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Use Bohr in gcp #438

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Use Bohr in gcp #438

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ad743d2
Update gcp.py
loriab Dec 1, 2023
53ce45b
fix canonical and qcel
loriab Dec 1, 2023
6390ac8
legacy dftd3, too
loriab Dec 1, 2023
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4 changes: 2 additions & 2 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -131,10 +131,10 @@ jobs:
qcore --accept-license

- name: Special Config - QCElemental Dep
if: false
if: true
run: |
conda remove qcelemental --force
python -m pip install 'git+https://github.com/MolSSI/QCElemental.git@loriab-patch-2' --no-deps
python -m pip install 'git+https://github.com/loriab/QCElemental.git@ghostformat' --no-deps

# note: conda remove --force, not mamba remove --force b/c https://github.com/mamba-org/mamba/issues/412
# alt. is micromamba but not yet ready for setup-miniconda https://github.com/conda-incubator/setup-miniconda/issues/75
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6 changes: 3 additions & 3 deletions qcengine/programs/dftd3.py
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Expand Up @@ -77,7 +77,7 @@ def compute(self, input_model: "AtomicInput", config: "TaskConfig") -> "AtomicRe
dexe["outfiles"]["stdout"] = dexe["stdout"]
dexe["outfiles"]["stderr"] = dexe["stderr"]
dexe["outfiles"]["input"] = job_inputs["infiles"][".dftd3par.local"]
dexe["outfiles"]["dftd3_geometry.xyz"] = job_inputs["infiles"]["dftd3_geometry.xyz"]
dexe["outfiles"]["dftd3_geometry.tmol"] = job_inputs["infiles"]["dftd3_geometry.tmol"]
output_model = self.parse_output(dexe["outfiles"], input_model)

else:
Expand Down Expand Up @@ -133,7 +133,7 @@ def build_input(
molrec = qcel.molparse.from_schema(input_model.molecule.dict())
# jobrec['molecule']['real'] = molrec['real']

command = ["dftd3", "dftd3_geometry.xyz"]
command = ["dftd3", "dftd3_geometry.tmol"]
if input_model.driver == "gradient":
command.append("-grad")
if input_model.extras["info"]["dashlevel"] == "atmgr":
Expand All @@ -147,7 +147,7 @@ def build_input(
".dftd3par.local": dftd3_coeff_formatter(
input_model.extras["info"]["dashlevel"], input_model.extras["info"]["dashparams"]
),
"dftd3_geometry.xyz": qcel.molparse.to_string(molrec, dtype="xyz", units="Angstrom", ghost_format=""),
"dftd3_geometry.tmol": qcel.molparse.to_string(molrec, dtype="turbomole", units="Bohr", ghost_format=""),
}

return {
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6 changes: 3 additions & 3 deletions qcengine/programs/gcp.py
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Expand Up @@ -86,7 +86,7 @@ def compute(self, input_model: "AtomicInput", config: "TaskConfig") -> "AtomicRe
dexe["outfiles"]["stdout"] = dexe["stdout"]
dexe["outfiles"]["stderr"] = dexe["stderr"]
dexe["outfiles"]["input"] = " ".join(job_inputs["command"]) # stretch to call this input
dexe["outfiles"]["gcp_geometry.xyz"] = job_inputs["infiles"]["gcp_geometry.xyz"]
dexe["outfiles"]["gcp_geometry.tmol"] = job_inputs["infiles"]["gcp_geometry.tmol"]
output_model = self.parse_output(dexe["outfiles"], input_model)

else:
Expand Down Expand Up @@ -181,13 +181,13 @@ def build_input(

calldash = {"gcp": "-", "mctc-gcp": "--"}[executable]

command = [executable, "gcp_geometry.xyz", calldash + "level", method]
command = [executable, "gcp_geometry.tmol", calldash + "level", method]

if input_model.driver == "gradient":
command.append(calldash + "grad")

infiles = {
"gcp_geometry.xyz": qcel.molparse.to_string(molrec, dtype="xyz", units="Angstrom", ghost_format=""),
"gcp_geometry.tmol": qcel.molparse.to_string(molrec, dtype="turbomole", units="Bohr", ghost_format=""),
}
if method == "FILE":
infiles[".gcppar"] = input_model.extras["parameters"]
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9 changes: 6 additions & 3 deletions qcengine/programs/tests/test_canonical_config.py
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Expand Up @@ -190,10 +190,13 @@ def test_local_options_scratch(program, model, keywords):
# a scratch file (preferrably output) expected after job if scratch not cleaned up
scratch_sample = {
"cfour": "*/NEWFOCK",
"dftd3": "*/dftd3_geometry.xyz", # no outfiles
# "dftd3": "*/dftd3_geometry.xyz", # no outfiles
"dftd3": "*/dftd3_geometry.tmol", # no outfiles
"gamess": "*/gamess.dat",
"gcp": "*/gcp_geometry.xyz", # no outfiles
"mctc-gcp": "*/gcp_geometry.xyz", # no outfiles
# "gcp": "*/gcp_geometry.xyz", # no outfiles
# "mctc-gcp": "*/gcp_geometry.xyz", # no outfiles
"gcp": "*/gcp_geometry.tmol", # no outfiles
"mctc-gcp": "*/gcp_geometry.tmol", # no outfiles
"mp2d": "*/mp2d_geometry", # no outfiles
"nwchem": "*/nwchem.db",
"psi4": "*/psi.*.35",
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9 changes: 6 additions & 3 deletions qcengine/programs/tests/test_canonical_fields.py
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Expand Up @@ -67,10 +67,13 @@ def test_protocol_native(program, model, keywords, native):

all_ref = {
"cfour": ("GRD", rf"1.0+\s+0.0+\s+0.0+\s+0.03"),
"dftd3": ("dftd3_geometry.xyz", rf"H\s+0.0+\s+0.0+\s+0.34"),
# "dftd3": ("dftd3_geometry.xyz", rf"H\s+0.0+\s+0.0+\s+0.34"),
"dftd3": ("dftd3_geometry.tmol", rf"\s+0.0+\s+0.0+\s+0.650+\s+h"),
"gamess": ("gamess.dat", rf"CLOSED SHELL ORBITALS --- GENERATED AT"),
"gcp": ("gcp_geometry.xyz", rf"H\s+0.0+\s+0.0+\s+0.34"),
"mctc-gcp": ("gcp_geometry.xyz", rf"H\s+0.0+\s+0.0+\s+0.34"),
# "gcp": ("gcp_geometry.tmol", rf"H\s+0.0+\s+0.0+\s+0.34"),
# "mctc-gcp": ("gcp_geometry.tmol", rf"H\s+0.0+\s+0.0+\s+0.34"),
"gcp": ("gcp_geometry.tmol", rf"\s+0.0+\s+0.0+\s+0.650+\s+h"),
"mctc-gcp": ("gcp_geometry.tmol", rf"\s+0.0+\s+0.0+\s+0.650+\s+h"),
"mp2d": ("mp2d_geometry", rf"H\s+0.0+\s+0.0+\s+0.34"),
"nwchem": ("nwchem.grad", rf"0.0, 0.0, 0.03"),
"psi4": ("psi4.grad", rf"1.0+\s+(-?)0.0+\s+(-?)0.0+\s+0.03"),
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