If you are using GitLab outside of the ILL, then you will need to use HTTPS and not SSH for clone/push/pull operations. If you are using the VPN, then SSH will work normally.

Commit 8320fc41 authored by eric pellegrini's avatar eric pellegrini

bug fix when transmutating atoms from an atom selection different to 'all'

parent 7c0d220c
......@@ -105,14 +105,17 @@ class AtomSelectionConfigurator(IConfigurator):
parser = AtomSelectionParser(trajConfig["instance"])
indexes.update(parser.parse(v))
indexes = sorted(list(indexes))
self["flatten_indexes"] = sorted(list(indexes))
trajConfig = self._configurable[self._dependencies['trajectory']]
atoms = sorted(trajConfig["universe"].atomList(), key = operator.attrgetter('index'))
selectedAtoms = [atoms[idx] for idx in indexes]
self["selection_length"] = len(indexes)
self["selection_length"] = len(self["flatten_indexes"])
self['indexes'] = [[idx] for idx in self["flatten_indexes"]]
self['elements'] = [[at.symbol] for at in selectedAtoms]
self['indexes'] = [[idx] for idx in indexes]
self['names'] = [at.symbol for at in selectedAtoms]
self['unique_names'] = sorted(set(self['names']))
self['masses'] = [[ELEMENTS[n,'atomic_weight']] for n in self['names']]
......
......@@ -112,12 +112,18 @@ class AtomTransmutationConfigurator(IConfigurator):
raise ConfiguratorError("the element %r is not registered in the database" % element, self)
atomSelConfigurator = self._configurable[self._dependencies['atom_selection']]
for idx in selection:
atomSelConfigurator["names"][idx] = element
atomSelConfigurator["elements"][idx] = [element]
try:
idxInSelection = atomSelConfigurator["flatten_indexes"].index(idx)
except ValueError:
pass
else:
atomSelConfigurator["names"][idxInSelection] = element
atomSelConfigurator["elements"][idxInSelection] = [element]
atomSelConfigurator['unique_names'] = sorted(set(atomSelConfigurator['names']))
atomSelConfigurator['masses'] = [[ELEMENTS[n,'atomic_weight']] for n in atomSelConfigurator['names']]
def get_information(self):
'''
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment