Updated to new system classes.

crystal_builder_step/crystal_builder.py

@@ -11,8 +11,8 @@
 import pprint
 
 import crystal_builder_step
+import molsystem
 import seamm
-from seamm_util import ureg, Q_  # noqa: F401
 import seamm_util.printing as printing
 from seamm_util.printing import FormattedText as __
 
@@ -180,7 +180,8 @@ def run(self):
         next_node = super().run(printer)
 
         # Get the system
-        system = self.get_variable('_system')
+        system_db = self.get_variable('_system_db')
+        configuration = system_db.system.configuration
 
         # Get the values of the parameters, dereferencing any variables
         P = self.parameters.current_values_to_dict(
@@ -197,20 +198,20 @@ def run(self):
         self.logger.debug(f'Formatted values:\n{pprint.pformat(PP)}')
         printer.important(__(self.description_text(PP), indent=self.indent))
 
-        # Create the system from the cif file for the prototype
+        # Create the configuration from the cif file for the prototype
         aflow_prototype = P['AFLOW prototype']
 
         package = self.__module__.split('.')[0]
         files = [p for p in implib.files(package) if aflow_prototype in str(p)]
         if len(files) > 0:
             path = files[0]
             data = path.read_text()
-            system.from_cif_text(data)
+            configuration.from_cif_text(data)
 
         # Now set the cell parameters. If unmentioned the lattice parameters
         # get the previous value, e.g. a, a, c. The angles are those of the
         # prototype if not mentioned.
-        a0, b0, c0, alpha0, beta0, gamma0 = system.cell.cell().parameters
+        a0, b0, c0, alpha0, beta0, gamma0 = configuration.cell.parameters
 
         data = crystal_builder_step.prototype_data[aflow_prototype]
         cell = data['cell']
@@ -242,7 +243,7 @@ def run(self):
             new_cell.append(last)
 
         self.logger.debug(f'cell = {new_cell}')
-        system.cell.set_cell(new_cell)
+        configuration.cell.parameters = new_cell
 
         # And the elements for the sites. Not that symmetry has been lowered
         # to P1
@@ -253,8 +254,8 @@ def run(self):
                 symbol = self.get_variable(symbol)
             symbols.extend([symbol] * mult)
         self.logger.debug(f'symbols = {symbols}')
-        atnos = system.atoms.to_atnos(symbols)
-        column = system.atoms.get_column('atno')
+        atnos = molsystem.elements.to_atnos(symbols)
+        column = configuration.atoms.get_column('atno')
         column[0:] = atnos
 
         # Requested citations for the AFLOW protoype library

crystal_builder_step/crystal_builder_parameters.py

@@ -5,7 +5,6 @@
 
 import logging
 import seamm
-import pprint  # noqa: F401
 
 logger = logging.getLogger(__name__)
 

crystal_builder_step/parse.py

@@ -195,7 +195,6 @@ def run(filename='prototypes.xlsx'):
     wb = openpyxl.load_workbook(filename=filename)
     ws = wb['Sheet1']
 
-    row = 1
     row_max = ws.max_row
 
     data = {
@@ -302,7 +301,7 @@ def get_bibtex(prototype):
     try:
         cif = CifFile.ReadCif(prototype + '.cif')
     except Exception:
-        print(f'Error in {new_path}\n\n')
+        print(f'Error in {prototype}.cif\n\n')
         raise
     tmp = cif['findsym-output']
     authors = tmp['_publ_author_name']
@@ -324,19 +323,18 @@ def get_bibtex(prototype):
     pages = f'{first}-{last}'
 
     template = string.Template(
-        textwrap.dedent(
-            """\
-            @article{$prototype,
-                author = {$author_list},
-                title = {$title},
-                journal = {$journal},
-                volume = {$volume},
-                pages = {$pages},
-                year = $year,
-            }
-            """
-        )
+        """\
+        @article{$prototype,
+        author = {$author_list},
+        title = {$title},
+        journal = {$journal},
+        volume = {$volume},
+        pages = {$pages},
+        year = $year,
+        }
+        """
     )
+
     citation = template.substitute(
         prototype=prototype,
         author_list=author_list,
@@ -351,7 +349,6 @@ def get_bibtex(prototype):
 
 
 def test():
-    import textwrap
     import bibtexparser
     import reference_handler
 
@@ -385,89 +382,91 @@ def test():
     import urllib.parse
     import urllib.request
 
-    if True:
-        test()
-    elif False:
-        bibtex = ''
-        with open('prototypes.json', 'r') as fd:
-            data = json.load(fd)
-
-        for prototype in data['AFLOW prototype']:
-            print(prototype)
-            if prototype in bib:
-                text = bib[prototype]
-            else:
-                text = get_bibtex(prototype)
-            bibtex += text
-        with open('references2.bib', 'w') as fd:
-            fd.write(bibtex)
-    elif False:
-        run()
-    elif False:
-        # Fix the prototypes to have added formula part in some cases
-        # Get the data from the json
-        with open('prototypes.json', 'r') as fd:
-            data = json.load(fd)
-
-        aflow_prototypes = []
-        for hyperlink in data['hyperlink']:
-            url = urllib.parse.urlsplit(hyperlink)
-            path = url.path
-            root, extension = os.path.splitext(os.path.basename(path))
-            aflow_prototypes.append(root)
-
-        data['AFLOW prototype'] = aflow_prototypes
-
-        with open('prototypes2.json', 'w') as fd:
-            json.dump(data, fd, indent=4)
-    else:
-        # Get the data from the json
-        with open('prototypes2.json', 'r') as fd:
-            data = json.load(fd)
-
-        cp = data['cell parameters'] = []
-        sites = data['sites'] = []
-        # Fetch the cif file to get the adjustable parameters
-        for hyperlink in data['hyperlink']:
-            url = urllib.parse.urlsplit(hyperlink)
-            path = url.path
-            root, extension = os.path.splitext(os.path.basename(path))
-            filename = root + '.cif'
-            new_path = os.path.join('.', filename)
-            if not os.path.exists(new_path):
-                print(f'{new_path} does not exist')
-            else:
-                try:
-                    cif = CifFile.ReadCif(new_path)
-                except Exception:
-                    print(f'Error in {new_path}\n\n')
-                    raise
-                tmp = cif['findsym-output']
-                params = tmp['_aflow_params'].split(',')
-                values = tmp['_aflow_params_values'].split(',')
-
-                cell_parameters = []
-                for param, value in zip(params, values):
-                    if param[0] in ('x', 'y', 'z'):
-                        break
-                    if param[0] == '\\':
-                        cell_parameters.append((param[1:], value))
-                    elif param == 'b/a':
-                        cell_parameters.append(('b', tmp['_cell_length_b']))
-                    elif param == 'c/a':
-                        cell_parameters.append(('c', tmp['_cell_length_c']))
-                    else:
-                        cell_parameters.append((param, value))
-                cp.append(cell_parameters)
-
-                site_data = []
-                for symbol, site, mult in zip(
-                    tmp['_atom_site_type_symbol'],
-                    tmp['_atom_site_Wyckoff_label'],
-                    tmp['_atom_site_symmetry_multiplicity']
-                ):
-                    site_data.append((site, int(mult), symbol))
-                sites.append(site_data)
-
-        with open('prototypes3.json', 'w') as fd:
-            json.dump(data, fd, indent=4)
+    test()
+
+    # if True:
+    #     test()
+    # elif False:
+    #     bibtex = ''
+    #     with open('prototypes.json', 'r') as fd:
+    #         data = json.load(fd)
+
+    #     for prototype in data['AFLOW prototype']:
+    #         print(prototype)
+    #         if prototype in bib:
+    #             text = bib[prototype]
+    #         else:
+    #             text = get_bibtex(prototype)
+    #         bibtex += text
+    #     with open('references2.bib', 'w') as fd:
+    #         fd.write(bibtex)
+    # elif False:
+    #     run()
+    # elif False:
+    #     # Fix the prototypes to have added formula part in some cases
+    #     # Get the data from the json
+    #     with open('prototypes.json', 'r') as fd:
+    #         data = json.load(fd)
+
+    #     aflow_prototypes = []
+    #     for hyperlink in data['hyperlink']:
+    #         url = urllib.parse.urlsplit(hyperlink)
+    #         path = url.path
+    #         root, extension = os.path.splitext(os.path.basename(path))
+    #         aflow_prototypes.append(root)
+
+    #     data['AFLOW prototype'] = aflow_prototypes
+
+    #     with open('prototypes2.json', 'w') as fd:
+    #         json.dump(data, fd, indent=4)
+    # else:
+    #     # Get the data from the json
+    #     with open('prototypes2.json', 'r') as fd:
+    #         data = json.load(fd)
+
+    #     cp = data['cell parameters'] = []
+    #     sites = data['sites'] = []
+    #     # Fetch the cif file to get the adjustable parameters
+    #     for hyperlink in data['hyperlink']:
+    #         url = urllib.parse.urlsplit(hyperlink)
+    #         path = url.path
+    #         root, extension = os.path.splitext(os.path.basename(path))
+    #         filename = root + '.cif'
+    #         new_path = os.path.join('.', filename)
+    #         if not os.path.exists(new_path):
+    #             print(f'{new_path} does not exist')
+    #         else:
+    #             try:
+    #                 cif = CifFile.ReadCif(new_path)
+    #             except Exception:
+    #                 print(f'Error in {new_path}\n\n')
+    #                 raise
+    #             tmp = cif['findsym-output']
+    #             params = tmp['_aflow_params'].split(',')
+    #             values = tmp['_aflow_params_values'].split(',')
+
+    #             cell_parameters = []
+    #             for param, value in zip(params, values):
+    #                 if param[0] in ('x', 'y', 'z'):
+    #                     break
+    #                 if param[0] == '\\':
+    #                     cell_parameters.append((param[1:], value))
+    #                 elif param == 'b/a':
+    #                     cell_parameters.append(('b', tmp['_cell_length_b']))
+    #                 elif param == 'c/a':
+    #                     cell_parameters.append(('c', tmp['_cell_length_c']))
+    #                 else:
+    #                     cell_parameters.append((param, value))
+    #             cp.append(cell_parameters)
+
+    #             site_data = []
+    #             for symbol, site, mult in zip(
+    #                 tmp['_atom_site_type_symbol'],
+    #                 tmp['_atom_site_Wyckoff_label'],
+    #                 tmp['_atom_site_symmetry_multiplicity']
+    #             ):
+    #                 site_data.append((site, int(mult), symbol))
+    #             sites.append(site_data)
+
+    #     with open('prototypes3.json', 'w') as fd:
+    #         json.dump(data, fd, indent=4)

crystal_builder_step/tk_crystal_builder.py

@@ -2,12 +2,10 @@
 
 """The graphical part of a Crystal Builder step"""
 
-import pprint  # noqa: F401
 import tkinter as tk
 import tkinter.ttk as ttk
 
 import seamm
-from seamm_util import ureg, Q_, units_class  # noqa: F401
 import seamm_widgets as sw
 import crystal_builder_step  # noqa: F401
 

requirements.txt

@@ -1,5 +1,5 @@
 openpyxl==3.0.5
 pycifrw==4.4.1
-seamm==2020.12.4
+seamm==2021.2.2
 seamm-util==2020.12.2
 seamm-widgets==2020.12.3