diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 25b331cf..f2513f3e 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -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 diff --git a/qcengine/programs/dftd3.py b/qcengine/programs/dftd3.py index 2f67fcfe..67726f7c 100644 --- a/qcengine/programs/dftd3.py +++ b/qcengine/programs/dftd3.py @@ -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: @@ -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": @@ -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 { diff --git a/qcengine/programs/gcp.py b/qcengine/programs/gcp.py index 368f8252..887dd06d 100644 --- a/qcengine/programs/gcp.py +++ b/qcengine/programs/gcp.py @@ -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: @@ -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"] diff --git a/qcengine/programs/tests/test_canonical_config.py b/qcengine/programs/tests/test_canonical_config.py index 72023850..b22c3d98 100644 --- a/qcengine/programs/tests/test_canonical_config.py +++ b/qcengine/programs/tests/test_canonical_config.py @@ -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", diff --git a/qcengine/programs/tests/test_canonical_fields.py b/qcengine/programs/tests/test_canonical_fields.py index ba4f809b..271525d0 100644 --- a/qcengine/programs/tests/test_canonical_fields.py +++ b/qcengine/programs/tests/test_canonical_fields.py @@ -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"),