def run_json_qcschema(json_data, clean, json_serialization, keep_wfn=False):
"""
An implementation of the QC JSON Schema (molssi-qc-schema.readthedocs.io/en/latest/index.html#) implementation in Psi4.
Parameters
----------
json_data : JSON
Please see molssi-qc-schema.readthedocs.io/en/latest/spec_components.html for further details.
Notes
-----
!Warning! This function is experimental and likely to change in the future.
Please report any suggestions or uses of this function on github.com/MolSSI/QC_JSON_Schema.
Examples
--------
"""
# Clean a few things
_clean_psi_environ(clean)
# This is currently a forced override
if json_data["schema_name"] in ["qc_schema_input", "qcschema_input"]:
json_data["schema_name"] = "qcschema_input"
else:
raise KeyError("Schema name of '{}' not understood".format(
json_data["schema_name"]))
if json_data["schema_version"] != 1:
raise KeyError("Schema version of '{}' not understood".format(
json_data["schema_version"]))
if json_data.get("nthreads", False) is not False:
core.set_num_threads(json_data["nthreads"], quiet=True)
# Build molecule
if "schema_name" in json_data["molecule"]:
molschemus = json_data["molecule"] # dtype >=2
else:
molschemus = json_data # dtype =1
mol = core.Molecule.from_schema(molschemus)
# Update molecule geometry as we orient and fix_com
json_data["molecule"]["geometry"] = mol.geometry().np.ravel().tolist()
# Set options
kwargs = json_data["keywords"].pop("function_kwargs", {})
p4util.set_options(json_data["keywords"])
# Setup the computation
method = json_data["model"]["method"]
core.set_global_option("BASIS", json_data["model"]["basis"])
kwargs.update({"return_wfn": True, "molecule": mol})
# Handle special properties case
if json_data["driver"] == "properties":
if "properties" not in kwargs:
kwargs["properties"] = list(default_properties_)
# Actual driver run
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
# Pull out a standard set of SCF properties
if "extras" not in json_data:
json_data["extras"] = {}
json_data["extras"]["qcvars"] = {}
current_qcvars_only = json_data["extras"].get("current_qcvars_only", False)
if json_data["extras"].get("wfn_qcvars_only", False):
psi_props = wfn.variables(
include_deprecated_keys=(not current_qcvars_only))
else:
psi_props = core.variables(
include_deprecated_keys=(not current_qcvars_only))
for k, v in psi_props.items():
if k not in json_data["extras"]["qcvars"]:
json_data["extras"]["qcvars"][k] = _serial_translation(
v, json=json_serialization)
# Still a bit of a mess at the moment add in local vars as well.
for k, v in wfn.variables().items():
if k not in json_data["extras"]["qcvars"]:
# interpreting wfn_qcvars_only as no deprecated qcvars either
if not (json_data["extras"].get("wfn_qcvars_only", False) and
(any([
k.upper().endswith(" DIPOLE " + cart)
for cart in ["X", "Y", "Z"]
]) or any([
k.upper().endswith(" QUADRUPOLE " + cart)
for cart in ["XX", "YY", "ZZ", "XY", "XZ", "YZ"]
]) or k.upper() in [
"SOS-MP2 CORRELATION ENERGY",
"SOS-MP2 TOTAL ENERGY",
"SOS-PI-MP2 CORRELATION ENERGY",
"SOS-PI-MP2 TOTAL ENERGY",
"SCS-MP3 CORRELATION ENERGY",
"SCS-MP3 TOTAL ENERGY",
])):
json_data["extras"]["qcvars"][k] = _serial_translation(
v, json=json_serialization)
# Handle the return result
if json_data["driver"] == "energy":
json_data["return_result"] = val
elif json_data["driver"] in ["gradient", "hessian"]:
json_data["return_result"] = _serial_translation(
val, json=json_serialization)
elif json_data["driver"] == "properties":
ret = {}
mtd = json_data["model"]["method"].upper()
# Dipole/quadrupole still special case
if "dipole" in kwargs["properties"]:
ret["dipole"] = _serial_translation(psi_props[mtd + " DIPOLE"],
json=json_serialization)
if "quadrupole" in kwargs["properties"]:
ret["quadrupole"] = _serial_translation(psi_props[mtd +
" QUADRUPOLE"],
json=json_serialization)
ret.update(
_convert_variables(wfn.variables(),
context="properties",
json=json_serialization))
json_data["return_result"] = ret
else:
raise KeyError("Did not understand Driver key %s." %
json_data["driver"])
props = {
"calcinfo_nbasis": wfn.nso(),
"calcinfo_nmo": wfn.nmo(),
"calcinfo_nalpha": wfn.nalpha(),
"calcinfo_nbeta": wfn.nbeta(),
"calcinfo_natom": mol.geometry().shape[0],
"nuclear_repulsion_energy": mol.nuclear_repulsion_energy(
), # use this b/c psivar is monomer for SAPT
}
props.update(
_convert_variables(psi_props,
context="generics",
json=json_serialization))
if not list(
set(['CBS NUMBER', 'NBODY NUMBER', 'FINDIF NUMBER'])
& set(json_data["extras"]["qcvars"].keys())):
props.update(
_convert_variables(psi_props,
context="scf",
json=json_serialization))
# Write out post-SCF keywords
if "MP2 CORRELATION ENERGY" in psi_props:
props.update(
_convert_variables(psi_props,
context="mp2",
json=json_serialization))
if "CCSD CORRELATION ENERGY" in psi_props:
props.update(
_convert_variables(psi_props,
context="ccsd",
json=json_serialization))
if "CCSD(T) CORRELATION ENERGY" in psi_props:
props.update(
_convert_variables(psi_props,
context="ccsd(t)",
json=json_serialization))
json_data["properties"] = props
json_data["success"] = True
json_data["provenance"]["module"] = wfn.module()
if keep_wfn:
json_data["wavefunction"] = _convert_wavefunction(wfn)
files = {
"psi4.grad":
Path(core.get_writer_file_prefix(wfn.molecule().name()) + ".grad"),
"psi4.hess":
Path(core.get_writer_file_prefix(wfn.molecule().name()) + ".hess"),
# binary "psi4.180.npy": Path(core.get_writer_file_prefix(wfn.molecule().name()) + ".180.npy"),
"timer.dat":
Path(
"timer.dat"
), # ok for `psi4 --qcschema` but no file collected for `qcengine.run_program(..., "psi4")`
}
json_data["native_files"] = {
fl: flpath.read_text()
for fl, flpath in files.items() if flpath.exists()
}
# Reset state
_clean_psi_environ(clean)
json_data["schema_name"] = "qcschema_output"
return json_data
def run_json_qcschema(json_data, clean, json_serialization, keep_wfn=False):
"""
An implementation of the QC JSON Schema (molssi-qc-schema.readthedocs.io/en/latest/index.html#) implementation in Psi4.
Parameters
----------
json_data : JSON
Please see molssi-qc-schema.readthedocs.io/en/latest/spec_components.html for further details.
Notes
-----
!Warning! This function is experimental and likely to change in the future.
Please report any suggestions or uses of this function on github.com/MolSSI/QC_JSON_Schema.
Examples
--------
"""
# Clean a few things
_clean_psi_environ(clean)
# This is currently a forced override
if json_data["schema_name"] in ["qc_schema_input", "qcschema_input"]:
json_data["schema_name"] = "qcschema_input"
else:
raise KeyError("Schema name of '{}' not understood".format(json_data["schema_name"]))
if json_data["schema_version"] != 1:
raise KeyError("Schema version of '{}' not understood".format(json_data["schema_version"]))
if json_data.get("nthreads", False) is not False:
core.set_num_threads(json_data["nthreads"], quiet=True)
# Build molecule
if "schema_name" in json_data["molecule"]:
molschemus = json_data["molecule"] # dtype >=2
else:
molschemus = json_data # dtype =1
mol = core.Molecule.from_schema(molschemus)
# Update molecule geometry as we orient and fix_com
json_data["molecule"]["geometry"] = mol.geometry().np.ravel().tolist()
# Set options
kwargs = json_data["keywords"].pop("function_kwargs", {})
p4util.set_options(json_data["keywords"])
# Setup the computation
method = json_data["model"]["method"]
core.set_global_option("BASIS", json_data["model"]["basis"])
kwargs.update({"return_wfn": True, "molecule": mol})
# Handle special properties case
if json_data["driver"] == "properties":
if "properties" in json_data["model"]:
kwargs["properties"] = [x.lower() for x in json_data["model"]["properties"]]
extra = set(kwargs["properties"]) - can_do_properties_
if len(extra):
raise KeyError("Did not understand property key %s." % kwargs["properties"])
else:
kwargs["properties"] = list(can_do_properties_)
# Actual driver run
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
# Pull out a standard set of SCF properties
if "extras" not in json_data:
json_data["extras"] = {}
json_data["extras"]["qcvars"] = {}
if json_data["extras"].get("wfn_qcvars_only", False):
psi_props = wfn.variables()
else:
psi_props = core.variables()
for k, v in psi_props.items():
if k not in json_data["extras"]["qcvars"]:
json_data["extras"]["qcvars"][k] = _serial_translation(v, json=json_serialization)
# Still a bit of a mess at the moment add in local vars as well.
for k, v in wfn.variables().items():
if k not in json_data["extras"]["qcvars"]:
json_data["extras"]["qcvars"][k] = _serial_translation(v, json=json_serialization)
# Handle the return result
if json_data["driver"] == "energy":
json_data["return_result"] = val
elif json_data["driver"] in ["gradient", "hessian"]:
json_data["return_result"] = _serial_translation(val, json=json_serialization)
elif json_data["driver"] == "properties":
ret = {}
mtd = json_data["model"]["method"].upper()
# Dipole/quadrupole still special case
if "dipole" in kwargs["properties"]:
ret["dipole"] = [psi_props[mtd + " DIPOLE " + x] for x in ["X", "Y", "Z"]]
if "quadrupole" in kwargs["properties"]:
ret["quadrupole"] = [psi_props[mtd + " QUADRUPOLE " + x] for x in ["XX", "XY", "XZ", "YY", "YZ", "ZZ"]]
ret.update(_convert_variables(wfn.variables(), context="properties", json=json_serialization))
json_data["return_result"] = ret
else:
raise KeyError("Did not understand Driver key %s." % json_data["driver"])
props = {
"calcinfo_nbasis": wfn.nso(),
"calcinfo_nmo": wfn.nmo(),
"calcinfo_nalpha": wfn.nalpha(),
"calcinfo_nbeta": wfn.nbeta(),
"calcinfo_natom": mol.geometry().shape[0],
}
props.update(_convert_variables(psi_props, context="generics", json=json_serialization))
if not list(set(['CBS NUMBER', 'NBODY NUMBER', 'FINDIF NUMBER']) & set(json_data["extras"]["qcvars"].keys())):
props.update(_convert_variables(psi_props, context="scf", json=json_serialization))
# Write out post-SCF keywords
if "MP2 CORRELATION ENERGY" in psi_props:
props.update(_convert_variables(psi_props, context="mp2", json=json_serialization))
if "CCSD CORRELATION ENERGY" in psi_props:
props.update(_convert_variables(psi_props, context="ccsd", json=json_serialization))
if "CCSD(T) CORRELATION ENERGY" in psi_props:
props.update(_convert_variables(psi_props, context="ccsd(t)", json=json_serialization))
json_data["properties"] = props
json_data["success"] = True
if keep_wfn:
json_data["wavefunction"] = _convert_wavefunction(wfn)
# Reset state
_clean_psi_environ(clean)
json_data["schema_name"] = "qcschema_output"
return json_data