def main():
atoms_ref = vf.my_read_vasp('../y_full_relax/CONTCAR') # for strain
natoms = atoms_ref.get_positions().shape[0]
dirlist = [
'y_convergence_encut',
'y_convergence_kp',
'y_convergence_sigma',
]
ljobn = [] # list of data
lEtot = []
lEent = []
for i in np.arange(len(dirlist)):
dirn = dirlist[i]
print(dirn)
os.chdir(dirn)
jobn, Etot, Eent, pres = vf.vasp_read_post_data()
os.chdir('..')
x = np.array([])
for j in np.arange(len(jobn)):
temp = float(jobn[j])
x = np.append(x, temp)
ljobn.append(x)
lEtot.append(Etot / natoms)
lEent.append(Eent / natoms)
plot_convergence(ljobn, lEtot, lEent)
def vasp_create_hcp_prism1(a, ca, ncell, bp=33):
print('==> create hcp prism plane: ')
print(a, ca, ncell, bp)
ncell2 = ncell.copy()
for i in np.arange(3):
ncell2[i] = ncell[np.mod(i + 2, 3)]
vasp_create_hcp_basal(a, ca, ncell2, bp=0)
atoms = vf.my_read_vasp('POSCAR')
atoms = vf.make_SFP_xy(atoms, i1=1)
atoms = vf.make_a3_ortho(atoms)
if bp == 33:
print('==> create prism1-W')
atoms.positions = atoms.positions + np.array([0, 0, 0.1]) * a
atoms.wrap()
elif bp == -33:
print('==> create prism1-N')
atoms.positions = atoms.positions + np.array([0, 0, -0.1]) * a
atoms.wrap()
atoms.pos_a0 = a
vf.my_write_vasp(atoms, filename='POSCAR', vasp5=True)
def run_MC_case(nstep=1000, T_list=[300.0, 1500.0], \
EPI_filename='y_post_EPI.beta_4.txt', \
pos_filename='CONTCAR'):
EPI_beta = np.loadtxt(EPI_filename)
atoms = vf.my_read_vasp(pos_filename)
for T in np.array(T_list):
print('==> MC starts, with T:', T)
MC_swap_with_EPI(atoms, EPI_beta, T, nstep)
def shift_to_complete_layers():
atoms = vf.my_read_vasp(filename='CONTCAR')
nlayers, nmiss = check_layers(atoms)
if nmiss > 0.1:
print('==> shift to POSCAR_layer, nmiss:', nmiss)
shift_to_poscar_layer(nmiss)
else:
print('==> no shift needed. ')
def shift_to_poscar_layer(nmiss):
atoms = vf.my_read_vasp(filename='CONTCAR')
z = atoms.get_positions()[:, -1]
z.sort()
natoms = len(z)
latt33 = atoms.get_cell()[2, 2]
temp1 = latt33 - z[int(-1 * nmiss)]
temp2 = z[int(-1 * nmiss)] - z[int(-1 * nmiss - 1)]
zshift = temp1 + 0.5 * temp2
pos = atoms.get_positions()
pos[:, 2] = pos[:, 2] + zshift
atoms.set_positions(pos)
atoms.wrap()
vf.my_write_vasp(atoms, filename='POSCAR_layer', vasp5=True)
# check
atoms2 = vf.my_read_vasp('POSCAR_layer')
atoms3 = vf.my_read_vasp('CONTCAR')
latt = atoms2.get_cell()[:]
vf.confirm_0(latt - atoms3.get_cell()[:])
dpos = atoms2.get_positions() - atoms3.get_positions()
dposD = dpos @ np.linalg.inv(latt)
dposD = dposD - np.around(dposD)
dpos = dposD @ latt
for i in np.arange(3):
dpos[:, i] = dpos[:, i] - dpos[:, i].mean()
vf.confirm_0(dpos)
def main():
atoms_ref = vf.my_read_vasp('../y_full_relax/CONTCAR') # for strain
dirlist = [
'y_cij_energy_c11',
'y_cij_energy_c12',
'y_cij_energy_c13',
'y_cij_energy_c33',
'y_cij_energy_c44',
]
ldata = [] # list of data
for i in np.arange(len(dirlist)):
dirn = dirlist[i]
print(dirn)
data = read_deform_data(dirn, atoms_ref)
ldata.append(data)
check_ldata(ldata)
plot_cij_energy(ldata)
def calc_gamma_s(EPI_beta, pos_filename, a_fcc, b_slip):
atoms = vf.my_read_vasp( pos_filename )
latt = atoms.get_cell()[:]
natoms = atoms.get_positions().shape[0]
b = atoms.pos_a0/np.sqrt(2)
nx = np.around( latt[0,0]/b )
vf.confirm_int(nx)
nx = int(nx)
nlayers, nmiss = vf_shift.check_layers(filename = pos_filename)
vf.confirm_0(nmiss)
nz = nlayers
E_s = calc_E_s(atoms, nx, nz, EPI_beta, b_slip)
vf.confirm_0( E_s.shape - np.array([nz/6, 2]) )
qe = vf.phy_const('qe')
gamma_s = E_s/(natoms/nz) / (np.sqrt(3)/2*a_fcc**2/2) *qe*1e23
return gamma_s, nz
def calc_pairs_per_shell_from_CONTCAR(shellmax=4):
atoms = vf.my_read_vasp('CONTCAR')
calc_pairs_per_shell(atoms, shellmax=shellmax)
def analyze_dump(jobname):
atoms = vf.my_read_vasp('../CONTCAR')
nelem = atoms.get_nelem()
EPI_beta = np.loadtxt('../y_post_EPI.beta_4.txt')
# extend EPIs to 10 shells
if nelem == 2:
EPI_beta = np.append(EPI_beta, np.zeros(11 - len(EPI_beta)))
else:
shellmax = calc_shellmax(atoms, EPI_beta)
temp = int((len(EPI_beta) - 1) / shellmax * (10 - shellmax))
temp2 = np.zeros(temp)
EPI_beta = np.append(EPI_beta, temp2)
print('==> extended EPI_beta:')
print(EPI_beta)
os.system('ls POSCAR_step_* > tmp_filelist')
f = open('tmp_filelist', 'r')
dp_shell_tot = np.zeros(len(EPI_beta) - 1)
WC_SRO_tot = np.zeros(len(EPI_beta) - 1)
for line in f:
filename = line.strip('\n')
print(filename)
atoms = vf.my_read_vasp(filename)
dp_shell = plot_dp_shell(atoms, EPI_beta=EPI_beta)
dp_shell_tot = np.vstack([dp_shell_tot, dp_shell])
filename2 = 'y_post_dp_shell_%s.pdf' % (filename)
os.rename('y_post_dp_shell.pdf', filename2)
os.remove('y_post_dp_shell.txt')
filename2 = 'y_post_WC_SRO_shell.txt'
temp = np.loadtxt(filename2)
WC_SRO_tot = np.vstack([WC_SRO_tot, temp])
os.remove(filename2)
os.remove('tmp_filelist')
dp_shell_tot = np.delete(dp_shell_tot, 0, 0)
print('==> dp_shell_tot.shape[0]:', dp_shell_tot.shape[0])
dp_shell_avg = np.mean(dp_shell_tot, axis=0)
filename2 = 'y_post_dp_shell_avg_%s.txt' % (jobname)
np.savetxt(filename2, dp_shell_avg)
plot_dp_shell(atoms, EPI_beta, dp_shell=dp_shell_avg)
filename2 = 'fig_dp_shell_avg_%s.pdf' % (jobname)
os.rename('y_post_dp_shell.pdf', filename2)
WC_SRO_tot = np.delete(WC_SRO_tot, 0, 0)
print('==> WC_SRO_tot.shape[0]:', WC_SRO_tot.shape[0])
WC_SRO_avg = np.mean(WC_SRO_tot, axis=0)
filename2 = 'y_post_WC_SRO_shell_avg_%s.txt' % (jobname)
np.savetxt(filename2, WC_SRO_avg)
plot_dp_shell(atoms, EPI_beta, dp_shell=WC_SRO_avg, dp_type='SRO')
filename2 = 'fig_WC_SRO_shell_avg_%s.pdf' % (jobname)
os.rename('y_post_WC_SRO_shell.pdf', filename2)