Fix for QCFractal next beta10

.github/workflows/ecosystem.yml

@@ -242,7 +242,7 @@ jobs:
  # "next" packages aren't self-contained, and "0.15.8" not available fro py310. try again someday
  # sed -i "s;- qcfractal;;g" aux.yaml
  # sed -i "s;- qcportal;;g" aux.yaml
- sed -i "s;- qcfractal;- qcarchive/label/next::qcfractal=0.50b7;g" aux.yaml
+ sed -i "s;- qcfractal;- qcarchive/label/next::qcfractal;g" aux.yaml # >=0.50b10
  sed -i "s;- qcportal;- postgresql;g" aux.yaml
  fi
  if [[ "${{ runner.os }}" == "macOS" ]]; then

external/upstream/libxc/CMakeLists.txt

@@ -19,7 +19,7 @@ else()
  # Default: use a stable release tarball of libxc. To use the
  # development version of libxc, instead, comment the URL line,
  # and uncomment the GIT lines.
- URL https://gitlab.com/libxc/libxc/-/archive/6.0.0/libxc-6.0.0.tar.gz
+ URL https://gitlab.com/libxc/libxc/-/archive/6.1.0/libxc-6.1.0.tar.gz
  #GIT_REPOSITORY https://gitlab.com/libxc/libxc.git
  #GIT_TAG 5.1.5
  #UPDATE_COMMAND ""

psi4/driver/driver.py

@@ -847,7 +847,7 @@ def calc(self, coords, dirname, read_data=False):
  step_coordinates = []
 
  # Make sure the molecule the user provided is the active one
- molecule = kwargs.get('molecule', core.get_active_molecule())
+ molecule = kwargs.pop('molecule', core.get_active_molecule())
 
  # Do not change orientation or COM
  molecule.fix_orientation(True)

psi4/driver/driver_cbs.py

@@ -1635,10 +1635,10 @@ def _prepare_results(self, client: Optional["qcportal.FractalClient"] = None):
  mc['f_gradient'] = task.extras['qcvars']['CURRENT GRADIENT']
 
  if 'CURRENT DIPOLE' in task.extras['qcvars']:
- mc['f_dipole'] = np.array(task.extras['qcvars']['CURRENT DIPOLE'])
+ mc['f_dipole'] = task.extras['qcvars']['CURRENT DIPOLE']
 
  if 'CURRENT DIPOLE GRADIENT' in task.extras['qcvars']:
- mc['f_dipder'] = np.array(task.extras['qcvars']['CURRENT DIPOLE GRADIENT'])
+ mc['f_dipder'] = task.extras['qcvars']['CURRENT DIPOLE GRADIENT']
 
  # Fill in energies for subsumed methods
  if self.metameta['ptype'] == 'energy':
@@ -1746,7 +1746,11 @@ def get_results(self, client: Optional["qcportal.FractalClient"] = None) -> Atom
 
  return cbs_model
 
- def get_psi_results(self, return_wfn: bool = False) -> EnergyGradientHessianWfnReturn:
+ def get_psi_results(
+ self,
+ client: Optional["qcportal.FractalClient"] = None,
+ *,
+ return_wfn: bool = False) -> EnergyGradientHessianWfnReturn:
  """Called by driver to assemble results into Composite-flavored QCSchema,
  then reshape and return them in the customary Psi4 driver interface: ``(e/g/h, wfn)``.
 
@@ -1770,7 +1774,7 @@ def get_psi_results(self, return_wfn: bool = False) -> EnergyGradientHessianWfnR
  Wavefunction described above when *return_wfn* specified.
 
  """
- cbs_model = self.get_results()
+ cbs_model = self.get_results(client=client)
 
  if cbs_model.driver == 'energy':
  ret_ptype = cbs_model.return_result

psi4/driver/driver_findif.py

@@ -1459,7 +1459,11 @@ def get_results(self, client: Optional["qcportal.FractalClient"] = None) -> Atom
 
  return findif_model
 
- def get_psi_results(self, return_wfn: bool = False) -> EnergyGradientHessianWfnReturn:
+ def get_psi_results(
+ self,
+ client: Optional["qcportal.FractalClient"] = None,
+ *,
+ return_wfn: bool = False) -> EnergyGradientHessianWfnReturn:
  """Called by driver to assemble results into FiniteDifference-flavored QCSchema,
  then reshape and return them in the customary Psi4 driver interface: ``(e/g/h, wfn)``.
 
@@ -1483,7 +1487,7 @@ def get_psi_results(self, return_wfn: bool = False) -> EnergyGradientHessianWfnR
  Wavefunction described above when *return_wfn* specified.
 
  """
- findif_model = self.get_results()
+ findif_model = self.get_results(client=client)
 
  ret_ptype = core.Matrix.from_array(findif_model.return_result)
  wfn = _findif_schema_to_wfn(findif_model)

psi4/driver/driver_nbody.py

@@ -1417,7 +1417,11 @@ def get_results(self, client: Optional["qcportal.FractalClient"] = None) -> Atom
 
  return nbody_model
 
- def get_psi_results(self, return_wfn: bool = False) -> EnergyGradientHessianWfnReturn:
+ def get_psi_results(
+ self,
+ client: Optional["qcportal.FractalClient"] = None,
+ *,
+ return_wfn: bool = False) -> EnergyGradientHessianWfnReturn:
  """Called by driver to assemble results into ManyBody-flavored QCSchema,
  then reshape and return them in the customary Psi4 driver interface: ``(e/g/h, wfn)``.
 
@@ -1440,7 +1444,7 @@ def get_psi_results(self, return_wfn: bool = False) -> EnergyGradientHessianWfnR
  Wavefunction described above when *return_wfn* specified.
 
  """
- nbody_model = self.get_results()
+ nbody_model = self.get_results(client=client)
  ret = nbody_model.return_result
 
  wfn = core.Wavefunction.build(self.molecule, "def2-svp", quiet=True)

psi4/driver/p4util/procutil.py

@@ -42,7 +42,6 @@
  "prepare_options_for_modules",
  "prepare_options_for_set_options",
  "provenance_stamp",
- "plump_qcvar",
  "state_to_atomicinput",
 ]
 
@@ -730,53 +729,3 @@ def provenance_stamp(routine: str, module: str = None) -> Dict[str, str]:
  prov["module"] = module
 
  return prov
-
-
-def plump_qcvar(
- val: Union[float, str, List],
- shape_clue: str,
- ret: str = 'np') -> Union[float, np.ndarray, core.Matrix]:
- """Prepare serialized QCVariable for :py:func:`~psi4.core.set_variable` by
- converting flat arrays into shaped ones and floating strings.
-
- Parameters
- ----------
- val
- flat (?, ) list or scalar or string, probably from JSON storage.
- shape_clue
- Label that includes (case insensitive) one of the following as
- a clue to the array's natural dimensions: 'gradient', 'hessian'
- ret
- {'np', 'psi4'}
- Whether for arrays to return :py:class:`numpy.ndarray` or
- :py:class:`psi4.core.Matrix`.
-
- Returns
- -------
- float or numpy.ndarray or Matrix
- Reshaped array of type `ret` with natural dimensions of `shape_clue`.
-
- """
- if isinstance(val, (np.ndarray, core.Matrix)):
- raise TypeError
- elif isinstance(val, list):
- tgt = np.asarray(val)
- else:
- # presumably scalar. may be string
- return float(val)
- # TODO choose float vs Decimal for return if string?
-
- if 'gradient' in shape_clue.lower():
- reshaper = (-1, 3)
- elif 'hessian' in shape_clue.lower():
- ndof = int(math.sqrt(len(tgt)))
- reshaper = (ndof, ndof)
- else:
- raise ValidationError(f'Uncertain how to reshape array: {shape_clue}')
-
- if ret == 'np':
- return tgt.reshape(reshaper)
- elif ret == 'psi4':
- return core.Matrix.from_array(tgt.reshape(reshaper))
- else:
- raise ValidationError(f'Return type not among [np, psi4]: {ret}')

psi4/driver/p4util/python_helpers.py

@@ -43,6 +43,7 @@
 __all__ = [
  "basis_helper",
  "pcm_helper",
+ "plump_qcvar",
  "set_options",
  "set_module_options",
  "temp_circular_import_blocker", # retire ASAP
@@ -52,6 +53,7 @@
 import os
 import re
 import sys
+import math
 import uuid
 import warnings
 from collections import Counter
@@ -839,6 +841,64 @@ def _qcvar_warnings(key: str) -> str:
  return key
 
 
+def plump_qcvar(
+ key: str,
+ val: Union[float, str, List]) -> Union[float, np.ndarray]:
+ """Prepare serialized QCVariables for QCSchema AtomicResult.extras["qcvars"] by
+ converting flat arrays into numpy, shaped ones and floating strings.
+ Unlike _qcvar_reshape_get/set, multipoles aren't compressed or plumped, only reshaped.
+
+ Parameters
+ ----------
+ key
+ Shape clue (usually QCVariable key) that includes (case insensitive) an identifier like
+ 'gradient' as a clue to the array's natural dimensions.
+ val
+ flat (?, ) list or scalar or string, probably from JSON storage.
+
+ Returns
+ -------
+ float or numpy.ndarray
+ Reshaped array of `val` with natural dimensions of `key`.
+
+ """
+ if isinstance(val, (np.ndarray, core.Matrix)):
+ raise TypeError
+ elif isinstance(val, list):
+ tgt = np.asarray(val)
+ else:
+ # presumably scalar. may be string
+ return float(val)
+
+ if key.upper().startswith("MBIS"):
+ if key.upper().endswith("CHARGES"):
+ reshaper = (-1, )
+ elif key.upper().endswith("DIPOLES"):
+ reshaper = (-1, 3)
+ elif key.upper().endswith("QUADRUPOLES"):
+ reshaper = (-1, 3, 3)
+ elif key.upper().endswith("OCTUPOLES"):
+ reshaper = (-1, 3, 3, 3)
+ elif key.upper().endswith("DIPOLE") or "DIPOLE -" in key.upper():
+ reshaper = (3, )
+ elif "QUADRUPOLE POLARIZABILITY TENSOR" in key.upper():
+ reshaper = (3, 3, 3)
+ elif any((key.upper().endswith(p) or f"{p} -" in key.upper()) for p in _multipole_order):
+ p = [p for p in _multipole_order if (key.upper().endswith(p) or f"{p} -" in key.upper())]
+ reshaper = tuple([3] * _multipole_order.index(p[0]))
+ elif key.upper() in ["MULLIKEN_CHARGES", "LOWDIN_CHARGES", "MULLIKEN CHARGES", "LOWDIN CHARGES"]:
+ reshaper = (-1, )
+ elif "GRADIENT" in key.upper():
+ reshaper = (-1, 3)
+ elif "HESSIAN" in key.upper():
+ ndof = int(math.sqrt(len(tgt)))
+ reshaper = (ndof, ndof)
+ else:
+ raise ValidationError(f'Uncertain how to reshape array: {key}')
+
+ return tgt.reshape(reshaper)
+
+
 _multipole_order = ["dummy", "dummy", "QUADRUPOLE", "OCTUPOLE", "HEXADECAPOLE"]
 for order in range(5, 10):
  _multipole_order.append(f"{int(2**order)}-POLE")
@@ -881,7 +941,7 @@ def _qcvar_reshape_set(key: str, val: np.ndarray) -> np.ndarray:
  return val
 
 
-def _qcvar_reshape_get(key: str, val: Union[core.Matrix, np.ndarray]) -> Union[core.Matrix, np.ndarray]:
+def _qcvar_reshape_get(key: str, val: core.Matrix) -> Union[core.Matrix, np.ndarray]:
  """For QCVariables where the 2D :py:class:`psi4.core.Matrix` shape is
  unnatural, convert to natural shape in :class:`numpy.ndarray`.
 

psi4/driver/task_base.py

@@ -35,6 +35,7 @@
 import abc
 import copy
 import logging
+import pprint
 from typing import Any, Dict, Optional, Tuple, Union, TYPE_CHECKING
 
 from pydantic import Field, validator
@@ -44,6 +45,7 @@
 import qcengine as qcng
 
 from psi4 import core
+from psi4.driver import p4util
 
 if TYPE_CHECKING:
  import qcportal
@@ -253,31 +255,16 @@ def get_results(self, client: Optional["qcportal.FractalClient"] = None) -> Atom
  return self.result
 
 
-def _singlepointrecord_to_atomicresult(spr) -> AtomicResult:
- extras = spr.raw_data.extras
- extras.pop("_qcfractal_compressed_outputs", None)
-
- atres = {
- "driver": spr.raw_data.specification.driver,
- "model": {
- "method": spr.raw_data.specification.method,
- "basis": spr.raw_data.specification.basis,
- },
- "molecule": spr.molecule,
- "keywords": spr.raw_data.specification.keywords,
- "properties": spr.properties,
- "protocols": spr.raw_data.specification.protocols,
- "return_result": spr.return_result,
- "extras": extras,
- "stdout": spr.stdout,
- "native_files": spr.native_files,
- "wavefunction": spr.wavefunction,
- "provenance": spr.raw_data.compute_history[0].provenance,
- "success": spr.status == "complete",
- }
-
- from qcelemental.models import AtomicResult
- atres = AtomicResult(**atres)
+def _singlepointrecord_to_atomicresult(spr: "qcportal.singlepoint.SinglepointRecord") -> AtomicResult:
+ atres = spr.to_qcschema_result()
+
+ # QCFractal `next` database stores return_result, properties, and extras["qcvars"] merged
+ # together and with lowercase keys. `to_qcschema_result` partitions properties back out,
+ # but we need to restore qcvars keys, types, and dimensions.
+ qcvars = atres.extras.pop("extra_properties")
+ qcvars.pop("return_result")
+ qcvars = {k.upper(): p4util.plump_qcvar(k, v) for k, v in qcvars.items()}
+ atres.extras["qcvars"] = qcvars
 
  return atres
 

pytest.ini

@@ -38,6 +38,7 @@ markers =
  cisd
  cubeprop
  dct
+ # ddd: "findif and cbs and nbody" (not defined, so use equiv. expansion)
  df: "tests that employ density-fitting"
  dfccd
  dfccd-grad
@@ -66,7 +67,7 @@ markers =
  extern: "tests that use the ExternalPotential object"
  fci
  fcidump
- findif
+ findif: "tests that run through the finite_difference wrapper"
  fnocc
  frac
  freq
@@ -160,7 +161,7 @@ markers =
  snsmp2
  v2rdm_casscf
  qcdb
- qcfractal: "tests suing QCFractal software; skip if unavailable"
- qcportal: "tests suing QCPortal software; skip if unavailable"
+ qcfractal: "tests using QCFractal software; skip if unavailable"
+ qcportal: "tests using QCPortal software; skip if unavailable"
  psi4