def main():
from MAST.structopt_stem import Optimizer
from MAST.structopt_stem import tools
#Test for cluster structures
parameters = {
'structure': 'Cluster',
'optimizer_type': 'GA',
'atomlist': [('Au', 10, 0, 0), ('Cu', 10, 0, 0)]
}
A = Optimizer(parameters)
A.algorithm_initialize()
A.calc = tools.setup_calculator(A)
offspring = A.generation_set([])
indiv = offspring[0].duplicate()
ind1 = offspring[1].duplicate()
ind2 = offspring[2].duplicate()
test_mutations(indiv)
test_cx(ind1, ind2)
A.close_output()
#Test for defect structures
parameters = {
'structure': 'Defect',
'optimizer_type': 'GA',
'atomlist': [('Au', 3, 0, 0), ('Cu', 3, 0, 0)],
'supercell': (3, 3, 3),
'SolidFile': 'BFe.xyz',
'SolidCell': [8.61, 8.61, 8.61]
}
A = Optimizer(parameters)
A.algorithm_initialize()
A.calc = tools.setup_calculator(A)
offspring = A.generation_set([])
indiv = offspring[0].duplicate()
ind1 = offspring[1].duplicate()
ind2 = offspring[2].duplicate()
test_mutations(indiv)
test_cx(ind1, ind2)
A.close_output()
#Test for crystal structures
parameters = {
'structure': 'Crystal',
'optimizer_type': 'GA',
'atomlist': [('Au', 10, 0, 0), ('Cu', 10, 0, 0)]
}
A = Optimizer(parameters)
A.algorithm_initialize()
A.calc = tools.setup_calculator(A)
offspring = A.generation_set([])
indiv = offspring[0].duplicate()
ind1 = offspring[1].duplicate()
ind2 = offspring[2].duplicate()
test_mutations(indiv)
test_cx(ind1, ind2)
A.close_output()
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
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)
'Aperture semiangle': 24.5,
'Source size': 0.882,
'Slice size': 20.0,
'Pixels': 800,
'aber': aber,
'Scale Factor': 0.00570113
}
A = ConvStem(parameters=autostemparameters, calc_exp=False)
#fig = plt.figure()
#ax = fig.add_subplot(111)
#psf = numpy.fft.fftshift(A.psf)
#ax.imshow(psf,cmap=cm.hot)
#plt.show()
imAu1 = A.get_image(A.psf, Au1, autostemparameters['Slice size'],
autostemparameters['Pixels'], 1)
#fig2 = plt.figure()
#ax2 = fig2.add_subplot(111)
#ax2.imshow(imAu1,cmap=cm.hot)
#plt.show()
autostemparameters['Exp_Image'] = imAu1
optparameters = {
'structure': 'Cluster',
'optimizer_type': 'BH',
'size': 10,
'atomlist': [('Au', 10, 0, 0), ('Cu', 10, 0, 0)],
'FIT_SCHEME': 'STEM_Cost',
'STEM_Parameters': autostemparameters
}
B = Optimizer(optparameters)
B.algorithm_serial()
from MAST.structopt_stem import Optimizer
from mpi4py import MPI
rank = MPI.COMM_WORLD.Get_rank()
if rank==0:
print 'Running Serial...'
A = Optimizer('input-clus.txt')
A.run()
done = True
else:
done = False
done = MPI.COMM_WORLD.bcast(done,root=0)
print done
print 'Running parallel...'
A = Optimizer('input-clus-p.txt')
A.run()
print 'Running Island_Method'
A = Optimizer('input-clus-im.txt')
A.run()
