def run_CNA_program(Cluster_1_name,Cluster_2_name):
Cluster_1 = ASE_read(Cluster_1_name+'.traj')
print 'Made ' + str(Cluster_1_name)
Cluster_2 = ASE_read(Cluster_2_name+'.traj')
print 'Made ' + str(Cluster_2_name)
CNA_run = Structural_Recognition_Program(Cluster_1,Cluster_2,rCut_low,rCut_high,rCut_resolution,mode,name_1=Cluster_1_name,name_2=Cluster_2_name,recognise_multimetallic=False,print_plots=True)
return CNA_run
def optimise(cluster_name):
cluster = ASE_read(cluster_name + '.traj')
cluster_optimised = RunMinimisation(cluster).get_cluster()
cluster_optimised.set_calculator(None)
cluster_name_opt = cluster_name + '_Opt'
ASE_write(cluster_name_opt + '.traj', cluster_optimised)
return cluster_name_opt, cluster_optimised
def Cluster_CNA_profile(Cluster_name, CNA_signature_to_monitor):
Cluster = ASE_read(Cluster_name + '.traj')
print 'Made ' + str(Cluster_name)
return Cluster_CNA_Profile(Cluster,
rCut_low,
rCut_high,
rCut_resolution,
CNA_signature_to_monitor,
name=Cluster_name,
recognise_multimetallic=False,
print_plots=True)
def load(self, file=None):
"""
Load structure from file
"""
# assume file can be read from within ASE
self._atoms = ASE_read(file)