Merge branch 'master' into orca

* master: (61 commits)
  Config: Changes new programs from job to task config
  Config: JobConfig -> TaskConfig
  Config: Adds nodes to config
  entos: Black reformat of entos.py and added @using_entos mark
  PR comments
  PR comments: TYPE_CHECKING, formatting, reduce redundant code
  entos: Added entos_policy to the input file
  entos: Updated commit for qcengine_records_commit
  hessparse and compute: Forgotten imports
  entos: Begun adding support for xtb in the entos Harness
  entos: Removed soon to be deprecated option
  entos: Added entos to the test_standard_suite_hf and did some minor cleanup in the entos Harness
  entos: Starting to add HF command to entos
  Fixed typo in error name
  Multiple changes based on review
  Gamess: replace print statements with logging
  Entos: add hessian and xtb support
  Parse named properties out of NWChem output
  Get more of the relevant fields from output
  Removed unncessary "pass" statement
  ...

.travis.yml

@@ -22,6 +22,10 @@ matrix:
 # env:
 # - PYTHON_VER=3.6
 # - PROG=ANI
+ - os: linux
+ env:
+ - PYTHON_VER=3.6
+ - PROG=OPENMM
 
 before_install:
  # Additional info about the build
@@ -45,6 +49,8 @@ install:
  python devtools/scripts/conda_env.py -n=test -p=$PYTHON_VER devtools/conda-envs/psi-nightly.yaml
  elif [ $PROG == "ANI" ]; then
  python devtools/scripts/conda_env.py -n=test -p=$PYTHON_VER devtools/conda-envs/torchani.yaml
+ elif [ $PROG == "OPENMM" ]; then
+ python devtools/scripts/conda_env.py -n=test -p=$PYTHON_VER devtools/conda-envs/openmm.yaml
  else
  echo "ERROR: No match for PROG ($PROG)."
  exit 1

devtools/conda-envs/openmm.yaml

@@ -0,0 +1,23 @@
+name: test
+channels:
+ - conda-forge
+ - omnia-dev
+ - omnia
+dependencies:
+ - conda-forge::rdkit
+ - omnia-dev::openmm
+ - omnia::openforcefield
+ - omnia::openforcefields
+
+ # Core
+ - python
+ - pyyaml
+ - py-cpuinfo
+ - psutil
+ - qcelemental >=0.11.1
+ - pydantic >=0.30.1
+
+ # Testing
+ - pytest
+ - pytest-cov
+ - codecov

docs/source/environment.rst

@@ -52,3 +52,32 @@ The global environment can also be inspected directly.
  },
  'cpu_brand': 'Intel(R) Core(TM) i7-7820HQ CPU @ 2.90GHz'
  }
+
+Configuration Files
+-------------------
+
+The computational environment defaults can be overridden by configuration files.
+
+Configuration files must be named ``qcengine.yaml`` and stored either in the directory
+from which you run QCEngine, a folder named ``.qcarchive`` in your home directory,
+or in a folder specified by the ``DQM_CONFIG_PATH`` environmental variable.
+Only one configuration file will be used if multiple are available.
+The ``DQM_CONFIG_PATH`` configuration file takes precedence over the current directory,
+which takes precedence over the ``.qcarchive`` folder.
+
+The configuration file is a YAML file that contains a dictionary of different node configurations.
+The keys in the YAML file are human-friendly names for the configurations.
+The values are dictionaries that define configurations for different nodes,
+following the ``NodeDescription`` schema:
+
+.. autoclass:: qcengine.config.NodeDescriptor
+
+When running QCEngine, the proper configuration for a node is determined based on the hostname of the node
+and matching the ``hostname_pattern`` to each of the configurations defined in ``qcengine.yaml``.
+
+An example ``qcengine.yaml`` file that sets the scratch directory for all nodes is as follows:
+
+.. code:: yaml
+ all:
+ hostname_pattern: "*"
+ scratch_directory: ./scratch

docs/source/program_overview.rst

@@ -1,7 +1,7 @@
 Program Overview
 ================
 
-The general capabalities available through QCEngine for each program can be
+The general capabilities available through QCEngine for each program can be
 found below:
 
 Quantum Chemistry
@@ -12,7 +12,7 @@ Quantum Chemistry
 +============+============+===+===+===+============+==============+
 | CFOUR | ✘ | ✓ | ✓ | ✘ | ✓ | ✘ |
 +------------+------------+---+---+---+------------+--------------+
-| Entos | ✘ | ✓ | ✓ | ✘ | ✘ | ✘ |
+| Entos | ✘ | ✓ | ✓ | ✓ | ✘ | ✘ |
 +------------+------------+---+---+---+------------+--------------+
 | GAMESS | ✘ | ✓ | ✓ | ✘ | ✓ | ✘ |
 +------------+------------+---+---+---+------------+--------------+
@@ -29,7 +29,7 @@ Quantum Chemistry
 | Turbomole | ✘ | ✓ | ✓ | ✘ | ✘ | ✘ |
 +------------+------------+---+---+---+------------+--------------+
 
-Semi-Emperical
+Semi-Empirical
 --------------
 
 +------------+------------+---+---+---+------------+--------------+

qcengine/compute.py

@@ -1,9 +1,13 @@
 """
 Integrates the computes together
 """
-from typing import Any, Dict, Optional, Union
+from typing import Any, Dict, Optional, Union, TYPE_CHECKING
 
-from qcelemental.models import AtomicInput, FailedOperation
+if TYPE_CHECKING:
+ from pydantic.main import BaseModel
+ from qcelemental.models import AtomicResult
+
+from qcelemental.models import AtomicInput, FailedOperation, AtomicResult
 
 from .config import get_config
 from .exceptions import InputError, RandomError

qcengine/config.py

@@ -43,6 +43,7 @@ def get_global(key: Optional[str] = None) -> Union[str, Dict[str, Any]]:
  cpu_cnt = psutil.cpu_count(logical=True)
 
  _global_values["ncores"] = cpu_cnt
+ _global_values["nnodes"] = 1
 
  _global_values["cpuinfo"] = cpuinfo.get_cpu_info()
  _global_values["cpu_brand"] = _global_values["cpuinfo"]["brand"]
@@ -80,10 +81,11 @@ class Config:
  extra = "forbid"
 
 
-class JobConfig(pydantic.BaseModel):
+class TaskConfig(pydantic.BaseModel):
 
  # Specifications
- ncores: int # Number of ncores per job
+ ncores: int # Number of ncores per task
+ nnodes: int # Number of nodes per task
  memory: float # Amount of memory in GiB per node
  scratch_directory: Optional[str] # What location to use as scratch
  retries: int # Number of retries on random failures
@@ -125,10 +127,6 @@ def _load_defaults() -> None:
  NODE_DESCRIPTORS[k] = NodeDescriptor(name=k, **v)
 
 
-# Pull in the local variables
-_load_defaults()
-
-
 def global_repr() -> str:
  """
  A representation of the current global configuration.
@@ -202,7 +200,7 @@ def parse_environment(data: Dict[str, Any]) -> Dict[str, Any]:
  return ret
 
 
-def get_config(*, hostname: Optional[str] = None, local_options: Dict[str, Any] = None) -> JobConfig:
+def get_config(*, hostname: Optional[str] = None, local_options: Dict[str, Any] = None) -> TaskConfig:
  """
  Returns the configuration key for qcengine.
  """
@@ -237,11 +235,12 @@ def get_config(*, hostname: Optional[str] = None, local_options: Dict[str, Any]
  raise KeyError("Number of jobs per node exceeds the number of available cores.")
 
  config["ncores"] = ncores
+ config["nnodes"] = local_options.pop("nnodes", 1)
 
  if local_options is not None:
  config.update(local_options)
 
- return JobConfig(**config)
+ return TaskConfig(**config)
 
 
 def get_provenance_augments() -> Dict[str, str]:
@@ -255,3 +254,7 @@ def get_provenance_augments() -> Dict[str, str]:
 
 def get_logger() -> "Logger":
  return LOGGER
+
+
+# Pull in the local variables
+_load_defaults()

qcengine/procedures/geometric.py

@@ -24,7 +24,7 @@ def found(self, raise_error: bool = False) -> bool:
  def build_input_model(self, data: Union[Dict[str, Any], "OptimizationInput"]) -> "OptimizationInput":
  return self._build_model(data, OptimizationInput)
 
- def compute(self, input_data: "OptimizationInput", config: "JobConfig") -> "OptimizationResult":
+ def compute(self, input_data: "OptimizationInput", config: "TaskConfig") -> "OptimizationResult":
  try:
  import geometric
  except ModuleNotFoundError:

qcengine/procedures/model.py

@@ -37,7 +37,7 @@ def build_input_model(self, data: Union[Dict[str, Any], "BaseModel"], raise_erro
  """
 
  @abc.abstractmethod
- def compute(self, input_data: "BaseModel", config: "JobConfig") -> "BaseModel":
+ def compute(self, input_data: "BaseModel", config: "TaskConfig") -> "BaseModel":
  pass
 
  @abc.abstractmethod

qcengine/programs/base.py

@@ -14,6 +14,7 @@
 from .mp2d import MP2DHarness
 from .nwchem import NWChemHarness
 from .orca import OrcaHarness
+from .openmm import OpenMMHarness 
 from .psi4 import Psi4Harness
 from .qchem import QChemHarness
 from .rdkit import RDKitHarness
@@ -112,6 +113,7 @@ def list_available_programs() -> Set[str]:
 
 # Molecular Mechanics
 register_program(RDKitHarness())
+register_program(OpenMMHarness())
 
 # Analytical Corrections
 register_program(DFTD3Harness())

qcengine/programs/cfour/runner.py

@@ -64,7 +64,7 @@ def get_version(self) -> str:
 
  return self.version_cache[which_prog]
 
- def compute(self, input_model: "AtomicInput", config: "JobConfig") -> "AtomicResult":
+ def compute(self, input_model: "AtomicInput", config: "TaskConfig") -> "AtomicResult":
  self.found(raise_error=True)
 
  job_inputs = self.build_input(input_model, config)
@@ -76,7 +76,7 @@ def compute(self, input_model: "AtomicInput", config: "JobConfig") -> "AtomicRes
  return self.parse_output(dexe["outfiles"], input_model)
 
  def build_input(
- self, input_model: "AtomicInput", config: "JobConfig", template: Optional[str] = None
+ self, input_model: "AtomicInput", config: "TaskConfig", template: Optional[str] = None
  ) -> Dict[str, Any]:
  cfourrec = {"infiles": {}, "scratch_directory": config.scratch_directory}
 

qcengine/programs/dftd3.py

@@ -61,7 +61,7 @@ def get_version(self) -> str:
 
  return self.version_cache[which_prog]
 
- def compute(self, input_model: "AtomicInput", config: "JobConfig") -> "AtomicResult":
+ def compute(self, input_model: "AtomicInput", config: "TaskConfig") -> "AtomicResult":
  self.found(raise_error=True)
 
  job_inputs = self.build_input(input_model, config)
@@ -98,7 +98,7 @@ def execute(
  return success, dexe
 
  def build_input(
- self, input_model: "AtomicInput", config: "JobConfig", template: Optional[str] = None
+ self, input_model: "AtomicInput", config: "TaskConfig", template: Optional[str] = None
  ) -> Dict[str, Any]:
 
  # strip engine hint