def found(raise_error: bool = False) -> bool:
"""Whether adcc harness is ready for operation.
Parameters
----------
raise_error: bool
Passed on to control negative return between False and ModuleNotFoundError raised.
Returns
-------
bool
If adcc and psi4 are found, returns True.
If raise_error is False and adcc or psi4 is missing, returns False.
If raise_error is True and adcc or psi4 are missing, the error message is raised.
"""
found_adcc = which_import(
"adcc",
return_bool=True,
raise_error=raise_error,
raise_msg="Please install via `conda install adcc -c adcc`.",
)
found_psi4 = which_import(
"psi4",
return_bool=True,
raise_error=raise_error,
raise_msg=
"Please install psi4 for adcc harness via `conda install psi4 -c psi4`.",
)
return found_adcc and found_psi4
def found(raise_error: bool = False) -> bool:
# this harness requires RDKit as well, so this needs checking too
rdkit_found = RDKitHarness.found(raise_error=raise_error)
openff_found = which_import(
"openforcefield",
return_bool=True,
raise_error=raise_error,
raise_msg=
"Please install via `conda install openforcefield -c omnia`.",
)
openmm_found = which_import(
".openmm",
return_bool=True,
raise_error=raise_error,
package="simtk",
raise_msg="Please install via `conda install openmm -c omnia`.",
)
openmmff_found = which_import(
".generators",
return_bool=True,
raise_error=raise_error,
package="openmmforcefields",
raise_msg=
"Please install via `conda install openmmforcefields -c conda-forge`",
)
return rdkit_found and openff_found and openmm_found and openmmff_found
def found(raise_error: bool = False) -> bool:
psithon = which("psi4", return_bool=True)
psiapi = which_import("psi4", return_bool=True)
if psithon and not psiapi:
with popen([which("psi4"), "--module"]) as exc:
exc["proc"].wait(timeout=30)
if "module does not exist" in exc["stderr"]:
pass
else:
sys.path.append(exc["stdout"].split()[-1])
if psiapi and not psithon:
psiimport = str(Path(which_import("psi4")).parent.parent)
env = os.environ.copy()
env["PYTHONPATH"] = psiimport
with popen(
["python", "-c", "import psi4; print(psi4.executable[:-5])"],
popen_kwargs={"env": env}) as exc:
exc["proc"].wait(timeout=30)
os.environ["PATH"] += os.pathsep + exc["stdout"].split()[-1]
if psithon or psiapi:
return True
return which(
"psi4",
return_bool=True,
raise_error=raise_error,
raise_msg="Please install via `conda install psi4 -c psi4`.",
)
def is_available(cls) -> bool:
"""
Check if any of the requested backend toolkits can be used.
"""
if len(cls._toolkits) == 1:
# the package needs a specific toolkit so raise the error
raise_error = True
else:
raise_error = False
for toolkit in cls._toolkits:
if toolkit == "openeye":
oe = which_import(
".oechem",
package="openeye",
return_bool=True,
raise_error=raise_error,
raise_msg="Please install via `conda install openeye-toolkits -c openeye`.",
)
if oe:
return True
elif toolkit == "rdkit":
rdkit = which_import(
"rdkit",
return_bool=True,
raise_error=raise_error,
raise_msg="Please install via `conda install rdkit -c conda-forge`.",
)
if rdkit:
return True
# if we are here both toolkits are missing
raise ModuleNotFoundError(
f"Openeye or RDKit is required to use this component please install via `conda install openeye-toolkits -c openeye` or `conda install rdkit -c conda-forge`."
)
def is_available(cls) -> bool:
"""
Make sure geometric and torsiondrive are installed.
"""
geo = which_import(
"geometric",
return_bool=True,
raise_error=True,
raise_msg=
"Please install via `conda install geometric -c conda-forge`.",
)
tdrive = which_import(
"torsiondrive",
return_bool=True,
raise_error=True,
raise_msg=
"Please install via `conda install torsiondrive -c conda-forge`.",
)
engine = which_import(
"qcengine",
return_bool=True,
raise_error=True,
raise_msg=
"Please install via `conda install qcengine -c conda-forge`.",
)
return geo and tdrive and engine
def load_options(options):
"""Initialize program options defaults onto `options`."""
load_qcdb_defaults(options)
if which('xcfour') and which_import('psi4'):
load_cfour_defaults_from_psi4(options)
if which('nwchem'):
load_nwchem_defaults(options)
if which('rungms'):
load_gamess_defaults(options)
if which('psi4') and which_import('psi4'):
load_psi4_defaults(options)
if which_import('resp'):
resp.load_defaults(nu_options)
def template_helper(*args):
"""
Store the _kind of object_ we want to I/O and _its dimensions_.
But in practice, given one piece of information, we can deduce the other.
If there's one dimension, it must be a Vector.
If there are two dimensions, it must be written to disk as a Matrix.
If it's a BlockedTensor, we can just read the dimensions.
"""
template = []
for arg in args:
if isinstance(arg, core.Vector):
template.append([arg.dimpi()])
elif isinstance(arg, (core.Matrix, core.dpdfile2, core.dpdbuf4)):
template.append([arg.rowdim(), arg.coldim()])
elif isinstance(arg, float):
template.append(float(0))
elif which_import("ambit", return_bool=True):
import ambit
if isinstance(arg, ambit.BlockedTensor):
template.append(ambit.BlockedTensor)
else:
raise TypeError("Unrecognized object type for DIIS.")
else:
raise TypeError("Unrecognized object type for DIIS.")
return template
def found(raise_error: bool = False) -> bool:
return which_import(
"torchani",
return_bool=True,
raise_error=raise_error,
raise_msg="Please install via `pip install torchani`.",
)
def copier(self, x, new_name: str):
""" Copy the object x and give it a new_name. Save it to disk if needed. """
if isinstance(x, (core.Matrix, core.Vector)):
copy = x.clone()
elif isinstance(x, (core.dpdbuf4, core.dpdfile2)):
copy = core.Matrix(x)
elif isinstance(x, float):
# Never cache a _number_.
return x
elif which_import("ambit", return_bool=True):
import ambit
if isinstance(x, ambit.BlockedTensor):
copy = x.clone()
else:
raise TypeError("Unrecognized object type for DIIS.")
else:
raise TypeError("Unrecognized object type for DIIS.")
copy.name = new_name
if self.storage_policy == StoragePolicy.OnDisk:
psio = core.IO.shared_object()
if isinstance(copy, core.Vector):
copy.save(psio, psif.PSIF_LIBDIIS)
elif isinstance(copy, core.Matrix):
copy.save(psio, psif.PSIF_LIBDIIS, core.SaveType.SubBlocks)
elif isinstance(copy, ambit.BlockedTensor):
filename = f"libdiis.{copy.name}"
copy.save(filename)
self.created_files.add(filename)
else:
raise TypeError("Unrecognized object type for DIIS. This shouldn't be possible.")
copy = None
return copy
def load_program_options(options: Keywords) -> None:
"""Initialize program keywords with defaults onto `options`."""
load_qcdb_keywords(options)
if which("xcfour"):
load_cfour_keywords(options)
if which("nwchem"):
load_nwchem_keywords(options)
if which("rungms"):
load_gamess_keywords(options)
if which("psi4") and which_import("psi4"):
load_psi4_keywords(options)
if which_import("resp_qcdb"):
pass
resp.load_keywords(nu_options)
def found(raise_error: bool=False) -> bool:
is_found = which_import("torchani", return_bool=True)
if not is_found and raise_error:
raise ModuleNotFoundError("Could not find 'torchani' in the Python path. Please 'pip install torchani'.")
return is_found
def found(self, raise_error: bool = False) -> bool:
return which_import(
'geometric',
return_bool=True,
raise_error=raise_error,
raise_msg=
'Please install via `conda install geometric -c conda-forge`.')
def found(raise_error: bool = False) -> bool:
return which_import(
"rdkit",
return_bool=True,
raise_error=raise_error,
raise_msg="Please install via `conda install rdkit -c conda-forge`.",
)
def test_mbis_available():
"""MBIS should always be available with the latest version of psi4."""
if which_import("psi4", return_bool=True, raise_error=False):
assert MBISCharges.is_available() is True
else:
with pytest.raises(ModuleNotFoundError):
MBISCharges.is_available()
def load_quantity(self, name, entry_num, item_num, force_new = True):
""" Load quantity from wherever it's stored, constructing a new object if needed. """
template_object = self.template[name][item_num]
if isinstance(template_object, float) or self.storage_policy == StoragePolicy.InCore:
quantity = self.stored_vectors[entry_num][name][item_num]
try:
quantity = quantity.clone()
except AttributeError:
# The quantity must have been a float. No need to clone.
pass
elif self.storage_policy == StoragePolicy.OnDisk:
full_name = self.get_name(name, entry_num, item_num)
psio = core.IO.shared_object()
if hasattr(template_object, "__len__"):
# Looks like we have dimensions.
if len(template_object) == 2:
quantity = core.Matrix(full_name, *template_object)
quantity.load(psio, psif.PSIF_LIBDIIS, core.SaveType.SubBlocks)
elif len(template_object) == 1:
quantity = core.Vector(full_name, *template_object)
quantity.load(psio, psif.PSIF_LIBDIIS)
elif which_import("ambit", return_bool=True):
import ambit
if template_object == ambit.BlockedTensor:
quantity = ambit.BlockedTensor.load_and_build(f"libdiis.{full_name}")
else:
raise Exception(f"StoragePolicy {self.storage_policy} not recognized. This is a bug: contact developers.")
return quantity
def found(raise_error: bool = False) -> bool:
"""Whether NWChem harness is ready for operation, with both the QC program and any particular dependencies found.
Parameters
----------
raise_error: bool
Passed on to control negative return between False and ModuleNotFoundError raised.
Returns
-------
bool
If both nwchem and its harness dependency networkx are found, returns True.
If raise_error is False and nwchem or networkx are missing, returns False.
If raise_error is True and nwchem or networkx are missing, the error message for the first missing one is raised.
"""
qc = which(
"nwchem",
return_bool=True,
raise_error=raise_error,
raise_msg=
"Please install via http://www.nwchem-sw.org/index.php/Download",
)
dep = which_import(
"networkx",
return_bool=True,
raise_error=raise_error,
raise_msg=
"For NWChem harness, please install via `conda install networkx -c conda-forge`.",
)
return qc and dep
def found(self, raise_error: bool = False) -> bool:
return which_import(
"berny",
return_bool=True,
raise_error=raise_error,
raise_msg="Please install via `pip install pyberny`.",
)
def found(raise_error: bool = False) -> bool:
"""Whether Psi4 harness is ready for operation.
Parameters
----------
raise_error: bool
Passed on to control negative return between False and ModuleNotFoundError raised.
Returns
-------
bool
If psi4 (psithon or psiapi) is found, returns True.
If raise_error is False and psi4 is missing, returns False.
If raise_error is True and psi4 is missing, the error message is raised.
"""
psithon = which("psi4", return_bool=True)
psiapi = which_import("psi4", return_bool=True)
if psithon and not psiapi:
with popen([which("psi4"), "--module"]) as exc:
exc["proc"].wait(timeout=30)
if "module does not exist" in exc["stderr"]:
pass # --module argument only in Psi4 DDD branch
else:
sys.path.append(exc["stdout"].split()[-1])
if psiapi and not psithon:
psiimport = str(Path(which_import("psi4")).parent.parent)
env = os.environ.copy()
env["PYTHONPATH"] = psiimport
with popen(
["python", "-c", "import psi4; print(psi4.executable[:-5])"],
popen_kwargs={"env": env}) as exc:
exc["proc"].wait(timeout=30)
os.environ["PATH"] += os.pathsep + exc["stdout"].split()[-1]
if psithon or psiapi:
return True
return which(
"psi4",
return_bool=True,
raise_error=raise_error,
raise_msg=
"Please install via `conda install psi4 -c psi4`. Check it's in your PATH with `which psi4`.",
)
def is_available(cls) -> bool:
qforce = which_import(
"qforce",
return_bool=True,
raise_error=True,
raise_msg="Please install via `pip install qforce`.",
)
return qforce
def found(self, raise_error: bool = False) -> bool:
return which_import(
"torsiondrive",
return_bool=True,
raise_error=raise_error,
raise_msg=
"Please install via `conda install torsiondrive -c conda-forge`.",
)
def is_available(cls) -> bool:
off = which_import(
"openff.toolkit",
return_bool=True,
raise_error=True,
raise_msg="Please install via `conda install openff-toolkit`.",
)
return off
def found(self, raise_error: bool = False) -> bool:
return which_import(
"qcore",
return_bool=True,
raise_error=raise_error,
raise_msg=
"Please install via `conda install py-qcore -c entos -c conda-forge`.",
)
def found(self, raise_error: bool = False) -> bool:
return which_import(
"optking",
return_bool=True,
raise_error=raise_error,
raise_msg=
"Please install via `conda install optking -c psi4/label/dev`.",
)
def is_available(cls) -> bool:
"""Make sure forcebalance can be imported."""
fb = which_import(
"forcebalance",
return_bool=True,
raise_error=True,
raise_msg=
"Please install via `conda install forcebalance -c conda-forge`.",
)
openmm = which_import(
".openmm",
return_bool=True,
raise_error=True,
package="simtk",
raise_msg=
"Please install via `conda install openmm -c conda-forge`.",
)
return fb and openmm
def found(raise_error: bool = False) -> bool:
is_found = which_import("rdkit", return_bool=True)
if not is_found and raise_error:
raise ModuleNotFoundError(
"Could not find 'rdkit' in the Python path. Please 'conda install rdkit -c conda-forge'."
)
return is_found
def found(raise_error: bool = False) -> bool:
"""Check for the availability of the Python API of xtb"""
return which_import(
"xtb",
return_bool=True,
raise_error=raise_error,
raise_msg="Please install via `conda install xtb-python -c conda-forge`.",
)
def get_version(self) -> str:
self.found(raise_error=True)
which_prog = which_import('torchani')
if which_prog not in self.version_cache:
import torchani
self.version_cache[which_prog] = safe_version(torchani.__version__)
return self.version_cache[which_prog]
def found(raise_error: bool = False) -> bool:
"""Check for the availability of the Python API of dftd4"""
return which_import(
"dftd4",
return_bool=True,
raise_error=raise_error,
raise_msg=
"Please install via a dftd4 version with enabled Python API",
)
def get_version(self) -> str:
self.found(raise_error=True)
which_prog = which_import("optking")
if which_prog not in self.version_cache:
import optking
self.version_cache[which_prog] = safe_version(optking.__version__)
return self.version_cache[which_prog]
def get_version(self) -> str:
self.found(raise_error=True)
which_prog = which_import("qcore")
if which_prog not in self.version_cache:
import qcore
self.version_cache[which_prog] = safe_version(qcore.__version__)
return self.version_cache[which_prog]
def is_numpy_new_enough(version_feature_introduced):
if not which_import('numpy', return_bool=True):
return False
import numpy
return parse_version(numpy.version.version) >= parse_version(version_feature_introduced)
def is_psi4_new_enough(version_feature_introduced):
if not which_import('psi4', return_bool=True):
return False
import psi4
return parse_version(psi4.__version__) >= parse_version(version_feature_introduced)
------
ModuleNotFoundError
When `raises_error=True` and command not found.
"""
lenv = (os.pathsep.join([os.path.abspath(x) for x in os.environ.get('PSIPATH', '').split(os.pathsep) if x != '']) +
os.pathsep + os.environ.get('PATH', ''))
return which(command=command, return_bool=return_bool, raise_error=raise_error, raise_msg=raise_msg, env=lenv)
_addons_ = {
"ambit": _CMake_to_Py_boolean("@ENABLE_ambit@"),
"chemps2": _CMake_to_Py_boolean("@ENABLE_CheMPS2@"),
"dkh": _CMake_to_Py_boolean("@ENABLE_dkh@"),
"libefp": which_import("pylibefp", return_bool=True),
"erd": _CMake_to_Py_boolean("@ENABLE_erd@"),
"gdma": _CMake_to_Py_boolean("@ENABLE_gdma@"),
"pcmsolver": _CMake_to_Py_boolean("@ENABLE_PCMSolver@"),
"simint": _CMake_to_Py_boolean("@ENABLE_simint@"),
"dftd3": psi4_which("dftd3", return_bool=True),
"cfour": psi4_which("xcfour", return_bool=True),
"mrcc": psi4_which("dmrcc", return_bool=True),
"gcp": psi4_which("gcp", return_bool=True),
"v2rdm_casscf": which_import("v2rdm_casscf", return_bool=True),
"gpu_dfcc": which_import("gpu_dfcc", return_bool=True),
"forte": which_import("forte", return_bool=True),
"snsmp2": which_import("snsmp2", return_bool=True),
"resp": which_import("resp", return_bool=True),
}
return gpu_dfcc.cudaGetDeviceCount() > 0
else:
try:
ngpu = len(GPUtil.getGPUs())
except FileNotFoundError:
# no `nvidia-smi`
return False
else:
return ngpu > 0
hardware_nvidia_gpu = pytest.mark.skipif(is_nvidia_gpu_present() is False,
reason='Psi4 not detecting Nvidia GPU via `nvidia-smi`. Install one')
using_memory_profiler = pytest.mark.skipif(
which_import('memory_profiler', return_bool=True) is False,
reason='Not detecting module memory_profiler. Install package if necessary and add to envvar PYTHONPATH')
using_psi4 = pytest.mark.skipif(
False, reason='Not detecting module psi4. Install package if necessary and add to envvar PYTHONPATH')
using_qcdb = pytest.mark.skipif(
True, reason='Not detecting common driver. Install package if necessary and add to envvar PYTHONPATH')
using_dftd3 = pytest.mark.skipif(
which('dftd3', return_bool=True) is False,
reason='Not detecting executable dftd3. Install package if necessary and add to envvar PATH or PSIPATH')
using_dftd3_321 = pytest.mark.skipif(is_dftd3_new_enough("3.2.1") is False,
reason='DFTD3 does not include 3.2.1 features. Update package and add to PATH')