Phase diagram from first principle calculation#
Author: S. Jung (v1, Apr14.2025., v1.1 May07.2025.) Revision: S. Tiwari (TBA)
In this Noteboook, we compute the Gibbs free energy of magnesium using the ab initio calculation. Electrons and phonons are computed with Quantum ESPRESSO (QE), electronic and vibrational entropy are computed with quasi-harmonic approximation (QHA). Finally, pressure-temperature phase diagram is drawn
Theory#
Here, we briefly introduce the main concepts and equations used in QE to obtain the Gibbs free energy. To draw a phase diagram, we need the Gibbs free energy for two different phases at a given temperature and pressure. The Gibbs free energy is given by
\[{G}(p,T) = {F}(p,T) + pV,\]
where \(G(p,T)\) and \(F(p,T)\) are the Gibbs and Helmholtz free energies at a given temperature (\(T\)) and pressure (\(p\)), respectively. To evaluate \(F\), we need the volume (\(V\)) and pressure (\(p\)), which can be obtained from the gradient of the \(V\)–\(F\) curve. The Helmholtz free energy \(F\) can be expressed as
\[{F}(p,T) = {F}(p;V,T) = {U}_{0}(V) + {F}_{\mathrm{vib}}(V,T) + {F}_{\mathrm{elec}}(V,T),\]
where \(U_{0}\), \({F}_{\mathrm{vib}}\), and \({F}_{\mathrm{elec}}\) are the internal, vibrational, and electronic free energies, respectively. \(U_{0}\) can be calculated using self-consistent field (SCF) calculations. The remaining two contributions to the free energy are derived from the phonon and electronic density of states (DOS).
First, the vibrational free energy is given by
\[{F}_{\mathrm{vib}}(V,T) = {E}_{\mathrm{zpe}}(V) - T{S}_{\mathrm{vib}}(V,T),\]
where \({E}_{\mathrm{zpe}}\) and \({S}_{\mathrm{vib}}\) are the zero-point energy and vibrational entropy, respectively. These quantities can be expressed using the phonon frequency (\(\omega_{\mathbf{q}\nu}\)) for a given wavevector (\(\mathbf{q}\)) and phonon mode (\(\nu\)),
\[{E}_{\mathrm{zpe}} = \sum_{\mathbf{q},\nu} \cfrac{\hbar \omega_{\mathbf{q}\nu}}{2},\]
\[{S}_{\mathrm{vib}} = -k_{B} \sum_{\mathbf{q},\nu} \log \left[ 1 - \exp \left( -\cfrac{\hbar \omega_{\mathbf{q}\nu}}{k_{B}T} \right) \right].\]
In this notebook, these equations are implemented using the phonon DOS instead of the individual phonon frequencies \(\omega_{\mathbf{q}\nu}\),
\[{E}_{\mathrm{zpe}} = \cfrac{1}{2} \int_{0}^{\infty} dE\, E\, g_{p}(E),\]
\[{S}_{\mathrm{vib}} = M \int_{0}^{\infty} dE\, \log(1 + n(E))\, g_{p}(E),\]
where \(E\), \(g_{p}\), and \(n\) denote the phonon energy, phonon DOS, and the Bose–Einstein distribution function, respectively. \(M\) represents the number of atoms in the unit cell, but \(M\) can be ignored since QE automatically normalizes the phonon DOS to the total number of phonon modes.
On the other hand, the electronic free energy is given by
\[{F}_{\mathrm{elec}}(V,T) = {E}_{\mathrm{exct}}(V,T) - T{S}_{\mathrm{elec}}(V,T),\]
where \({E}_{\mathrm{exct}}\) and \({S}_{\mathrm{elec}}\) are the electronic excitation energy and entropy, respectively.
\[{E}_{\mathrm{exct}} = \int_{-\infty}^{\infty} d\varepsilon\, \varepsilon\, g_{e}(\varepsilon) f(\varepsilon) - \int_{-\infty}^{E_{F}} d\varepsilon\, \varepsilon\, g_{e}(\varepsilon),\]
\[{S}_{\mathrm{elec}} = -k_{B} \int_{-\infty}^{\infty} d\varepsilon \left[ f(\varepsilon)\log(f(\varepsilon)) + (1 - f(\varepsilon))\log(1 - f(\varepsilon)) \right] g_{e}(\varepsilon),\]
where \(\varepsilon\), \(g_{e}\), and \(f\) represent the electronic energy, electronic DOS, and the Fermi–Dirac distribution function, respectively.
Finally, we obtain \(F(V,T)\) for each phase. This \(F(V,T)\) is then interpolated and expressed as a function of pressure, i.e., \(F(p;V,T)\). The final step is to compare the Gibbs free energies \(G\) of the different phases at a given temperature and pressure.
Calculation steps#
Construct a volume set for each phase via structural relaxation calculations under pressure. (
pw.x)Perform phonon dispersion and DOS calculations. (
ph.x,q2r.x, andmatdyn.x)Conduct non-self-consistent field (NSCF) and electronic DOS calculations. (
pw.xanddos.x)Calculate the zero-point energy and vibrational entropy from step 2.
Calculate the electronic excitation energy and entropy from step 3.
Using the results from steps 4 and 5, calculate and interpolate the Helmholtz free energy as a function of pressure.
Finally, compute and compare the Gibbs free energy of each phase.
Basic steups#
We need to set paths, constants, pararellization parameters.
[2]:
import os
import math
import numpy as np
import EPWpy
from EPWpy import EPWpy
from EPWpy.QE.PW_util import *
from scipy.integrate import simpson
from scipy.interpolate import interp1d
# Set your pseudopotential dir. This tutorial use LDA
# paramiterized by Pseudodojo
pseudo = '/work2/08400/jsyeb/frontera/epwpy/pseudos'
workdir = '/scratch/08400/jsyeb/'
cores = 48
bccnk = 24
hcpnk = 12
[3]:
# Move to your working directory and make dirs for each phase
os.chdir(workdir)
os.mkdir("mg-epwpy")
os.chdir("./mg-epwpy")
os.mkdir("bcc")
os.mkdir("hcp")
[4]:
# Set constant values
kb = 8.617333E-05 # Boltzmann [eV/K]
ry2ev = 13.6057 # rydberg to electronvolt
ry2cmm1 = 109677.57 # rydberg to cm-1
ry2k = 157887.6634 # rydberg to kelvin
# this constant standing for Ry/bohr3 -> kbar
pressunit = 147105.371715 # pressure unit conversion
Input values#
The following are input values. All values depend on the specific system and the pseudopotential used. You can manually control how many volume and temperature points are considered.
[5]:
# Set input values
bccnatom = 1.0 # number of atoms for BCC Mg
hcpnatom = 2.0 # number of atoms for HCP Mg
bccnelec = 10.0 # number of electrons for BCC Mg
hcpnelec = 20.0 # number of electrons for HCP Mg
numvol = 6 # numver of volume to consider
ntemp = 50 # number of temperature to consider
tstep = 40.0 # temperature interval
pmin = 50.0 # minimum pressure value
pmax = 550.0 # maximum pressure value
pstep = 5.0 # pressure interval
[6]:
# We will consider six different volume and 20 temperature points
# for each BCC and HCP Mg:
bcclat = [None]*numvol
bccenergy = [None]*numvol
bcchelm = [[0.0 for x in range(numvol)] for y in range(ntemp)]
bccgibbs = [[0.0 for x in range(numvol)] for y in range(ntemp)]
hcplat = [None]*numvol
hcpcoa = [None]*numvol
hcpenergy = [None]*numvol
hcphelm = [[0.0 for x in range(numvol)] for y in range(ntemp)]
hcpgibbs = [[0.0 for x in range(numvol)] for y in range(ntemp)]
# interpolation arrays:
bccvol = [None]*numvol
hcpvol = [None]*numvol
bccitpv = [None]*ntemp
hcpitpv = [None]*ntemp
bccpress = [[0.0 for x in range(numvol)] for y in range(ntemp)]
hcppress = [[0.0 for x in range(numvol)] for y in range(ntemp)]
bccitpg = [None]*ntemp
hcpitpg = [None]*ntemp
# Set volume and phase boundary arrays:
nump = int((pmax - pmin)/pstep)
press = [None]*nump
pb = [None]*nump
top = [None]*nump
BCC Mg calculaions#
First, we define the general calculation parameters for body-centered cubic (BCC) magnesium (Mg).
[7]:
bccrelax=EPWpy.EPWpy({'prefix':'\'bccrelax\'','restart_mode':'\'from_scratch\'',
'calculation':'\'scf\'',
'ibrav':3,'celldm(1)':'6.41680','ntyp':1,'nat':1,
'atomic_species':['Mg'],'mass':[24.305],'atoms':['Mg'],'pseudo':['Mg.upf'],
'atomic_pos':np.array([[0.0, 0.0, 0.0]]),'atomic_position_type':'crystal',
'ecutwfc':'100','occupations':'\'smearing\'','smearing':'\'gaussian\'','degauss':'0.05',
'verbosity':'\'low\'','pseudo_dir':'\''+str(pseudo)+'\''
},env='mpirun',system='bccrelax')
bccrelax.run_serial = True
bccrelax.verbosity = 2
bccrelax.iondynamics = True
bccrelax.celldynamics = True
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==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Structure relaxation calculations with pressure#
Relax the BCC Mg lattice parameter without applying external pressure. All subsequent relaxation calculations under finite pressure will be carried out. Each calculation is named according to its pressure value in kbar.
[8]:
bccrelax.scf(ions={'ion_dynamics':'bfgs'},
cell={'press':'0','press_conv_thr':'0.1'},
system={'nbnd':10},
control = {'calculation':'\'vc-relax\'','nstep':50},
electrons = {'conv_thr':'1E-12'},
kpoints={'kpoints':[[12,12,12]]},
name = '0')
bccrelax.prepare(cores,'scf',infile = '0.in')
bccrelax.run(cores,'scf',infile='0')
-- -- -- -- -- -- -- -- -- -- -- Calculation: 0 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 48 -nt 1 -in 0.in > 0.out
Running 0 |████████████████████████████████████████| in 14.5s (0.10/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Now, we have relaxed BCC Mg structure, and we will check the values. All the values should be zero, because this was a first calculation of this tutorial.
[9]:
bccrelax.pw_util = bccrelax.PW_utilities()
print(bccrelax.pw_cell_parameters)
print('old_positions:', bccrelax.pw_atomic_positions['atomic_pos'])
print('old_cell_parameters:', bccrelax.pw_cell_parameters['lattice_vector'])
{'cell_type': 'alat', 'lattice_vector': array([['0.000 0.000 0.000'],
['0.000 0.000 0.00'],
['0.000 0.000 0.000']], dtype='<U17')}
old_positions: [[0. 0. 0.]]
old_cell_parameters: [['0.000 0.000 0.000']
['0.000 0.000 0.00']
['0.000 0.000 0.000']]
We can check the change of lattice parameter by comparing first and second line of the output. At the first, our input has lattice parameter 1 with (0.5,0.5,0,5) vector in unit of alat. After relax calculation, the second line informs that lattice 1 has become (0.518083,0.518083,0.518083).
[10]:
bccrelax.pw_cell_parameters['lattice_vector'] = obtain_cell_parameters(bccrelax.pw_util.file)
print('new_cell_parameters:', bccrelax.pw_cell_parameters['lattice_vector'])
['a(1)', '=', '(', '0.500000', '0.500000', '0.500000', ')']
['a(1)', '=', '(', '0.518083', '0.518083', '0.518083', ')']
new_cell_parameters: [[ 1.75921454 1.75921454 1.75921454]
[-1.75921454 1.75921454 1.75921454]
[-1.75921454 -1.75921454 1.75921454]]
We can apply pressure to the relax calculation. For automatic calculation, the relax calculation setup will be recycled with a loop. We consider six differet pressure from 50 to 550 kbar, and each relax calculation will give us lattice parameter at given pressure.
[11]:
for prs in range(50, 650, 100):
bccrelax.scf(ions={'ion_dynamics':'bfgs'},
cell={'press':''+str(prs)+'','press_conv_thr':'0.1'},
control = {'calculation':'\'vc-relax\'','nstep':50},
system={'nbnd':10},
electrons = {'conv_thr':'1E-12'},
kpoints={'kpoints':[[12,12,12]]},
name = ''+str(prs)+'')
bccrelax.prepare(cores,'scf',infile = ''+str(prs)+'.in')
bccrelax.run(cores,'scf',infile=''+str(prs)+'')
bccrelax.pw_util = bccrelax.PW_utilities()
bccrelax.pw_cell_parameters['lattice_vector'] = obtain_cell_parameters(bccrelax.pw_util.file)
print('new_cell_parameters:', bccrelax.pw_cell_parameters['lattice_vector'])
-- -- -- -- -- -- -- -- -- -- -- Calculation: 50 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 48 -nt 1 -in 50.in > 50.out
Running 50 |████████████████████████████████████████| in 3.3s (0.53/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '0.500000', '0.500000', '0.500000', ')']
['a(1)', '=', '(', '0.500000', '0.500000', '0.500000', ')']
new_cell_parameters: [[ 1.69781149 1.69781149 1.69781149]
[-1.69781149 1.69781149 1.69781149]
[-1.69781149 -1.69781149 1.69781149]]
-- -- -- -- -- -- -- -- -- -- -- Calculation: 150 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 48 -nt 1 -in 150.in > 150.out
Running 150 |████████████████████████████████████████| in 5.2s (0.30/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '0.500000', '0.500000', '0.500000', ')']
['a(1)', '=', '(', '0.477690', '0.477690', '0.477690', ')']
new_cell_parameters: [[ 1.62205514 1.62205514 1.62205514]
[-1.62205514 1.62205514 1.62205514]
[-1.62205514 -1.62205514 1.62205514]]
-- -- -- -- -- -- -- -- -- -- -- Calculation: 250 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 48 -nt 1 -in 250.in > 250.out
Running 250 |████████████████████████████████████████| in 5.6s (0.27/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '0.500000', '0.500000', '0.500000', ')']
['a(1)', '=', '(', '0.462946', '0.462946', '0.462946', ')']
new_cell_parameters: [[ 1.57199007 1.57199007 1.57199007]
[-1.57199007 1.57199007 1.57199007]
[-1.57199007 -1.57199007 1.57199007]]
-- -- -- -- -- -- -- -- -- -- -- Calculation: 350 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 48 -nt 1 -in 350.in > 350.out
Running 350 |████████████████████████████████████████| in 5.9s (0.26/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '0.500000', '0.500000', '0.500000', ')']
['a(1)', '=', '(', '0.451870', '0.451870', '0.451870', ')']
new_cell_parameters: [[ 1.53438015 1.53438015 1.53438015]
[-1.53438015 1.53438015 1.53438015]
[-1.53438015 -1.53438015 1.53438015]]
-- -- -- -- -- -- -- -- -- -- -- Calculation: 450 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 48 -nt 1 -in 450.in > 450.out
Running 450 |████████████████████████████████████████| in 5.9s (0.26/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '0.500000', '0.500000', '0.500000', ')']
['a(1)', '=', '(', '0.442987', '0.442987', '0.442987', ')']
new_cell_parameters: [[ 1.50421683 1.50421683 1.50421683]
[-1.50421683 1.50421683 1.50421683]
[-1.50421683 -1.50421683 1.50421683]]
-- -- -- -- -- -- -- -- -- -- -- Calculation: 550 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 48 -nt 1 -in 550.in > 550.out
Running 550 |████████████████████████████████████████| in 5.5s (0.28/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '0.500000', '0.500000', '0.500000', ')']
['a(1)', '=', '(', '0.435573', '0.435573', '0.435573', ')']
new_cell_parameters: [[ 1.47904169 1.47904169 1.47904169]
[-1.47904169 1.47904169 1.47904169]
[-1.47904169 -1.47904169 1.47904169]]
The relaxed lattice parameters are saved as an array.
[12]:
# Save the relaxed lattice parameters as a array manually
bcclat =[6.41680,6.13032,5.94124,5.79916,5.68522,5.59006]
[13]:
# Move to BCC workplace
os.chdir(workdir)
os.chdir("./mg-epwpy/bcc/")
cwd = os.getcwd()
print(cwd)
/scratch/08400/jsyeb/mg-epwpy/bcc
SCF, phonon, band, and DOS calculations#
Here, we enter the main loop over numvol, performing SCF and phonon calculations. This is one of the most powerful features of epwpy. An outer loop over volume is constructed to sequentially run SCF, NSCF, electronic DOS, phonon, and phonon DOS calculations. Each volume is calculated in its own independent directory.
[14]:
for i in range(0, numvol):
# Define bcc calculation as a function of lattice parameter
bcc=EPWpy.EPWpy({'prefix':'\'bcc'+str(i)+'\'','restart_mode':'\'from_scratch\'',
'calculation':'\'scf\'',
'ibrav':3,'celldm(1)':''+str(bcclat[i])+'','ntyp':1,'nat':1,
'atomic_species':['Mg'],'mass':[24.305],'atoms':['Mg'],'pseudo':['Mg.upf'],
'atomic_pos':np.array([[0.0, 0.0, 0.0]]),'atomic_position_type':'crystal',
'ecutwfc':'100','occupations':'\'smearing\'',
'smearing':'\'gaussian\'','degauss':'0.05',
'verbosity':'\'low\'','pseudo_dir':'\''+str(pseudo)+'\''
},env='mpirun',system='bcc'+str(i)+'')
# SCF block
bcc.run_serial = True
bcc.Run.serial = True
bcc.verbosity = 2
bcc.Run.verbosity = 2
bcc.scf(control = {'calculation':'\'scf\''},system={'nbnd':10},
electrons = {'conv_thr':'1E-12'},kpoints={'kpoints':[[12,12,12]]},
name = 'bcc'+str(i)+'')
bcc.prepare(1,type_run='scf',infile = 'bcc'+str(i)+'.in')
bcc.run(cores,type_run='scf',infile='bcc'+str(i)+'',parallelization='-nk '+str(bccnk)+'')
# NB: We need the total energy values to calculate Gibbs free energies.
bcc.pw_util = bcc.PW_utilities()
print('Total Energy: ',bcc.pw_util.total_energy)
bccenergy[i]=bcc.pw_util.total_energy
# Electronic density of state (DOS) block
bcc.scf(control = {'calculation':'\'nscf\''},system={'nbnd':10},
electrons = {'conv_thr':'1E-12'},kpoints={'kpoints':[[24,24,24]]},
name = 'nscf')
bcc.prepare(1,type_run='nscf',infile = 'nscf.in')
bcc.run(cores,type_run='nscf',infile = 'nscf',parallelization='-nk '+str(bccnk)+'')
bcc.dos(dos={'DeltaE':'0.01','degauss':'0.02'})
# NB: The DOS calculation was implemented by using manual call in EPWpy.
# Following six lines could be change in future.
bcc.set_work()
bcc.Prepare.prepare_dos(name = 'nscf')
bcc.set_home()
bcc.set_work()
bcc.Run.run_dos(type_run='nscf',name='dos')
bcc.set_home()
# Phonon block
bcc.ph(phonons={'fildyn':'"bcc'+str(i)+'.dyn"','nq1':3,'nq2':3,'nq3':3,
'fildvscf':'"dvscf"','tr2_ph':'1.0d-14'})
bcc.prepare(1,type_run='ph')
bcc.run(cores,type_run='ph',parallelization='-nk '+str(bccnk)+'')
# q2r and matdyn block
bcc.q2r(name='q2r')
bcc.prepare(type_run='q2r')
bcc.run(1,type_run='q2r')
bcc.matdyn(name='matdyn',matdyn={'flfrq':'\'bcc'+str(i)+'.freq\''},
kpoints={'kpoints':[
['0.00','0.00','0.00','20'],
['-0.50','0.50','0.50','20'],
['0.00','0.50','0.00','20'],
['0.00','0.00','0.00','20'],
['0.25','0.25','0.25','20']
],
'kpoints_type':'{crystal_b}'
},
)
bcc.prepare(type_run='matdyn')
bcc.run(1,type_run='matdyn')
# Phonon DOS block
bcc.phdos(name='phdos',phdos={'flfrq':'\'bcc'+str(i)+'.dos.freq\'','flfrc':'\'bcc'+str(i)+'.fc\'','asr':'\'simple\'',
'fldos':'\'bcc'+str(i)+'.dos\'','dos':'.true.','nk1':30,'nk2':30,'nk3':30})
bcc.prepare(type_run='phdos')
bcc.run(1,type_run='phdos')
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*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: bcc0 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in bcc0.in > bcc0.out
Running bcc0 |████████████████████████████████████████| in 2.5s (0.80/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -118.55802521
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 4.3s (0.38/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.6s (1.96/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 24 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 57.0s (0.02/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 1.0s (7.26/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (14.36/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 20.5s (0.07/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: bcc1 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in bcc1.in > bcc1.out
Running bcc1 |████████████████████████████████████████| in 2.3s (0.93/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -118.54710635
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 3.9s (0.42/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.7s (1.62/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 24 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 43.1s (0.03/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (19.63/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (15.51/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 19.5s (0.07/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: bcc2 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in bcc2.in > bcc2.out
Running bcc2 |████████████████████████████████████████| in 2.3s (0.93/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -118.53328093
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 3.9s (0.43/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.4s (2.51/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 24 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 41.7s (0.03/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (13.73/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (19.70/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 20.5s (0.07/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: bcc3 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in bcc3.in > bcc3.out
Running bcc3 |████████████████████████████████████████| in 2.3s (0.96/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -118.51841918
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 3.6s (0.48/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.6s (1.98/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 24 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 33.5s (0.04/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (13.94/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (14.39/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 21.3s (0.06/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: bcc4 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in bcc4.in > bcc4.out
Running bcc4 |████████████████████████████████████████| in 2.3s (0.95/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -118.50316494
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 3.9s (0.43/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.5s (2.25/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 24 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 33.1s (0.04/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (14.05/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (16.14/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 24.6s (0.05/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: bcc5 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in bcc5.in > bcc5.out
Running bcc5 |████████████████████████████████████████| in 2.3s (0.95/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -118.48779427
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 24 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 3.9s (0.42/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.6s (1.99/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 24
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 24 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 34.0s (0.04/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (14.55/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (15.31/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 22.7s (0.06/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Calculation of vibrational entropy#
This section provides a short code to calculate the zero-point energy and vibrational entropy, as described in the theory section.
[15]:
for v in range(0, numvol):
# Go to actual working dir
os.chdir(workdir)
os.chdir('./mg-epwpy/bcc/bcc'+str(v)+'/ph')
# Read phonon DOS result
pdata = []
with open('bcc'+str(v)+'.dos', 'r') as f:
next(f)
for line in f:
row = [float(x) for x in line.split()]
pdata.append(row)
if abs(pdata[0][0]) < 0.01:
pdata[0][0] = 0.0
numpdat = len(pdata)
# Set data arrays
etemps=[None]*ntemp
temps=[None]*ntemp
for i in range(0, ntemp):
etemps[i]=i*tstep/ry2k
temps[i]=i*tstep
energy = [None]*numpdat
phdos = [None]*numpdat
logdos = [None]*numpdat
vibent = [None]*ntemp
# Calculate zero-point energy
for i in range(0,numpdat):
energy[i]=pdata[i][0]/ry2cmm1
phdos[i]=pdata[i][1]*ry2cmm1*energy[i]
zpe = simpson(phdos, x=energy)
zpe = 0.5*zpe
# Set temperature loop and calculate zero-point energy and
# vibrational entropy at given temperature to calculate
# Helmholtz free energy
for i in range(0, ntemp):
if etemps[i] == 0.0:
vibent[i] = 0.0
bcchelm[i][v] = bccenergy[v] + zpe
continue
for j in range(0,numpdat):
if energy[j] == 0.0:
logdos[j] = 0.0
continue
logdos[j]=pdata[j][1]*ry2cmm1*math.log(1.0+(1.0/(math.exp(energy[j]/etemps[i])-1.0)))
# phonon DOS in QE was already normalized to # of phonons
vibent[i] = -etemps[i]*simpson(logdos, x=energy)
bcchelm[i][v] = vibent[i] + bccenergy[v] + zpe
Calculation of electronic excitation entropy#
This section provides a short code to calculate the electronic excitation energy and entropy, as described in the theory section.
[16]:
for v in range(0, numvol):
os.chdir(workdir)
os.chdir('./mg-epwpy/bcc/bcc'+str(v)+'/nscf')
edata = []
with open('bcc'+str(v)+'.dos', 'r') as f:
next(f)
for line in f:
row = [float(x) for x in line.split()]
edata.append(row)
numedat = len(edata)
en = [None]*numedat
edos = [None]*numedat
edosfd = [None]*numedat
doslog = [None]*numedat
tfermi = [None]*ntemp
exce = [None]*ntemp
excent = [None]*ntemp
niter = 200
for i in range(0,numedat):
en[i]=edata[i][0]/ry2ev
edos[i]=edata[i][1]*ry2ev*en[i]
# Get fermi energy in DOS by using bisection method
for i in range(0, ntemp):
if etemps[i] == 0.0:
# Set lower limit of calculation as 10K
etemps[i] = 10.0/ry2k
tmpfermi1 = max(en)
tmpfermi2 = min(en)
for k in range(0,niter):
dosfd = [0]*numedat
tmpfermi = (tmpfermi1+tmpfermi2)/2.0
tmpelec = 0.0
for j in range(0,numedat):
etmp = (en[j]-tmpfermi)/etemps[i]
if abs(etmp) > 10e+0:
if etmp < 0.0:
dosfd[j] = edata[j][1]*ry2ev
else:
dosfd[j] = 0.0
continue
dosfd[j] = edata[j][1]*ry2ev*(1.0/(math.exp(etmp)+1.0))
tmpelec = simpson(dosfd, x=en)
if abs(tmpelec - bccnelec) < 1.0e-12:
tfermi[i] = tmpfermi
break
if tmpelec < bccnelec:
tmpfermi2 = tmpfermi
if tmpelec > bccnelec:
tmpfermi1 = tmpfermi
print('Fermienergy calculation was finished for volume '+str(v)+'')
# Calculate electronic excitations energy
for i in range(0, ntemp):
for j in range(0,numedat):
etmp = (en[j]-tfermi[i])/etemps[i]
if abs(etmp) > 1.0e+2:
if etmp < 0.0:
edosfd[j] = edos[j]
else:
edosfd[j] = 0.0
continue
edosfd[j] = edos[j]*(1.0/(math.exp(etmp)+1.0))
exce[i] = simpson(edosfd, x=en)
uzero = exce[0]
for i in range(0, ntemp):
exce[i] = exce[i] - uzero
# Calculate electronic excitations entropy
for i in range(0, ntemp):
for j in range(0,numedat):
etmp = (en[j]-tfermi[i])/etemps[i]
if abs(etmp) > 1.0e+2:
if etmp < 0.0:
fd = 1.0
else:
fd = 0.0
else:
fd = (1.0/(math.exp(etmp)+1.0))
if fd>0.0 and fd<1.0:
# kb has an unit of eV/K. So, we don't need ry2ev here:
doslog[j] = (fd*math.log(fd)+(1.0-fd)*math.log(1.0-fd))*edata[j][1]
else:
doslog[j] = 0.0
excent[i] = -kb*simpson(doslog, x=en)
# Now, exce is electronic free energy:
exce[i] = exce[i] - excent[i]*temps[i]
bcchelm[i][v] = bcchelm[i][v] + exce[i]
Fermienergy calculation was finished for volume 0
Fermienergy calculation was finished for volume 1
Fermienergy calculation was finished for volume 2
Fermienergy calculation was finished for volume 3
Fermienergy calculation was finished for volume 4
Fermienergy calculation was finished for volume 5
HCP Mg calculations#
Next, we perform the same procedure for hexagonal close-packed (HCP) magnesium (Mg). In the case of HCP Mg, there are two atoms in the unit cell, so the calculations will take more time compared to BCC Mg.
[17]:
os.chdir(workdir)
os.chdir("./mg-epwpy/")
Structure relaxation calculations with pressure#
[18]:
hcprelax=EPWpy.EPWpy({'prefix':'\'hcprelax\'','restart_mode':'\'from_scratch\'',
'calculation':'\'scf\'',
'ibrav':4,'celldm(1)':'5.92367','celldm(3)':'1.62803','ntyp':1,'nat':2,
'atomic_species':['Mg'],'mass':[24.305],'atoms':['Mg','Mg'],'pseudo':['Mg.upf'],
'atomic_pos':np.array([[0.3333333, 0.6666667, 0.25],
[0.6666667, 0.3333333, 0.75]]),
'atomic_position_type':'crystal',
'ecutwfc':'100','occupations':'\'smearing\'','smearing':'\'gaussian\'','degauss':'0.045',
'verbosity':'\'low\'','pseudo_dir':'\''+str(pseudo)+'\''
},env='mpirun',system='hcprelax')
hcprelax.run_serial = True
hcprelax.verbosity = 2
hcprelax.iondynamics = True
hcprelax.celldynamics = True
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
[19]:
for prs in range(50, 650, 100):
hcprelax.scf(ions={'ion_dynamics':'bfgs'},
cell={'press':''+str(prs)+'','press_conv_thr':'0.1'},
control = {'calculation':'\'vc-relax\'','nstep':50},
system={'nbnd':20},
electrons = {'conv_thr':'1E-12'},
kpoints={'kpoints':[[8,8,8]]},
name = ''+str(prs)+'')
hcprelax.prepare(cores,'scf',infile = ''+str(prs)+'.in')
hcprelax.run(cores,'scf',infile=''+str(prs)+'',parallelization='-nk '+str(hcpnk)+'')
hcprelax.pw_util = hcprelax.PW_utilities()
hcprelax.pw_cell_parameters['lattice_vector'] = obtain_cell_parameters(hcprelax.pw_util.file)
print('new_cell_parameters:', hcprelax.pw_cell_parameters['lattice_vector'])
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: 50 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in 50.in > 50.out
Running 50 |████████████████████████████████████████| in 14.8s (0.09/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '1.000000', '0.000000', '0.000000', ')']
['a(1)', '=', '(', '0.969953', '-0.000000', '0.000000', ')']
new_cell_parameters: [[ 3.04048249 -0. 0. ]
[-1.52023968 2.63313527 0. ]
[ 0. 0. 4.90030096]]
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: 150 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in 150.in > 150.out
Running 150 |████████████████████████████████████████| in 13.1s (0.11/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '1.000000', '0.000000', '0.000000', ')']
['a(1)', '=', '(', '0.926960', '0.000000', '-0.000000', ')']
new_cell_parameters: [[ 2.90571363 0. -0. ]
[-1.45285681 2.51642211 0. ]
[-0. -0. 4.6862657 ]]
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: 250 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in 250.in > 250.out
Running 250 |████████████████████████████████████████| in 10.9s (0.13/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '1.000000', '0.000000', '0.000000', ')']
['a(1)', '=', '(', '0.898446', '-0.000000', '0.000000', ')']
new_cell_parameters: [[ 2.81633165 -0. 0. ]
[-1.40816583 2.43901457 0. ]
[-0. -0. 4.5444595 ]]
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: 350 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in 350.in > 350.out
Running 350 |████████████████████████████████████████| in 13.6s (0.10/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '1.000000', '0.000000', '0.000000', ')']
['a(1)', '=', '(', '0.876982', '-0.000000', '0.000000', ')']
new_cell_parameters: [[ 2.7490491 -0. 0. ]
[-1.37452455 2.38074732 0. ]
[-0. -0. 4.43762682]]
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: 450 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in 450.in > 450.out
Running 450 |████████████████████████████████████████| in 13.1s (0.11/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '1.000000', '0.000000', '0.000000', ')']
['a(1)', '=', '(', '0.859735', '-0.000000', '0.000000', ')']
new_cell_parameters: [[ 2.69498544 -0. 0. ]
[-1.34749429 2.33392476 0. ]
[ 0. 0. 4.35199391]]
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: 550 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in 550.in > 550.out
Running 550 |████████████████████████████████████████| in 13.1s (0.11/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
['a(1)', '=', '(', '1.000000', '0.000000', '0.000000', ')']
['a(1)', '=', '(', '0.845289', '-0.000000', '0.000000', ')']
new_cell_parameters: [[ 2.649702 -0. 0. ]
[-1.32484943 2.2947069 0. ]
[-0. -0. 4.28038551]]
[20]:
# Save the relaxed lattice parameters as a array manually
hcplat =[5.745679,5.491004,5.322100,5.194951,5.092787,5.007211]
hcpcoa =[1.611686,1.612777,1.613609,1.614240,1.614848,1.615422]
[21]:
# Move to HCP workplace
os.chdir(workdir)
os.chdir("./mg-epwpy/hcp/")
SCF, phonon, band, and DOS calculations#
[22]:
for i in range(0, numvol):
# Define HCP calculation as a function of lattice parameter
hcp=EPWpy.EPWpy({'prefix':'\'hcp'+str(i)+'\'','restart_mode':'\'from_scratch\'',
'calculation':'\'scf\'',
'ibrav':4,'celldm(1)':''+str(hcplat[i])+'','celldm(3)':''+str(hcpcoa[i])+'','ntyp':1,'nat':2,
'atomic_species':['Mg'],'mass':[24.305],'atoms':['Mg','Mg'],'pseudo':['Mg.upf'],
'atomic_pos':np.array([[0.3333333, 0.6666667, 0.25],
[0.6666667, 0.3333333, 0.75]]),
'atomic_position_type':'crystal',
'ecutwfc':'100','occupations':'\'smearing\'',
'smearing':'\'gaussian\'','degauss':'0.045',
'verbosity':'\'low\'','pseudo_dir':'\''+str(pseudo)+'\''
},env='mpirun',system='hcp'+str(i)+'')
# SCF block
hcp.run_serial = True
hcp.Run.serial = True
hcp.verbosity = 2
hcp.Run.verbosity = 2
hcp.scf(control = {'calculation':'\'scf\''},system={'nbnd':20},
electrons = {'conv_thr':'1E-12'},kpoints={'kpoints':[[8,8,8]]},
name = 'hcp'+str(i)+'')
hcp.prepare(1,type_run='scf',infile = 'hcp'+str(i)+'.in')
hcp.run(cores,type_run='scf',infile='hcp'+str(i)+'',parallelization='-nk '+str(hcpnk)+'')
# NB: We need the total energy values to calculate Gibbs free energies.
hcp.pw_util = hcp.PW_utilities()
print('Total Energy: ',hcp.pw_util.total_energy)
hcpenergy[i]=hcp.pw_util.total_energy
# Electronic density of state (DOS) block
hcp.scf(control = {'calculation':'\'nscf\''},system={'nbnd':20},
electrons = {'conv_thr':'1E-12'},kpoints={'kpoints':[[16,16,16]]},
name = 'nscf')
hcp.prepare(1,type_run='nscf',infile = 'nscf.in')
hcp.run(cores,type_run='nscf',infile = 'nscf',parallelization='-nk '+str(hcpnk)+'')
hcp.dos(dos={'DeltaE':'0.01','degauss':'0.02'})
# NB: The DOS calculation was implemented by using manual call in EPWpy.
# Following six lines could be change in future.
hcp.set_work()
hcp.Prepare.prepare_dos(name = 'nscf')
hcp.set_home()
hcp.set_work()
hcp.Run.run_dos(type_run='nscf',name='dos')
hcp.set_home()
# Phonon block
hcp.ph(phonons={'fildyn':'"hcp'+str(i)+'.dyn"','nq1':3,'nq2':3,'nq3':3,
'fildvscf':'"dvscf"','tr2_ph':'1.0d-14'})
hcp.prepare(1,type_run='ph')
hcp.run(cores,type_run='ph',parallelization='-nk '+str(hcpnk)+'')
# q2r and matdyn block
hcp.q2r(name='q2r')
hcp.prepare(type_run='q2r')
hcp.run(1,type_run='q2r')
hcp.matdyn(name='matdyn',matdyn={'flfrq':'\'hcp'+str(i)+'.freq\''},
kpoints={'kpoints':[
['0.00000','0.00000','0.00000','20'],
['0.50000','0.00000','0.00000','20'],
['0.33333','0.33333','0.00000','20'],
['0.00000','0.00000','0.00000','20'],
['0.00000','0.00000','0.50000','20']
],
'kpoints_type':'{crystal_b}'
},
)
hcp.prepare(type_run='matdyn')
hcp.run(1,type_run='matdyn')
# Phonon DOS block
hcp.phdos(name='phdos',phdos={'flfrq':'\'hcp'+str(i)+'.dos.freq\'','flfrc':'\'hcp'+str(i)+'.fc\'','asr':'\'simple\'',
'fldos':'\'hcp'+str(i)+'.dos\'','dos':'.true.','nk1':30,'nk2':30,'nk3':30})
hcp.prepare(type_run='phdos')
hcp.run(1,type_run='phdos')
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: hcp0 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in hcp0.in > hcp0.out
Running hcp0 |████████████████████████████████████████| in 3.7s (0.46/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -237.11964833
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 7.8s (0.19/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.7s (1.65/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 12 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 3:51.3 (0.01/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (14.50/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (13.95/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 40.4s (0.03/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: hcp1 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in hcp1.in > hcp1.out
Running hcp1 |████████████████████████████████████████| in 3.0s (0.61/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -237.09800288
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 7.0s (0.21/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.7s (1.62/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 12 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 3:08.5 (0.01/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (19.50/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.9s (13.11/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 44.0s (0.03/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: hcp2 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in hcp2.in > hcp2.out
Running hcp2 |████████████████████████████████████████| in 2.9s (0.65/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -237.07046548
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 6.7s (0.22/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.7s (1.78/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 12 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 2:59.6 (0.01/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (19.64/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (14.68/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 48.1s (0.03/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
.. .%S: +%%%%*. :*%%%#= %%= -=. :==-
:=#%%*- .#S- .. .%%= :*#*: -=. :==-
-%S:.=#%%*==%# *%%=::=##-+%%. . .=-. :==- .=
:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
:%%- -%S.
.-=*####SS%#########: -###########*+: +#######= =%SS####+::.
=+#**%SSSSSSSSSSSSSSSS= =SSSSSSSSSSSSSSS= #SSSSSSS*. +SSSSSSSS%%%%-
*%% =SSS.. .SSS= SSS=. .:+SSS+ -SSS:. .-::. .SSS+. #%*
#%#. =SSS. *S# *S%: SSS= %SS%. .SSS= #SSS%. :SSS: =%#.
*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: hcp3 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in hcp3.in > hcp3.out
Running hcp3 |████████████████████████████████████████| in 2.8s (0.69/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -237.04079096
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 6.3s (0.24/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.8s (1.58/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 12 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 2:53.7 (0.01/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.9s (13.93/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (15.65/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 51.8s (0.03/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
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.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
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==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: hcp4 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in hcp4.in > hcp4.out
Running hcp4 |████████████████████████████████████████| in 3.1s (0.60/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -237.01029264
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 6.0s (0.26/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.8s (1.45/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 12 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 2:59.8 (0.01/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (20.03/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.8s (19.72/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 54.8s (0.02/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-*#*- ...............-
.+*= .+%*-=%%: .=#*- -===============-:.
:*%=*%%- *%* #%* :+%+-%%+ .:. -=. :==-.
-%S -%%*: :#%. -%%-. -##: #%* -=. :==-
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:%%- .-+++: -+##*=. =%S :-::==: .==- --.
*%# #%+ -=--:. .----:.
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*%%: =SSS#*#SSS- SSS= .+SSS+. %SS*.=SSSSS+ +SS%.:+%+
+%%:=SSSSSSSSS- SSSSSSSSSSSSS=. +SSS:SSS%SSS:%SS*-#%=
....#S==SSS:..SSS: =+- SSS%######+=. -SSS%SS%.#SS%SSS==%%=.
.:+##%%#*- =SSS. ::. :SSS. SSS=. SSSSSS:..SSSSSS: :*%%%*=-
#%+. -+#SSS*+++++++*SSS: .=+SSS#++++: %SSSS+. =SSSS%. :-+#%%+
#%* .SSSSSSSSSSSSSSSSSS: *SSSSSSSSSSS. +SSS%. %SSS*. . .%%=
=%S :::::::::::::::::. .:::::::::. :::. :::. =+=-.#%+
-%S: =+===#S:
==*------------------------------=========+++++++++++++++++++++++========++-+##
=+++++++++++*******++++++++++++++++========------------------==========+++++++-
-- -- -- -- -- -- -- -- -- -- -- -- Structure Info -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: hcp5 -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in hcp5.in > hcp5.out
Running hcp5 |████████████████████████████████████████| in 2.8s (0.71/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Total Energy: -236.97947762
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: nscf -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/pw.x -nk 12 -in nscf.in > nscf.out
Running nscf |████████████████████████████████████████| in 5.2s (0.30/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: dos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/dos.x -in dos.in > dos.out
Running dos |████████████████████████████████████████| in 1.8s (1.59/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
parallelization chosen: -nk 12
-- -- -- -- -- -- -- -- -- -- -- Calculation: ph -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 48 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/ph.x -nk 12 -in ph.in > ph.out
Running ph |████████████████████████████████████████| in 2:22.0 (0.01/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: q2r -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/q2r.x -in q2r.in > q2r.out
Running q2r |████████████████████████████████████████| in 0.8s (12.85/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: matdyn -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in matdyn.in > matdyn.out
Running matdyn |████████████████████████████████████████| in 0.9s (12.04/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- -- -- -- -- -- -- -- -- -- -- Calculation: phdos -- -- -- -- -- -- -- -- -- -- --
on 1: running: mpirun -np 1 /work2/08400/jsyeb/frontera/epwpy/build/q-e-EPW-5.9s/bin/matdyn.x -in phdos.in > phdos.out
Running phdos |████████████████████████████████████████| in 57.3s (0.02/s)
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Calculation of vibrational entropy#
[23]:
for v in range(0, numvol):
# Go to actual working dir
os.chdir(workdir)
os.chdir('./mg-epwpy/hcp/hcp'+str(v)+'/ph')
# Read phonon DOS result
pdata = []
with open('hcp'+str(v)+'.dos', 'r') as f:
next(f)
for line in f:
row = [float(x) for x in line.split()]
pdata.append(row)
if abs(pdata[0][0]) < 0.01:
pdata[0][0] = 0.0
numpdat = len(pdata)
# Set data arrays
etemps=[None]*ntemp
temps=[None]*ntemp
for i in range(0, ntemp):
etemps[i]=i*tstep/ry2k
temps[i]=i*tstep
energy = [None]*numpdat
phdos = [None]*numpdat
logdos = [None]*numpdat
vibent = [None]*ntemp
# Calculate zero-point energy
for i in range(0,numpdat):
energy[i]=pdata[i][0]/ry2cmm1
phdos[i]=pdata[i][1]*ry2cmm1*energy[i]
zpe = simpson(phdos, x=energy)
zpe = 0.5*zpe
# Set temperature loop and calculate zero-point energy and
# vibrational entropy at given temperature to calculate
# Helmholtz free energy
for i in range(0, ntemp):
if etemps[i] == 0.0:
vibent[i] = 0.0
hcphelm[i][v] = hcpenergy[v] + zpe
continue
for j in range(0,numpdat):
if energy[j] == 0.0:
logdos[j] = 0.0
continue
logdos[j]=pdata[j][1]*ry2cmm1*math.log(1.0+(1.0/(math.exp(energy[j]/etemps[i])-1.0)))
# phonon DOS in QE was already normalized to # of phonons
vibent[i] = -etemps[i]*simpson(logdos, x=energy)
hcphelm[i][v] = vibent[i] + hcpenergy[v] + zpe
Calculation of electronic excitation entropy#
[24]:
for v in range(0, numvol):
os.chdir(workdir)
os.chdir('./mg-epwpy/hcp/hcp'+str(v)+'/nscf')
edata = []
with open('hcp'+str(v)+'.dos', 'r') as f:
next(f)
for line in f:
row = [float(x) for x in line.split()]
edata.append(row)
numedat = len(edata)
en = [None]*numedat
edos = [None]*numedat
edosfd = [None]*numedat
doslog = [None]*numedat
tfermi = [None]*ntemp
exce = [None]*ntemp
excent = [None]*ntemp
niter = 200
for i in range(0,numedat):
en[i]=edata[i][0]/ry2ev
edos[i]=edata[i][1]*ry2ev*en[i]
# Get fermi energy in DOS by using bisection method
for i in range(0, ntemp):
if etemps[i] == 0.0:
# Set lower limit of calculation as 10K
etemps[i] = 10.0/ry2k
tmpfermi1 = max(en)
tmpfermi2 = min(en)
for k in range(0,niter):
dosfd = [0]*numedat
tmpfermi = (tmpfermi1+tmpfermi2)/2.0
tmpelec = 0.0
for j in range(0,numedat):
etmp = (en[j]-tmpfermi)/etemps[i]
if abs(etmp) > 10e+0:
if etmp < 0.0:
dosfd[j] = edata[j][1]*ry2ev
else:
dosfd[j] = 0.0
continue
dosfd[j] = edata[j][1]*ry2ev*(1.0/(math.exp(etmp)+1.0))
tmpelec = simpson(dosfd, x=en)
if abs(tmpelec - hcpnelec) < 1.0e-12:
tfermi[i] = tmpfermi
break
if tmpelec < hcpnelec:
tmpfermi2 = tmpfermi
if tmpelec > hcpnelec:
tmpfermi1 = tmpfermi
print('Fermienergy calculation was finished for volume '+str(v)+'')
# Calculate electronic excitations energy
for i in range(0, ntemp):
for j in range(0,numedat):
etmp = (en[j]-tfermi[i])/etemps[i]
if abs(etmp) > 1.0e+2:
if etmp < 0.0:
edosfd[j] = edos[j]
else:
edosfd[j] = 0.0
continue
edosfd[j] = edos[j]*(1.0/(math.exp(etmp)+1.0))
exce[i] = simpson(edosfd, x=en)
uzero = exce[0]
for i in range(0, ntemp):
exce[i] = exce[i] - uzero
# Calculate electronic excitations entropy
for i in range(0, ntemp):
doslog = [None]*numedat
for j in range(0,numedat):
etmp = (en[j]-tfermi[i])/etemps[i]
if abs(etmp) > 1.0e+2:
if etmp < 0.0:
fd = 1.0
else:
fd = 0.0
else:
fd = (1.0/(math.exp(etmp)+1.0))
if fd>0.0 and fd<1.0:
# kb has an unit of eV/K. So, we don't need ry2ev here:
doslog[j] = (fd*math.log(fd)+(1.0-fd)*math.log(1.0-fd))*edata[j][1]
else:
doslog[j] = 0.0
excent[i] = -kb*simpson(doslog, x=en)
# Now, exce is electronic free energy:
exce[i] = exce[i] - excent[i]*temps[i]
hcphelm[i][v] = hcphelm[i][v] + exce[i]
Fermienergy calculation was finished for volume 0
Fermienergy calculation was finished for volume 1
Fermienergy calculation was finished for volume 2
Fermienergy calculation was finished for volume 3
Fermienergy calculation was finished for volume 4
Fermienergy calculation was finished for volume 5
Calculation of Gibbs free energy as a function of pressure#
Finally, we obtain the Gibbs free energies at given temperatures and pressures by interpolating the pressure-dependent values. The calculated Gibbs free energies for each phase are then compared, and the phase boundary is determined and saved.
[25]:
#Calculate volume
for i in range(0,numvol):
bccvol[i] = (bcclat[i] ** 3.0)/2.0
hcpvol[i] = (hcplat[i] ** 3.0)*(math.sqrt(3.0)/2.0)*hcpcoa[i]
# Helmholtz free energy interolation as a function of volume
for i in range(0,ntemp):
bccitpv[i] = interp1d(bccvol, bcchelm[i][:], kind='quadratic',fill_value='extrapolate')
hcpitpv[i] = interp1d(hcpvol, hcphelm[i][:], kind='quadratic',fill_value='extrapolate')
# Calculate pressure
control = 100.0
tmpup = max(bccvol)
tmplw = min(bccvol)
# Calculate Gibbs free energy as a function of
interval = (tmpup - tmplw)/((numvol-1)*control)
for i in range(0,ntemp):
for j in range(0,numvol):
abc = np.array([bccitpv[i](bccvol[j]-interval), bccitpv[i](bccvol[j]), bccitpv[i](bccvol[j]+interval)])
defg = np.array([bccvol[j]-interval,bccvol[j],bccvol[j]+interval])
bccpress[i][j] = -np.gradient(abc, defg)[1] * pressunit
bccgibbs[i][j] = bcchelm[i][j] + (bccpress[i][j]*bccvol[j]/pressunit)
tmpup = max(hcpvol)/2.0
tmplw = min(hcpvol)/2.0
interval = (tmpup - tmplw)/((numvol-1)*control)
for i in range(0,ntemp):
for j in range(0,numvol):
abc = np.array([hcpitpv[i](hcpvol[j]-interval), hcpitpv[i](hcpvol[j]), hcpitpv[i](hcpvol[j]+interval)])
defg = np.array([hcpvol[j]-interval,hcpvol[j],hcpvol[j]+interval])
hcppress[i][j] = -np.gradient(abc, defg)[1] * pressunit
hcpgibbs[i][j] = hcphelm[i][j] + (hcppress[i][j]*hcpvol[j]/pressunit)
# Interpolate Gibbs free energy
for i in range(0,ntemp):
bccitpg[i] = interp1d(bccpress[i][:], bccgibbs[i][:], kind='quadratic',fill_value='extrapolate')
hcpitpg[i] = interp1d(hcppress[i][:], hcpgibbs[i][:], kind='quadratic',fill_value='extrapolate')
for p in range(0,nump):
press[p] = pmin + p*pstep
top[p] = 2400.0
# Compare
for p in range(0,nump):
for i in range(0,ntemp):
if (bccitpg[i](press[p])/bccnatom)<(hcpitpg[i](press[p])/hcpnatom):
#print(press[p],i*tstep)
pb[p] = i*tstep
break
Visualization of phase diagram#
[26]:
import matplotlib.pyplot as plt
plt.plot(press, pb, color='Black', marker='.', label='Phase boundary')
plt.fill_between(press, pb, color='forestgreen', alpha=.6)
plt.fill_between(press, pb, 2400.0, color='bisque', alpha=.8)
plt.xlim(50,545)
plt.ylim(0,2400)
plt.legend()
plt.xlabel(r'$Pressure (kbar)$')
plt.ylabel(r'$Temperature (K)$')
plt.figtext(0.3, 0.3, 'HCP', size=20)
plt.figtext(0.6, 0.7, 'BCC', size=20)
plt.show()
Note: The overall shape and trend of the phase diagram agree well with previous experimental measurements and theoretical calculations. [Olijnyk and Holzapfel (1985)], [Moriarty and Althoff (1995)], and [Mehta et al. (2006)] However, the phase boundary is slightly overestimated. This is because the calculations in this tutorial use unconverged parameters. For more accurate results, one should consider using a denser k-point grid and a higher ecutwfc value in the SCF calculations.
Converged calculation parameters can be found in the original epwpy paper.