments and arguments["--ele"]
elif "--like_toulouse" in arguments and arguments["--like_toulouse"]:
from src.misc_info import list_toulouse
l_ele = list_toulouse
elif "--like_applencourt" in arguments and arguments["--like_applencourt"]:
from src.misc_info import list_applencourt
l_ele = list_applencourt
elif "--like_run_id" in arguments and arguments["--like_run_id"]:
c.execute("""SELECT name FROM output_tab
WHERE run_id = {0}""".format(arguments["--like_run_id"]))
l_ele = [i[0] for i in c.fetchall()]
else:
l_ele = list()
return l_ele
def get_l_ele(arguments):
"""
Return the good list of element needed using arguments dict.
arguments need to have all this key:
--ele ; --like_toulouse ; --like_applencourt ; --like_run_id
"""
if "--ele" in arguments and arguments["--ele"]:
l_ele = "--ele" in arguments and arguments["--ele"]
elif "--like_toulouse" in arguments and arguments["--like_toulouse"]:
from src.misc_info import list_toulouse
l_ele = list_toulouse
elif "--like_applencourt" in arguments and arguments["--like_applencourt"]:
from src.misc_info import list_applencourt
l_ele = list_applencourt
elif "--like_run_id" in arguments and arguments["--like_run_id"]:
c.execute("""SELECT name FROM output_tab
WHERE run_id = {0}""".format(
arguments["--like_run_id"]))
l_ele = [i[0] for i in c.fetchall()]
else:
l_ele = list()
return l_ele
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_dict_element():
c.execute('''SELECT id,name,charge,multiplicity,
num_atoms,num_elec,symmetry FROM ele_tab''')
d = defaultdict(dict)
for i in c.fetchall():
d[str(i[1])] = {"id": str(i[0]),
"charge": int(i[2]),
"multiplicity": int(i[3]),
"num_atoms": int(i[4]),
"symmetry": str(i[6])}
for ele in d:
f = get_formula(ele)
d[ele]["formula"] = f
for geo in list_geo():
l = [get_coord(ele, a, geo) for a in f]
d[ele][geo] = l
return d
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]
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]