def db_get(self, table_name):
"""
Get a table from the database
Return a dict[run_id][ele] = Value
TableName is eather e_tab _ae_tab
"""
l = {
cond_sql_or(k, v)
for k, v in (["ele_name", self.l_element_whe_want],
["run_id", self.l_run_id])
}
sql_cmd_where = " AND ".join(l)
cursor = c_row.execute("""SELECT *
FROM {0}
WHERE {1}
""".format(table_name, sql_cmd_where))
from src.object import Energie
d = defaultdict(dict)
for r in cursor:
e = r["energy"]
err = r["err"] if r["err"] else 0
d[r["run_id"]][r["ele_name"]] = Energie(e, err)
return d
def db_get(self, table_name):
"""
Get a table from the database
Return a dict[run_id][ele] = Value
TableName is eather e_tab _ae_tab
"""
l = {
cond_sql_or(k, v)
for k, v in (["ele_name", self.l_element_whe_want],
["run_id", self.l_run_id])
}
sql_cmd_where = " AND ".join(l)
cursor = c_row.execute("""SELECT *
FROM {0}
WHERE {1}
""".format(table_name, sql_cmd_where))
from src.object import Energie
d = defaultdict(dict)
for r in cursor:
e = r["energy"]
err = r["err"] if r["err"] else 0
d[r["run_id"]][r["ele_name"]] = Energie(e, err)
return d
def get_zpe_aeexp(cond_filter_ele):
"""
Return 2 dict:
* zpe_exp Dict of zpe experimental (zpe_exp[name])
* ae_exp Dict of atomization experimental energis (ae_ext[name])
"""
# -#-#- #
# S Q L #
# -#-#- #
try:
zpe_ae_user = config.get("ZPE_AE", "value")
except KeyError:
print "WARNING bad ZPE AE type"
raise
if zpe_ae_user == "recomended":
cond = ['basis_id=(1)']
else:
method_id = ae_zpe_exp_dict[zpe_ae_user]
cond = ['(basis_id=1)', '(method_id=%d)' % (method_id)]
cond_filter = cond_filter_ele + cond
cmd_where = " AND ".join(cond_filter)
cursor = c_row.execute("""SELECT name,
formula,
zpe,
kcal,
min(kcal_err) as kcal_err
FROM id_tab
NATURAL JOIN zpe_tab
NATURAL JOIN atomization_tab
WHERE {cmd_where}
GROUP BY name""".format(cmd_where=cmd_where))
# -#-#-#- #
# I n i t #
# -#-#-#- #
ae_exp = defaultdict()
zpe_exp = defaultdict()
# -#-#-#-#-#-#- #
# F i l l _ i n #
# -#-#-#-#-#-#- #
for r in cursor:
zpe = r['zpe'] * 4.55633e-06
energy = r['kcal'] * 0.00159362
energy_err = r['kcal_err'] * 0.00159362 if r['kcal_err'] else 0.
ae_exp[r['name']] = v_un(energy, energy_err)
zpe_exp[r['name']] = zpe
return [ae_exp, zpe_exp]
def get_zpe_aeexp(cond_filter_ele):
"""
Return 2 dict:
* zpe_exp Dict of zpe experimental (zpe_exp[name])
* ae_exp Dict of atomization experimental energis (ae_ext[name])
"""
# -#-#- #
# S Q L #
# -#-#- #
try:
zpe_ae_user = config.get("ZPE_AE", "value")
except KeyError:
print "WARNING bad ZPE AE type"
raise
if zpe_ae_user == "recomended":
cond = ['basis_id=(1)']
else:
method_id = ae_zpe_exp_dict[zpe_ae_user]
cond = ['(basis_id=1)', '(method_id=%d)' % (method_id)]
cond_filter = cond_filter_ele + cond
cmd_where = " AND ".join(cond_filter)
cursor = c_row.execute("""SELECT name,
formula,
zpe,
kcal,
min(kcal_err) as kcal_err
FROM id_tab
NATURAL JOIN zpe_tab
NATURAL JOIN atomization_tab
WHERE {cmd_where}
GROUP BY name""".format(cmd_where=cmd_where))
# -#-#-#- #
# I n i t #
# -#-#-#- #
ae_exp = defaultdict()
zpe_exp = defaultdict()
# -#-#-#-#-#-#- #
# F i l l _ i n #
# -#-#-#-#-#-#- #
for r in cursor:
zpe = r['zpe'] * 4.55633e-06
energy = r['kcal'] * 0.00159362
energy_err = r['kcal_err'] * 0.00159362 if r['kcal_err'] else 0.
ae_exp[r['name']] = v_un(energy, energy_err)
zpe_exp[r['name']] = zpe
return [ae_exp, zpe_exp]
def db_list_element(self, run_id):
"""
Get the element listed in a run_id
"""
sql_cmd_where = cond_sql_or("run_id", [run_id])
cursor = c_row.execute("""SELECT ele_name
FROM run_tab_ele
WHERE {0}
""".format(sql_cmd_where))
l_ele = {i[0] for i in cursor}
str_ = "No element in run_id: {0}"
assert (l_ele), str_.format(run_id)
return l_ele
def l_element(self):
"""
Get the element from the databse
"""
l = {
cond_sql_or(k, v)
for k, v in (["ele_name", self.l_element_whe_want],
["run_id", self.l_run_id])
}
sql_cmd_where = " AND ".join(l)
cursor = c_row.execute("""SELECT DISTINCT ele_name
FROM run_tab_ele
WHERE {0}
""".format(sql_cmd_where))
return {i[0] for i in cursor.fetchall()}
def db_list_element(self, run_id):
"""
Get the element listed in a run_id
"""
sql_cmd_where = cond_sql_or("run_id", [run_id])
cursor = c_row.execute("""SELECT ele_name
FROM run_tab_ele
WHERE {0}
""".format(sql_cmd_where))
l_ele = {i[0] for i in cursor}
str_ = "No element in run_id: {0}"
assert (l_ele), str_.format(run_id)
return l_ele
def l_element(self):
"""
Get the element from the databse
"""
l = {
cond_sql_or(k, v)
for k, v in (["ele_name", self.l_element_whe_want],
["run_id", self.l_run_id])
}
sql_cmd_where = " AND ".join(l)
cursor = c_row.execute("""SELECT DISTINCT ele_name
FROM run_tab_ele
WHERE {0}
""".format(sql_cmd_where))
return {i[0] for i in cursor.fetchall()}
def d_run_info(self):
"Return a dict in adecation with d_arguments"
d_arg2db = self.d_arg_to_db
d_arg2value = self.d_arguments
l = d_arg2db.viewkeys() & d_arg2value.viewkeys()
if l:
l_cond_filter = [
cond_sql_or(table_name=d_arg2db[k], l_value=d_arg2value[k])
for k in l
]
else:
l_cond_filter = ["(1)"]
sql_cmd_where = " AND ".join(l_cond_filter)
# -#-#- #
# S Q L #
# -#-#- #
cursor = c_row.execute("""SELECT run_id,
method,
basis,
geo,
comments
FROM run_tab_expended
WHERE {0}
""".format(sql_cmd_where))
RunInfo = namedtuple('RunInfo', 'run_id, method, basis, geo, comments')
d_run_info = dict()
for emp in map(RunInfo._make, cursor.fetchall()):
d_run_info[emp.run_id] = emp
assert d_run_info, "No run_id with: {0}".format(sql_cmd_where)
return d_run_info
def d_run_info(self):
"Return a dict in adecation with d_arguments"
d_arg2db = self.d_arg_to_db
d_arg2value = self.d_arguments
l = d_arg2db.viewkeys() & d_arg2value.viewkeys()
if l:
l_cond_filter = [cond_sql_or(table_name=d_arg2db[k],
l_value=d_arg2value[k]) for k in l]
else:
l_cond_filter = ["(1)"]
sql_cmd_where = " AND ".join(l_cond_filter)
# -#-#- #
# S Q L #
# -#-#- #
cursor = c_row.execute("""SELECT run_id,
method,
basis,
geo,
comments
FROM run_tab_expended
WHERE {0}
""".format(sql_cmd_where))
RunInfo = namedtuple('RunInfo', 'run_id, method, basis, geo, comments')
d_run_info = dict()
for emp in map(RunInfo._make, cursor.fetchall()):
d_run_info[emp.run_id] = emp
assert d_run_info, "No run_id with: {0}".format(sql_cmd_where)
return d_run_info
def get_ecal_runinfo_finfo(cmd_where, cipsi_type):
"""
Return 3 dict:
* e_cal Dict of energies theorical / calculated (e_cal[run_id][name])
* run_info Dict of the geo,basis,method,comments (run_info[run_id])
* f_info Dict of formula (run_id[name])
"""
# -#-#- #
# S Q L #
# -#-#- #
cursor = c_row.execute("""SELECT formula,
num_atoms,
run_id,
method_name method,
basis_name basis,
geo_name geo,
comments,
output_tab.name ele,
s_energy,
c_energy,
c_pt2,
q_energy,
q_err
FROM output_tab
INNER JOIN id_tab
ON output_tab.name = id_tab.name
WHERE {0}""".format(cmd_where.replace("name", "ele")))
# -#-#-#- #
# I n i t #
# -#-#-#- #
e_cal = defaultdict(dict)
run_info = defaultdict()
f_info = defaultdict()
# -#-#-#-#-#-#- #
# F i l l _ i n #
# -#-#-#-#-#-#- #
num_formula = namedtuple('num_formula', ['num_atoms', 'formula'])
for r in cursor:
# Energy
if r['s_energy']:
value = float(r['s_energy'])
if r['c_energy']:
if cipsi_type == "var":
value = float(r['c_energy'])
elif cipsi_type == "pt2":
value = float(r['c_pt2'])
elif cipsi_type == "var+pt2":
value = float(r['c_energy']) + float(r['c_pt2'])
if r['q_energy']:
value = v_un(float(r['q_energy']),
float(r['q_err']))
e_cal[r['run_id']][r['ele']] = value
# Info
run_info[r['run_id']] = [r['method'], r['basis'],
r['geo'], r['comments']]
if not r['ele'] in f_info:
f_info[r['ele']] = num_formula(r['num_atoms'], eval(r['formula']))
return [e_cal, run_info, f_info]
def get_ecal_runinfo_finfo(cmd_where, cipsi_type):
"""
Return 3 dict:
* e_cal Dict of energies theorical / calculated (e_cal[run_id][name])
* run_info Dict of the geo,basis,method,comments (run_info[run_id])
* f_info Dict of formula (run_id[name])
"""
# -#-#- #
# S Q L #
# -#-#- #
cursor = c_row.execute("""SELECT formula,
num_atoms,
run_id,
method_name method,
basis_name basis,
geo_name geo,
comments,
output_tab.name ele,
s_energy,
c_energy,
c_pt2,
q_energy,
q_err
FROM output_tab
INNER JOIN id_tab
ON output_tab.name = id_tab.name
WHERE {0}""".format(cmd_where.replace("name",
"ele")))
# -#-#-#- #
# I n i t #
# -#-#-#- #
e_cal = defaultdict(dict)
run_info = defaultdict()
f_info = defaultdict()
# -#-#-#-#-#-#- #
# F i l l _ i n #
# -#-#-#-#-#-#- #
num_formula = namedtuple('num_formula', ['num_atoms', 'formula'])
for r in cursor:
# Energy
if r['s_energy']:
value = float(r['s_energy'])
if r['c_energy']:
if cipsi_type == "var":
value = float(r['c_energy'])
elif cipsi_type == "pt2":
value = float(r['c_pt2'])
elif cipsi_type == "var+pt2":
value = float(r['c_energy']) + float(r['c_pt2'])
if r['q_energy']:
value = v_un(float(r['q_energy']), float(r['q_err']))
e_cal[r['run_id']][r['ele']] = value
# Info
run_info[r['run_id']] = [
r['method'], r['basis'], r['geo'], r['comments']
]
if not r['ele'] in f_info:
f_info[r['ele']] = num_formula(r['num_atoms'], eval(r['formula']))
return [e_cal, run_info, f_info]
