def run_json(json_data, clean=True):
warnings.warn(
"Using `psi4.schema_wrapper.run_json` or `psi4.json_wrapper.run_json` instead of `psi4.schema_wrapper.run_qcschema` is deprecated, and in 1.7 it will stop working\n",
category=FutureWarning)
# Set scratch
if "scratch_location" in json_data:
psi4_io = core.IOManager.shared_object()
psi4_io.set_default_path(json_data["scratch_location"])
# Direct output
outfile = os.path.join(core.IOManager.shared_object().get_default_path(),
str(uuid.uuid4()) + ".json_out")
core.set_output_file(outfile, False)
# Set memory
if "memory" in json_data:
p4util.set_memory(json_data["memory"])
# Do we return the output?
return_output = json_data.pop("return_output", False)
if return_output:
json_data["raw_output"] = "Not yet run."
# Set a few flags
json_data["raw_output"] = None
json_data["success"] = False
json_data["provenance"] = {
"creator": "Psi4",
"version": __version__,
"routine": "psi4.json_wrapper.run_json"
}
# Attempt to run the computer
try:
# qcschema should be copied
json_data = run_json_qcschema(copy.deepcopy(json_data), clean, True)
except Exception as exc:
json_data["error"] = {
'error_type': type(exc).__name__,
'error_message':
''.join(traceback.format_exception(*sys.exc_info())),
}
json_data["success"] = False
json_data["raw_output"] = _read_output(outfile)
if return_output:
json_data["raw_output"] = _read_output(outfile)
atexit.register(_quiet_remove, outfile)
return json_data
def run_json(json_data, clean=True):
# Set scratch
if "scratch_location" in json_data:
psi4_io = core.IOManager.shared_object()
psi4_io.set_default_path(json_data["scratch_location"])
# Direct output
outfile = os.path.join(core.IOManager.shared_object().get_default_path(),
str(uuid.uuid4()) + ".json_out")
core.set_output_file(outfile, False)
# Set memory
if "memory" in json_data:
psi4.set_memory(json_data["memory"])
# Do we return the output?
return_output = json_data.pop("return_output", False)
if return_output:
json_data["raw_output"] = "Not yet run."
# Set a few flags
json_data["raw_output"] = None
json_data["success"] = False
# Attempt to run the computer
try:
# qcschema should be copied
json_data = run_json_qcschema(copy.deepcopy(json_data), clean)
except Exception as exc:
json_data["error"] = {
'error_type': type(exc).__name__,
'error_message':
''.join(traceback.format_exception(*sys.exc_info())),
}
json_data["success"] = False
json_data["raw_output"] = _read_output(outfile)
if return_output:
json_data["raw_output"] = _read_output(outfile)
# Destroy the created file at exit
def _quiet_remove(filename):
try:
os.unlink(filename)
except OSError:
pass
atexit.register(_quiet_remove, outfile)
return json_data
def run_json(json_data, clean=True):
# Set scratch
if "scratch_location" in json_data:
psi4_io = core.IOManager.shared_object()
psi4_io.set_default_path(json_data["scratch_location"])
# Direct output
outfile = os.path.join(core.IOManager.shared_object().get_default_path(), str(uuid.uuid4()) + ".json_out")
core.set_output_file(outfile, False)
# Set memory
if "memory" in json_data:
psi4.set_memory(json_data["memory"])
# Do we return the output?
return_output = json_data.pop("return_output", False)
if return_output:
json_data["raw_output"] = "Not yet run."
# Set a few flags
json_data["raw_output"] = None
json_data["success"] = False
# Attempt to run the computer
try:
# qcschema should be copied
json_data = run_json_qcschema(copy.deepcopy(json_data), clean)
except Exception as exc:
json_data["error"] = {
'error_type': type(exc).__name__,
'error_message': ''.join(traceback.format_exception(*sys.exc_info())),
}
json_data["success"] = False
json_data["raw_output"] = _read_output(outfile)
if return_output:
json_data["raw_output"] = _read_output(outfile)
# Destroy the created file at exit
def _quiet_remove(filename):
try:
os.unlink(filename)
except OSError:
pass
atexit.register(_quiet_remove, outfile)
return json_data
def run_qcschema(input_data, clean=True):
outfile = os.path.join(core.IOManager.shared_object().get_default_path(),
str(uuid.uuid4()) + ".qcschema_tmpout")
core.set_output_file(outfile, False)
print_header()
start_time = datetime.datetime.now()
try:
input_model = qcng.util.model_wrapper(input_data,
qcel.models.AtomicInput)
keep_wfn = input_model.protocols.wavefunction != 'none'
# qcschema should be copied
ret_data = run_json_qcschema(input_model.dict(),
clean,
False,
keep_wfn=keep_wfn)
ret_data["provenance"] = {
"creator": "Psi4",
"version": __version__,
"routine": "psi4.schema_runner.run_qcschema"
}
exit_printing(start_time=start_time, success=True)
ret = qcel.models.AtomicResult(**ret_data,
stdout=_read_output(outfile))
except Exception as exc:
if not isinstance(input_data, dict):
input_data = input_data.dict()
input_data = input_data.copy()
input_data["stdout"] = _read_output(outfile)
ret = qcel.models.FailedOperation(
input_data=input_data,
success=False,
error={
'error_type':
type(exc).__name__,
'error_message':
''.join(traceback.format_exception(*sys.exc_info())),
})
atexit.register(_quiet_remove, outfile)
return ret
def run_json(json_data, clean=True):
# Set scratch
if "scratch_location" in json_data:
psi4_io = core.IOManager.shared_object()
psi4_io.set_default_path(json_data["scratch_location"])
# Direct output
outfile = os.path.join(core.IOManager.shared_object().get_default_path(), str(uuid.uuid4()) + ".json_out")
core.set_output_file(outfile, False)
# Set memory
if "memory" in json_data:
psi4.set_memory(json_data["memory"])
# Do we return the output?
return_output = json_data.pop("return_output", False)
if return_output:
json_data["raw_output"] = "Not yet run."
# Set a few flags
json_data["raw_output"] = None
json_data["success"] = False
# Attempt to run the computer
try:
if json_data.get("schema_name", "").startswith("qc_schema"):
# qc_schema should be copied
json_data = run_json_qc_schema(copy.deepcopy(json_data), clean)
else:
# Original run updates inplace
run_json_original_v1_1(json_data, clean)
except Exception as error:
json_data["error"] = repr(error)
json_data["success"] = False
if return_output:
with open(outfile, 'r') as f:
json_data["raw_output"] = f.read()
atexit.register(os.unlink, outfile)
return json_data
def run_json(json_data, clean=True):
# Set scratch
if "scratch_location" in json_data:
psi4_io = core.IOManager.shared_object()
psi4_io.set_default_path(json_data["scratch_location"])
# Direct output
outfile = os.path.join(core.IOManager.shared_object().get_default_path(), str(uuid.uuid4()) + ".json_out")
core.set_output_file(outfile, False)
# Set memory
if "memory" in json_data:
psi4.set_memory(json_data["memory"])
# Do we return the output?
return_output = json_data.pop("return_output", False)
if return_output:
json_data["raw_output"] = "Not yet run."
# Set a few flags
json_data["raw_output"] = None
json_data["success"] = False
# Attempt to run the computer
try:
# qc_schema should be copied
json_data = run_json_qc_schema(copy.deepcopy(json_data), clean)
except Exception as error:
exc_type, exc_value, exc_traceback = sys.exc_info()
json_data["error"] = repr(traceback.format_exception(exc_type, exc_value,
exc_traceback))
json_data["success"] = False
with open(outfile, 'r') as f:
json_data["raw_output"] = f.read()
if return_output:
with open(outfile, 'r') as f:
json_data["raw_output"] = f.read()
atexit.register(os.unlink, outfile)
return json_data
def run_json(json_data, clean=True):
# Set scratch
if "scratch_location" in json_data:
psi4_io = core.IOManager.shared_object()
psi4_io.set_default_path(json_data["scratch_location"])
# Direct output
outfile = os.path.join(core.IOManager.shared_object().get_default_path(), str(uuid.uuid4()) + ".json_out")
core.set_output_file(outfile, False)
# Set memory
if "memory" in json_data:
psi4.set_memory(json_data["memory"])
# Do we return the output?
return_output = json_data.pop("return_output", False)
if return_output:
json_data["raw_output"] = "Not yet run."
# Set a few flags
json_data["raw_output"] = None
json_data["success"] = False
# Attempt to run the computer
try:
if json_data.get("schema_name", "").startswith("qc_schema"):
# qc_schema should be copied
json_data = run_json_qc_schema(copy.deepcopy(json_data), clean)
else:
# Original run updates inplace
run_json_original_v1_1(json_data, clean)
except Exception as error:
json_data["error"] = repr(error)
json_data["success"] = False
if return_output:
with open(outfile, 'r') as f:
json_data["raw_output"] = f.read()
os.unlink(outfile)
return json_data
def run_json(json_data, clean=True):
# Set scratch
if "scratch_location" in json_data:
psi4_io = core.IOManager.shared_object()
psi4_io.set_default_path(json_data["scratch_location"])
# Set memory
if "memory" in json_data:
psi4.set_memory(json_data["memory"])
# Do we return the output?
return_output = json_data.pop("return_output", False)
if return_output:
outfile = os.path.join(
core.IOManager.shared_object().get_default_path(),
str(uuid.uuid4()) + ".json_out")
core.set_output_file(outfile, False)
json_data["raw_output"] = "Not yet run."
# Set a few flags
json_data["raw_output"] = None
json_data["success"] = False
# Attempt to run the computer
try:
if ("schema_name" in json_data) and (json_data["schema_name"]
== "QC_JSON"):
run_json_qc_schema(json_data, clean)
else:
run_json_original_v1_1(json_data, clean)
except Exception as error:
json_data["error"] = repr(error)
json_data["success"] = False
if return_output:
with open(outfile, 'r') as f:
json_data["raw_output"] = f.read()
os.unlink(outfile)
return json_data
def run_qcschema(
input_data: Union[Dict[str, Any], qcel.models.AtomicInput],
clean: bool = True,
postclean: bool = True
) -> Union[qcel.models.AtomicResult, qcel.models.FailedOperation]:
"""Run a quantum chemistry job specified by :py:class:`qcelemental.models.AtomicInput` **input_data** in |PSIfour|.
Parameters
----------
input_data
Quantum chemistry job in either AtomicInput class or dictionary form.
clean
Reset global QCVariables, options, and scratch files to default state.
postclean
When ``False``, *remove* the output file since absorbed into AtomicResult.
When ``True``, simply *close* the output file. True is useful when calling
from a Psi4 session to avoid removing the parent Psi4's output file.
Returns
-------
qcelemental.models.AtomicResult
Full record of quantum chemistry calculation, including output text. Returned upon job success.
qcelemental.models.FailedOperation
Record to diagnose calculation failure, including output text and input specification. Returned upon job failure.
"""
outfile = os.path.join(core.IOManager.shared_object().get_default_path(),
str(uuid.uuid4()) + ".qcschema_tmpout")
core.set_output_file(outfile, False)
print_header()
start_time = datetime.datetime.now()
try:
input_model = qcng.util.model_wrapper(input_data,
qcel.models.AtomicInput)
# Echo the infile on the outfile
core.print_out("\n ==> Input QCSchema <==\n")
core.print_out(
"\n--------------------------------------------------------------------------\n"
)
core.print_out(pp.pformat(json.loads(input_model.json())))
core.print_out(
"\n--------------------------------------------------------------------------\n"
)
keep_wfn = input_model.protocols.wavefunction != 'none'
# qcschema should be copied
ret_data = run_json_qcschema(input_model.dict(),
clean,
False,
keep_wfn=keep_wfn)
ret_data["provenance"].update({
"creator":
"Psi4",
"version":
__version__,
"routine":
"psi4.schema_runner.run_qcschema"
})
ret_data["native_files"]["input"] = json.dumps(json.loads(
input_model.json()),
indent=1)
exit_printing(start_time=start_time, success=True)
ret = qcel.models.AtomicResult(**ret_data,
stdout=_read_output(outfile))
except Exception as exc:
if not isinstance(input_data, dict):
input_data = input_data.dict()
input_data = input_data.copy()
input_data["stdout"] = _read_output(outfile)
ret = qcel.models.FailedOperation(
input_data=input_data,
success=False,
error={
'error_type':
type(exc).__name__,
'error_message':
''.join(traceback.format_exception(*sys.exc_info())),
})
_clean_psi_output(postclean, outfile)
return ret
def run_json(json_data):
"""
Runs and updates the input JSON data.
Parameters
----------
json_data : JSON input
Required input fields:
- molecule : str
A string representation of the molecule. Any valid psi4 synatx is valid.
- driver : str
The driver method to use valid arguments are "energy", "gradient", "property"
- args : str
Input arguments to the driver function
- kwargs : dict
Input dictionary to the driver function
Optional input fields:
- kwargs : dict
Additional kwargs to be passed to the driver.
- options : dict
Global options to set in the Psi4 run.
- scratch_location : str
Overide the default scratch location.
- return_output : bool
Return the full string reprsentation of the output or not.
Output fields:
- return_value : float, psi4.core.Vector, psi4.core.Matrix
The return value of the input function.
- variables : dict
The list of Psi4 variables generated from the run.
- success : bool
Indicates if the run was successful or not.
- error : str
If an error is raised the result is returned here.
- raw_output : str
The full Psi4 output if requested.
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/psi4/psi4.
Examples
--------
# CP corrected Helium dimer energy in the STO-3G basis.
>>> json_data = {}
>>> json_data["molecule"] = "He 0 0 0\n--\nHe 0 0 1"
>>> json_data["driver"] = "energy"
>>> json_data["method"] = 'SCF'
>>> json_data["kwargs"] = {"bsse_type": "cp"}
>>> json_data["options"] = {"BASIS": "STO-3G"}
>>> run_json(json_data)
{
"raw_output": "Output storing was not requested.",
"options": {
"BASIS": "STO-3G"
},
"driver": "energy",
"molecule": "He 0 0 0\n--\nHe 0 0 1",
"method": "SCF",
"variables": {
"SCF N ITERS": 2.0,
"SCF DIPOLE Y": 0.0,
"CURRENT DIPOLE Y": 0.0,
"CP-CORRECTED 2-BODY INTERACTION ENERGY": 0.1839360538612116,
"HF TOTAL ENERGY": -5.433191881443323,
"SCF TOTAL ENERGY": -5.433191881443323,
"TWO-ELECTRON ENERGY": 4.124089347186247,
"SCF ITERATION ENERGY": -5.433191881443323,
"CURRENT DIPOLE X": 0.0,
"CURRENT DIPOLE Z": 0.0,
"CURRENT REFERENCE ENERGY": -5.433191881443323,
"CURRENT ENERGY": 0.1839360538612116,
"COUNTERPOISE CORRECTED TOTAL ENERGY": -5.433191881443323,
"SCF DIPOLE Z": 0.0,
"COUNTERPOISE CORRECTED INTERACTION ENERGY": 0.1839360538612116,
"NUCLEAR REPULSION ENERGY": 2.11670883436,
"SCF DIPOLE X": 0.0,
"ONE-ELECTRON ENERGY": -11.67399006298957
},
"return_value": 0.1839360538612116,
"error": "",
"success": true,
"provenance": {
"creator": "Psi4",
"routine": "psi4.run_json",
"version": "1.1a1"
},
"kwargs": {
"bsse_type": "cp"
}
}
"""
# Set a few variables
json_data["error"] = ""
json_data["raw_output"] = "Output storing was not requested."
json_data["success"] = False
json_data["raw_output"] = None
# Check input
for check in ["driver", "method", "molecule"]:
if check not in list(json_data):
json_data["error"] = "Minimum input requires the %s field." % check
return json_data
# Check driver call
if json_data["driver"] not in list(methods_dict):
json_data["error"] = "Driver parameters '%s' not recognized" % str(json_data["driver"])
return json_data
# Set scratch
if "scratch_location" in list(json_data):
psi4_io = core.IOManager.shared_object()
psi4_io.set_default_path(json_data["scratch_location"])
# Set memory
if "memory" in list(json_data):
psi4.core.set_memory(int(json_data["memory"]))
# Do we return the output?
return_output = json_data.pop("return_output", False)
if return_output:
outfile = str(uuid.uuid4()) + ".json_out"
core.set_output_file(outfile, False)
json_data["raw_output"] = "Not yet run."
try:
# Set options
if "options" in json_data.keys() and (json_data["options"] is not None):
for k, v in json_data["options"].items():
core.set_global_option(k, v)
# Rework args
args = json_data["method"]
if not isinstance(args, (list, tuple)):
args = [args]
# Deep copy kwargs
if "kwargs" in list(json_data):
kwargs = copy.deepcopy(json_data["kwargs"])
else:
kwargs = {}
kwargs["molecule"] = molutil.geometry(json_data["molecule"])
# Full driver call
kwargs["return_wfn"] = True
val, wfn = methods_dict[json_data["driver"]](*args, **kwargs)
if isinstance(val, (float)):
json_data["return_value"] = val
elif isinstance(val, (core.Matrix, core.Vector)):
json_data["return_value"] = val.to_serial()
else:
json_data["error"] += "Unrecognized return value of type %s\n" % type(val)
json_data["return_value"] = val
json_data["variables"] = core.get_variables()
json_data["success"] = True
prov = {}
prov["version"] = psi4.__version__
prov["routine"] = "psi4.run_json"
prov["creator"] = "Psi4"
json_data["provenance"] = prov
except Exception as error:
json_data["error"] += repr(error)
json_data["success"] = False
if return_output:
with open(outfile, 'r') as f:
json_data["raw_output"] = f.read()
os.unlink(outfile)
return json_data
def compute(self, client: Optional["FractalClient"] = None):
"""Run quantum chemistry."""
from psi4.driver import pp
if self.computed:
return
if client:
self.computed = True
from qcportal.models import KeywordSet, Molecule
# Build the keywords
keyword_id = client.add_keywords(
[KeywordSet(values=self.keywords)])[0]
# Build the molecule
mol = Molecule(**self.molecule.to_schema(dtype=2))
r = client.add_compute("psi4", self.method, self.basis,
self.driver, keyword_id, [mol])
self.result_id = r.ids[0]
# NOTE: The following will re-run errored jobs by default
if self.result_id in r.existing:
ret = client.query_tasks(base_result=self.result_id)
if ret:
if ret[0].status == "ERROR":
client.modify_tasks("restart",
base_result=self.result_id)
logger.info("Resubmitting Errored Job {}".format(
self.result_id))
elif ret[0].status == "COMPLETE":
logger.debug("Job already completed {}".format(
self.result_id))
else:
logger.debug("Job already completed {}".format(
self.result_id))
else:
logger.debug("Submitting AtomicResult {}".format(
self.result_id))
return
logger.info(
f'<<< JSON launch ... {self.molecule.schoenflies_symbol()} {self.molecule.nuclear_repulsion_energy()}'
)
gof = core.get_output_file()
# EITHER ...
# from psi4.driver import schema_wrapper
# self.result = schema_wrapper.run_qcschema(self.plan())
# ... OR ...
self.result = qcng.compute(
self.plan(),
"psi4",
raise_error=True,
# local_options below suitable for serial mode where each job takes all the resources of the parent Psi4 job.
# distributed runs through QCFractal will likely need a different setup.
local_options={
# B -> GiB
"memory": core.get_memory() / (2**30),
"ncores": core.get_num_threads(),
},
)
# ... END
#pp.pprint(self.result.dict())
#print("... JSON returns >>>")
core.set_output_file(gof, True)
core.reopen_outfile()
logger.debug(pp.pformat(self.result.dict()))
core.print_out(_drink_filter(self.result.dict()["stdout"]))
self.computed = True
def run_json(json_data):
"""
Runs and updates the input JSON data.
Parameters
----------
json_data : JSON input
Required input fields:
- molecule : str
A string representation of the molecule. Any valid psi4 synatx is valid.
- driver : str
The driver method to use valid arguments are "energy", "gradient", "property"
- args : str
Input arguments to the driver function
- kwargs : dict
Input dictionary to the driver function
Optional input fields:
- kwargs : dict
Additional kwargs to be passed to the driver.
- options : dict
Global options to set in the Psi4 run.
- scratch_location : str
Overide the default scratch location.
- return_output : bool
Return the full string reprsentation of the output or not.
Output fields:
- return_value : float, psi4.core.Vector, psi4.core.Matrix
The return value of the input function.
- variables : dict
The list of Psi4 variables generated from the run.
- success : bool
Indicates if the run was successful or not.
- error : str
If an error is raised the result is returned here.
- output : str
The full Psi4 output if requested.
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/psi4/psi4.
Examples
--------
# CP corrected Helium dimer energy in the STO-3G basis.
>>> json_data = {}
>>> json_data["molecule"] = "He 0 0 0\n--\nHe 0 0 1"
>>> json_data["driver"] = "energy"
>>> json_data["args"] = 'SCF'
>>> json_data["kwargs"] = {"bsse_type": "cp"}
>>> json_data["options"] = {"BASIS": "STO-3G"}
>>> run_json(json_data)
{'status': 'finished', 'success': True, 'kwargs': {'bsse_type': 'cp'},
'molecule': 'He 0 0 0\n--\nHe 0 0 1', 'variables': {u'CURRENT REFERENCE
ENERGY': -5.433191881443323, u'HF TOTAL ENERGY': -5.433191881443323, u'CURRENT
DIPOLE Z': 0.0, u'COUNTERPOISE CORRECTED INTERACTION ENERGY':
0.1839360538612116, u'CURRENT DIPOLE X': 0.0, u'CURRENT DIPOLE Y': 0.0,
u'NUCLEAR REPULSION ENERGY': 2.11670883436, u'TWO-ELECTRON ENERGY':
4.124089347186247, u'SCF ITERATION ENERGY': -5.433191881443323, u'CP-CORRECTED
2-BODY INTERACTION ENERGY': 0.1839360538612116, u'SCF DIPOLE Y': 0.0,
u'COUNTERPOISE CORRECTED TOTAL ENERGY': -5.433191881443323, u'CURRENT ENERGY':
0.1839360538612116, u'SCF TOTAL ENERGY': -5.433191881443323, u'SCF DIPOLE Z':
0.0, u'ONE-ELECTRON ENERGY': -11.67399006298957, u'SCF DIPOLE X': 0.0}, 'args':
'SCF', 'driver': 'energy', 'return_value': 0.1839360538612116, 'error': '',
'output': '', 'options': {'BASIS': 'STO-3G'}}
"""
# Set a few variables
json_data["error"] = ""
json_data["output"] = ""
# Check input
for check in ["driver", "args", "molecule"]:
if check not in list(json_data):
json_data["error"] = "Minimum input requires the %s field." % check
return False
if json_data["driver"] not in list(methods_dict):
json_data["error"] = "Driver parameters '%s' not recognized" % str(
json_data["driver"])
return False
if "scratch_location" in list(json_data):
psi4_io = core.IOManager.shared_object()
psi4_io.set_default_path(json_data["scratch_location"])
# Do we return the output?
return_output = json_data.pop("return_output", False)
if return_output:
outfile = str(uuid.uuid4()) + ".json_out"
core.set_output_file(outfile, False)
json_data["output"] = "Not yet run."
try:
# Set options
if "options" in json_data.keys() and (json_data["options"]
is not None):
for k, v in json_data["options"].items():
core.set_global_option(k, v)
# Rework args
args = json_data["args"]
if not isinstance(args, (list, tuple)):
args = [args]
# Deep copy kwargs
if "kwargs" in list(json_data):
kwargs = copy.deepcopy(json_data["kwargs"])
kwargs["molecule"] = molutil.geometry(json_data["molecule"])
else:
kwargs = {}
# Full driver call
kwargs["return_wfn"] = True
val, wfn = methods_dict[json_data["driver"]](*args, **kwargs)
if isinstance(val, (float)):
json_data["return_value"] = val
elif isinstance(val, (core.Matrix, core.Vector)):
json_data["return_value"] = val.to_serial()
else:
json_data[
"error"] += "Unrecognized return value of type %s\n" % type(
val)
json_data["return_value"] = val
json_data["variables"] = core.get_variables()
json_data["success"] = True
except Exception as error:
json_data["error"] += repr(error)
json_data["success"] = False
if return_output:
with open(outfile, 'r') as f:
json_data["output"] = f.read()
os.unlink(outfile)
return json_data
def run_psi4(self):
core.set_output_file(self.output + '.dat')
import psi4
psi4.set_memory('1 GB')
psi_molecule = psi4.geometry(self.psi_geom)
psi4.set_options({
'basis': self.basis,
'molden_write': False,
'WRITER_FILE_LABEL': str(self.output) + '.dat',
'maxiter': 500,
'fail_on_maxiter': False
})
if self.multiplicity != 1:
psi4.set_options({'reference': 'ROHF'})
e, wfn = psi4.energy('scf', return_wfn=True)
self.molecule.hf_energy = e
if os.path.exists('./scr.molden'):
os.system('rm scr.molden')
if self.active != None:
cb = wfn.Cb().to_array()
ca = wfn.Ca().to_array()
self.molecule.n_orbitals = len(ca)
ca[:, self.active + self.reorder] = ca[:,
self.reorder + self.active]
cb[:, self.active + self.reorder] = cb[:,
self.reorder + self.active]
if self.loc == 'True':
acs = psi4.core.Matrix('null')
acs = acs.from_array(ca[:, self.active])
Local = psi4.core.Localizer.build("BOYS", wfn.basisset(), acs)
Local.localize()
acs = Local.L
ca[:, self.active] = acs
acs2 = psi4.core.Matrix('null2')
acs2 = acs2.from_array(cb[:, self.active])
Local = psi4.core.Localizer.build("BOYS", wfn.basisset(), acs2)
Local.localize()
acs2 = Local.L
cb[:, self.active] = acs2
ca = psi4.core.Matrix.from_array(ca)
cb = psi4.core.Matrix.from_array(cb)
wfn.Cb().copy(cb)
wfn.Ca().copy(ca)
psi4.molden(wfn, 'scr.molden')
psi4.set_options({'frozen_docc': [self.n_fdoccs]})
self.n_fnoccs = self.molecule.n_orbitals - self.n_fdoccs - len(
self.active)
psi4.set_options({'frozen_uocc': [self.n_fnoccs]})
self.CASCI = psi4.energy('fci', ref_wfn=wfn)
self.molecule.CASCI = self.CASCI
self.fci_energy = self.CASCI
self.molecule.fci_energy = self.CASCI
else:
self.CASCI = psi4.energy('fci', ref_wfn=wfn)
self.molecule.CASCI = self.CASCI
self.fci_energy = self.CASCI
self.molecule.fci_energy = self.CASCI
self.molecule.n_orbitals = len(wfn.Ca().to_array())
psi4.molden(wfn, 'scr.molden')
self.molecule.nuclear_repulsion = psi_molecule.nuclear_repulsion_energy(
)
self.molecule.canonical_orbitals = np.asarray(wfn.Ca())
if self.active == None:
self.active = [i for i in range(0, self.molecule.n_orbitals)]
self.molecule.overlap_integrals = np.asarray(wfn.S())
self.molecule.n_qubits = 2 * self.molecule.n_orbitals
self.molecule.orbital_energies = np.asarray(wfn.epsilon_a())
self.molecule.fock_matrix = np.asarray(wfn.Fa())
mints = psi4.core.MintsHelper(wfn.basisset())
self.molecule.one_body_integrals = general_basis_change(
np.asarray(mints.ao_kinetic()), self.molecule.canonical_orbitals,
(1, 0))
self.molecule.one_body_integrals += general_basis_change(
np.asarray(mints.ao_potential()), self.molecule.canonical_orbitals,
(1, 0))
two_body_integrals = np.asarray(mints.ao_eri())
two_body_integrals.reshape(
(self.molecule.n_orbitals, self.molecule.n_orbitals,
self.molecule.n_orbitals, self.molecule.n_orbitals))
two_body_integrals = np.einsum('psqr', two_body_integrals)
two_body_integrals = general_basis_change(
two_body_integrals, self.molecule.canonical_orbitals, (1, 1, 0, 0))
self.molecule.two_body_integrals = two_body_integrals
doccs = [i for i in range(0, self.n_fdoccs)]
if self.active != None:
self.molecule.n_orbitals = len(self.active)
self.molecule.n_qubits = 2 * self.molecule.n_orbitals
else:
self.molecule.n_orbitals = len(self.molecule.canonical_orbitals)
self.molecule.n_qubits = 2 * self.molecule.n_orbitals
self.molecule.n_fdoccs = self.n_fdoccs
self.molecule.hamiltonian = self.molecule.get_molecular_hamiltonian(
occupied_indices=doccs, active_indices=self.active)
self.molecule.save()
return self.molecule
def pre_processing(self):
"""
Process local run dictionary to create the input directory and identify
the command to be passed
Returns:
:py:class:`dict`: dictionary containing the command to be passed to
:meth:`process_run`
"""
from psi4 import set_options, energy, optimize, frequency
from psi4.core import set_output_file
from BigDFT.Systems import System
from os.path import join
# Check Arguments
try:
self.sys = self.run_options["sys"]
except KeyError:
raise ValueError("sys= must be provided as an argument")
try:
action = self.run_options["action"]
except KeyError:
raise ValueError("You must specify a valid action=(energy,"
" optimize, frequency")
try:
method = self.run_options["method"]
except KeyError:
raise ValueError("You must specify an ab initio method=")
try:
basis = self.run_options["basis"]
except KeyError:
raise ValueError("You must specify a basis=")
# Run directory
self._ensure_run_directory()
# Check skip
if self.run_options["skip"]:
try:
log = PSI4Logfile(self.sys, self._get_logname(True),
action, method)
return {"command": None}
except ValueError: # invalid logfile, so we can't skip.
pass
except IOError: # no logfile, so we can't skip.
pass
# Convert system
if "sapt" in method:
keys = list(self.sys)
if len(keys) != 2:
raise ValueError("For SAPT method, your system must be"
" composed of exactly two fragments.")
sysA = System()
sysA[keys[0]] = self.sys[keys[0]]
sysB = System()
sysB[keys[1]] = self.sys[keys[1]]
mol = bigdft_to_psi4(sysA=sysA, sysB=sysB)
else:
mol = bigdft_to_psi4(sysA=self.sys)
# Set extra options.
if "psi4_options" in self.run_options:
set_options(self.run_options["psi4_options"])
set_output_file(self._get_logname(True), False)
# Instead of a command, we return a closure.
if action == "energy":
def cmd(method, mol):
energy(method, molecule=mol)
elif action == "optimize":
def cmd(method, mol):
optimize(method, molecule=mol)
elif action == "frequency":
def cmd(method, mol):
frequency(method, molecule=mol)
return {"command": cmd(join(method, basis), mol)}