def _getBasisAtoms(self, ilayer):
atom_numbers = Uniqify(
[atom.GetAtomicNum() for atom in self._fragmentation.getAtoms()])
atom_numbers.sort()
atoms = [
self._elements.GetSymbol(atom_number)
for atom_number in atom_numbers
]
return "".join(
[self._formatSingleAtomBasis(ilayer, atom) for atom in atoms])
def _setupActiveFragmentsInformation(self):
active_atoms = self._getActiveAtomsFromFragments()
if self._active_atoms_distance > 0.0:
active_atoms = self._getActiveAtomsFromDistance()
if self._verbose:
print("Info: FragIt [GAMESS-FMO] found {0:d} atoms which should be active".format(len(active_atoms)))
self._active_atoms = active_atoms[:]
atoms = self._active_atoms[:]
frags = self._fragmentation.getFragments()
fragment_layers = self._fragment_layers[:]
if self._central_fragment == 0:
self._active_frags = []
return
# 1) If there are active atoms, we must find the associated fragments
# 2) The associated fragments are labelled active
# 3) The active fragments have their atoms made flexible
# we now have region A
if len(self._active_atoms) > 0:
active_frags = [] #self._active_fragments[:]
active_frags.append(self._central_fragment -1) # central must also be active
for atom in atoms:
ifrg = self._getFragmentFromAtom(atom)
active_frags.extend([ifrg])
active_frags = Uniqify(active_frags)
active_frags = sorted(active_frags)
self._active_fragments = active_frags[:]
# promote active fragments to layer 2
for active_fragment_id in active_frags:
self._fragment_layers[active_fragment_id] = 2
# add active fragment atoms to list of active atoms
fragments = self._fragmentation.getFragments()
for frag in active_frags:
atoms.extend(fragments[frag])
atoms = Uniqify(atoms)
atoms = sorted(atoms)
if self._verbose and len(atoms) != len(self._active_atoms):
print("Info: FragIt [GAMESS-FMO] active region is now {0:d} atoms ({1:d} fragments) ".format(len(active_atoms), len(active_frags)))
# Optionally freeze backbone atoms in the active region
if self._freeze_backbone:
for item in self._fragmentation.getBackboneAtoms():
if item in atoms:
atoms.remove(item)
continue
atoms = Uniqify(atoms)
atoms = sorted(atoms)
self._active_atoms = atoms[:]
def _setupActiveFragmentsInformation(self): active_atoms = self._getActiveAtomsFromFragments() if self._active_atoms_distance > 0.0: active_atoms = self._getActiveAtomsFromDistance() #print "found %i atoms which should be active" % (len(active_atoms)) self._active_atoms = active_atoms[:] atoms = self._active_atoms[:] frags = self._fragmentation.getFragments() fragment_layers = self._fragment_layers[:] if self._central_fragment == 0: self._active_frags = [] return if len(self._active_atoms) > 0: #print "extending region A to include all atoms of close fragments" active_frags = [] #self._active_fragments[:] active_frags.append(self._central_fragment -1) # central must also be active for atom in atoms: ifrg = self._getFragmentFromAtom(atom) active_frags.extend([ifrg]) active_frags = Uniqify(active_frags) active_frags = sorted(active_frags) self._active_fragments = active_frags[:] # promote active fragments to layer 2 for active_fragment_id in active_frags: self._fragment_layers[active_fragment_id] = 2 # add active fragment atoms to list of active atoms fragments = self._fragmentation.getFragments() for frag in active_frags: atoms.extend(fragments[frag]) atoms = Uniqify(atoms) atoms = sorted(atoms) #print "active region is now %i atoms large (%i fragments)" % (len(atoms),len(active_frags)) #print atoms if self._freeze_backbone: #print "attempting to find and freeze backbone atoms in the active region" for item in self._fragmentation.getBackboneAtoms(): if item in atoms: atoms.remove(item) continue #print "active region is now %i atoms large (%i fragments)" % (len(atoms),len(active_frags)) #print atoms atoms = Uniqify(atoms) atoms = sorted(atoms) self._active_atoms = atoms[:]
def _getActiveAtomsFromDistance(self):
atoms = []
central_atoms = self._fragmentation.getFragments()[
self._central_fragment - 1]
atoms.extend(central_atoms)
all_atoms = range(1, len(self._fragmentation.getAtoms()) + 1)
for atom_idx in central_atoms:
for atom_jdx in all_atoms:
if atom_jdx in central_atoms: continue
if atom_jdx in atoms: continue
R = self._getDistanceBetweenAtoms(atom_idx, atom_jdx)
if R < self._active_atoms_distance:
atoms.append(atom_jdx)
continue
atoms = Uniqify(atoms)
return sorted(atoms)
def _setupActiveFragmentsInformation(self):
active_atoms = self._getActiveAtomsFromFragments()
if self._active_atoms_distance > 0.0:
active_atoms = self._getActiveAtomsFromDistance()
#print "found %i atoms which should be active" % (len(active_atoms))
self._active_atoms = active_atoms[:]
atoms = self._active_atoms[:]
frags = self._fragmentation.getFragments()
fragment_layers = self._fragment_layers[:]
if self._central_fragment == 0:
self._active_frags = []
return
if len(self._active_atoms) > 0:
#print "extending region A to include all atoms of close fragments"
active_frags = [] #self._active_fragments[:]
active_frags.append(self._central_fragment -
1) # central must also be active
for atom in atoms:
ifrg = self._getFragmentFromAtom(atom)
active_frags.extend([ifrg])
active_frags = Uniqify(active_frags)
active_frags = sorted(active_frags)
self._active_fragments = active_frags[:]
# promote active fragments to layer 2
for active_fragment_id in active_frags:
self._fragment_layers[active_fragment_id] = 2
# add active fragment atoms to list of active atoms
fragments = self._fragmentation.getFragments()
for frag in active_frags:
atoms.extend(fragments[frag])
atoms = Uniqify(atoms)
atoms = sorted(atoms)
#print "active region is now %i atoms large (%i fragments)" % (len(atoms),len(active_frags))
#print atoms
if self._freeze_backbone:
#print "attempting to find and freeze backbone atoms in the active region"
for item in self._fragmentation.getBackboneAtoms():
if item in atoms:
atoms.remove(item)
continue
#print "active region is now %i atoms large (%i fragments)" % (len(atoms),len(active_frags))
#print atoms
atoms = Uniqify(atoms)
atoms = sorted(atoms)
self._active_atoms = atoms[:]
def pop_qm_fragment(self):
""" Remove the qm fragments from the fragmentation. Adds hydrogens to both the
qm-fragment that is returned and to the neighbouring fragments if bonds were cut.
"""
# at this point, fragments have been generated
fragments = self._fragmentation.getFragments()
# investigate which fragments should be included in the QM-region
qmfrags = self._qmfrags[:]
distance = self._fragmentation.getActiveAtomsDistance()
qmfrags = Uniqify(self._add_fragments_to_QM(qmfrags))
qmfrags.sort()
qmfrags.reverse()
qm_region_charge = 0
fragments_for_qm_no_hydrogens = []
# instead of removing the qm-fragment, we rather adopt a quite novel approach
# in which we signal to the user of the API that the fragment is not to be used
# further by setting its original atom numbers to -1
for idx in qmfrags:
qm_region_charge += self._qm_charges[idx]
old_fragment = fragments.pop(idx)
fragments.insert(idx, [-1 for i in old_fragment])
fragments_for_qm_no_hydrogens.insert(0,old_fragment[:])
# for simplicity, let us just squash the qm fragments into one big fragment
fragments_for_qm_no_hydrogens = ravel2D(fragments_for_qm_no_hydrogens)
breaks = self._fragmentation.getExplicitlyBreakAtomPairs()
if len(breaks) == 0:
return (fragments_for_qm_no_hydrogens, qm_region_charge)
# below here: add hydrogens to qm-fragment and to the rest of the capped structure
fragment_for_qm = fragments_for_qm_no_hydrogens[:]
# first, fix the QM-fragment, removing any bond-breaks that reside
# inside (or bordering) the qm-fragment. if breaks are bordering,
# add appropriate hydrogen atoms.
lenqmfrags = len(fragments_for_qm_no_hydrogens)
remove_breaks = []
for ibreak, bbreak in enumerate(breaks):
lendiff = len(listDiff(fragments_for_qm_no_hydrogens, list(bbreak)))
difflen = lenqmfrags - lendiff
# the break is not present in the qm-region, leave it
if difflen == 0: continue
# mark the ibreak'th item for removal. no hydrogens to be added
if difflen == 2: remove_breaks.append(ibreak)
# the break is bordering the qm-region and the mm-region
if difflen == 1:
for iibreak in bbreak:
# fix the qm-fragment first
if iibreak in fragments_for_qm_no_hydrogens:
new_atoms = self.satisfyValency(fragments_for_qm_no_hydrogens, iibreak, bbreak)
if len(new_atoms) > 0:
print("Info: FragIt adds", len(new_atoms), "atom(s) to the QM fragment.")
self._fragmentation._atom_names.extend([' H '] * len(new_atoms))
fragment_for_qm.extend(new_atoms)
# then fix the fragments themselves
# INFO/WARNING: this is a lists of lists thing. BE CAREFULL
for ifragment, fragment in enumerate(fragments):
if iibreak in fragment:
new_atoms = self.satisfyValency(fragment, iibreak, bbreak)
print("Info: FragIt adds", len(new_atoms), "atom(s) to MM fragment", ifragment+1)
self._fragmentation._atom_names.extend([' H '] * len(new_atoms))
fragments[ifragment].extend(new_atoms)
# also mark the ibreak'th item for removal
remove_breaks.append(ibreak)
for ibreak in remove_breaks:
self._fragmentation.popExplicitlyBreakAtomPairs(breaks[ibreak])
#print("FRAGIT: [qm] {0}".format(fragment_for_qm))
return (fragment_for_qm, qm_region_charge)
def _getBasisAtoms(self, ilayer): atom_numbers = Uniqify([atom.GetAtomicNum() for atom in self._fragmentation.getAtoms()]) atom_numbers.sort() atoms = [self._elements.GetSymbol(atom_number) for atom_number in atom_numbers] return "".join([self._formatSingleAtomBasis(ilayer,atom) for atom in atoms])
