def relax_structure(system, potential, potential_filename=None, relax_positions=True, relax_cell=True): """ Run a geometry optimisation on the structure to find the energy minimum. Parameters ---------- system : ase.Atoms A system of atoms to run the minimisation on. The structure is altered in-place. potential : Potential or str A quippy Potential object with the desired potential, or a potential_str to initialise a new potential. Returns ------- minimised_structure : Atoms The geometry optimised structure. """ info("Inside minimiser.") qsystem = Atoms(system) if not isinstance(potential, Potential): if potential_filename: potential = Potential(potential, param_filename=potential_filename) else: potential = Potential(potential) qsystem.set_calculator(potential) minimiser = Minim(qsystem, relax_positions=relax_positions, relax_cell=relax_cell) with Capturing(debug_on_exit=True): minimiser.run() system.set_cell(qsystem.cell) system.set_positions(qsystem.positions) system.energy = qsystem.get_potential_energy() info("Minimiser done.") return system
def h2_formation_energy(pot): """ Given a potential calculate the H2 formation energy and equilibrium bond spacing. Args: pot(:quippy:class:`Potential`) potential object. Returns: float: Hydrogen molecule formation energy. """ h2 = aseAtoms('H2', positions=[[0, 0, 0], [0, 0, 0.7]]) h2 = Atoms(h2) h2.set_calculator(pot) opt = BFGS(h2) opt.run(fmax=0.0001) E_h2 = h2.get_potential_energy() return E_h2
block=block, corner=corner, shape=shape, exe = vasp, ediffg = -0.05, nelmin = 6, nelmdl = -15, kpar = 32, parmode='cobalt', xc='PBE', lreal=False, ibrion=13, nsw=40, algo='VeryFast', npar=8, lplane=False, lwave=False, lcharg=False, nsim=1, voskown=1, ismear=1, sigma=0.01, iwavpr=11, isym=2, nelm=100) sock_calc = SocketCalculator(vasp_client, ip=ip, bgq=True) bulk.set_calculator(sock_calc) opt = LBFGS(bulk) opt.run(fmax=0.05, steps=100) sock_e = bulk.get_potential_energy() sock_f = bulk.get_forces() sock_s = bulk.get_stress() print 'energy', sock_e print 'forces', sock_f print 'stress', sock_s sock_calc.shutdown()
ibrion=13, nsw=40, algo='VeryFast', npar=8, lplane=False, lwave=False, lcharg=False, nsim=1, voskown=1, ismear=1, sigma=0.01, iwavpr=11, isym=2, nelm=100) sock_calc = SocketCalculator(vasp_client, ip=ip, bgq=True) bulk.set_calculator(sock_calc) opt = LBFGS(bulk) opt.run(fmax=0.05, steps=100) sock_e = bulk.get_potential_energy() sock_f = bulk.get_forces() sock_s = bulk.get_stress() print 'energy', sock_e print 'forces', sock_f print 'stress', sock_s sock_calc.shutdown()
def calc_bulk_dissolution(args): """Calculate the bulk dissolution energy for hydrogen in a tetrahedral position in bcc iron. Args: args(list): determine applied strain to unit cell. """ POT_DIR = os.path.join(app.root_path, 'potentials') eam_pot = os.path.join(POT_DIR, 'PotBH.xml') r_scale = 1.00894848312 pot = Potential( 'IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale), param_filename=eam_pot) alat = 2.83 gb = BodyCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]], size=(6, 6, 6), symbol='Fe', pbc=(1, 1, 1), latticeconstant=alat) cell = gb.get_cell() print 'Fe Cell', cell e1 = np.array([1, 0, 0]) e2 = np.array([0, 1, 0]) e3 = np.array([0, 0, 1]) if args.hydrostatic != 0.0: strain_tensor = np.eye(3) + args.hydrostatic * np.eye(3) cell = cell * strain_tensor gb.set_cell(cell, scale_atoms=True) print 'Hydrostatic strain', args.hydrostatic print 'strain tensor', strain_tensor print gb.get_cell() elif args.stretch != 0.0: strain_tensor = np.tensordot(e2, e2, axes=0) strain_tensor = np.eye(3) + args.stretch * strain_tensor cell = strain_tensor * cell print 'Stretch strain' print 'Cell:', cell gb.set_cell(cell, scale_atoms=True) elif args.shear != 0.0: strain_tensor = np.tensordot(e1, e2, axes=0) strain_tensor = np.eye(3) + args.shear * strain_tensor cell = strain_tensor.dot(cell) print 'Shear Strain', strain_tensor print 'Cell:', cell gb.set_cell(cell, scale_atoms=True) gb.write('sheared.xyz') else: print 'No strain applied.' tetra_pos = alat * np.array([0.25, 0.0, 0.5]) h2 = aseAtoms('H2', positions=[[0, 0, 0], [0, 0, 0.7]]) h2 = Atoms(h2) gb = Atoms(gb) gb_h = gb.copy() gb_h.add_atoms(tetra_pos, 1) #caclulators gb.set_calculator(pot) h2.set_calculator(pot) gb_h.set_calculator(pot) gb_h.write('hydrogen_bcc.xyz') #Calc Hydrogen molecule energy opt = BFGS(h2) opt.run(fmax=0.0001) E_h2 = h2.get_potential_energy() h2.write('h2mol.xyz') #strain_mask = [1,1,1,0,0,0] strain_mask = [0, 0, 0, 0, 0, 0] ucf = UnitCellFilter(gb_h, strain_mask) #opt = BFGS(gb_h) opt = FIRE(ucf) opt.run(fmax=0.0001) E_gb = gb.get_potential_energy() E_gbh = gb_h.get_potential_energy() E_dis = E_gbh - E_gb - 0.5 * E_h2 print 'E_gb', E_gb print 'E_gbh', E_gbh print 'H2 Formation Energy', E_h2 print 'Dissolution Energy', E_dis
h2 = Atoms(h2) gb = Atoms(gb) gb_h = gb.copy() gb_h.add_atoms(tetra_pos, 1) #caclulators gb.set_calculator(pot) h2.set_calculator(pot) gb_h.set_calculator(pot) gb_h.write('hydrogen_bcc.xyz') #Calc Hydrogen molecule energy opt = BFGS(h2) opt.run(fmax=0.0001) E_h2 = h2.get_potential_energy() strain_mask = [1, 1, 1, 0, 0, 0] ucf = UnitCellFilter(gb_h, strain_mask) #opt = BFGS(gb_h) opt = FIRE(ucf) opt.run(fmax=0.0001) E_gb = gb.get_potential_energy() E_gbh = gb_h.get_potential_energy() E_dis = E_gbh - E_gb - 0.5 * E_h2 print 'E_gb', E_gb print 'E_gbh', E_gbh print 'H2 Formation Energy', E_h2 print 'Dissolution Energy', E_dis