Merge pull request #6 from molssi-seamm/structure

Updated to the new system classes.

devtools/conda-envs/test_env.yaml

@@ -2,6 +2,7 @@ name: test
 
 channels:
   - default
+  - conda-forge
 
 dependencies:
     # Base depends
@@ -10,6 +11,7 @@ dependencies:
   - configargparse
   - psutil
   - py-cpuinfo
+  - openbabel
 
     # Testing
   - coverage
@@ -20,9 +22,9 @@ dependencies:
 
     # Pip-only installs
   - pip:
-    - seamm>=0.9
-    - seamm-util>=0.9
-    - seamm-widgets>=0.9
+    - seamm>=2020.9.23
+    - seamm-util>=2020.9.23
+    - seamm-widgets>=2020.8.1
 
       # Testing
     - codecov

docs/conf.py

@@ -20,7 +20,7 @@
 # directory, add these directories to sys.path here. If the directory is
 # relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('.'))
 
 # Get the project root dir, which is the parent dir of this
 cwd = os.getcwd()
@@ -31,16 +31,18 @@
 # version is used.
 sys.path.insert(0, project_root)
 
-import psi4_step
+import psi4_step  # noqa: E402
 
 # -- General configuration ---------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+extensions = [
+    'sphinx.ext.napoleon', 'sphinx.ext.autodoc', 'sphinx.ext.viewcode'
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -49,7 +51,7 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
@@ -69,42 +71,42 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to
 # some non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = ['_build']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built
 # documents.
-#keep_warnings = False
+# keep_warnings = False
 
 
 # -- Options for HTML output -------------------------------------------
@@ -116,27 +118,27 @@
 # 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
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as
 # html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the
 # top of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon
 # of the docs.  This file should be a Windows icon file (.ico) being
 # 16x16 or 32x32 pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets)
 # here, relative to this directory. They are copied after the builtin
@@ -146,46 +148,46 @@
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page
 # bottom, using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names
 # to template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer.
 # Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer.
 # Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages
 # will contain a <link> tag referring to it.  The value of this option
 # must be the base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'psi4_stepdoc'
@@ -195,13 +197,13 @@
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
-    #'papersize': 'letterpaper',
+    # 'papersize': 'letterpaper',
 
     # The font size ('10pt', '11pt' or '12pt').
-    #'pointsize': '10pt',
+    # 'pointsize': '10pt',
 
     # Additional stuff for the LaTeX preamble.
-    #'preamble': '',
+    # 'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
@@ -215,23 +217,23 @@
 
 # The name of an image file (relative to this directory) to place at
 # the top of the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings
 # are parts, not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output ------------------------------------
@@ -245,7 +247,7 @@
 ]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -263,13 +265,13 @@
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False

psi4_step/energy_parameters.py

@@ -90,6 +90,18 @@ class EnergyParameters(seamm.Parameters):
                 "(UHF, UKS)"
             )
         },
+        "freeze-cores": {
+            "default": "yes",
+            "kind": "enumeration",
+            "default_units": "",
+            "enumeration": ('yes', 'no'),
+            "format_string": "s",
+            "description": "Freeze core orbitals:",
+            "help_text": (
+                "Whether to freeze the core orbitals in correlated "
+                "methods"
+            )
+        },
         "results": {
             "default": {},
             "kind": "dictionary",

psi4_step/psi4.py

@@ -13,7 +13,6 @@
 
 import psi4_step
 import seamm
-from seamm import data  # noqa: F401
 from seamm_util import ureg, Q_  # noqa: F401
 import seamm_util.printing as printing
 from seamm_util.printing import FormattedText as __
@@ -298,7 +297,9 @@ def run(self):
         printer.important(self.header)
         printer.important('')
 
-        if data.structure is None:
+        system = self.get_variable('_system')
+        n_atoms = system.n_atoms()
+        if n_atoms == 0:
             logger.error('Psi4 run(): there is no structure!')
             raise RuntimeError('Psi4 run(): there is no structure!')
 
@@ -483,13 +484,18 @@ def analyze(self, indent='', **kwargs):
             with structure_file.open(mode='r') as fd:
                 structure = json.load(fd)
         if 'geom' in structure:
-            system = seamm.data.structure
-            atoms = system['atoms']
-            xyz = []
+            system = self.get_variable('_system')
+            xs = []
+            ys = []
+            zs = []
             it = iter(structure['geom'])
             for x in it:
-                xyz.append([x, next(it), next(it)])
-            atoms['coordinates'] = xyz
+                xs.append(x)
+                ys.append(next(it))
+                zs.append(next(it))
+            system.atoms['x'][0:] = xs
+            system.atoms['y'][0:] = ys
+            system.atoms['z'][0:] = zs
             printer.important(
                 self.indent +
                 '    Updated the system with the structure from Psi4',
@@ -499,7 +505,7 @@ def analyze(self, indent='', **kwargs):
     def _convert_structure(self, name=None):
         """Convert the structure to the input for Psi4."""
 
-        system = seamm.data.structure
+        system = self.get_variable('_system')
 
         structure = []
         if name is None:
@@ -537,11 +543,11 @@ def _convert_structure(self, name=None):
                 if 'net_charge' in extras and extras['net_charge'] is not None:
                     structure.append(f"    {extras['net_charge']}   1")
 
-        elements = system['atoms']['elements']
-        coordinates = system['atoms']['coordinates']
+        elements = system.atoms.symbols()
+        coordinates = system.atoms.coordinates()
 
-        if 'freeze' in system['atoms']:
-            freeze = system['atoms']['freeze']
+        if 'freeze' in system.atoms:
+            freeze = system.atoms['freeze']
         else:
             freeze = [''] * len(elements)