Simplify a bit

Author: jensj

ase/atom.py

@@ -1,21 +1,18 @@
 """This module defines the Atom object."""
 
-import warnings
-
 import numpy as np
 
 from ase.data import atomic_numbers, chemical_symbols, atomic_masses
 
 
-#         singular,    plural,     default value
+# Singular, plural, default value:
 names = {'position': ('positions', np.zeros(3)),
-         'number':   ('numbers',   0),
-         'tag':      ('tags',      0),
-         'momentum': ('momenta',   np.zeros(3)),
-         'mass':     ('masses',    None),
-         'magmom':   ('magmoms',   0.0),
-         'charge':   ('charges',   0.0)
-         }
+         'number': ('numbers', 0),
+         'tag': ('tags', 0),
+         'momentum': ('momenta', np.zeros(3)),
+         'mass': ('masses', None),
+         'magmom': ('magmoms', 0.0),
+         'charge': ('charges', 0.0)}
 
 
 def atomproperty(name, doc):

ase/cli/run.py

@@ -17,53 +17,73 @@
 from ase.optimize import LBFGS
 from ase.io.trajectory import PickleTrajectory
 from ase.utils.eos import EquationOfState
-from ase.calculators.calculator import get_calculator
+from ase.calculators.calculator import get_calculator, names as calcnames
 import ase.db as db
 
 
-def main(runner=None):
-    if runner is None:
-        runner = Runner()
+def main():
+    runner = Runner()
     runner.parse()
     if runner.errors:
         sys.exit(runner.errors)
 
 
 class Runner:
-    names = []
-
-    parameter_namespace = {}
-
-    calculator_name = None
-
     def __init__(self):
         self.db = None
         self.opts = None
         self.errors = 0
+        self.names = []
+        self.calculator_name = None
 
         if world.rank == 0:
             self.logfile = sys.stdout
         else:
             self.logfile = devnull
 
     def parse(self, args=None):
-        # create the top-level parser
+        parser = self.make_parser()
+        self.add_options(parser)
+        self.opts, names = parser.parse_args(args)
+
+        if args is None and self.opts.interactive_python_session:
+            file = tempfile.NamedTemporaryFile()
+            file.write('import os\n')
+            file.write('if "PYTHONSTARTUP" in os.environ:\n')
+            file.write('    execfile(os.environ["PYTHONSTARTUP"])\n')
+            file.write('from ase.cli.run import Runner\n')
+            file.write('atoms = Runner().parse(%r)\n' %
+                       ([self.calculator_name] + sys.argv[1:]))
+            file.flush()
+            os.system('python -i %s' % file.name)
+            return
+
+        if self.calculator_name is None:
+            if names:
+                self.calculator_name = names.pop(0)
+            else:
+                parser.error('Missing calculator name')
+                
+        atoms = self.run(names)
+        return atoms
+        
+    def make_parser(self):
         parser = optparse.OptionParser(
-            usage='%prog calculator [options] [name, name, ...]')
+            usage='ase-run calculator [options] [system, ...]',
+            description="Run calculation with one of ASE's calculators: " +
+            ', '.join(calcnames) + '.')
+        return parser
+        
+    def add_options(self, parser):
         add = parser.add_option
-        add('-q', '--quiet', action='store_const', const=0, default=1,
-            dest='verbosity')
-        add('-V', '--verbose', action='store_const', const=2, default=1,
-            dest='verbosity')
         add('-t', '--tag',
             help='String tag added to filenames.')
-        add('--plugin')
         add('-p', '--parameters', default='',
             metavar='key=value,...',
             help='Comma-separated key=value pairs of ' +
             'calculator specific parameters.')
         add('-d', '--database',
-            help='Use a filename with a ".sqlite" extension for a sqlite3 ' +
+            help='Use a filename with a ".db" extension for a sqlite3 ' +
             'database or a ".json" extension for a simple json database.  ' +
             'Default is no database')
         add('-S', '--skip', action='store_true',
@@ -81,42 +101,13 @@ def parse(self, args=None):
             help='Relax unit-cell and internal coordinates.')
         add('-E', '--equation-of-state', help='Equation of state ...')
         add('--eos-type', default='sjeos', help='Selects the type of eos.')
-        add('-i', '--interactive-python-session', action='store_true',
-           )  # help=optparse.SUPPRESS)
+        add('-i', '--interactive-python-session', action='store_true')
         add('-c', '--collection')
         add('--modify', metavar='...',
             help='Modify atoms with Python statement.  ' +
             'Example: --modify="atoms.positions[-1,2]+=0.1".')
         add('--after', help='Perform operation after calculation.  ' +
             'Example: --after="atoms.calc.write(...)"')
-            
-        self.opts, names = parser.parse_args(args)
-
-        if args is None and self.opts.interactive_python_session:
-            file = tempfile.NamedTemporaryFile()
-            file.write('import os\n')
-            file.write('if "PYTHONSTARTUP" in os.environ:\n')
-            file.write('    execfile(os.environ["PYTHONSTARTUP"])\n')
-            file.write('from ase.cli.run import Runner\n')
-            file.write('atoms = Runner().parse(%r)\n' %
-                       ([self.calculator_name] + sys.argv[1:]))
-            file.flush()
-            os.system('python -i %s' % file.name)
-            return
-
-        if self.calculator_name is None:
-            if names:
-                self.calculator_name = names.pop(0)
-            else:
-                parser.error('Missing calculator name')
-                
-        if self.opts.plugin:
-            runner = self.get_runner()
-        else:
-            runner = self
-
-        atoms = runner.run(names)
-        return atoms
 
     def log(self, *args, **kwargs):
         print(file=self.logfile, *args, **kwargs)
@@ -193,20 +184,6 @@ def calculate(self, atoms, name):
 
         return data
 
-    def get_plugin(self, name):
-        f = open(self.opts.plugin)
-        script = f.read()
-        f.close()
-        namespace = {}
-        exec script in namespace
-        for cls in namespace:
-            if issubclass(namespace[cls], Runner):
-                runner = namespace[cls]()
-                runner.opts = self.opts
-                runner.calculator_name = self.calculator_name
-                runner.parameter_namespace = self.parameter_namespace
-                return runner
-
     def expand(self, names):
         if not self.names and self.opts.collection:
             con = db.connect(self.opts.collection)
@@ -240,17 +217,12 @@ def build(self, name):
 
     def set_calculator(self, atoms, name):
         cls = get_calculator(self.calculator_name)
-        parameters = self.get_parameters()
+        parameters = str2dict(self.opts.parameters)
         if getattr(cls, 'nolabel', False):
             atoms.calc = cls(**parameters)
         else:
             atoms.calc = cls(label=self.get_filename(name), **parameters)
 
-    def get_parameters(self):
-        namespace = self.parameter_namespace
-        parameters = str2dict(self.opts.parameters, namespace)
-        return parameters
-
     def calculate_once(self, atoms, name):
         opts = self.opts