def load():
import qcfractal.interface as ptl
NAME = "QCA"
# this builds the index, starting with the client node
NAMEP = NAME + ".p"
if os.path.exists( NAMEP ):
with open( NAMEP, 'rb') as fid:
QCA = pickle.load( fid)
if QCA.db is None:
with open( NAME + ".db.p", 'rb') as fid:
QCA.db = pickle.load( fid).db
else:
client = ptl.FractalClient()
client_node = Node.Node( payload=client, name="client")
QCA = qca.QCATree( NAME, root_payload=client, node_index=None, db=None )
DS_NAME = "OpenFF Trivalent Nitrogen Set 1"
DS_NAME = "SMIRNOFF Coverage Torsion Set 1"
DS_TYPE = "TorsionDriveDataset"
DS_NAME = "OpenFF Gen 2 Torsion Set 2 Coverage"
client.get_collection( DS_TYPE, DS_NAME)
ds = client.get_collection( DS_TYPE, DS_NAME)
drop=[]
# since we know there are no Hessians, skip looking for them
#drop.append("Hessian")
QCA.build_index( ds, drop=drop)
DS_TYPE = "OptimizationDataset"
DS_NAME = "OpenFF Gen 2 Opt Set 2 Coverage"
ds = client.get_collection( DS_TYPE, DS_NAME)
QCA.build_index( ds, drop=drop)
# this will download the final structure of *all* minimizations found
# for a gridopt, this will just be the final structure of each point
QCA.cache_optimization_minimum_molecules()
# save the index and data to disk for future analysis
QCA.to_pickle( db=False)
QCA.to_pickle( name=QCA.name + ".db.p", index=False, db=True)
return QCA
if False:
# TODO: needs work still as ui can't be imported
# Load a list of datasets and build the index
# "datasets" is a file of datasets to load
datasets = offsb.ui.qcasb.load_dataset_input("datasets")
QCA = offsb.ui.qcasb.QCArchiveSpellBook(datasets=datasets).QCA
else:
# Just a quick shortcut to get something going
client = ptl.FractalClient()
ds = client.get_collection("TorsionDriveDataset",
"OpenFF Gen 2 Torsion Set 1 Roche")
QCA = QCA = qca.QCATree("QCA",
root_payload=client,
node_index=dict(),
db=dict())
drop = ["Intermediates", "Hessian"]
QCA.build_index(ds, drop=drop, keep_specs=["default"])
save(QCA)
entries = list(QCA.node_iter_depth_first(QCA.root(), select="Entry"))
print("There are {:d} entries total".format(len(entries)))
# The general query on the dataset.
# The results respect the key, and will only return those indices if specified
# If no key is specified, then the indices are in order as they appear in the string
query = smiles.SmilesSearchTree("[#7X3:2](~[#1:1])(~[#6])~[#6:3]=[O:4]",
QCA,
name="smiles")
def generate_status_report( collection, name, logname):
"""
Iterates a dataset, checking for errors, and saves errors to the log file.
"""
client = ptl.FractalClient()
QCA = qca.QCATree( "QCA", root_payload=client, node_index=dict(), db=dict())
for s in sets:
ds = client.get_collection( collection, name)
QCA.build_index( ds, drop=["Gradient"], keep_specs=["default"],
start=0, limit=0)
default = [n for n in QCA.node_iter_depth_first(QCA.root())
if "QCS-default" in n.payload]
mindepth = QCA.node_depth(default[0])
tdfailures= 0
fid = open(logname, 'w')
for node in QCA.node_iter_dive(default):
i = QCA.node_depth(node) - mindepth+1
status=""
statbar= " "
errmsg = ""
hasstat = False
qcp = QCA.db[node.payload]['data']
try:
hasstat = "status" in QCA.db[node.payload]["data"]
except Exception:
pass
if hasstat:
status = qcp["status"][:]
if status != "COMPLETE" and node.name == "Optimization":
try:
statbar = "----"
client = qcp['client']
print("error", qcp['error'], qcp['error'] is None)
if not (qcp['error'] is None):
key=int(qcp['error'])
err = list(client.query_kvstore(key).values())[0]
errmsg += "####ERROR####\n"
errmsg += "Error type: " + err['error_type'] + "\n"
errmsg += "Error:\n" + err['error_message']
errmsg += "############\n"
elif status == "ERROR":
errmsg += "####FATAL####\n"
errmsg += "Job errored and no error on record. "
errmsg += "Input likely bogus; check your settings\n"
errmsg += "############\n"
if not (qcp['stdout'] is None):
key=int(qcp['stdout'])
msg = list(client.query_kvstore(key)).values())[0]
errmsg += "----ISSUE----\n"
errmsg += "Status was not complete; stdout is:\n"
errmsg += msg
errmsg += "-------------\n"
if not (qcp['stderr'] is None):
key=int(qcp['stderr'])
msg = list(client.query_kvstore(key)).values())[0]
errmsg += "####ISSUE####\n"
errmsg += "Status was not complete; stderr is:\n"
errmsg += msg
errmsg += "-------------\n"
except Exception as e:
fid.write("Internal issue:\n" + str(e) + '\n')
if status != "COMPLETE" and node.name == "TorsionDrive":
statbar = "XXXX"
if node.name == "TorsionDrive" and status != "COMPLETE":
tdfailures += 1
fid.write("{:2d} {} {} {}\n".format(tdi,statbar*i,
" ".join([str(node.index),str(node.name), str(node.payload)]),
status))
if errmsg != "":
fid.write("\n{}\n".format(errmsg))