Merge remote-tracking branch 'upstream/master' into orca

* upstream/master:
  Qchem: SCF-> Total energy in the final basis set for correctly catching -D, etc.
  Qchem: PR comments
  Testing: Finishes up using conversion on several straglers
  Testing: Applies new using strategy to all files
  Testing: New using strategy
  Psi4: Fixes issue with HF3c execution
  PR comments
  PR comments: parse logfile for fields not available in QCSCR also, fix dipole parsing
  nwc: add hessian file; minor testing updates (#177)
  PR comments: use qcel's NUMBER regex also, blacken and isort
  fix test until next qcel version
  PR comments: added ability to ingest logfile+QCSCR
  Blacken QCEngine
  PR comments: rename input, refactor NUMBER into regex snippet file
  Update QCENGINE_RECORDS_COMMIT
  Update QCENGINE_RECORDS_COMMIT
  Qchem: add tests for log parser for archival data
  Qchem: add log parser for archival data

qcengine/compute.py

@@ -1,20 +1,21 @@
 """
 Integrates the computes together
 """
-from typing import Any, Dict, Optional, Union, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any, Dict, Optional, Union
 
-if TYPE_CHECKING:
- from pydantic.main import BaseModel
- from qcelemental.models import AtomicResult
-
-from qcelemental.models import AtomicInput, FailedOperation, AtomicResult
+from qcelemental.models import AtomicInput, AtomicResult, FailedOperation
 
 from .config import get_config
 from .exceptions import InputError, RandomError
 from .procedures import get_procedure
 from .programs import get_program
 from .util import compute_wrapper, environ_context, handle_output_metadata, model_wrapper
 
+if TYPE_CHECKING:
+ from pydantic.main import BaseModel
+ from qcelemental.models import AtomicResult
+
+
 __all__ = ["compute", "compute_procedure"]
 
 

qcengine/mdi_server.py

@@ -5,7 +5,6 @@
 from typing import Any, Dict, List, Optional
 
 import numpy as np
-
 import qcelemental as qcel
 from qcelemental.util import which_import
 

qcengine/programs/base.py

@@ -13,8 +13,8 @@
 from .mopac import MopacHarness
 from .mp2d import MP2DHarness
 from .nwchem import NWChemHarness
+from .openmm import OpenMMHarness
 from .orca import OrcaHarness
-from .openmm import OpenMMHarness 
 from .psi4 import Psi4Harness
 from .qchem import QChemHarness
 from .rdkit import RDKitHarness

qcengine/programs/cfour/harvester.py

@@ -2,9 +2,9 @@
 from decimal import Decimal
 
 import numpy as np
-
 import qcelemental as qcel
 from qcelemental.models import Molecule
+from qcelemental.molparse import regex
 
 from ..util import PreservingDict, load_hessian
 
@@ -63,7 +63,7 @@ def harvest_outfile_pass(outtext):
  # vcc/ecc
 
  # fmt: off
- NUMBER = "((?:[-+]?\\d*\\.\\d+(?:[DdEe][-+]?\\d+)?)|(?:[-+]?\\d+\\.\\d*(?:[DdEe][-+]?\\d+)?))"
+ NUMBER = r'(?x:' + regex.NUMBER + ')'
 
  # Process version
  mobj = re.search(r'^\s*' + r'Version' + r'\s+' + r'(?P<version>[\w.]+)' + r'\s*$',

qcengine/programs/cfour/runner.py

@@ -7,7 +7,6 @@
 from typing import Any, Dict, Optional, Tuple
 
 import numpy as np
-
 import qcelemental as qcel
 from qcelemental.models import AtomicResult, Provenance
 from qcelemental.util import safe_version, which

qcengine/programs/dftd3.py

@@ -10,7 +10,6 @@
 from typing import Any, Dict, Optional, Tuple
 
 import numpy as np
-
 import qcelemental as qcel
 from qcelemental.models import AtomicResult, FailedOperation, Provenance
 from qcelemental.util import safe_version, which

qcengine/programs/entos.py

@@ -4,11 +4,7 @@
 
 import json
 import string
-from typing import Any, Dict, List, Optional, Set, Tuple, TYPE_CHECKING
-
-if TYPE_CHECKING:
- from ..config import TaskConfig
- from qcelemental.models import AtomicInput
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Set, Tuple
 
 from qcelemental.models import AtomicResult
 from qcelemental.util import parse_version, safe_version, which
@@ -17,6 +13,10 @@
 from ..util import execute, popen
 from .model import ProgramHarness
 
+if TYPE_CHECKING:
+ from ..config import TaskConfig
+ from qcelemental.models import AtomicInput
+
 
 class EntosHarness(ProgramHarness):
  _defaults: Dict[str, Any] = {

qcengine/programs/gamess/harvester.py

@@ -6,9 +6,9 @@
 from decimal import Decimal
 
 import numpy as np
-
 import qcelemental as qcel
 from qcelemental.models import Molecule
+from qcelemental.molparse import regex
 
 from ..util import PreservingDict
 
@@ -71,7 +71,7 @@ def harvest_outfile_pass(outtext):
  qcvar_coord = None
  qcvar_grad = None
 
- NUMBER = "((?:[-+]?\\d*\\.\\d+(?:[DdEe][-+]?\\d+)?)|(?:[-+]?\\d+\\.\\d*(?:[DdEe][-+]?\\d+)?))"
+ NUMBER = r"(?x:" + regex.NUMBER + ")"
 
  # If calculation fail to converge
  mobj = re.search(r"^\s+" + r"(?:GAMESS TERMINATED ABNORMALLY)" + r"\s*$", outtext, re.MULTILINE)

qcengine/programs/gamess/runner.py

@@ -169,20 +169,22 @@ def parse_output(self, outfiles: Dict[str, str], input_model: "AtomicInput") ->
  "TWO-ELECTRON ENERGY": "scf_two_electron_energy",
  "SCF TOTAL ENERGY": "scf_total_energy",
  "MP2 CORRELATION ENERGY": "mp2_correlation_energy",
- 'MP2 TOTAL ENERGY': "mp2_total_energy",
+ "MP2 TOTAL ENERGY": "mp2_total_energy",
  "CCSD CORRELATION ENERGY": "ccsd_correlation_energy",
  "CCSD TOTAL ENERGY": "ccsd_total_energy",
  "CCSD(T) CORRELATION ENERGY": "ccsd_prt_pr_correlation_energy",
- "CCSD(T) TOTAL ENERGY": "ccsd_prt_pr_total_energy"
+ "CCSD(T) TOTAL ENERGY": "ccsd_prt_pr_total_energy",
  }
  for qcvar in qcvars:
  if qcvar in qcvars_to_properties:
- output_data['properties'][qcvars_to_properties[qcvar]] = qcvars[qcvar]
- if {'SCF DIPOLE X', 'SCF DIPOLE Y', 'SCF DIPOLE Z'} & set(qcvars.keys()):
- conv = Decimal(qcel.constants.conversion_factor('debye', 'e * bohr'))
- output_data['properties']['scf_dipole_moment'] = [qcvars['SCF DIPOLE X'] * conv,
- qcvars['SCF DIPOLE Y'] * conv,
- qcvars['SCF DIPOLE Z'] * conv]
+ output_data["properties"][qcvars_to_properties[qcvar]] = qcvars[qcvar]
+ if {"SCF DIPOLE X", "SCF DIPOLE Y", "SCF DIPOLE Z"} & set(qcvars.keys()):
+ conv = Decimal(qcel.constants.conversion_factor("debye", "e * bohr"))
+ output_data["properties"]["scf_dipole_moment"] = [
+ qcvars["SCF DIPOLE X"] * conv,
+ qcvars["SCF DIPOLE Y"] * conv,
+ qcvars["SCF DIPOLE Z"] * conv,
+ ]
  output_data["success"] = True
 
  return AtomicResult(**{**input_model.dict(), **output_data})

qcengine/programs/mp2d.py

@@ -7,7 +7,6 @@
 from typing import Any, Dict, Optional, Tuple
 
 import numpy as np
-
 import qcelemental as qcel
 from qcelemental.models import AtomicResult, Provenance
 from qcelemental.util import safe_version, which

qcengine/programs/nwchem/germinate.py

@@ -3,15 +3,89 @@
 from qcengine.exceptions import InputError
 
 # List of XC functionals known to NWChem
-_xc_functionals = ['acm', 'b3lyp', 'beckehandh', 'pbe0', 'becke97', 'becke97-1', 'becke97-2', 'becke97-3', 'becke97-d',
- 'becke98', 'hcth', 'hcth120', 'hcth147', 'hcth407', 'becke97gga1', 'hcth407p', 'mpw91', 'mpw1k',
- 'xft97', 'cft97', 'ft97', 'op', 'bop', 'pbeop', 'xpkzb99', 'cpkzb99', 'xtpss03', 'ctpss03',
- 'xctpssh', 'b1b95', 'bb1k', 'mpw1b95', 'mpwb1k', 'pw6b95', 'pwb6k', 'm05', 'm05-2x', 'vs98', 'm06',
- 'm06-hf', 'm06-L', 'm06-2x', 'HFexch', 'becke88', 'xperdew91', 'xpbe96', 'gill96', 'lyp', 'perdew81',
- 'perdew86', 'perdew91', 'cpbe96', 'pw91lda', 'slater', 'vwn_1', 'vwn_2', 'vwn_3', 'vwn_4', 'vwn_5',
- 'vwn_1_rpa', 'xtpss03', 'ctpss03', 'bc95', 'xpw6b95', 'xpwb6k', 'xm05', 'xm05-2x', 'cpw6b95',
- 'cpwb6k', 'cm05', 'cm05-2x', 'xvs98', 'cvs98', 'xm06-L', 'xm06-hf', 'xm06', 'xm06-2x', 'cm06-L',
- 'cm06-hf', 'cm06', 'cm06-2x']
+_xc_functionals = [
+ "acm",
+ "b3lyp",
+ "beckehandh",
+ "pbe0",
+ "becke97",
+ "becke97-1",
+ "becke97-2",
+ "becke97-3",
+ "becke97-d",
+ "becke98",
+ "hcth",
+ "hcth120",
+ "hcth147",
+ "hcth407",
+ "becke97gga1",
+ "hcth407p",
+ "mpw91",
+ "mpw1k",
+ "xft97",
+ "cft97",
+ "ft97",
+ "op",
+ "bop",
+ "pbeop",
+ "xpkzb99",
+ "cpkzb99",
+ "xtpss03",
+ "ctpss03",
+ "xctpssh",
+ "b1b95",
+ "bb1k",
+ "mpw1b95",
+ "mpwb1k",
+ "pw6b95",
+ "pwb6k",
+ "m05",
+ "m05-2x",
+ "vs98",
+ "m06",
+ "m06-hf",
+ "m06-L",
+ "m06-2x",
+ "HFexch",
+ "becke88",
+ "xperdew91",
+ "xpbe96",
+ "gill96",
+ "lyp",
+ "perdew81",
+ "perdew86",
+ "perdew91",
+ "cpbe96",
+ "pw91lda",
+ "slater",
+ "vwn_1",
+ "vwn_2",
+ "vwn_3",
+ "vwn_4",
+ "vwn_5",
+ "vwn_1_rpa",
+ "xtpss03",
+ "ctpss03",
+ "bc95",
+ "xpw6b95",
+ "xpwb6k",
+ "xm05",
+ "xm05-2x",
+ "cpw6b95",
+ "cpwb6k",
+ "cm05",
+ "cm05-2x",
+ "xvs98",
+ "cvs98",
+ "xm06-L",
+ "xm06-hf",
+ "xm06",
+ "xm06-2x",
+ "cm06-L",
+ "cm06-hf",
+ "cm06",
+ "cm06-2x",
+]
 
 
 def muster_modelchem(method: str, derint: int, use_tce: bool) -> Tuple[str, Dict[str, Any]]:
@@ -88,12 +162,17 @@ def muster_modelchem(method: str, derint: int, use_tce: bool) -> Tuple[str, Dict
  else:
  mdccmd = f"task ccsd(t) {runtyp}\n\n"
 
- elif method in ['sodft', 'direct_mp2', 'rimp2', 'mcscf', 'selci', 'md', 'pspw', 'band']:
- raise InputError(f"Method \"{method}\" not yet supported by QCEngine")
+ elif method == "tddft":
+ mdccmd = f"task tddft {runtyp}\n\n"
+
+ elif method in ["sodft", "direct_mp2", "rimp2", "mcscf", "selci", "md", "pspw", "band"]:
+ raise InputError(f'Method "{method}" not yet supported by QCEngine')
 
  elif method == "tce":
- raise InputError(f"Do not specify TCE as a method. Instead specify the desired method "
- f"and \"qc_module=True\" in the run configuration")
+ raise InputError(
+ f"Do not specify TCE as a method. Instead specify the desired method "
+ f'as a keyword and "qc_module=True".'
+ )
 
  elif method in _xc_functionals:
  opts["dft__xc"] = method