autostemparameters['Grid_sim2exp'] = 1
autostemparameters['Pixelshift'] = False
parameters={'structure':'Cluster',
'optimizer_type':'GA',
'atomlist':[('Au',1,196.9665,-3.6)],'natoms': 309,
'nindiv': 60, 'maxgen': 100, 'reqrep': 10,
'restart': True,
'generate_flag': 'sphere',
'tolerance': 0.01,
'r_ab': 2.5, 'size': 23.0,
'cxpb': 0.8, 'mutpb': 0.2, 'cx_scheme': 'cxtp', #rotct_rand',
'mutation_options': ['lattice_alteration','lattice_alteration_group','rotation','stem_mutation','zp_rotation'],
'selection_scheme': 'tournament2', 'natural_selection_scheme': 'fuss', 'tournsize': 3, 'fusslimit': 10,
'convergence_scheme': 'gen-rep-min', 'fingerprinting': False, 'predator': 'fitpred', 'demin': 0.05,
'pair_style': 'eam', 'pot_file': 'Au_u3.eam',
'filename': 'Output',
'lammps_keep_files': True, 'lammps_min': '1e-8 1e-8 5000 10000', 'lammps_min_style': 'cg\nmin_modify line quadratic', 'lammps_thermo_steps': 1000,
'genealogy': True, 'allenergyfile': True, 'best_inds_list': True, 'postprocessing': True,
'parallel': True,
'energy_cutoff_factor': 4.0,
'stem_keep_files': False, 'stem_coeff': 10.0
}
parameters['stem_parameters']=autostemparameters
parameters['fitness_scheme']='stem_cost'
else:
parameters=None
parameters = MPI.COMM_WORLD.bcast(parameters,root=0)
C = Optimizer(parameters)
C.run()
def main():
from MAST.structopt import Optimizer
from MAST.structopt 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
print 'Running parallel...'
parameters['filename'] = 'Test-Parallel'
parameters['parallel'] = True
A = Optimizer(parameters)
A.algorithm_parallel()
print 'Running Island_Method'
parameters['filename'] = 'Test-IM'
'forcing': 'Concentration',
'calc_method': 'LAMMPS',
'pair_style':'eam/fs',
'pot_file':'Fe_mm.eam.fs',
'lammps_thermo_steps':100,
'keep_Lammps_files': True,
'ase_min': False,
'lammps_min': mincomd,
'lammps_min_style': 'cg\nmin_modify line quadratic',
'genealogy': True,
'output_format': 'FormationEnergyPerInt',
'allenergyfile':True,
'bestindslist': True,
'finddefects':True,
'parallel' : True,
'algorithm_type' : 'lambda+mu',
'debug':['None']}
bsfe = BCC('Fe', size=parameters['supercell'])
rank = MPI.COMM_WORLD.Get_rank()
if rank==0:
write(parameters['SolidFile'],bsfe)
cell=numpy.maximum.reduce(bsfe.get_cell())
parameters['SolidCell']=cell
A = Optimizer(parameters)
A.algorithm_parallel()
if __name__ == "__main__":
main()
'lammps_min':
'1e-8 1e-8 5000 10000',
'lammps_min_style':
'cg\nmin_modify line quadratic',
'lammps_thermo_steps':
1000,
'genealogy':
True,
'allenergyfile':
True,
'best_inds_list':
True,
'postprocessing':
True,
'parallel':
True,
'energy_cutoff_factor':
4.0,
'stem_keep_files':
False,
'stem_coeff':
10.0
}
parameters['stem_parameters'] = autostemparameters
parameters['fitness_scheme'] = 'stem_cost'
else:
parameters = None
parameters = MPI.COMM_WORLD.bcast(parameters, root=0)
C = Optimizer(parameters)
C.run()
'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 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()
#import matplotlib.pyplot as plt
#import matplotlib.cm as cm
from MAST.structopt.tools.StemCalc import ConvStem
from MAST.structopt.generate.gen_pop_box import gen_pop_box as gpb
from MAST.structopt import Optimizer
import numpy
size = 10.0
Au1 = gpb([('Au',10,0,0),('Cu',10,0,0)],size)
aber=[[0,0],[0,0],[22.56,-20.1],[22.08,-7.5],[0.1198,0],[0.9018,-170.1],[0.04964,20.9],[28.43,-120.6],[11.84,153.8],[8.456,76.1],[0.622,0],[2.811,-125.5]]
autostemparameters={'Electron energy': 200,'Spherical aberration': 1.4,'Defocus':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()
"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"
def main():
from MAST.structopt import Optimizer
from MAST.structopt 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()