def test_fig2a_txt(qcprog):
"""
Execution (a; txt)
cp infile . && xcfour > outfile
rungms infile > outfile
nwchem infile > outfile
psi4 infile outfile
"""
sin = _fig2_ins[qcprog]["a"]
from qcelemental.util import which
from qcengine.util import execute
if qcprog == "cfour":
success, dexe = execute([which("xcfour")], {"ZMAT": sin})
if qcprog == "gamess":
success, dexe = execute([which("rungms"), "input"], {"input.inp": sin})
if qcprog == "nwchem":
success, dexe = execute([which("nwchem"), "input"], {"input": sin})
if qcprog == "psi4":
success, dexe = execute([which("psi4"), "input", "-o", "stdout"],
{"input": sin})
pprint.pprint(dexe, width=180)
assert success
assert _the_short_fig2_energy in dexe["stdout"]
def execute(
self,
inputs: Dict[str, Any],
extra_outfiles: Optional[List[str]] = None,
extra_commands: Optional[List[str]] = None,
scratch_name: Optional[str] = None,
timeout: Optional[int] = None,
) -> Tuple[bool, Dict[str, Any]]:
"""
Run the gaussian single point job and fchk conversion
"""
# collect together inputs
infiles = inputs["infiles"]
outfiles = ["gaussian.log", "lig.chk"]
if extra_outfiles is not None:
outfiles.extend(extra_outfiles)
gaussian_version = self.get_version()
commands = [gaussian_version, "gaussian.com"]
scratch_directory = inputs["scratch_directory"]
# remember before formatting lig.chk is binary, run calculation
exe_success, proc = execute(
command=commands,
infiles=infiles,
outfiles=outfiles,
scratch_directory=scratch_directory,
as_binary=["lig.chk"],
)
if exe_success:
# now we need to run the conversion of the chk file
commands = ["formchk", "lig.chk", "lig.fchk"]
infiles = {"lig.chk": proc["outfiles"]["lig.chk"]}
chk_success, proc_chk = execute(
command=commands,
infiles=infiles,
outfiles=["lig.fchk"],
scratch_directory=scratch_directory,
as_binary=["lig.chk"],
)
# now we want to put this out file into the main proc
proc["outfiles"]["lig.fchk"] = proc_chk["outfiles"]["lig.fchk"]
# we can dump the chk file
del proc["outfiles"]["lig.chk"]
return exe_success, proc
def execute(self, inputs, extra_outfiles=None, extra_commands=None, scratch_name=None, timeout=None):
exe_success, proc = uti.execute(inputs["commands"],
infiles = inputs["infiles"],
outfiles = ["tc.out"],
scratch_location = inputs["scratch_location"],
timeout = timeout
)
proc["outfiles"]["tc.out"] = proc["stdout"]
return exe_success, proc
def ctest_runner(inputdatloc,
extra_infiles: List = None,
outfiles: List = None):
"""Called from a mock PyTest function, this takes a full path ``inputdatloc`` to an ``"input.dat"`` file set up for
CTest and submits it to the ``psi4`` executable. Any auxiliary files with names listed in ``extra_infiles`` that reside
alongside ``inputdatloc`` are placed in the Psi4 execution directory.
"""
from qcengine.util import execute
import psi4
# Pass runtime env through to `execute`
# * appending Psi4 import path (after all, it worked previous line) since partial/relative paths not robust
psiimport = Path(psi4.__file__).parent.parent
env = os.environ.copy()
if "PYTHONPATH" in env:
env["PYTHONPATH"] += os.pathsep + str(psiimport)
else:
env["PYTHONPATH"] = str(psiimport)
ctestdir = Path(inputdatloc).resolve().parent
if (ctestdir / "input.dat").exists():
inputdat = "input.dat"
elif (ctestdir / "input.py").exists():
inputdat = "input.py"
infiles = [inputdat]
if extra_infiles:
infiles.extend(extra_infiles)
infiles_with_contents = {(Path(fl).name if Path(fl).is_absolute() else fl):
(ctestdir / fl).read_text()
for fl in infiles}
# Note: The simple `command = ["psi4", "input.dat"]` works fine for Linux and Mac but not for Windows.
# L/M/W ok with `command = [which("psi4"), "input.dat"]` where `which` on Windows finds the psi4.bat file that points to the psi4 python script. -or-
# L/M/W ok with `command = [sys.executable, psi4.executable, "input.dat"]` aka `python /full/path/bin/psi4 input.dat`.
# Latter chosen as `psi4.executable` is path computed by `import psi4`, so assured correspondence.
# Note: The input.py in json/, python/, and psi4numpy/ are not being treated best.
# Properly, as in CTest, it's `command = [sys.executable, "input.py"]`.
# Have to either have 3-item `command` or pass PYTHONPATH through env. Since some tests (fsapt) "import psi4" internally, doing both.
# The "exe" rerouting is for Windows conda package Scripts/psi4.exe file. It gives an encoding error if Python in command.
# * Toggle `scratch_messy` to examine scratch contents.
if Path(psi4.executable).suffix == ".exe":
command = [psi4.executable, inputdat]
else:
command = [sys.executable, psi4.executable, inputdat]
_, output = execute(command,
infiles_with_contents,
outfiles,
environment=env,
scratch_messy=False)
success = output["proc"].poll() == 0
assert success, output["stdout"] + output["stderr"]
def execute(self, inputs, extra_outfiles=None, extra_commands=None, scratch_name=None, timeout=None):
binaries = []
for filename in extra_outfiles:
if filename in ['scr/ca0', 'scr/cb0','scr/c0']:
binaries.append(filename)
exe_success, proc = uti.execute(inputs["commands"],
infiles = inputs["infiles"],
outfiles = extra_outfiles,
as_binary = binaries,
scratch_directory=inputs["scratch_directory"],
timeout = timeout
)
proc["outfiles"]["tc.out"] = proc["stdout"]
return exe_success, proc