'LammpsMin':
'1e-8 1e-8 5000 10000',
'Lmin_style':
'cg\nmin_modify line quadratic',
'genealogy':
True,
'allenergyfile':
True,
'BestIndsList':
True
}
if rank == 0:
print 'Running Serial...'
parameters['filename'] = 'Test-Serial'
A = Optimizer(parameters)
A.run()
done = True
else:
done = False
done = MPI.COMM_WORLD.bcast(done, root=0)
print done
if rank == 0:
print 'Running parallel...'
parameters['filename'] = 'Test-Parallel'
parameters['parallel'] = True
A = Optimizer(parameters)
else:
A = None
A = MPI.COMM_WORLD.bcast(A, root=0)
A.algorithm_parallel()
'convergence_scheme': 'Gen-Rep-Min',
'predator' : 'Mutation_Dups',
'mutation_options' : ['Lattice_Alteration','Lattice_Alteration_Group','Rotation_geo','Rotation'],
'pair_style' : 'eam',
'pot_file' : 'Au_u3.eam',
'keep_Lammps_files' : True,
'LammpsMin' : '1e-8 1e-8 5000 10000',
'Lmin_style' : 'cg\nmin_modify line quadratic',
'genealogy' : True,
'allenergyfile' : True,
'BestIndsList' : True}
if rank==0:
print 'Running Serial...'
parameters['filename'] = 'Test-Serial'
A = Optimizer(parameters)
A.run()
done = True
else:
done = False
done = MPI.COMM_WORLD.bcast(done,root=0)
print done
print 'Running parallel...'
parameters['filename'] = 'Test-Parallel'
parameters['parallel'] = True
A = Optimizer(parameters)
A.algorithm_parallel()
print 'Running Island_Method'
parameters['filename'] = 'Test-IM'
A = ConvStem(parameters=autostemparameters, calc_exp=False)
try:
atoms_ref = inp_out.read_xyz(parameters['stem_ref'], 0)
except KeyError:
atoms_ref = inp_out.read_xyz(
'/home/usitguest/USIT/dropbox_app/STEM_ref', 0)
nk = autostemparameters['Pixels']
A.psf = np.empty([nk, nk], dtype=float)
try:
fileobj = open(parameters['psf'], 'r')
except KeyError:
fileobj = open('/home/usitguest/USIT/dropbox_app/PSF.txt', 'r')
lines = fileobj.readlines()
for x in range(0, nk):
A.psf[x] = lines[x].split()
fileobj.close()
STEM_ref = A.get_image(A.psf, atoms_ref, autostemparameters['Slice size'],
autostemparameters['Pixels'])
parameters['stem_parameters'] = autostemparameters
autostemparameters['Exp_Image'] = STEM_ref
autostemparameters['Grid_sim2exp'] = 1
autostemparameters['Pixelshift'] = False
else:
parameters = None
parameters = MPI.COMM_WORLD.bcast(parameters, root=0)
C = Optimizer(parameters)
C.run()
parameters['stem_ref'] = ast.literal_eval(data[line].strip())['stem_ref']
'''
A = ConvStem(parameters=autostemparameters,calc_exp=False)
try:
atoms_ref=inp_out.read_xyz(parameters['stem_ref'],0)
except KeyError:
atoms_ref=inp_out.read_xyz('/home/usitguest/USIT/dropbox_app/STEM_ref',0)
nk = autostemparameters['Pixels']
A.psf = np.empty([nk,nk],dtype=float)
try:
fileobj = open(parameters['psf'], 'r')
except KeyError:
fileobj = open('/home/usitguest/USIT/dropbox_app/PSF.txt', 'r')
lines = fileobj.readlines()
for x in range(0,nk):
A.psf[x] = lines[x].split()
fileobj.close()
STEM_ref = A.get_image(A.psf, atoms_ref, autostemparameters['Slice size'], autostemparameters['Pixels'])
parameters['stem_parameters']=autostemparameters
autostemparameters['Exp_Image'] = STEM_ref
autostemparameters['Grid_sim2exp'] = 1
autostemparameters['Pixelshift'] = False
else:
parameters=None
parameters = MPI.COMM_WORLD.bcast(parameters,root=0)
C = Optimizer(parameters)
C.run()
