running Madness with QCengine

devtools/scripts/conda_env.py

@@ -4,10 +4,10 @@
 import subprocess as sp
 
 # Args
-parser = argparse.ArgumentParser(description='Creates a conda environment from file for a given Python version.')
-parser.add_argument('-n', '--name', type=str, nargs=1, help='The name of the created Python environment')
-parser.add_argument('-p', '--python', type=str, nargs=1, help='The version of the created Python environment')
-parser.add_argument('conda_file', nargs='*', help='The file for the created Python environment')
+parser = argparse.ArgumentParser(description="Creates a conda environment from file for a given Python version.")
+parser.add_argument("-n", "--name", type=str, nargs=1, help="The name of the created Python environment")
+parser.add_argument("-p", "--python", type=str, nargs=1, help="The version of the created Python environment")
+parser.add_argument("conda_file", nargs="*", help="The file for the created Python environment")
 
 args = parser.parse_args()
 

docs/source/conf.py

@@ -10,7 +10,7 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath("../.."))
 import qcengine
 
 # -- Path setup --------------------------------------------------------------
@@ -26,9 +26,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'QCEngine'
-copyright = f'2018-{datetime.datetime.today().year}, The Molecular Sciences Software Institute'
-author = 'The QCArchive Development Team'
+project = "QCEngine"
+copyright = f"2018-{datetime.datetime.today().year}, The Molecular Sciences Software Institute"
+author = "The QCArchive Development Team"
 
 # The short X.Y version
 version = qcengine.__version__
@@ -46,26 +46,26 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.doctest',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.extlinks',
-    'sphinx.ext.graphviz',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon',
-    'sphinx_automodapi.automodapi',
-    'sphinx_automodapi.automodsumm',
-    'sphinx_automodapi.smart_resolver',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.graphviz",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx_automodapi.automodapi",
+    "sphinx_automodapi.automodsumm",
+    "sphinx_automodapi.smart_resolver",
     "sphinx_autodoc_typehints",
     "sphinxcontrib.autodoc_pydantic",
 ]
 
 autosummary_generate = True
-automodapi_toctreedirnm = 'api'
+automodapi_toctreedirnm = "api"
 autodoc_typehints = "description"
 napoleon_use_param = True
 napoleon_use_rtype = True
@@ -74,16 +74,16 @@
 autodoc_pydantic_field_swap_name_and_alias = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -98,15 +98,15 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'default'
+pygments_style = "default"
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -117,7 +117,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -133,7 +133,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'QCEnginedoc'
+htmlhelp_basename = "QCEnginedoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -142,15 +142,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -160,19 +157,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'QCEngine.tex', 'QCEngine Documentation',
-     'The QCArchive Development Team', 'manual'),
+    (master_doc, "QCEngine.tex", "QCEngine Documentation", "The QCArchive Development Team", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'qcengine', 'QCEngine Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "qcengine", "QCEngine Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -181,30 +174,37 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'QCEngine', 'QCEngine Documentation',
-     author, 'QCEngine', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "QCEngine",
+        "QCEngine Documentation",
+        author,
+        "QCEngine",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 
 # -- Extension configuration -------------------------------------------------
 
 extlinks = {
-    'issue': ('https://github.com/MolSSI/QCEngine/issues/%s', 'GH#%s'),
-    'pr': ('https://github.com/MolSSI/QCEngine/pull/%s', 'GH#%s')
+    "issue": ("https://github.com/MolSSI/QCEngine/issues/%s", "GH#%s"),
+    "pr": ("https://github.com/MolSSI/QCEngine/pull/%s", "GH#%s"),
 }
 
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'python': ('https://docs.python.org/3.10', None),
-                       "numpy": ("https://numpy.org/doc/stable/", None),
-                       'scipy': ('https://docs.scipy.org/doc/scipy/', None),
-                       'matplotlib': ('https://matplotlib.org/stable/', None),
-                       "qcelemental": ("http://docs.qcarchive.molssi.org/projects/QCElemental/en/latest/", None),
-                       "qcportal": ("http://docs.qcarchive.molssi.org/projects/QCPortal/en/latest/", None),
-                       "qcfractal": ("http://docs.qcarchive.molssi.org/projects/QCFractal/en/latest/", None),
-                      }
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3.10", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+    "qcelemental": ("http://docs.qcarchive.molssi.org/projects/QCElemental/en/latest/", None),
+    "qcportal": ("http://docs.qcarchive.molssi.org/projects/QCPortal/en/latest/", None),
+    "qcfractal": ("http://docs.qcarchive.molssi.org/projects/QCFractal/en/latest/", None),
+}
 
 # -- Options for todo extension ----------------------------------------------
 

examples/terachem_pbs.py

@@ -22,4 +22,4 @@
     model={"method": "pbe0", "basis": "6-31g"},
 )
 ret = prog.compute(inp)
-print(ret)
+print(ret)

qcengine/compute.py

@@ -1,6 +1,7 @@
 """
 Integrates the computes together
 """
+
 import warnings
 from typing import TYPE_CHECKING, Any, Dict, Optional, Union
 

qcengine/mdi_server.py

@@ -2,6 +2,7 @@
 For details regarding MDI, see https://molssi.github.io/MDI_Library/html/index.html.
 
 """
+
 from typing import Any, Dict, List, Optional
 
 import numpy as np

qcengine/programs/adcc.py

@@ -1,6 +1,7 @@
 """
 Calls adcc
 """
+
 from typing import TYPE_CHECKING, Dict
 
 from qcelemental.models import AtomicResult, BasisSet, Provenance

qcengine/programs/base.py

@@ -17,6 +17,7 @@
 from .mp2d import MP2DHarness
 from .mrchem import MRChemHarness
 from .nwchem import NWChemHarness
+from .madness import MadnessHarness
 from .openmm import OpenMMHarness
 from .psi4 import Psi4Harness
 from .qchem import QChemHarness
@@ -108,6 +109,7 @@ def list_available_programs() -> Set[str]:
 register_program(CFOURHarness())
 register_program(EntosHarness())  # Duplicate of Qcore harness to transition the namespace, to be deprecated
 register_program(GAMESSHarness())
+register_program(MadnessHarness())
 register_program(MRChemHarness())
 register_program(MolproHarness())
 register_program(NWChemHarness())

qcengine/programs/cfour/runner.py

@@ -90,7 +90,7 @@ def build_input(
 
         # Handle memory
         # for cfour, [GiB] --> [QW]
-        opts["memory_size"] = int(config.memory * (1024**3) / 8)
+        opts["memory_size"] = int(config.memory * (1024 ** 3) / 8)
         opts["mem_unit"] = "integerwords"
 
         # Handle molecule

qcengine/programs/empirical_dispersion_resources.py

@@ -1159,9 +1159,9 @@ def from_arrays(
                 "d3mbj2b",
             ]
             for d in ["d3zero", "d3bj", "d3mzero", "d3mbj"]:
-                psi4.procrouting.empirical_dispersion._capable_engines_for_disp[
-                    d + "2b"
-                ] = psi4.procrouting.empirical_dispersion._capable_engines_for_disp.pop(d)
+                psi4.procrouting.empirical_dispersion._capable_engines_for_disp[d + "2b"] = (
+                    psi4.procrouting.empirical_dispersion._capable_engines_for_disp.pop(d)
+                )
     except ImportError:
         pass
 

qcengine/programs/madness/__init__.py

@@ -0,0 +1 @@
+from .runner import MadnessHarness

qcengine/programs/madness/germinate.py

@@ -0,0 +1,60 @@
+from typing import Any, Dict, Tuple
+
+from qcengine.exceptions import InputError
+
+# List of XC functionals known to NWChem
+_xc_functionals = [
+    "hf",
+    "lda",
+    "b3lyp",
+]
+
+
+def muster_modelchem(
+    method: str,
+    derint: int,
+) -> Tuple[str, Dict[str, Any]]:
+    """Converts the QC method into MADNESS keywords
+    Options include energy calculation with moldft
+    Geometry optimization with moldft
+    propreties calculation with molresponse...runs moldft then molresponse
+
+    Args:
+       method (str): Name of the QC method to use
+       derint (str): Index of the run type
+    Returns:
+       (str): Task command for MADNESS
+       (dict): Any options for MADNESS
+    """
+
+    # Standardize the method name
+    method = method.lower()
+
+    opts = {}
+
+    # Map the run type to
+    # runtyp = {"energy": "energy", "gradient": "gradient", "hessian": "hessian", "properties": "property"}[derint]
+    runtyp = {"energy": "energy", "optimization": "gopt", "hessian": "hessian", "properties": "molresponse"}[derint]
+
+    # Write out the theory directive
+    if runtyp == "energy":
+        if method == "optimization":
+            opts["dft__gopt"] = True
+        elif method.split()[0] in _xc_functionals:
+            opts["dft__xc"] = method
+        else:
+            raise InputError(f"Method not recognized: {method}")
+        mdccmd = f""
+    elif runtyp == "molresponse":
+        if method.split()[0] in _xc_functionals:
+            opts["dft__xc"] = method
+            opts["response__xc"] = method
+            opts["response__archive"] = "restartdata"
+        else:
+            raise InputError(f"Method not recognized: {method}")
+        mdccmd = f"response"  ## we will split the options with the word response later
+
+    ## all we have to do is add options to the dft block in order to change the run type
+    ## default in energy
+    # do nothing
+    return mdccmd, opts