'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()