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add abacus-phonopy interface

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jiyuang 2022-07-18 16:17:09 +08:00
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.. _abacus_interface:
ABACUS & phonopy calculation
=========================================
How to run
-----------
A procedure of ABACUS-phonopy calculation is as follows:
1) Prepare a 'setting.conf' with following tags
::
DIM = 2 2 2
ATOM_NAME = Al
* when three integers are specified after ``DIM =``, a supercell elongated along axes of unit cell is created
* chemical symbols are specified after ``ATOM_NAME =``, and number of symbols should match ``ntype`` in ABACUS INPUT file.
The interface reads ABACUS STRU file according to the settings of this tag.
2) To obtain supercells with displacements, run phonopy:
::
% phonopy setting.conf --abacus -d
In this example, 2x2x2 supercells are created. ``STRU.in`` and
``STRU-{number}`` give the perfect supercell and supercells
with displacements, respectively. ``phonopy_disp.yaml`` is also created.
This file contains information on displacements. Perhaps the supercell files are
stored in ``disp-{number}`` directories, then ABACUS calculations are
executed in these directories.
3) Calculate forces on atoms in the supercells with displacements. For each SCF calculation,
you should specify ``stru_file`` with ``STRU-{number}`` and ``cal_force=1`` in INPUT in order to calculate force using ABACUS.
Be careful not to relax the structures
4) Then create ``FORCE_SETS`` file using ABACUS inteface
::
% phonopy -f ./disp-001//OUT*/running*.log ./disp-002//OUT*/running*.log ...
Two examples with different settings of basis sets are found in ``example/Al-ABACUS``.

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INPUT_PARAMETERS
#Parameters (1.General)
suffix ABACUS
calculation scf
ntype 1
symmetry 1
pseudo_type upf201
#Parameters (2.Iteration)
ecutwfc 80
scf_thr 1e-8
scf_nmax 100
cal_force 1
cal_stress 1
#Parameters (3.Basis)
basis_type lcao
#kspacing 0.06
#Parameters (4.Smearing)
smearing_method gauss
smearing_sigma 0.01
#Parameters (5.Mixing)
mixing_type pulay
mixing_beta 0.7
pseudo_mesh 1
pseudo_rcut 10.0

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K_POINTS
0
Gamma
4 4 4 0 0 0

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ATOMIC_SPECIES
Al 26.982 Al.PD04.PBE.UPF
NUMERICAL_ORBITAL
Al_gga_10au_100Ry_3s3p2d.orb
LATTICE_CONSTANT
1.8897261254578281
LATTICE_VECTORS
4.04495 0.0 0.0
0.0 4.04495 0.0
0.0 0.0 4.04495
ATOMIC_POSITIONS
Direct
Al
0.0
4
0.00 0.00 0.00 1 1 1
0.50 0.50 0.00 1 1 1
0.50 0.00 0.50 1 1 1
0.00 0.50 0.50 1 1 1

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ATOM_NAME = Al
DIM = 2 2 2
MESH = 8 8 8
PRIMITIVE_AXES = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
BAND= 1 1 1 1/2 1/2 1 3/8 3/8 3/4 0 0 0 1/2 1/2 1/2
BAND_POINTS = 21
BAND_CONNECTION = .TRUE.

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program main
implicit none
integer nelec,nkpt,nbnd
integer lowbound,highbound
real,allocatable :: k(:,:), kk(:), ene(:,:)
integer i,j, m,l
real vbm
real b1, b2, b3
open(unit=11,file='band.yaml')
open(unit=12,file='phonon.dat')
do i=1,24
read(11,*)
enddo
!read(11,*) nelec,nkpt,nbnd
nkpt = 84
nbnd = 3
allocate(kk(1:nkpt))
allocate(ene(nbnd,nkpt))
do j=1,nkpt
read(11,*)
read(11,*)
read(11,'(11X,F13.7)') kk(j)
read(11,*)
do i=1,nbnd
read(11,*)
read(11,'(14X,F16.10)') ene(i,j)
read(11,*)
read(11,*)
read(11,*)
read(11,*)
read(11,*)
enddo
enddo
!do i = 1, nbnd
! write(12,*)
do j=1, nkpt
write(12,'(f17.7,1000f14.6)') kk(j), ene(1:3,j) !*33.35641
enddo
!enddo
close(11)
close(12)
end

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#!/bin/bash
phonopy setting.conf --abacus -d
echo 'stru_file ./STRU-001' >> INPUT
OMP_NUM_THREADS=1 mpirun -n 8 abacus > log
phonopy -f OUT.ABACUS/running_scf.log
phonopy band.conf --abacus

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DIM=2 2 2
ATOM_NAME = Al

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32
1
1
0.0200000000000000 0.0000000000000000 0.0000000000000000
-0.0493525900 0.0000000000 0.0000000000
0.0021020094 0.0000000000 0.0000000000
-0.0012176302 0.0000000000 0.0000000000
0.0007156342 0.0000000000 0.0000000000
-0.0012176302 0.0000000000 0.0000000000
0.0007156342 0.0000000000 0.0000000000
-0.0020298652 0.0000000000 0.0000000000
0.0015348267 0.0000000000 0.0000000000
0.0071358330 0.0067554795 0.0000000000
0.0069649910 -0.0065265932 0.0000000000
0.0071358330 -0.0067554795 0.0000000000
0.0069649910 0.0065265932 0.0000000000
0.0002814260 -0.0009371985 0.0000000000
0.0002792955 0.0009498415 0.0000000000
0.0002814260 0.0009371985 0.0000000000
0.0002792955 -0.0009498415 0.0000000000
0.0071358330 0.0000000000 0.0067554795
0.0069649910 0.0000000000 -0.0065265932
0.0002814260 0.0000000000 -0.0009371985
0.0002792955 0.0000000000 0.0009498415
0.0071358330 0.0000000000 -0.0067554795
0.0069649910 0.0000000000 0.0065265932
0.0002814260 0.0000000000 0.0009371985
0.0002792955 0.0000000000 -0.0009498415
-0.0024694104 -0.0000223750 -0.0000223750
-0.0000047323 -0.0000008412 -0.0000008412
-0.0024694104 0.0000223750 -0.0000223750
-0.0000047323 0.0000008412 -0.0000008412
-0.0024694104 -0.0000223750 0.0000223750
-0.0000047323 -0.0000008412 0.0000008412
-0.0024694104 0.0000223750 0.0000223750
-0.0000047323 0.0000008412 0.0000008412

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INPUT_PARAMETERS
#Parameters (1.General)
suffix ABACUS
calculation scf
ntype 1
symmetry 1
pseudo_type upf201
#Parameters (2.Iteration)
ecutwfc 80
scf_thr 1e-8
scf_nmax 100
cal_force 1
cal_stress 1
#Parameters (3.Basis)
basis_type lcao
#kspacing 0.06
#Parameters (4.Smearing)
smearing_method gauss
smearing_sigma 0.01
#Parameters (5.Mixing)
mixing_type pulay
mixing_beta 0.7
pseudo_mesh 1
pseudo_rcut 10.0
stru_file ./STRU-001

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K_POINTS
0
Gamma
4 4 4 0 0 0

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INPUT_PARAMETERS
#Parameters (1.General)
suffix ABACUS #the name of main output directory
latname test #the name of lattice name
stru_file ./STRU-001 #the filename of file containing atom positions
kpoint_file KPT #the name of file containing k points
pseudo_dir #the directory containing pseudo files
orbital_dir #the directory containing orbital files
pseudo_type upf201 #the type pseudo files
pseudo_rcut 10 #cut-off radius for radial integration
pseudo_mesh 1 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE
lmaxmax 2 #maximum of l channels used
dft_functional default #exchange correlation functional
calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md
ntype 1 #atom species number
nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin
kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file
nbands 0 #number of bands
nbands_sto 256 #number of stochastic bands
nbands_istate 5 #number of bands around Fermi level for istate calulation
nche_sto 100 #number of orders for Chebyshev expansion in stochastic DFT
symmetry 1 #turn symmetry on or off
init_vel 0 #read velocity from STRU or not
symmetry_prec 1e-05 #accuracy for symmetry
nelec 0 #input number of electrons
tot_magnetization 0 #total magnetization of the system
out_mul 0 # mulliken charge or not
noncolin 0 #using non-collinear-spin
lspinorb 0 #consider the spin-orbit interaction
kpar 1 #devide all processors into kpar groups and k points will be distributed among each group
bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group
#Parameters (2.PW)
ecutwfc 80 ##energy cutoff for wave functions
pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations
scf_thr 1e-08 #charge density error
init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file'
init_chg atomic #start charge is from 'atomic' or file
chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA
out_chg 0 #>0 output charge density for selected electron steps
out_pot 0 #output realspace potential
out_wfc_pw 0 #output wave functions
out_wfc_r 0 #output wave functions in realspace
out_dos 0 #output energy and dos
out_band 0 #output energy and band structure
out_proj_band 0 #output projected band structure
restart_save 0 #print to disk every step for restart
restart_load 0 #restart from disk
read_file_dir auto #directory of files for reading
nx 0 #number of points along x axis for FFT grid
ny 0 #number of points along y axis for FFT grid
nz 0 #number of points along z axis for FFT grid
cell_factor 1.2 #used in the construction of the pseudopotential tables
#Parameters (3.Stochastic DFT)
method_sto 1 #1: slow and save memory, 2: fast and waste memory
nbands_sto 256 #number of stochstic orbitals
nche_sto 100 #Chebyshev expansion orders
emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator
emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator
seed_sto 0 #the random seed to generate stochastic orbitals
initsto_freq 1000 #frequency to generate new stochastic orbitals when running md
#Parameters (4.Relaxation)
ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver
scf_nmax 100 ##number of electron iterations
out_force 0 #output the out_force or not
relax_nmax 1 #number of ion iteration steps
out_stru 0 #output the structure files after each ion step
force_thr 0.001 #force threshold, unit: Ry/Bohr
force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom
force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom
relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom
stress_thr 0.01 #stress threshold
press1 0 #target pressure, unit: KBar
press2 0 #target pressure, unit: KBar
press3 0 #target pressure, unit: KBar
relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs
relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs
relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr
relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr
relax_bfgs_init 0.5 #initial trust radius, unit: Bohr
cal_stress 1 #calculate the stress or not
fixed_axes None #which axes are fixed
relax_method cg #bfgs; sd; cg; cg_bfgs;
out_level ie #ie(for electrons); i(for ions);
out_dm 0 #>0 output density matrix
deepks_out_labels 0 #>0 compute descriptor for deepks
deepks_scf 0 #>0 add V_delta to Hamiltonian
deepks_bandgap 0 #>0 for bandgap label
deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test
deepks_model #file dir of traced pytorch model: 'model.ptg
deepks_descriptor_lmax2 #lmax used in generating descriptor
deepks_descriptor_rcut0 #rcut used in generating descriptor
deepks_descriptor_ecut0 #ecut used in generating descriptor
#Parameters (5.LCAO)
basis_type lcao #PW; LCAO in pw; LCAO
nb2d 0 #2d distribution of atoms
search_radius -1 #input search radius (Bohr)
search_pbc 1 #input periodic boundary condition
lcao_ecut 80 #energy cutoff for LCAO
lcao_dk 0.01 #delta k for 1D integration in LCAO
lcao_dr 0.01 #delta r for 1D integration in LCAO
lcao_rmax 30 #max R for 1D two-center integration table
out_mat_hs 0 #output H and S matrix
out_mat_hs2 0 #output H(R) and S(R) matrix
out_mat_r 0 #output r(R) matrix
out_wfc_lcao 0 #ouput LCAO wave functions
bx 2 #division of an element grid in FFT grid along x
by 2 #division of an element grid in FFT grid along y
bz 2 #division of an element grid in FFT grid along z
#Parameters (6.Smearing)
smearing_method gauss #type of smearing_method: gauss; fd; fixed; mp; mp2; mv
smearing_sigma 0.01 #energy range for smearing
#Parameters (7.Charge Mixing)
mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden
mixing_beta 0.7 #mixing parameter: 0 means no new charge
mixing_ndim 8 #mixing dimension in pulay
mixing_gg0 0 #mixing parameter in kerker
#Parameters (8.DOS)
dos_emin_ev -15 #minimal range for dos
dos_emax_ev 15 #maximal range for dos
dos_edelta_ev 0.01 #delta energy for dos
dos_scale 0.01 #scale dos range by
dos_sigma 0.07 #gauss b coefficeinet(default=0.07)
#Parameters (9.Molecular dynamics)
md_type 1 #choose ensemble
md_nstep 10 #md steps
md_ensolver FP #choose potential
md_dt 1 #time step
md_mnhc 4 #number of Nose-Hoover chains
md_tfirst -1 #temperature first
md_tlast -1 #temperature last
md_dumpfreq 1 #The period to dump MD information
md_restartfreq 5 #The period to output MD restart information
md_seed -1 #random seed for MD
md_restart 0 #whether restart
lj_rcut 8.5 #cutoff radius of LJ potential
lj_epsilon 0.01032 #the value of epsilon for LJ potential
lj_sigma 3.405 #the value of sigma for LJ potential
msst_direction 2 #the direction of shock wave
msst_vel 0 #the velocity of shock wave
msst_vis 0 #artificial viscosity
msst_tscale 0.01 #reduction in initial temperature
msst_qmass -1 #mass of thermostat
md_tfreq 0 #oscillation frequency, used to determine qmass of NHC
md_damp 1 #damping parameter (time units) used to add force in Langevin method
#Parameters (10.Electric field and dipole correction)
efield_flag 0 #add electric field
dip_cor_flag 0 #dipole correction
efield_dir 2 #the direction of the electric field or dipole correction
efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir
efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases
efield_amp 0 #amplitude of the electric field
#Parameters (11.Test)
out_alllog 0 #output information for each processor, when parallel
nurse 0 #for coders
colour 0 #for coders, make their live colourful
t_in_h 1 #calculate the kinetic energy or not
vl_in_h 1 #calculate the local potential or not
vnl_in_h 1 #calculate the nonlocal potential or not
vh_in_h 1 #calculate the hartree potential or not
vion_in_h 1 #calculate the local ionic potential or not
test_force 0 #test the force
test_stress 0 #test the force
#Parameters (13.vdW Correction)
vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj
vdw_s6 default #scale parameter of d2/d3_0/d3_bj
vdw_s8 default #scale parameter of d3_0/d3_bj
vdw_a1 default #damping parameter of d3_0/d3_bj
vdw_a2 default #damping parameter of d3_bj
vdw_d 20 #damping parameter of d2
vdw_abc 0 #third-order term?
vdw_C6_file default #filename of C6
vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6
vdw_R0_file default #filename of R0
vdw_R0_unit A #unit of R0, A or Bohr
vdw_model radius #expression model of periodic structure, radius or period
vdw_radius default #radius cutoff for periodic structure
vdw_radius_unit Bohr #unit of radius cutoff for periodic structure
vdw_cn_thr 40 #radius cutoff for cn
vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom
vdw_period 3 3 3 #periods of periodic structure
#Parameters (14.exx)
dft_functional default #no, hf, pbe0, hse or opt_orb
exx_hybrid_alpha 0.25 #
exx_hse_omega 0.11 #
exx_separate_loop 1 #0 or 1
exx_hybrid_step 100 #
exx_lambda 0.3 #
exx_pca_threshold 0 #
exx_c_threshold 0 #
exx_v_threshold 0 #
exx_dm_threshold 0 #
exx_schwarz_threshold0 #
exx_cauchy_threshold0 #
exx_ccp_threshold 1e-08 #
exx_ccp_rmesh_times 10 #
exx_distribute_type htime #htime or kmeans1 or kmeans2
exx_opt_orb_lmax 0 #
exx_opt_orb_ecut 0 #
exx_opt_orb_tolerence0 #
#Parameters (16.tddft)
tddft 0 #calculate tddft or not
td_scf_thr 1e-09 #threshold for electronic iteration of tddft
td_dt 0.02 #time of ion step
td_force_dt 0.02 #time of force change
td_val_elec_01 1 #td_val_elec_01
td_val_elec_02 1 #td_val_elec_02
td_val_elec_03 1 #td_val_elec_03
td_vext 0 #add extern potential or not
td_vext_dire 1 #extern potential direction
td_timescale 0.5 #extern potential td_timescale
td_vexttype 1 #extern potential type
td_vextout 0 #output extern potential or not
td_dipoleout 0 #output dipole or not
ocp 0 #change occupation or not
ocp_set none #set occupation
#Parameters (17.berry_wannier)
berry_phase 0 #calculate berry phase or not
gdir 3 #calculate the polarization in the direction of the lattice vector
towannier90 0 #use wannier90 code interface or not
nnkpfile seedname.nnkp #the wannier90 code nnkp file name
wannier_spin up #calculate spin in wannier90 code interface
#Parameters (18.implicit_solvation)
imp_sol 0 #calculate implicit solvation correction or not
eb_k 80 #the relative permittivity of the bulk solvent
tau 1.0798e-05 #the effective surface tension parameter
sigma_k 0.6 # the width of the diffuse cavity
nc_k 0.00037 # the cut-off charge density
#Parameters (19.compensating_charge)
comp_chg 0 # add compensating charge
comp_q 0 # total charge of compensating charge
comp_l 1 # total length of compensating charge
comp_center 0 # center of compensating charge on dim
comp_dim 2 # dimension of compensating charge(x, y or z)

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data_test
_audit_creation_method generated by ABACUS
_cell_length_a 8.0899
_cell_length_b 8.0899
_cell_length_c 8.0899
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_symmetry_space_group_name_H-M
_symmetry_Int_Tables_number
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Al 0.00130824 0 0
Al 0.5 0 0
Al 0 0.5 0
Al 0.5 0.5 0
Al 0 0 0.5
Al 0.5 0 0.5
Al 0 0.5 0.5
Al 0.5 0.5 0.5
Al 0.25 0.25 0
Al 0.75 0.25 0
Al 0.25 0.75 0
Al 0.75 0.75 0
Al 0.25 0.25 0.5
Al 0.75 0.25 0.5
Al 0.25 0.75 0.5
Al 0.75 0.75 0.5
Al 0.25 0 0.25
Al 0.75 0 0.25
Al 0.25 0.5 0.25
Al 0.75 0.5 0.25
Al 0.25 0 0.75
Al 0.75 0 0.75
Al 0.25 0.5 0.75
Al 0.75 0.5 0.75
Al 0 0.25 0.25
Al 0.5 0.25 0.25
Al 0 0.75 0.25
Al 0.5 0.75 0.25
Al 0 0.25 0.75
Al 0.5 0.25 0.75
Al 0 0.75 0.75
Al 0.5 0.75 0.75

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AUTO_SET ks_solver to genelpa
Input warning : gamma_only_local algorithm is not used.
AUTO_SET lcao_ecut to 80
In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block.
AUTO_SET NBANDS to 0
AUTO_SET NBANDS to 58
startmag_type = 2
charge from rho_at = 2.99755
charge should be = 3
SETUP ATOMIC RHO FOR SPIN 1
Electron number from rho = 96
total electron number from rho = 96
should be = 96
charge before normalized = 96
charge after normalized = 96
cpu 2D distribution : 2*4
but, the number of bands-row-block is 2
Processor Atom
1 48
2 48
3 48
4 48
5 48
6 48
7 48
8 48
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.000061748641
charge after normalized = 96
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000614083239
charge after normalized = 96.0000000000001
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000617032261
charge after normalized = 96.0000000000001
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000617004812
charge after normalized = 96
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616881486
charge after normalized = 96
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616852643
charge after normalized = 96
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616851719
charge after normalized = 96.0000000000001
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.000061685274
charge after normalized = 96.0000000000001
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616851274
charge after normalized = 96.0000000000001
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616850981
charge after normalized = 96
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616851286
charge after normalized = 96
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616852008
charge after normalized = 96
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616852035
charge after normalized = 96
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616850972
charge after normalized = 96
CHECK UPDATE INPUT INFORMATION
charge before normalized = 96.0000616852347
charge after normalized = 96
charge before normalized = 96.0000000000001
charge after normalized = 96

23
example/Al-ABACUS/abacus-lcao/reference/STRU Normal file
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@ -0,0 +1,23 @@
ATOMIC_SPECIES
Al 26.982 Al.PD04.PBE.UPF
NUMERICAL_ORBITAL
Al_gga_10au_100Ry_3s3p2d.orb
LATTICE_CONSTANT
1.8897261254578281
LATTICE_VECTORS
4.04495 0.0 0.0
0.0 4.04495 0.0
0.0 0.0 4.04495
ATOMIC_POSITIONS
Direct
Al
0.0
4
0.00 0.00 0.00 1 1 1
0.50 0.50 0.00 1 1 1
0.50 0.00 0.50 1 1 1
0.00 0.50 0.50 1 1 1

52
example/Al-ABACUS/abacus-lcao/reference/STRU-001 Normal file
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@ -0,0 +1,52 @@
ATOMIC_SPECIES
Al 26.9815386 Al.PD04.PBE.UPF
NUMERICAL_ORBITAL
Al_gga_10au_100Ry_3s3p2d.orb
LATTICE_CONSTANT
1.0
LATTICE_VECTORS
15.287695382341283 0.0 0.0
0.0 15.287695382341283 0.0
0.0 0.0 15.287695382341283
ATOMIC_POSITIONS
Direct
Al
0.0
32
0.0013082416610094069 0.0 0.0 1 1 1
0.5 0.0 0.0 1 1 1
0.0 0.5 0.0 1 1 1
0.5 0.5 0.0 1 1 1
0.0 0.0 0.5 1 1 1
0.5 0.0 0.5 1 1 1
0.0 0.5 0.5 1 1 1
0.5 0.5 0.5 1 1 1
0.25 0.25 0.0 1 1 1
0.75 0.25 0.0 1 1 1
0.25 0.75 0.0 1 1 1
0.75 0.75 0.0 1 1 1
0.25 0.25 0.5 1 1 1
0.75 0.25 0.5 1 1 1
0.25 0.75 0.5 1 1 1
0.75 0.75 0.5 1 1 1
0.25 0.0 0.25 1 1 1
0.75 0.0 0.25 1 1 1
0.25 0.5 0.25 1 1 1
0.75 0.5 0.25 1 1 1
0.25 0.0 0.75 1 1 1
0.75 0.0 0.75 1 1 1
0.25 0.5 0.75 1 1 1
0.75 0.5 0.75 1 1 1
0.0 0.25 0.25 1 1 1
0.5 0.25 0.25 1 1 1
0.0 0.75 0.25 1 1 1
0.5 0.75 0.25 1 1 1
0.0 0.25 0.75 1 1 1
0.5 0.25 0.75 1 1 1
0.0 0.75 0.75 1 1 1
0.5 0.75 0.75 1 1 1

49
example/Al-ABACUS/abacus-lcao/reference/STRU.in Normal file
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@ -0,0 +1,49 @@
ATOMIC_SPECIES
Al 26.9815386 Al.PD04.PBE.UPF
LATTICE_CONSTANT
1.0
LATTICE_VECTORS
15.287695382341283 0.0 0.0
0.0 15.287695382341283 0.0
0.0 0.0 15.287695382341283
ATOMIC_POSITIONS
Direct
Al
0.0
32
0.0 0.0 0.0 1 1 1
0.5 0.0 0.0 1 1 1
0.0 0.5 0.0 1 1 1
0.5 0.5 0.0 1 1 1
0.0 0.0 0.5 1 1 1
0.5 0.0 0.5 1 1 1
0.0 0.5 0.5 1 1 1
0.5 0.5 0.5 1 1 1
0.25 0.25 0.0 1 1 1
0.75 0.25 0.0 1 1 1
0.25 0.75 0.0 1 1 1
0.75 0.75 0.0 1 1 1
0.25 0.25 0.5 1 1 1
0.75 0.25 0.5 1 1 1
0.25 0.75 0.5 1 1 1
0.75 0.75 0.5 1 1 1
0.25 0.0 0.25 1 1 1
0.75 0.0 0.25 1 1 1
0.25 0.5 0.25 1 1 1
0.75 0.5 0.25 1 1 1
0.25 0.0 0.75 1 1 1
0.75 0.0 0.75 1 1 1
0.25 0.5 0.75 1 1 1
0.75 0.5 0.75 1 1 1
0.0 0.25 0.25 1 1 1
0.5 0.25 0.25 1 1 1
0.0 0.75 0.25 1 1 1
0.5 0.75 0.25 1 1 1
0.0 0.25 0.75 1 1 1
0.5 0.25 0.75 1 1 1
0.0 0.75 0.75 1 1 1
0.5 0.75 0.75 1 1 1

7
example/Al-ABACUS/abacus-lcao/reference/band.conf Normal file
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@ -0,0 +1,7 @@
ATOM_NAME = Al
DIM = 2 2 2
MESH = 8 8 8
PRIMITIVE_AXES = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
BAND= 1 1 1 1/2 1/2 1 3/8 3/8 3/4 0 0 0 1/2 1/2 1/2
BAND_POINTS = 21
BAND_CONNECTION = .TRUE.

52
example/Al-ABACUS/abacus-lcao/reference/band.f90 Normal file
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@ -0,0 +1,52 @@
program main
implicit none
integer nelec,nkpt,nbnd
integer lowbound,highbound
real,allocatable :: k(:,:), kk(:), ene(:,:)
integer i,j, m,l
real vbm
real b1, b2, b3
open(unit=11,file='band.yaml')
open(unit=12,file='phonon.dat')
do i=1,24
read(11,*)
enddo
!read(11,*) nelec,nkpt,nbnd
nkpt = 84
nbnd = 3
allocate(kk(1:nkpt))
allocate(ene(nbnd,nkpt))
do j=1,nkpt
read(11,*)
read(11,*)
read(11,'(11X,F13.7)') kk(j)
read(11,*)
do i=1,nbnd
read(11,*)
read(11,'(14X,F16.10)') ene(i,j)
read(11,*)
read(11,*)
read(11,*)
read(11,*)
read(11,*)
enddo
enddo
!do i = 1, nbnd
! write(12,*)
do j=1, nkpt
write(12,'(f17.7,1000f14.6)') kk(j), ene(1:3,j) !*33.35641
enddo
!enddo
close(11)
close(12)
end

2125
example/Al-ABACUS/abacus-lcao/reference/band.yaml Normal file
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File diff suppressed because it is too large Load Diff

122
example/Al-ABACUS/abacus-lcao/reference/log Normal file
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@ -0,0 +1,122 @@
*********************************************************
* *
* WELCOME TO ABACUS *
* *
* 'Atomic-orbital Based Ab-initio *
* Computation at UStc' *
* *
* Website: http://abacus.ustc.edu.cn/ *
* *
*********************************************************
Mon Jul 18 11:02:22 2022
MAKE THE DIR : OUT.ABACUS/
UNIFORM GRID DIM : 90 * 90 * 90
UNIFORM GRID DIM(BIG): 45 * 45 * 45
DONE(0.0887968 SEC) : SETUP UNITCELL
DONE(0.152374 SEC) : SYMMETRY
DONE(0.153268 SEC) : INIT K-POINTS
---------------------------------------------------------
Self-consistent calculations for electrons
---------------------------------------------------------
SPIN KPOINTS PROCESSORS NBASE
1 18 8 704
---------------------------------------------------------
Use Systematically Improvable Atomic bases
---------------------------------------------------------
ELEMENT ORBITALS NBASE NATOM XC
Al 3s3p2d-10au 22 32
---------------------------------------------------------
Initial plane wave basis and FFT box
---------------------------------------------------------
DONE(0.173506 SEC) : INIT PLANEWAVE
DONE(0.233752 SEC) : INIT CHARGE
START POTENTIAL : atomic
DONE(0.380414 SEC) : INIT POTENTIAL
-------------------------------------------
SELF-CONSISTENT :
-------------------------------------------
ITER ETOT(eV) EDIFF(eV) DRHO TIME(s)
GE1 -2.017000e+03 0.000000e+00 9.519e-02 2.721e+01
GE2 -2.016968e+03 3.171577e-02 2.625e-02 2.680e+01
GE3 -2.016962e+03 6.352559e-03 2.693e-03 2.690e+01
GE4 -2.016964e+03 -2.272341e-03 3.710e-03 2.679e+01
GE5 -2.016971e+03 -6.543145e-03 1.525e-03 2.685e+01
GE6 -2.016972e+03 -9.679255e-04 9.489e-05 2.704e+01
GE7 -2.016972e+03 -3.133626e-06 1.593e-05 2.714e+01
GE8 -2.016972e+03 -4.547868e-08 3.181e-06 2.772e+01
GE9 -2.016972e+03 5.911053e-09 5.285e-06 2.745e+01
GE10 -2.016972e+03 -1.558158e-08 9.145e-07 2.699e+01
GE11 -2.016972e+03 -4.060321e-11 6.326e-07 2.687e+01
GE12 -2.016972e+03 3.886307e-10 1.272e-07 2.693e+01
GE13 -2.016972e+03 1.469449e-11 3.477e-08 2.751e+01
GE14 -2.016972e+03 -8.414531e-10 8.572e-08 2.682e+01
GE15 -2.016972e+03 1.124902e-09 9.909e-09 2.673e+01
><><><><><><><><><><><><><><><><><><><><><><
TOTAL-STRESS (KBAR):
><><><><><><><><><><><><><><><><><><><><><><
-5.257e-01 1.365e-16 0.000e+00
1.365e-16 -5.261e-01 0.000e+00
0.000e+00 0.000e+00 -5.261e-01
TOTAL-PRESSURE: -5.260e-01 KBAR
|CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%-------
total 478.91 13 37 1e+02 %
Run_lcao lcao_line 478.89 1 4.8e+02 1e+02 %
Potential init_pot 0.2093 2 0.1 0.044 %
PW_Basis recip2real 0.22177 101 0.0022 0.046 %
PW_Basis gathers_scatterp 0.10299 101 0.001 0.022 %
Potential v_of_rho 0.96207 17 0.057 0.2 %
XC_Functional v_xc 0.96289 19 0.051 0.2 %
PW_Basis real2recip 0.27633 150 0.0018 0.058 %
PW_Basis gatherp_scatters 0.1184 150 0.00079 0.025 %
ORB_control read_orb_first 0.21339 1 0.21 0.045 %
LCAO_Orbitals Read_Orbitals 0.21339 1 0.21 0.045 %
NOrbital_Lm extra_uniform 0.15193 8 0.019 0.032 %
Mathzone_Add1 Uni_Deriv_Phi 0.14416 8 0.018 0.03 %
ORB_control set_orb_tables 2.3656 1 2.4 0.49 %
ORB_gen_tables gen_tables 2.3656 1 2.4 0.49 %
ORB_table_phi init_Table 1.5061 1 1.5 0.31 %
ORB_table_phi cal_ST_Phi12_R 1.4931 186 0.008 0.31 %
ORB_table_beta init_Table_Beta 0.49308 1 0.49 0.1 %
ORB_table_beta VNL_PhiBeta_R 0.49051 72 0.0068 0.1 %
LOOP_ions opt_ions 475.89 1 4.8e+02 99 %
ESolver_KS_LCAO Run 407.94 1 4.1e+02 85 %
ESolver_KS_LCAO beforescf 2.1944 1 2.2 0.46 %
ESolver_KS_LCAO set_matrix_grid 0.23403 1 0.23 0.049 %
Grid_Technique init 0.17127 1 0.17 0.036 %
Grid_Driver Find_atom 0.29418 19712 1.5e-05 0.061 %
LCAO_Hamilt set_lcao_matrices 1.6719 1 1.7 0.35 %
LCAO_gen_fixedH calculate_S_no 0.23734 1 0.24 0.05 %
LCAO_gen_fixedH build_Nonlocal_mu_new4.1635 2 2.1 0.87 %
ORB_gen_tables snap_psibeta_half 0.32988 58080 5.7e-06 0.069 %
H_Ewald_pw compute_ewald 0.11569 1 0.12 0.024 %
Symmetry rho_symmetry 0.4139 16 0.026 0.086 %
HSolverLCAO solve 404.14 15 27 84 %
HamiltLCAO each_k 173.49 270 0.64 36 %
Gint_interface cal_gint 350.59 31 11 73 %
HamiltLCAO H_k 27.688 135 0.21 5.8 %
LCAO_Hamilt calculate_Hk 20.968 270 0.078 4.4 %
Gint_k folding_vl_k 13.019 270 0.048 2.7 %
Gint_k Distri 9.6214 270 0.036 2 %
LCAO_nnr folding_fixedH 7.7757 270 0.029 1.6 %
Efficience H_k 24.598 135 0.18 5.1 %
DiagoElpa elpa_solve 31.037 270 0.11 6.5 %
ElecStateLCAO psiToRho 178.05 15 12 37 %
Local_Orbital_wfc wfc_2d_to_grid 0.14392 270 0.00053 0.03 %
LCAO_Charge cal_dk_k 26.976 15 1.8 5.6 %
Charge mix_rho 0.17432 14 0.012 0.036 %
LOOP_ions force_stress 67.947 1 68 14 %
Force_Stress_LCAO getForceStress 67.947 1 68 14 %
Force_LCAO_k ftable_k 67.549 1 68 14 %
Force_LCAO_k allocate_k 4.9257 1 4.9 1 %
Force_LCAO_k cal_foverlap_k 0.49157 1 0.49 0.1 %
Force_LCAO_k cal_edm_2d 0.46163 1 0.46 0.096 %
Local_Orbital_Chargecal_dm_R 0.10869 1 0.11 0.023 %
Force_LCAO_k cal_fvl_dphi_k 29.31 1 29 6.1 %
Force_LCAO_k cal_fvnl_dbeta_k_new32.506 1 33 6.8 %
----------------------------------------------------------------------------------------
START Time : Mon Jul 18 11:02:22 2022
FINISH Time : Mon Jul 18 11:10:21 2022
TOTAL Time : 4.8e+02
SEE INFORMATION IN : OUT.ABACUS/

677
example/Al-ABACUS/abacus-lcao/reference/mesh.yaml Normal file
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@ -0,0 +1,677 @@
mesh: [ 8, 8, 8 ]
nqpoint: 60
reciprocal_lattice:
- [ -0.13082417, 0.13082417, 0.13082417 ] # a*
- [ 0.13082417, -0.13082417, 0.13082417 ] # b*
- [ 0.13082417, 0.13082417, -0.13082417 ] # c*
natom: 1
lattice:
- [ 0.000000000000000, 3.821923845585321, 3.821923845585321 ] # a
- [ 3.821923845585321, 0.000000000000000, 3.821923845585321 ] # b
- [ 3.821923845585321, 3.821923845585321, 0.000000000000000 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
phonon:
- q-position: [ 0.0625000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.014162131
weight: 2
band:
- # 1
frequency: 1.0754588523
- # 2
frequency: 1.0754588523
- # 3
frequency: 1.8471050830
- q-position: [ 0.1875000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.035640582
weight: 6
band:
- # 1
frequency: 2.4601577018
- # 2
frequency: 2.5617592884
- # 3
frequency: 4.4283350763
- q-position: [ 0.3125000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.062804968
weight: 6
band:
- # 1
frequency: 3.6187140693
- # 2
frequency: 3.6636930806
- # 3
frequency: 7.1528503588
- q-position: [ 0.4375000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.090681887
weight: 6
band:
- # 1
frequency: 4.1562575691
- # 2
frequency: 4.2738323537
- # 3
frequency: 9.1043434563
- q-position: [ -0.4375000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.109394253
weight: 6
band:
- # 1
frequency: 4.2879955835
- # 2
frequency: 4.4696100994
- # 3
frequency: 9.6659328733
- q-position: [ -0.3125000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.081355251
weight: 6
band:
- # 1
frequency: 3.9285712032
- # 2
frequency: 4.2001009151
- # 3
frequency: 8.5970574374
- q-position: [ -0.1875000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.053616964
weight: 6
band:
- # 1
frequency: 3.1822432936
- # 2
frequency: 3.4753933510
- # 3
frequency: 6.3466681017
- q-position: [ -0.0625000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.027118417
weight: 6
band:
- # 1
frequency: 1.8693641783
- # 2
frequency: 1.9775740401
- # 3
frequency: 3.5555967539
- q-position: [ 0.1875000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.042486394
weight: 6
band:
- # 1
frequency: 2.8021240600
- # 2
frequency: 2.9360236056
- # 3
frequency: 5.3953973361
- q-position: [ 0.3125000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.062804968
weight: 12
band:
- # 1
frequency: 3.8254211859
- # 2
frequency: 4.2103349879
- # 3
frequency: 7.0550581774
- q-position: [ 0.4375000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.087683305
weight: 12
band:
- # 1
frequency: 4.4474455994
- # 2
frequency: 5.2754054193
- # 3
frequency: 8.4492349378
- q-position: [ 0.5625000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.114178754
weight: 12
band:
- # 1
frequency: 4.7636313146
- # 2
frequency: 5.6288712249
- # 3
frequency: 9.1965824364
- q-position: [ -0.3125000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.096399636
weight: 12
band:
- # 1
frequency: 4.5902817218
- # 2
frequency: 5.4885270626
- # 3
frequency: 8.6853650944
- q-position: [ -0.1875000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.070810657
weight: 12
band:
- # 1
frequency: 4.0603902494
- # 2
frequency: 4.7642236832
- # 3
frequency: 7.2782693671
- q-position: [ -0.0625000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.048372888
weight: 12
band:
- # 1
frequency: 3.1458120964
- # 2
frequency: 3.3537599066
- # 3
frequency: 5.7545931753
- q-position: [ 0.3125000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.074491555
weight: 6
band:
- # 1
frequency: 4.4669390047
- # 2
frequency: 4.6138488042
- # 3
frequency: 8.2285182310
- q-position: [ 0.4375000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.093584439
weight: 12
band:
- # 1
frequency: 5.1445834306
- # 2
frequency: 5.5874850616
- # 3
frequency: 8.8979934794
- q-position: [ 0.5625000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.116497341
weight: 12
band:
- # 1
frequency: 5.4841285414
- # 2
frequency: 6.7462214491
- # 3
frequency: 8.8549485079
- q-position: [ -0.3125000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.116497341
weight: 12
band:
- # 1
frequency: 5.3362879232
- # 2
frequency: 7.3289284552
- # 3
frequency: 8.1490299979
- q-position: [ -0.1875000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.093584439
weight: 12
band:
- # 1
frequency: 4.7245214827
- # 2
frequency: 6.1604611507
- # 3
frequency: 8.0136530087
- q-position: [ -0.0625000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.074491555
weight: 12
band:
- # 1
frequency: 3.9523989028
- # 2
frequency: 4.4199870051
- # 3
frequency: 7.8974516797
- q-position: [ 0.4375000, 0.4375000, 0.0625000 ]
distance_from_gamma: 0.106921747
weight: 6
band:
- # 1
frequency: 5.5222123544
- # 2
frequency: 5.6551978114
- # 3
frequency: 9.6539072603
- q-position: [ 0.5625000, 0.4375000, 0.0625000 ]
distance_from_gamma: 0.125343531
weight: 12
band:
- # 1
frequency: 5.8711493201
- # 2
frequency: 6.2478175993
- # 3
frequency: 9.6106457402
- q-position: [ -0.3125000, -0.5625000, 0.0625000 ]
distance_from_gamma: 0.131588481
weight: 12
band:
- # 1
frequency: 5.7536170714
- # 2
frequency: 7.1585251613
- # 3
frequency: 8.8236284738
- q-position: [ -0.1875000, 0.4375000, 0.0625000 ]
distance_from_gamma: 0.118770674
weight: 12
band:
- # 1
frequency: 5.1208242587
- # 2
frequency: 6.4786506832
- # 3
frequency: 8.7850781310
- q-position: [ -0.0625000, 0.4375000, 0.0625000 ]
distance_from_gamma: 0.101796733
weight: 12
band:
- # 1
frequency: 4.3997759661
- # 2
frequency: 4.8549417889
- # 3
frequency: 9.3127293260
- q-position: [ -0.4375000, -0.4375000, 0.0625000 ]
distance_from_gamma: 0.123191550
weight: 6
band:
- # 1
frequency: 5.7450539802
- # 2
frequency: 5.8729345409
- # 3
frequency: 9.9101107059
- q-position: [ -0.3125000, -0.4375000, 0.0625000 ]
distance_from_gamma: 0.109394253
weight: 12
band:
- # 1
frequency: 5.6181092260
- # 2
frequency: 6.0209654132
- # 3
frequency: 9.3825552607
- q-position: [ -0.1875000, -0.4375000, 0.0625000 ]
distance_from_gamma: 0.101796733
weight: 12
band:
- # 1
frequency: 5.0080357649
- # 2
frequency: 6.0805415728
- # 3
frequency: 8.7620773386
- q-position: [ -0.3125000, -0.3125000, 0.0625000 ]
distance_from_gamma: 0.090681887
weight: 6
band:
- # 1
frequency: 5.0885093599
- # 2
frequency: 5.2293457126
- # 3
frequency: 9.1085752761
- q-position: [ -0.1875000, -0.3125000, 0.0625000 ]
distance_from_gamma: 0.077998938
weight: 12
band:
- # 1
frequency: 4.5180208832
- # 2
frequency: 4.9731797521
- # 3
frequency: 8.1237608972
- q-position: [ -0.1875000, -0.1875000, 0.0625000 ]
distance_from_gamma: 0.058391964
weight: 6
band:
- # 1
frequency: 3.6903085807
- # 2
frequency: 3.8361700397
- # 3
frequency: 6.9851718168
- q-position: [ 0.1875000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.042486394
weight: 2
band:
- # 1
frequency: 2.7714962644
- # 2
frequency: 2.7714962644
- # 3
frequency: 5.2525087926
- q-position: [ 0.3125000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.058391964
weight: 6
band:
- # 1
frequency: 3.6192837816
- # 2
frequency: 3.9713932784
- # 3
frequency: 6.4526006659
- q-position: [ 0.4375000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.081355251
weight: 6
band:
- # 1
frequency: 4.3123862376
- # 2
frequency: 5.4556047415
- # 3
frequency: 7.6420194461
- q-position: [ 0.5625000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.106921747
weight: 6
band:
- # 1
frequency: 4.7724806798
- # 2
frequency: 5.9445584668
- # 3
frequency: 8.8191377283
- q-position: [ -0.3125000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.106921747
weight: 6
band:
- # 1
frequency: 4.8061058449
- # 2
frequency: 5.8656501635
- # 3
frequency: 9.0220156991
- q-position: [ -0.1875000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.081355251
weight: 6
band:
- # 1
frequency: 4.3894431584
- # 2
frequency: 5.1700651689
- # 3
frequency: 8.2317958569
- q-position: [ 0.3125000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.066927622
weight: 6
band:
- # 1
frequency: 3.7499587069
- # 2
frequency: 4.3361959595
- # 3
frequency: 7.3881712045
- q-position: [ 0.4375000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.084578481
weight: 12
band:
- # 1
frequency: 4.6267770312
- # 2
frequency: 5.5138046060
- # 3
frequency: 8.0200503439
- q-position: [ 0.5625000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.106921747
weight: 12
band:
- # 1
frequency: 5.3175656390
- # 2
frequency: 6.7774132937
- # 3
frequency: 8.2728153993
- q-position: [ -0.3125000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.123191550
weight: 12
band:
- # 1
frequency: 5.5799076670
- # 2
frequency: 6.9444781601
- # 3
frequency: 8.5947509183
- q-position: [ -0.1875000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.099134920
weight: 12
band:
- # 1
frequency: 5.2622877793
- # 2
frequency: 6.1326276524
- # 3
frequency: 8.5717199069
- q-position: [ 0.4375000, 0.4375000, 0.1875000 ]
distance_from_gamma: 0.096399636
weight: 6
band:
- # 1
frequency: 4.9949292223
- # 2
frequency: 5.8800289362
- # 3
frequency: 8.8251894696
- q-position: [ 0.5625000, 0.4375000, 0.1875000 ]
distance_from_gamma: 0.114178754
weight: 12
band:
- # 1
frequency: 5.8126908668
- # 2
frequency: 6.5787258339
- # 3
frequency: 8.9085558974
- q-position: [ 0.6875000, 0.4375000, 0.1875000 ]
distance_from_gamma: 0.135592085
weight: 12
band:
- # 1
frequency: 6.3207504972
- # 2
frequency: 7.5321855052
- # 3
frequency: 8.3413149018
- q-position: [ -0.1875000, 0.4375000, 0.1875000 ]
distance_from_gamma: 0.121001304
weight: 12
band:
- # 1
frequency: 5.9266218831
- # 2
frequency: 7.2490736992
- # 3
frequency: 8.3681885863
- q-position: [ 0.5625000, 0.5625000, 0.1875000 ]
distance_from_gamma: 0.127459183
weight: 6
band:
- # 1
frequency: 5.7210154662
- # 2
frequency: 6.6831989518
- # 3
frequency: 9.3325345220
- q-position: [ -0.3125000, -0.4375000, 0.1875000 ]
distance_from_gamma: 0.129540286
weight: 12
band:
- # 1
frequency: 6.1285301765
- # 2
frequency: 6.8192598466
- # 3
frequency: 9.0575505282
- q-position: [ -0.3125000, -0.3125000, 0.1875000 ]
distance_from_gamma: 0.111812098
weight: 6
band:
- # 1
frequency: 5.4648740425
- # 2
frequency: 6.4025852132
- # 3
frequency: 9.1773187997
- q-position: [ 0.3125000, 0.3125000, 0.3125000 ]
distance_from_gamma: 0.070810657
weight: 2
band:
- # 1
frequency: 3.6932782343
- # 2
frequency: 3.6932782343
- # 3
frequency: 7.9597400720
- q-position: [ 0.4375000, 0.3125000, 0.3125000 ]
distance_from_gamma: 0.084578481
weight: 6
band:
- # 1
frequency: 4.2392833555
- # 2
frequency: 4.8022335696
- # 3
frequency: 8.3763239192
- q-position: [ 0.5625000, 0.3125000, 0.3125000 ]
distance_from_gamma: 0.104390696
weight: 6
band:
- # 1
frequency: 4.9259127265
- # 2
frequency: 6.8062201847
- # 3
frequency: 8.0809745921
- q-position: [ 0.6875000, 0.3125000, 0.3125000 ]
distance_from_gamma: 0.127459183
weight: 6
band:
- # 1
frequency: 5.4586327500
- # 2
frequency: 7.4112974269
- # 3
frequency: 8.4252888393
- q-position: [ 0.4375000, 0.4375000, 0.3125000 ]
distance_from_gamma: 0.093584439
weight: 6
band:
- # 1
frequency: 4.3307045941
- # 2
frequency: 4.9888539995
- # 3
frequency: 8.9603589394
- q-position: [ 0.5625000, 0.4375000, 0.3125000 ]
distance_from_gamma: 0.109394253
weight: 12
band:
- # 1
frequency: 5.0881239354
- # 2
frequency: 6.2319863162
- # 3
frequency: 8.7609534814
- q-position: [ 0.6875000, 0.4375000, 0.3125000 ]
distance_from_gamma: 0.129540286
weight: 12
band:
- # 1
frequency: 5.8781600355
- # 2
frequency: 7.5748420911
- # 3
frequency: 8.2339317253
- q-position: [ 0.5625000, 0.5625000, 0.3125000 ]
distance_from_gamma: 0.121001304
weight: 6
band:
- # 1
frequency: 5.2202022516
- # 2
frequency: 6.7139235853
- # 3
frequency: 8.8082184312
- q-position: [ 0.4375000, 0.4375000, 0.4375000 ]
distance_from_gamma: 0.099134920
weight: 2
band:
- # 1
frequency: 4.1544533378
- # 2
frequency: 4.1544533378
- # 3
frequency: 9.5645788805
- q-position: [ 0.5625000, 0.4375000, 0.4375000 ]
distance_from_gamma: 0.111812098
weight: 6
band:
- # 1
frequency: 4.5260476934
- # 2
frequency: 5.1100820129
- # 3
frequency: 9.3985278683

7
example/Al-ABACUS/abacus-lcao/reference/myrun.sh Normal file
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@ -0,0 +1,7 @@
#!/bin/bash
phonopy setting.conf --abacus -d
echo 'stru_file ./STRU-001' >> INPUT
OMP_NUM_THREADS=1 mpirun -n 8 abacus > log
phonopy -f OUT.ABACUS/running_scf.log
phonopy band.conf --abacus

84
example/Al-ABACUS/abacus-lcao/reference/phonon.dat Normal file
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@ -0,0 +1,84 @@
0.0000000 -0.000293 -0.000293 -0.000293
0.0065412 0.458159 0.910749 0.458159
0.0130824 0.913285 1.811611 0.913285
0.0196236 1.362374 2.692964 1.362374
0.0261648 1.802481 3.545705 1.802481
0.0327060 2.230749 4.361490 2.230749
0.0392472 2.644434 5.132941 2.644434
0.0457885 3.040928 5.853829 3.040928
0.0523297 3.417775 6.519203 3.417775
0.0588709 3.772693 7.125475 3.772693
0.0654121 4.103580 7.670451 4.103580
0.0719533 4.408526 8.153296 4.408526
0.0784945 4.685817 8.574439 4.685817
0.0850357 4.933935 8.935414 4.933935
0.0915769 5.151559 9.238643 5.151559
0.0981181 5.337560 9.487163 5.337560
0.1046593 5.490996 9.684319 5.490996
0.1112005 5.611110 9.833447 5.611110
0.1177417 5.697316 9.937542 5.697316
0.1242830 5.749204 9.998980 5.749204
0.1308242 5.766527 10.019283 5.766527
0.1308242 5.766527 5.766527 10.019283
0.1331368 5.772051 5.766840 10.016143
0.1354495 5.788537 5.767757 10.006731
0.1377622 5.815726 5.769206 9.991076
0.1400748 5.853197 5.771071 9.969228
0.1423875 5.900383 5.773195 9.941251
0.1447002 5.956590 5.775382 9.907229
0.1470128 6.021016 5.777400 9.867267
0.1493255 6.092778 5.778996 9.821479
0.1516382 6.170937 5.779891 9.770000
0.1539508 6.254513 5.779793 9.712978
0.1562635 6.342516 5.778403 9.650573
0.1585762 6.433957 5.775422 9.582955
0.1608888 6.527866 5.770555 9.510306
0.1632015 6.623305 5.763521 9.432817
0.1655142 6.719377 5.754057 9.350682
0.1678268 6.815235 5.741925 9.264104
0.1701395 6.910087 5.726913 9.173287
0.1724522 7.003198 5.708845 9.078439
0.1747648 7.093895 5.687579 8.979765
0.1770775 7.181564 5.663013 8.877470
0.1770775 5.663013 7.181564 8.877470
0.1840155 5.569097 7.421144 8.550860
0.1909535 5.445725 7.616838 8.198598
0.1978915 5.296586 7.760577 7.825179
0.2048295 5.127780 7.847246 7.434267
0.2117675 4.946590 7.873646 7.028641
0.2187055 4.759892 7.837521 6.610254
0.2256435 4.572482 7.736780 6.180404
0.2325815 4.385675 7.569002 5.739966
0.2395195 4.196606 7.331270 5.289642
0.2464575 3.998467 7.020335 4.830178
0.2533955 3.781656 6.633060 4.362518
0.2603335 3.535513 6.167043 3.887866
0.2672715 3.250179 5.621313 3.407656
0.2742095 2.918186 4.996967 2.923451
0.2811475 2.535570 4.297670 2.436779
0.2880855 2.102415 3.529938 1.948972
0.2950235 1.622910 2.703175 1.461023
0.3019615 1.104983 1.829459 0.973503
0.3088995 0.559627 0.923099 0.486559
0.3158375 -0.000293 -0.000293 -0.000293
0.3158375 -0.000293 -0.000293 -0.000293
0.3215023 0.437822 0.437822 0.743393
0.3271672 0.866849 0.866849 1.481556
0.3328320 1.278863 1.278863 2.209513
0.3384969 1.666754 1.666754 2.922759
0.3441617 2.024968 2.024968 3.617393
0.3498266 2.349823 2.349823 4.290154
0.3554914 2.639668 2.639668 4.938350
0.3611563 2.894844 2.894844 5.559681
0.3668211 3.117436 3.117436 6.151994
0.3724860 3.310833 3.310833 6.713007
0.3781509 3.479118 3.479118 7.240062
0.3838157 3.626395 3.626395 7.729932
0.3894806 3.756130 3.756130 8.178753
0.3951454 3.870656 3.870656 8.582065
0.4008103 3.970932 3.970932 8.934994
0.4064751 4.056584 4.056584 9.232524
0.4121400 4.126226 4.126226 9.469849
0.4178048 4.177954 4.177954 9.642736
0.4234697 4.209897 4.209897 9.747878
0.4291345 4.220707 4.220707 9.783167

243
example/Al-ABACUS/abacus-lcao/reference/phonopy.yaml Normal file
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@ -0,0 +1,243 @@
phonopy:
version: 2.15.1
calculator: abacus
frequency_unit_conversion_factor: 21.490680
symmetry_tolerance: 1.00000e-05
configuration:
atom_name: "Al"
dim: "2 2 2"
mesh: "8 8 8"
primitive_axes: "0 1/2 1/2 1/2 0 1/2 1/2 1/2 0"
band: "1 1 1 1/2 1/2 1 3/8 3/8 3/4 0 0 0 1/2 1/2 1/2"
band_points: "21"
band_connection: ".TRUE."
calculator: "abacus"
physical_unit:
atomic_mass: "AMU"
length: "au"
force_constants: "eV/angstrom.au"
space_group:
type: "Fm-3m"
number: 225
Hall_symbol: "-F 4 2 3"
primitive_matrix:
- [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
- [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
- [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
supercell_matrix:
- [ 2, 0, 0 ]
- [ 0, 2, 0 ]
- [ 0, 0, 2 ]
primitive_cell:
lattice:
- [ 0.000000000000000, 3.821923845585321, 3.821923845585321 ] # a
- [ 3.821923845585321, 0.000000000000000, 3.821923845585321 ] # b
- [ 3.821923845585321, 3.821923845585321, 0.000000000000000 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
reciprocal_lattice: # without 2pi
- [ -0.130824166100941, 0.130824166100941, 0.130824166100941 ] # a*
- [ 0.130824166100941, -0.130824166100941, 0.130824166100941 ] # b*
- [ 0.130824166100941, 0.130824166100941, -0.130824166100941 ] # c*
unit_cell:
lattice:
- [ 7.643847691170642, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 7.643847691170642, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 7.643847691170642 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
supercell:
lattice:
- [ 15.287695382341283, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 15.287695382341283, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 15.287695382341283 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 5
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 6
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 7
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 8
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 9
coordinates: [ 0.250000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 10
coordinates: [ 0.750000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 11
coordinates: [ 0.250000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 12
coordinates: [ 0.750000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 13
coordinates: [ 0.250000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 14
coordinates: [ 0.750000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 15
coordinates: [ 0.250000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 16
coordinates: [ 0.750000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 17
coordinates: [ 0.250000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 18
coordinates: [ 0.750000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 19
coordinates: [ 0.250000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 20
coordinates: [ 0.750000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 21
coordinates: [ 0.250000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 22
coordinates: [ 0.750000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 23
coordinates: [ 0.250000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 24
coordinates: [ 0.750000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 25
coordinates: [ 0.000000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 26
coordinates: [ 0.500000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 27
coordinates: [ 0.000000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 28
coordinates: [ 0.500000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 29
coordinates: [ 0.000000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 30
coordinates: [ 0.500000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 31
coordinates: [ 0.000000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 32
coordinates: [ 0.500000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000

251
example/Al-ABACUS/abacus-lcao/reference/phonopy_disp.yaml Normal file
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@ -0,0 +1,251 @@
phonopy:
version: 2.15.1
calculator: abacus
frequency_unit_conversion_factor: 15.633302
symmetry_tolerance: 1.00000e-05
configuration:
dim: "2 2 2"
atom_name: "Al"
create_displacements: ".true."
calculator: "abacus"
physical_unit:
atomic_mass: "AMU"
length: "au"
force_constants: "eV/angstrom.au"
space_group:
type: "Fm-3m"
number: 225
Hall_symbol: "-F 4 2 3"
supercell_matrix:
- [ 2, 0, 0 ]
- [ 0, 2, 0 ]
- [ 0, 0, 2 ]
primitive_cell:
lattice:
- [ 7.643847691170642, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 7.643847691170642, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 7.643847691170642 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
reciprocal_lattice: # without 2pi
- [ 0.130824166100941, 0.000000000000000, 0.000000000000000 ] # a*
- [ 0.000000000000000, 0.130824166100941, 0.000000000000000 ] # b*
- [ 0.000000000000000, 0.000000000000000, 0.130824166100941 ] # c*
unit_cell:
lattice:
- [ 7.643847691170642, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 7.643847691170642, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 7.643847691170642 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 2
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 3
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 4
magnetic_moment: 0.00000000
supercell:
lattice:
- [ 15.287695382341283, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 15.287695382341283, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 15.287695382341283 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 5
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 6
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 7
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 8
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 9
coordinates: [ 0.250000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 10
coordinates: [ 0.750000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 11
coordinates: [ 0.250000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 12
coordinates: [ 0.750000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 13
coordinates: [ 0.250000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 14
coordinates: [ 0.750000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 15
coordinates: [ 0.250000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 16
coordinates: [ 0.750000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 17
coordinates: [ 0.250000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 18
coordinates: [ 0.750000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 19
coordinates: [ 0.250000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 20
coordinates: [ 0.750000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 21
coordinates: [ 0.250000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 22
coordinates: [ 0.750000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 23
coordinates: [ 0.250000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 24
coordinates: [ 0.750000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 25
coordinates: [ 0.000000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 26
coordinates: [ 0.500000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 27
coordinates: [ 0.000000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 28
coordinates: [ 0.500000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 29
coordinates: [ 0.000000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 30
coordinates: [ 0.500000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 31
coordinates: [ 0.000000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 32
coordinates: [ 0.500000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
displacements:
- atom: 1
displacement:
[ 0.0200000000000000, 0.0000000000000000, 0.0000000000000000 ]

2
example/Al-ABACUS/abacus-lcao/reference/setting.conf Normal file
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DIM=2 2 2
ATOM_NAME = Al

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19
example/Al-ABACUS/abacus-pw/inputs/INPUT Normal file
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INPUT_PARAMETERS
# Created by Atomic Simulation Enviroment
ntype 1
calculation scf
pseudo_rcut 10.0
pseudo_mesh 1
ecutwfc 80
basis_type pw
ks_solver cg
smearing_method gaussian
smearing_sigma 0.01
mixing_type pulay
mixing_beta 0.7
scf_nmax 100
scf_thr 1e-08
cal_force 1
force_thr 0.001
cal_stress 1
out_stru 1

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example/Al-ABACUS/abacus-pw/inputs/KPT Normal file
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K_POINTS
0
Gamma
4 4 4 0 0 0

22
example/Al-ABACUS/abacus-pw/inputs/STRU Normal file
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ATOMIC_SPECIES
Al 26.9815385 Al.PD04.PBE.UPF
LATTICE_CONSTANT
1.889726125
LATTICE_VECTORS
4.0443360000 0.0000000000 0.0000000000
0.0000000000 4.0443360000 0.0000000000
0.0000000000 0.0000000000 4.0443360000
ATOMIC_POSITIONS
Direct
Al
0.0000000000
4
0.0000000000 0.0000000000 0.0000000000 1 1 1
0.0000000000 0.5000000000 0.5000000000 1 1 1
0.5000000000 0.0000000000 0.5000000000 1 1 1
0.5000000000 0.5000000000 0.0000000000 1 1 1

7
example/Al-ABACUS/abacus-pw/inputs/band.conf Normal file
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ATOM_NAME = Al
DIM = 2 2 2
MESH = 8 8 8
PRIMITIVE_AXES = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
BAND= 1 1 1 1/2 1/2 1 3/8 3/8 3/4 0 0 0 1/2 1/2 1/2
BAND_POINTS = 21
BAND_CONNECTION = .TRUE.

52
example/Al-ABACUS/abacus-pw/inputs/band.f90 Normal file
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program main
implicit none
integer nelec,nkpt,nbnd
integer lowbound,highbound
real,allocatable :: k(:,:), kk(:), ene(:,:)
integer i,j, m,l
real vbm
real b1, b2, b3
open(unit=11,file='band.yaml')
open(unit=12,file='phonon.dat')
do i=1,24
read(11,*)
enddo
!read(11,*) nelec,nkpt,nbnd
nkpt = 84
nbnd = 3
allocate(kk(1:nkpt))
allocate(ene(nbnd,nkpt))
do j=1,nkpt
read(11,*)
read(11,*)
read(11,'(11X,F13.7)') kk(j)
read(11,*)
do i=1,nbnd
read(11,*)
read(11,'(14X,F16.10)') ene(i,j)
read(11,*)
read(11,*)
read(11,*)
read(11,*)
read(11,*)
enddo
enddo
!do i = 1, nbnd
! write(12,*)
do j=1, nkpt
write(12,'(f17.7,1000f14.6)') kk(j), ene(1:3,j) !*33.35641
enddo
!enddo
close(11)
close(12)
end

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example/Al-ABACUS/abacus-pw/inputs/myrun.sh Normal file
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#!/bin/bash
phonopy setting.conf --abacus -d
echo 'stru_file ./STRU-001' >> INPUT
OMP_NUM_THREADS=1 mpirun -n 8 abacus > log
phonopy -f OUT.ABACUS/running_scf.log
phonopy band.conf --abacus

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example/Al-ABACUS/abacus-pw/inputs/setting.conf Normal file
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DIM=2 2 2
ATOM_NAME = Al

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example/Al-ABACUS/abacus-pw/reference/FORCE_SETS Normal file
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32
1
1
0.0200000000000000 0.0000000000000000 0.0000000000000000
-0.0487262119 0.0000000000 -0.0000000000
0.0018861981 0.0000000000 -0.0000000000
-0.0012557519 0.0000000000 -0.0000000000
0.0007399781 0.0000000000 -0.0000000000
-0.0012779419 0.0000000000 -0.0000000000
0.0007617081 0.0000000000 -0.0000000000
-0.0019987519 0.0000000000 -0.0000000000
0.0014663981 0.0000000000 -0.0000000000
-0.0024751619 0.0002696100 0.0004027500
0.0000529281 0.0003608900 0.0005002700
-0.0024751719 -0.0002696600 0.0004027600
0.0000529381 -0.0003609500 0.0005002900
-0.0024751719 0.0002696600 -0.0004027600
0.0000529381 0.0003609500 -0.0005002900
-0.0024751619 -0.0002696100 -0.0004027500
0.0000529281 -0.0003608900 -0.0005002700
0.0067310581 0.0000000000 0.0071752700
0.0072285281 0.0000000000 -0.0060528800
0.0000176281 0.0000000000 -0.0004076500
0.0005461481 0.0000000000 0.0013741800
0.0067310581 0.0000000000 -0.0071752700
0.0072285281 0.0000000000 0.0060528800
0.0000176281 0.0000000000 0.0004076500
0.0005461481 0.0000000000 -0.0013741800
0.0067277281 0.0070496000 -0.0000000000
0.0072316381 -0.0062000800 -0.0000000000
0.0067277281 -0.0070496000 -0.0000000000
0.0072316381 0.0062000800 -0.0000000000
0.0000208381 -0.0005328600 -0.0000000000
0.0005430881 0.0012268700 -0.0000000000
0.0000208381 0.0005328600 -0.0000000000
0.0005430881 -0.0012268700 -0.0000000000

20
example/Al-ABACUS/abacus-pw/reference/INPUT Normal file
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INPUT_PARAMETERS
# Created by Atomic Simulation Enviroment
ntype 1
calculation scf
pseudo_rcut 10.0
pseudo_mesh 1
ecutwfc 80
basis_type pw
ks_solver cg
smearing_method gaussian
smearing_sigma 0.01
mixing_type pulay
mixing_beta 0.7
scf_nmax 100
scf_thr 1e-08
cal_force 1
force_thr 0.001
cal_stress 1
out_stru 1
stru_file ./STRU-001

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example/Al-ABACUS/abacus-pw/reference/KPT Normal file
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K_POINTS
0
Gamma
4 4 4 0 0 0

250
example/Al-ABACUS/abacus-pw/reference/OUT.ABACUS/INPUT Normal file
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INPUT_PARAMETERS
#Parameters (1.General)
suffix ABACUS #the name of main output directory
latname test #the name of lattice name
stru_file ./STRU-001 #the filename of file containing atom positions
kpoint_file KPT #the name of file containing k points
pseudo_dir #the directory containing pseudo files
orbital_dir #the directory containing orbital files
pseudo_type auto #the type pseudo files
pseudo_rcut 10 #cut-off radius for radial integration
pseudo_mesh 1 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE
lmaxmax 2 #maximum of l channels used
dft_functional default #exchange correlation functional
calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md
ntype 1 #atom species number
nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin
kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file
nbands 0 #number of bands
nbands_sto 256 #number of stochastic bands
nbands_istate 5 #number of bands around Fermi level for istate calulation
nche_sto 100 #number of orders for Chebyshev expansion in stochastic DFT
symmetry 0 #turn symmetry on or off
init_vel 0 #read velocity from STRU or not
symmetry_prec 1e-05 #accuracy for symmetry
nelec 0 #input number of electrons
tot_magnetization 0 #total magnetization of the system
out_mul 0 # mulliken charge or not
noncolin 0 #using non-collinear-spin
lspinorb 0 #consider the spin-orbit interaction
kpar 1 #devide all processors into kpar groups and k points will be distributed among each group
bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group
#Parameters (2.PW)
ecutwfc 80 ##energy cutoff for wave functions
pw_diag_nmax 50 #max iteration number for cg
diago_cg_prec 1 #diago_cg_prec
pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations
scf_thr 1e-08 #charge density error
init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file'
init_chg atomic #start charge is from 'atomic' or file
chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA
out_chg 0 #>0 output charge density for selected electron steps
out_pot 0 #output realspace potential
out_wfc_pw 0 #output wave functions
out_wfc_r 0 #output wave functions in realspace
out_dos 0 #output energy and dos
out_band 0 #output energy and band structure
out_proj_band 0 #output projected band structure
restart_save 0 #print to disk every step for restart
restart_load 0 #restart from disk
read_file_dir auto #directory of files for reading
nx 0 #number of points along x axis for FFT grid
ny 0 #number of points along y axis for FFT grid
nz 0 #number of points along z axis for FFT grid
cell_factor 1.2 #used in the construction of the pseudopotential tables
#Parameters (3.Stochastic DFT)
method_sto 1 #1: slow and save memory, 2: fast and waste memory
nbands_sto 256 #number of stochstic orbitals
nche_sto 100 #Chebyshev expansion orders
emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator
emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator
seed_sto 0 #the random seed to generate stochastic orbitals
initsto_freq 1000 #frequency to generate new stochastic orbitals when running md
#Parameters (4.Relaxation)
ks_solver cg #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver
scf_nmax 100 ##number of electron iterations
out_force 0 #output the out_force or not
relax_nmax 1 #number of ion iteration steps
out_stru 1 #output the structure files after each ion step
force_thr 0.001 #force threshold, unit: Ry/Bohr
force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom
force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom
relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom
stress_thr 0.01 #stress threshold
press1 0 #target pressure, unit: KBar
press2 0 #target pressure, unit: KBar
press3 0 #target pressure, unit: KBar
relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs
relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs
relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr
relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr
relax_bfgs_init 0.5 #initial trust radius, unit: Bohr
cal_stress 1 #calculate the stress or not
fixed_axes None #which axes are fixed
relax_method cg #bfgs; sd; cg; cg_bfgs;
out_level ie #ie(for electrons); i(for ions);
out_dm 0 #>0 output density matrix
deepks_out_labels 0 #>0 compute descriptor for deepks
deepks_scf 0 #>0 add V_delta to Hamiltonian
deepks_bandgap 0 #>0 for bandgap label
deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test
deepks_model #file dir of traced pytorch model: 'model.ptg
deepks_descriptor_lmax2 #lmax used in generating descriptor
deepks_descriptor_rcut0 #rcut used in generating descriptor
deepks_descriptor_ecut0 #ecut used in generating descriptor
#Parameters (5.LCAO)
basis_type pw #PW; LCAO in pw; LCAO
search_radius -1 #input search radius (Bohr)
search_pbc 1 #input periodic boundary condition
lcao_ecut 0 #energy cutoff for LCAO
lcao_dk 0.01 #delta k for 1D integration in LCAO
lcao_dr 0.01 #delta r for 1D integration in LCAO
lcao_rmax 30 #max R for 1D two-center integration table
out_mat_hs 0 #output H and S matrix
out_mat_hs2 0 #output H(R) and S(R) matrix
out_mat_r 0 #output r(R) matrix
out_wfc_lcao 0 #ouput LCAO wave functions
bx 1 #division of an element grid in FFT grid along x
by 1 #division of an element grid in FFT grid along y
bz 1 #division of an element grid in FFT grid along z
#Parameters (6.Smearing)
smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv
smearing_sigma 0.01 #energy range for smearing
#Parameters (7.Charge Mixing)
mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden
mixing_beta 0.7 #mixing parameter: 0 means no new charge
mixing_ndim 8 #mixing dimension in pulay
mixing_gg0 0 #mixing parameter in kerker
#Parameters (8.DOS)
dos_emin_ev -15 #minimal range for dos
dos_emax_ev 15 #maximal range for dos
dos_edelta_ev 0.01 #delta energy for dos
dos_scale 0.01 #scale dos range by
dos_sigma 0.07 #gauss b coefficeinet(default=0.07)
#Parameters (9.Molecular dynamics)
md_type 1 #choose ensemble
md_nstep 10 #md steps
md_ensolver FP #choose potential
md_dt 1 #time step
md_mnhc 4 #number of Nose-Hoover chains
md_tfirst -1 #temperature first
md_tlast -1 #temperature last
md_dumpfreq 1 #The period to dump MD information
md_restartfreq 5 #The period to output MD restart information
md_seed -1 #random seed for MD
md_restart 0 #whether restart
lj_rcut 8.5 #cutoff radius of LJ potential
lj_epsilon 0.01032 #the value of epsilon for LJ potential
lj_sigma 3.405 #the value of sigma for LJ potential
msst_direction 2 #the direction of shock wave
msst_vel 0 #the velocity of shock wave
msst_vis 0 #artificial viscosity
msst_tscale 0.01 #reduction in initial temperature
msst_qmass -1 #mass of thermostat
md_tfreq 0 #oscillation frequency, used to determine qmass of NHC
md_damp 1 #damping parameter (time units) used to add force in Langevin method
#Parameters (10.Electric field and dipole correction)
efield_flag 0 #add electric field
dip_cor_flag 0 #dipole correction
efield_dir 2 #the direction of the electric field or dipole correction
efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir
efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases
efield_amp 0 #amplitude of the electric field
#Parameters (11.Test)
out_alllog 0 #output information for each processor, when parallel
nurse 0 #for coders
colour 0 #for coders, make their live colourful
t_in_h 1 #calculate the kinetic energy or not
vl_in_h 1 #calculate the local potential or not
vnl_in_h 1 #calculate the nonlocal potential or not
vh_in_h 1 #calculate the hartree potential or not
vion_in_h 1 #calculate the local ionic potential or not
test_force 0 #test the force
test_stress 0 #test the force
#Parameters (13.vdW Correction)
vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj
vdw_s6 default #scale parameter of d2/d3_0/d3_bj
vdw_s8 default #scale parameter of d3_0/d3_bj
vdw_a1 default #damping parameter of d3_0/d3_bj
vdw_a2 default #damping parameter of d3_bj
vdw_d 20 #damping parameter of d2
vdw_abc 0 #third-order term?
vdw_C6_file default #filename of C6
vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6
vdw_R0_file default #filename of R0
vdw_R0_unit A #unit of R0, A or Bohr
vdw_model radius #expression model of periodic structure, radius or period
vdw_radius default #radius cutoff for periodic structure
vdw_radius_unit Bohr #unit of radius cutoff for periodic structure
vdw_cn_thr 40 #radius cutoff for cn
vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom
vdw_period 3 3 3 #periods of periodic structure
#Parameters (14.exx)
dft_functional default #no, hf, pbe0, hse or opt_orb
exx_hybrid_alpha 0.25 #
exx_hse_omega 0.11 #
exx_separate_loop 1 #0 or 1
exx_hybrid_step 100 #
exx_lambda 0.3 #
exx_pca_threshold 0 #
exx_c_threshold 0 #
exx_v_threshold 0 #
exx_dm_threshold 0 #
exx_schwarz_threshold0 #
exx_cauchy_threshold0 #
exx_ccp_threshold 1e-08 #
exx_ccp_rmesh_times 10 #
exx_distribute_type htime #htime or kmeans1 or kmeans2
exx_opt_orb_lmax 0 #
exx_opt_orb_ecut 0 #
exx_opt_orb_tolerence0 #
#Parameters (16.tddft)
tddft 0 #calculate tddft or not
td_scf_thr 1e-09 #threshold for electronic iteration of tddft
td_dt 0.02 #time of ion step
td_force_dt 0.02 #time of force change
td_val_elec_01 1 #td_val_elec_01
td_val_elec_02 1 #td_val_elec_02
td_val_elec_03 1 #td_val_elec_03
td_vext 0 #add extern potential or not
td_vext_dire 1 #extern potential direction
td_timescale 0.5 #extern potential td_timescale
td_vexttype 1 #extern potential type
td_vextout 0 #output extern potential or not
td_dipoleout 0 #output dipole or not
ocp 0 #change occupation or not
ocp_set none #set occupation
#Parameters (17.berry_wannier)
berry_phase 0 #calculate berry phase or not
gdir 3 #calculate the polarization in the direction of the lattice vector
towannier90 0 #use wannier90 code interface or not
nnkpfile seedname.nnkp #the wannier90 code nnkp file name
wannier_spin up #calculate spin in wannier90 code interface
#Parameters (18.implicit_solvation)
imp_sol 0 #calculate implicit solvation correction or not
eb_k 80 #the relative permittivity of the bulk solvent
tau 1.0798e-05 #the effective surface tension parameter
sigma_k 0.6 # the width of the diffuse cavity
nc_k 0.00037 # the cut-off charge density
#Parameters (19.compensating_charge)
comp_chg 0 # add compensating charge
comp_q 0 # total charge of compensating charge
comp_l 1 # total length of compensating charge
comp_center 0 # center of compensating charge on dim
comp_dim 2 # dimension of compensating charge(x, y or z)

51
example/Al-ABACUS/abacus-pw/reference/OUT.ABACUS/STRU_READIN_ADJUST.cif Normal file
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data_test
_audit_creation_method generated by ABACUS
_cell_length_a 8.08867
_cell_length_b 8.08867
_cell_length_c 8.08867
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_symmetry_space_group_name_H-M
_symmetry_Int_Tables_number
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Al 0.00130844 0 0
Al 0.5 0 0
Al 0 0.5 0
Al 0.5 0.5 0
Al 0 0 0.5
Al 0.5 0 0.5
Al 0 0.5 0.5
Al 0.5 0.5 0.5
Al 0 0.25 0.25
Al 0.5 0.25 0.25
Al 0 0.75 0.25
Al 0.5 0.75 0.25
Al 0 0.25 0.75
Al 0.5 0.25 0.75
Al 0 0.75 0.75
Al 0.5 0.75 0.75
Al 0.25 0 0.25
Al 0.75 0 0.25
Al 0.25 0.5 0.25
Al 0.75 0.5 0.25
Al 0.25 0 0.75
Al 0.75 0 0.75
Al 0.25 0.5 0.75
Al 0.75 0.5 0.75
Al 0.25 0.25 0
Al 0.75 0.25 0
Al 0.25 0.75 0
Al 0.75 0.75 0
Al 0.25 0.25 0.5
Al 0.75 0.25 0.5
Al 0.25 0.75 0.5
Al 0.75 0.75 0.5

2196
example/Al-ABACUS/abacus-pw/reference/OUT.ABACUS/istate.info Normal file
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2899
example/Al-ABACUS/abacus-pw/reference/OUT.ABACUS/running_scf.log Normal file
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14
example/Al-ABACUS/abacus-pw/reference/OUT.ABACUS/warning.log Normal file
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It's ok to use cg.
In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block.
AUTO_SET NBANDS to 58
startmag_type = 2
charge from rho_at = 2.99755
charge should be = 3
SETUP ATOMIC RHO FOR SPIN 1
Electron number from rho = 96
total electron number from rho = 96
should be = 96
charge before normalized = 96
charge after normalized = 96
scf warning : Threshold on eigenvalues was too large.

22
example/Al-ABACUS/abacus-pw/reference/STRU Normal file
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ATOMIC_SPECIES
Al 26.9815385 Al.PD04.PBE.UPF
LATTICE_CONSTANT
1.889726125
LATTICE_VECTORS
4.0443360000 0.0000000000 0.0000000000
0.0000000000 4.0443360000 0.0000000000
0.0000000000 0.0000000000 4.0443360000
ATOMIC_POSITIONS
Direct
Al
0.0000000000
4
0.0000000000 0.0000000000 0.0000000000 1 1 1
0.0000000000 0.5000000000 0.5000000000 1 1 1
0.5000000000 0.0000000000 0.5000000000 1 1 1
0.5000000000 0.5000000000 0.0000000000 1 1 1

49
example/Al-ABACUS/abacus-pw/reference/STRU-001 Normal file
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ATOMIC_SPECIES
Al 26.9815386 Al.PD04.PBE.UPF
LATTICE_CONSTANT
1.0
LATTICE_VECTORS
15.285374794956 0.0 0.0
0.0 15.285374794956 0.0
0.0 0.0 15.285374794956
ATOMIC_POSITIONS
Direct
Al
0.0
32
0.0013084402749875504 0.0 0.0 1 1 1
0.5 0.0 0.0 1 1 1
0.0 0.5 0.0 1 1 1
0.5 0.5 0.0 1 1 1
0.0 0.0 0.5 1 1 1
0.5 0.0 0.5 1 1 1
0.0 0.5 0.5 1 1 1
0.5 0.5 0.5 1 1 1
0.0 0.25 0.25 1 1 1
0.5 0.25 0.25 1 1 1
0.0 0.7500000000000001 0.25 1 1 1
0.5 0.7500000000000001 0.25 1 1 1
0.0 0.25 0.7500000000000001 1 1 1
0.5 0.25 0.7500000000000001 1 1 1
0.0 0.7500000000000001 0.7500000000000001 1 1 1
0.5 0.7500000000000001 0.7500000000000001 1 1 1
0.25 0.0 0.25 1 1 1
0.7500000000000001 0.0 0.25 1 1 1
0.25 0.5 0.25 1 1 1
0.7500000000000001 0.5 0.25 1 1 1
0.25 0.0 0.7500000000000001 1 1 1
0.7500000000000001 0.0 0.7500000000000001 1 1 1
0.25 0.5 0.7500000000000001 1 1 1
0.7500000000000001 0.5 0.7500000000000001 1 1 1
0.25 0.25 0.0 1 1 1
0.7500000000000001 0.25 0.0 1 1 1
0.25 0.7500000000000001 0.0 1 1 1
0.7500000000000001 0.7500000000000001 0.0 1 1 1
0.25 0.25 0.5 1 1 1
0.7500000000000001 0.25 0.5 1 1 1
0.25 0.7500000000000001 0.5 1 1 1
0.7500000000000001 0.7500000000000001 0.5 1 1 1

49
example/Al-ABACUS/abacus-pw/reference/STRU.in Normal file
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ATOMIC_SPECIES
Al 26.9815386 Al.PD04.PBE.UPF
LATTICE_CONSTANT
1.0
LATTICE_VECTORS
15.285374794956 0.0 0.0
0.0 15.285374794956 0.0
0.0 0.0 15.285374794956
ATOMIC_POSITIONS
Direct
Al
0.0
32
0.0 0.0 0.0 1 1 1
0.5 0.0 0.0 1 1 1
0.0 0.5 0.0 1 1 1
0.5 0.5 0.0 1 1 1
0.0 0.0 0.5 1 1 1
0.5 0.0 0.5 1 1 1
0.0 0.5 0.5 1 1 1
0.5 0.5 0.5 1 1 1
0.0 0.25 0.25 1 1 1
0.5 0.25 0.25 1 1 1
0.0 0.75 0.25 1 1 1
0.5 0.75 0.25 1 1 1
0.0 0.25 0.75 1 1 1
0.5 0.25 0.75 1 1 1
0.0 0.75 0.75 1 1 1
0.5 0.75 0.75 1 1 1
0.25 0.0 0.25 1 1 1
0.75 0.0 0.25 1 1 1
0.25 0.5 0.25 1 1 1
0.75 0.5 0.25 1 1 1
0.25 0.0 0.75 1 1 1
0.75 0.0 0.75 1 1 1
0.25 0.5 0.75 1 1 1
0.75 0.5 0.75 1 1 1
0.25 0.25 0.0 1 1 1
0.75 0.25 0.0 1 1 1
0.25 0.75 0.0 1 1 1
0.75 0.75 0.0 1 1 1
0.25 0.25 0.5 1 1 1
0.75 0.25 0.5 1 1 1
0.25 0.75 0.5 1 1 1
0.75 0.75 0.5 1 1 1

7
example/Al-ABACUS/abacus-pw/reference/band.conf Normal file
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ATOM_NAME = Al
DIM = 2 2 2
MESH = 8 8 8
PRIMITIVE_AXES = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
BAND= 1 1 1 1/2 1/2 1 3/8 3/8 3/4 0 0 0 1/2 1/2 1/2
BAND_POINTS = 21
BAND_CONNECTION = .TRUE.

52
example/Al-ABACUS/abacus-pw/reference/band.f90 Normal file
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program main
implicit none
integer nelec,nkpt,nbnd
integer lowbound,highbound
real,allocatable :: k(:,:), kk(:), ene(:,:)
integer i,j, m,l
real vbm
real b1, b2, b3
open(unit=11,file='band.yaml')
open(unit=12,file='phonon.dat')
do i=1,24
read(11,*)
enddo
!read(11,*) nelec,nkpt,nbnd
nkpt = 84
nbnd = 3
allocate(kk(1:nkpt))
allocate(ene(nbnd,nkpt))
do j=1,nkpt
read(11,*)
read(11,*)
read(11,'(11X,F13.7)') kk(j)
read(11,*)
do i=1,nbnd
read(11,*)
read(11,'(14X,F16.10)') ene(i,j)
read(11,*)
read(11,*)
read(11,*)
read(11,*)
read(11,*)
enddo
enddo
!do i = 1, nbnd
! write(12,*)
do j=1, nkpt
write(12,'(f17.7,1000f14.6)') kk(j), ene(1:3,j) !*33.35641
enddo
!enddo
close(11)
close(12)
end

2125
example/Al-ABACUS/abacus-pw/reference/band.yaml Normal file
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100
example/Al-ABACUS/abacus-pw/reference/log Normal file
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*********************************************************
* *
* WELCOME TO ABACUS *
* *
* 'Atomic-orbital Based Ab-initio *
* Computation at UStc' *
* *
* Website: http://abacus.ustc.edu.cn/ *
* *
*********************************************************
Mon Jul 18 11:26:18 2022
MAKE THE DIR : OUT.ABACUS/
UNIFORM GRID DIM : 90 * 90 * 90
UNIFORM GRID DIM(BIG): 90 * 90 * 90
DONE(0.0591953 SEC) : SETUP UNITCELL
DONE(0.0762966 SEC) : INIT K-POINTS
---------------------------------------------------------
Self-consistent calculations for electrons
---------------------------------------------------------
SPIN KPOINTS PROCESSORS
1 36 8
---------------------------------------------------------
Use plane wave basis
---------------------------------------------------------
ELEMENT NATOM XC
Al 32
---------------------------------------------------------
Initial plane wave basis and FFT box
---------------------------------------------------------
DONE(0.0943999 SEC) : INIT PLANEWAVE
DONE(0.134182 SEC) : INIT CHARGE
MEMORY FOR PSI (MB) : 172.492
DONE(0.264528 SEC) : LOCAL POTENTIAL
DONE(0.274519 SEC) : NON-LOCAL POTENTIAL
START POTENTIAL : atomic
DONE(0.360893 SEC) : INIT POTENTIAL
DONE(13.397 SEC) : INIT BASIS
-------------------------------------------
SELF-CONSISTENT :
-------------------------------------------
ITER ETOT(eV) EDIFF(eV) DRHO TIME(s)
CG1 -2.018266e+03 0.000000e+00 1.806e-01 1.733e+02
CG2 -2.018253e+03 1.280875e-02 1.343e-02 5.978e+01
CG3 -2.018266e+03 -1.230611e-02 1.695e-04 6.503e+01
CG4 -2.018273e+03 -7.128246e-03 9.605e-04 1.349e+02
CG5 -2.018275e+03 -2.470117e-03 9.431e-04 1.090e+02
CG6 -2.018277e+03 -1.548126e-03 3.792e-05 9.129e+01
CG7 -2.018277e+03 -9.650275e-05 5.293e-07 7.998e+01
CG8 -2.018277e+03 -7.519853e-05 5.191e-07 1.379e+02
CG9 -2.018277e+03 -4.039296e-07 3.200e-07 8.448e+01
CG10 -2.018277e+03 -1.850996e-07 4.517e-08 6.919e+01
CG11 -2.018277e+03 -2.073130e-07 1.696e-08 1.110e+02
CG12 -2.018277e+03 5.269909e-08 5.601e-09 7.039e+01
><><><><><><><><><><><><><><><><><><><><><><
TOTAL-STRESS (KBAR):
><><><><><><><><><><><><><><><><><><><><><><
-1.950e+00 -8.950e-11 -1.286e-10
-8.950e-11 -1.951e+00 5.901e-07
-1.286e-10 5.901e-07 -1.951e+00
TOTAL-PRESSURE: -1.950e+00 KBAR
|CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%-------
total 1234.5 17 73 1e+02 %
Run_pw plane_wave_line 1234.5 1 1.2e+03 1e+02 %
PW_Basis recip2real 0.12745 79 0.0016 0.01 %
Potential v_of_rho 0.54791 13 0.042 0.044 %
XC_Functional v_xc 0.56685 15 0.038 0.046 %
PW_Basis real2recip 0.17407 122 0.0014 0.014 %
wavefunc wfcinit 13.021 1 13 1.1 %
pp_cell_vnl getvnl 8.1342 576 0.014 0.66 %
WF_igk get_sk 2.4525 24192 0.0001 0.2 %
WF_atomic atomic_wfc 0.54595 36 0.015 0.044 %
Hamilt_PW diagH_subspace 11.596 36 0.32 0.94 %
Hamilt_PW h_psi 1081.6 86741 0.012 88 %
Hamilt_PW vloc 209.26 86741 0.0024 17 %
PW_Basis_K recip2real 124.09 138442 0.0009 10 %
PW_Basis_K gathers_scatterp 40.47 138442 0.00029 3.3 %
PW_Basis_K real2recip 66.596 113885 0.00058 5.4 %
PW_Basis_K gatherp_scatters 15.539 113885 0.00014 1.3 %
Hamilt_PW vnl 870.02 86741 0.01 70 %
Hamilt_PW add_nonlocal_pp 433.49 86741 0.005 35 %
Hamilt diagH_LAPACK 0.22914 36 0.0064 0.019 %
Cell_PW opt_cells_pw 1221.1 1 1.2e+03 99 %
Ions opt_ions_pw 1221.1 1 1.2e+03 99 %
ESolver_KS_PW Run 1186.2 1 1.2e+03 96 %
HSolverPW solve 1185.5 13 91 96 %
DiagoCG diag 1102.1 468 2.4 89 %
ElecStatePW psiToRho 19.352 13 1.5 1.6 %
Charge rho_mpi 0.14826 13 0.011 0.012 %
DiagoIterAssist diagH_subspace 57.369 396 0.14 4.6 %
DiagoIterAssist diagH_LAPACK 0.32581 396 0.00082 0.026 %
Forces cal_force_nl 5.3906 1 5.4 0.44 %
Stress_PW cal_stress 29.335 1 29 2.4 %
Stress_Func stres_nl 28.998 1 29 2.3 %
----------------------------------------------------------------------------------------
START Time : Mon Jul 18 11:26:18 2022
FINISH Time : Mon Jul 18 11:46:53 2022
TOTAL Time : 1.2e+03
SEE INFORMATION IN : OUT.ABACUS/

677
example/Al-ABACUS/abacus-pw/reference/mesh.yaml Normal file
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mesh: [ 8, 8, 8 ]
nqpoint: 60
reciprocal_lattice:
- [ -0.13084403, 0.13084403, 0.13084403 ] # a*
- [ 0.13084403, -0.13084403, 0.13084403 ] # b*
- [ 0.13084403, 0.13084403, -0.13084403 ] # c*
natom: 1
lattice:
- [ 0.000000000000000, 3.821343698739000, 3.821343698739000 ] # a
- [ 3.821343698739000, 0.000000000000000, 3.821343698739000 ] # b
- [ 3.821343698739000, 3.821343698739000, 0.000000000000000 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
phonon:
- q-position: [ 0.0625000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.014164281
weight: 2
band:
- # 1
frequency: 1.0659698966
- # 2
frequency: 1.0659698966
- # 3
frequency: 1.8450027513
- q-position: [ 0.1875000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.035645993
weight: 6
band:
- # 1
frequency: 2.4454146225
- # 2
frequency: 2.5329187709
- # 3
frequency: 4.4194735273
- q-position: [ 0.3125000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.062814503
weight: 6
band:
- # 1
frequency: 3.5671669824
- # 2
frequency: 3.6336916223
- # 3
frequency: 7.1227588399
- q-position: [ 0.4375000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.090695654
weight: 6
band:
- # 1
frequency: 4.0804478636
- # 2
frequency: 4.2167240392
- # 3
frequency: 9.0426909517
- q-position: [ -0.4375000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.109410861
weight: 6
band:
- # 1
frequency: 4.2097756303
- # 2
frequency: 4.3943504578
- # 3
frequency: 9.5927468259
- q-position: [ -0.3125000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.081367602
weight: 6
band:
- # 1
frequency: 3.8769332192
- # 2
frequency: 4.1366957283
- # 3
frequency: 8.5452755322
- q-position: [ -0.1875000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.053625104
weight: 6
band:
- # 1
frequency: 3.1562475018
- # 2
frequency: 3.4360903763
- # 3
frequency: 6.3252703653
- q-position: [ -0.0625000, 0.0625000, 0.0625000 ]
distance_from_gamma: 0.027122534
weight: 6
band:
- # 1
frequency: 1.8570777577
- # 2
frequency: 1.9618037232
- # 3
frequency: 3.5467063065
- q-position: [ 0.1875000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.042492844
weight: 6
band:
- # 1
frequency: 2.7866437656
- # 2
frequency: 2.9164704738
- # 3
frequency: 5.3784034923
- q-position: [ 0.3125000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.062814503
weight: 12
band:
- # 1
frequency: 3.7944793194
- # 2
frequency: 4.1843482523
- # 3
frequency: 7.0312380369
- q-position: [ 0.4375000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.087696617
weight: 12
band:
- # 1
frequency: 4.3974749150
- # 2
frequency: 5.2277382593
- # 3
frequency: 8.4079040996
- q-position: [ 0.5625000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.114196088
weight: 12
band:
- # 1
frequency: 4.6894039194
- # 2
frequency: 5.5751864725
- # 3
frequency: 9.1381044652
- q-position: [ -0.3125000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.096414271
weight: 12
band:
- # 1
frequency: 4.5137402168
- # 2
frequency: 5.4490541780
- # 3
frequency: 8.6365709017
- q-position: [ -0.1875000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.070821407
weight: 12
band:
- # 1
frequency: 4.0014121637
- # 2
frequency: 4.7417353153
- # 3
frequency: 7.2530915140
- q-position: [ -0.0625000, 0.1875000, 0.0625000 ]
distance_from_gamma: 0.048380232
weight: 12
band:
- # 1
frequency: 3.1186375256
- # 2
frequency: 3.3280866423
- # 3
frequency: 5.7390532998
- q-position: [ 0.3125000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.074502864
weight: 6
band:
- # 1
frequency: 4.4494641303
- # 2
frequency: 4.5935032152
- # 3
frequency: 8.1962028155
- q-position: [ 0.4375000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.093598647
weight: 12
band:
- # 1
frequency: 5.1141094285
- # 2
frequency: 5.5628142787
- # 3
frequency: 8.8595691765
- q-position: [ 0.5625000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.116515027
weight: 12
band:
- # 1
frequency: 5.4294603906
- # 2
frequency: 6.7054634843
- # 3
frequency: 8.8118839632
- q-position: [ -0.3125000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.116515027
weight: 12
band:
- # 1
frequency: 5.2580793913
- # 2
frequency: 7.2915514531
- # 3
frequency: 8.1083317341
- q-position: [ -0.1875000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.093598647
weight: 12
band:
- # 1
frequency: 4.6454257584
- # 2
frequency: 6.1324490211
- # 3
frequency: 7.9779837063
- q-position: [ -0.0625000, 0.3125000, 0.0625000 ]
distance_from_gamma: 0.074502864
weight: 12
band:
- # 1
frequency: 3.9033592979
- # 2
frequency: 4.3761677248
- # 3
frequency: 7.8601646626
- q-position: [ 0.4375000, 0.4375000, 0.0625000 ]
distance_from_gamma: 0.106937980
weight: 6
band:
- # 1
frequency: 5.5070710537
- # 2
frequency: 5.6401282472
- # 3
frequency: 9.6098166456
- q-position: [ 0.5625000, 0.4375000, 0.0625000 ]
distance_from_gamma: 0.125362560
weight: 12
band:
- # 1
frequency: 5.8425461995
- # 2
frequency: 6.2263689588
- # 3
frequency: 9.5641343355
- q-position: [ -0.3125000, -0.5625000, 0.0625000 ]
distance_from_gamma: 0.131608459
weight: 12
band:
- # 1
frequency: 5.6970273867
- # 2
frequency: 7.1225170005
- # 3
frequency: 8.7798038294
- q-position: [ -0.1875000, 0.4375000, 0.0625000 ]
distance_from_gamma: 0.118788705
weight: 12
band:
- # 1
frequency: 5.0445285872
- # 2
frequency: 6.4356583851
- # 3
frequency: 8.7360178848
- q-position: [ -0.0625000, 0.4375000, 0.0625000 ]
distance_from_gamma: 0.101812188
weight: 12
band:
- # 1
frequency: 4.3253934674
- # 2
frequency: 4.7937196049
- # 3
frequency: 9.2489609440
- q-position: [ -0.4375000, -0.4375000, 0.0625000 ]
distance_from_gamma: 0.123210253
weight: 6
band:
- # 1
frequency: 5.7308240905
- # 2
frequency: 5.8596939457
- # 3
frequency: 9.8631974420
- q-position: [ -0.3125000, -0.4375000, 0.0625000 ]
distance_from_gamma: 0.109410861
weight: 12
band:
- # 1
frequency: 5.5887979833
- # 2
frequency: 5.9981267561
- # 3
frequency: 9.3389372449
- q-position: [ -0.1875000, -0.4375000, 0.0625000 ]
distance_from_gamma: 0.101812188
weight: 12
band:
- # 1
frequency: 4.9560363622
- # 2
frequency: 6.0347386762
- # 3
frequency: 8.7193780001
- q-position: [ -0.3125000, -0.3125000, 0.0625000 ]
distance_from_gamma: 0.090695654
weight: 6
band:
- # 1
frequency: 5.0720232408
- # 2
frequency: 5.2114626878
- # 3
frequency: 9.0696076898
- q-position: [ -0.1875000, -0.3125000, 0.0625000 ]
distance_from_gamma: 0.078010779
weight: 12
band:
- # 1
frequency: 4.4866372494
- # 2
frequency: 4.9472762092
- # 3
frequency: 8.0921173507
- q-position: [ -0.1875000, -0.1875000, 0.0625000 ]
distance_from_gamma: 0.058400829
weight: 6
band:
- # 1
frequency: 3.6730103453
- # 2
frequency: 3.8150168229
- # 3
frequency: 6.9603307100
- q-position: [ 0.1875000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.042492844
weight: 2
band:
- # 1
frequency: 2.7442616567
- # 2
frequency: 2.7442616567
- # 3
frequency: 5.2383911705
- q-position: [ 0.3125000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.058400829
weight: 6
band:
- # 1
frequency: 3.5666213764
- # 2
frequency: 3.9530521095
- # 3
frequency: 6.4341574506
- q-position: [ 0.4375000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.081367602
weight: 6
band:
- # 1
frequency: 4.2365061369
- # 2
frequency: 5.4320819067
- # 3
frequency: 7.6117922016
- q-position: [ 0.5625000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.106937980
weight: 6
band:
- # 1
frequency: 4.6898420752
- # 2
frequency: 5.9043157925
- # 3
frequency: 8.7674796483
- q-position: [ -0.3125000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.106937980
weight: 6
band:
- # 1
frequency: 4.7453082813
- # 2
frequency: 5.8111572807
- # 3
frequency: 8.9704334696
- q-position: [ -0.1875000, 0.1875000, 0.1875000 ]
distance_from_gamma: 0.081367602
weight: 6
band:
- # 1
frequency: 4.3597157890
- # 2
frequency: 5.1255345579
- # 3
frequency: 8.1974761291
- q-position: [ 0.3125000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.066937783
weight: 6
band:
- # 1
frequency: 3.7231456544
- # 2
frequency: 4.2911601432
- # 3
frequency: 7.3598006906
- q-position: [ 0.4375000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.084591322
weight: 12
band:
- # 1
frequency: 4.5679478142
- # 2
frequency: 5.4874792455
- # 3
frequency: 7.9878621232
- q-position: [ 0.5625000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.106937980
weight: 12
band:
- # 1
frequency: 5.2424837466
- # 2
frequency: 6.7448599169
- # 3
frequency: 8.2335635124
- q-position: [ -0.3125000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.123210253
weight: 12
band:
- # 1
frequency: 5.5095279504
- # 2
frequency: 6.9030782286
- # 3
frequency: 8.5508152687
- q-position: [ -0.1875000, 0.3125000, 0.1875000 ]
distance_from_gamma: 0.099149970
weight: 12
band:
- # 1
frequency: 5.2063151968
- # 2
frequency: 6.1038560492
- # 3
frequency: 8.5336482904
- q-position: [ 0.4375000, 0.4375000, 0.1875000 ]
distance_from_gamma: 0.096414271
weight: 6
band:
- # 1
frequency: 4.9612998653
- # 2
frequency: 5.8403879810
- # 3
frequency: 8.7859241618
- q-position: [ 0.5625000, 0.4375000, 0.1875000 ]
distance_from_gamma: 0.114196088
weight: 12
band:
- # 1
frequency: 5.7598956125
- # 2
frequency: 6.5488486227
- # 3
frequency: 8.8660181500
- q-position: [ 0.6875000, 0.4375000, 0.1875000 ]
distance_from_gamma: 0.135612670
weight: 12
band:
- # 1
frequency: 6.2540118558
- # 2
frequency: 7.4952498976
- # 3
frequency: 8.2992902587
- q-position: [ -0.1875000, 0.4375000, 0.1875000 ]
distance_from_gamma: 0.121019674
weight: 12
band:
- # 1
frequency: 5.8567582699
- # 2
frequency: 7.2133712856
- # 3
frequency: 8.3271067388
- q-position: [ 0.5625000, 0.5625000, 0.1875000 ]
distance_from_gamma: 0.127478533
weight: 6
band:
- # 1
frequency: 5.6818032876
- # 2
frequency: 6.6545430300
- # 3
frequency: 9.2868153660
- q-position: [ -0.3125000, -0.4375000, 0.1875000 ]
distance_from_gamma: 0.129559953
weight: 12
band:
- # 1
frequency: 6.0776916618
- # 2
frequency: 6.7892122945
- # 3
frequency: 9.0123944756
- q-position: [ -0.3125000, -0.3125000, 0.1875000 ]
distance_from_gamma: 0.111829073
weight: 6
band:
- # 1
frequency: 5.4277191100
- # 2
frequency: 6.3693689910
- # 3
frequency: 9.1340675297
- q-position: [ 0.3125000, 0.3125000, 0.3125000 ]
distance_from_gamma: 0.070821407
weight: 2
band:
- # 1
frequency: 3.6426676706
- # 2
frequency: 3.6426676706
- # 3
frequency: 7.9167556333
- q-position: [ 0.4375000, 0.3125000, 0.3125000 ]
distance_from_gamma: 0.084591322
weight: 6
band:
- # 1
frequency: 4.1635602192
- # 2
frequency: 4.7685034770
- # 3
frequency: 8.3310362641
- q-position: [ 0.5625000, 0.3125000, 0.3125000 ]
distance_from_gamma: 0.104406545
weight: 6
band:
- # 1
frequency: 4.8419111502
- # 2
frequency: 6.7737972352
- # 3
frequency: 8.0414224794
- q-position: [ 0.6875000, 0.3125000, 0.3125000 ]
distance_from_gamma: 0.127478533
weight: 6
band:
- # 1
frequency: 5.3896688313
- # 2
frequency: 7.3717224096
- # 3
frequency: 8.3836737086
- q-position: [ 0.4375000, 0.4375000, 0.3125000 ]
distance_from_gamma: 0.093598647
weight: 6
band:
- # 1
frequency: 4.2753246677
- # 2
frequency: 4.9260273733
- # 3
frequency: 8.9059175201
- q-position: [ 0.5625000, 0.4375000, 0.3125000 ]
distance_from_gamma: 0.109410861
weight: 12
band:
- # 1
frequency: 5.0155602982
- # 2
frequency: 6.1895381564
- # 3
frequency: 8.7133046221
- q-position: [ 0.6875000, 0.4375000, 0.3125000 ]
distance_from_gamma: 0.129559953
weight: 12
band:
- # 1
frequency: 5.8078831716
- # 2
frequency: 7.5353416275
- # 3
frequency: 8.1932325622
- q-position: [ 0.5625000, 0.5625000, 0.3125000 ]
distance_from_gamma: 0.121019674
weight: 6
band:
- # 1
frequency: 5.1542867237
- # 2
frequency: 6.6687100155
- # 3
frequency: 8.7622487174
- q-position: [ 0.4375000, 0.4375000, 0.4375000 ]
distance_from_gamma: 0.099149970
weight: 2
band:
- # 1
frequency: 4.0778627672
- # 2
frequency: 4.0778627672
- # 3
frequency: 9.4924647607
- q-position: [ 0.5625000, 0.4375000, 0.4375000 ]
distance_from_gamma: 0.111829073
weight: 6
band:
- # 1
frequency: 4.4455996541
- # 2
frequency: 5.0521655965
- # 3
frequency: 9.3334251451

7
example/Al-ABACUS/abacus-pw/reference/myrun.sh Normal file
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@ -0,0 +1,7 @@
#!/bin/bash
phonopy setting.conf --abacus -d
echo 'stru_file ./STRU-001' >> INPUT
OMP_NUM_THREADS=1 mpirun -n 8 abacus > log
phonopy -f OUT.ABACUS/running_scf.log
phonopy band.conf --abacus

84
example/Al-ABACUS/abacus-pw/reference/phonon.dat Normal file
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@ -0,0 +1,84 @@
0.0000000 0.000827 0.000827 0.000827
0.0065422 0.455300 0.907934 0.455300
0.0130844 0.907658 1.805970 0.907658
0.0196266 1.354159 2.684478 1.354159
0.0261688 1.791938 3.534348 1.791938
0.0327110 2.218204 4.347230 2.218204
0.0392532 2.630261 5.115750 2.630261
0.0457954 3.025534 5.833682 3.025534
0.0523376 3.401578 6.496085 3.401578
0.0588798 3.756101 7.099391 3.756101
0.0654220 4.086973 7.641430 4.086973
0.0719642 4.392239 8.121401 4.392239
0.0785064 4.670121 8.539770 4.670121
0.0850486 4.919030 8.898118 4.919030
0.0915908 5.137565 9.198917 5.137565
0.0981330 5.324514 9.445257 5.324514
0.1046752 5.478857 9.640540 5.478857
0.1112174 5.599759 9.788147 5.599759
0.1177596 5.686577 9.891122 5.686577
0.1243018 5.738851 9.951872 5.738851
0.1308440 5.756307 9.971945 5.756307
0.1308440 5.756307 5.756307 9.971945
0.1331570 5.756461 5.761715 9.968806
0.1354701 5.756903 5.777855 9.959400
0.1377831 5.757566 5.804477 9.943756
0.1400961 5.758345 5.841173 9.921924
0.1424091 5.759091 5.887393 9.893970
0.1447221 5.759626 5.942463 9.859982
0.1470351 5.759737 6.005604 9.820065
0.1493482 5.759187 6.075960 9.774337
0.1516612 5.757722 6.152614 9.722935
0.1539742 5.755072 6.234615 9.666010
0.1562872 5.750963 6.320998 9.603724
0.1586002 5.745121 6.410795 9.536254
0.1609133 5.737275 6.503062 9.463783
0.1632263 5.727172 6.596879 9.386505
0.1655393 5.714574 6.691371 9.304619
0.1678523 5.699265 6.785707 9.218328
0.1701653 5.681061 6.879109 9.127843
0.1724783 5.659808 6.970857 9.033369
0.1747914 5.635386 7.060288 8.935117
0.1771044 5.607714 7.146799 8.833293
0.1771044 5.607714 7.146799 8.833293
0.1840434 5.504992 7.383617 8.508391
0.1909825 5.373957 7.577707 8.158274
0.1979215 5.218715 7.721017 7.787379
0.2048606 5.045696 7.808364 7.399275
0.2117996 4.862404 7.836406 6.996600
0.2187387 4.675813 7.802698 6.581159
0.2256777 4.490654 7.704935 6.154103
0.2326168 4.308013 7.540474 5.716192
0.2395558 4.124642 7.306197 5.268058
0.2464949 3.933264 6.998682 4.810437
0.2534340 3.723803 6.614664 4.344320
0.2603730 3.485185 6.151657 3.871011
0.2673121 3.207253 5.608647 3.392080
0.2742511 2.882362 4.986726 2.909234
0.2811902 2.506466 4.289577 2.424136
0.2881292 2.079650 3.523752 1.938220
0.2950683 1.606146 2.698704 1.452523
0.3020073 1.093957 1.826558 0.967604
0.3089464 0.554160 0.921672 0.483536
0.3158854 0.000827 0.000827 0.000827
0.3158854 0.000827 0.000827 0.000827
0.3215511 0.742665 0.433981 0.433981
0.3272169 1.479970 0.859221 0.859221
0.3328826 2.206814 1.267540 1.267540
0.3385483 2.918562 1.651845 1.651845
0.3442140 3.611189 2.006560 2.006560
0.3498797 4.281324 2.327947 2.327947
0.3555454 4.926185 2.614260 2.614260
0.3612111 5.543417 2.865722 2.865722
0.3668768 6.130857 3.084296 3.084296
0.3725426 6.686277 3.273264 3.273264
0.3782083 7.207128 3.436656 3.436656
0.3838740 7.690360 3.578592 3.578592
0.3895397 8.132338 3.702647 3.702647
0.3952054 8.528876 3.811352 3.811352
0.4008711 8.875396 3.905937 3.905937
0.4065368 9.167181 3.986342 3.986342
0.4122025 9.399704 4.051499 4.051499
0.4178683 9.568974 4.099794 4.099794
0.4235340 9.671868 4.129580 4.129580
0.4291997 9.706394 4.139655 4.139655

243
example/Al-ABACUS/abacus-pw/reference/phonopy.yaml Normal file
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@ -0,0 +1,243 @@
phonopy:
version: 2.15.1
calculator: abacus
frequency_unit_conversion_factor: 21.490680
symmetry_tolerance: 1.00000e-05
configuration:
atom_name: "Al"
dim: "2 2 2"
mesh: "8 8 8"
primitive_axes: "0 1/2 1/2 1/2 0 1/2 1/2 1/2 0"
band: "1 1 1 1/2 1/2 1 3/8 3/8 3/4 0 0 0 1/2 1/2 1/2"
band_points: "21"
band_connection: ".TRUE."
calculator: "abacus"
physical_unit:
atomic_mass: "AMU"
length: "au"
force_constants: "eV/angstrom.au"
space_group:
type: "Fm-3m"
number: 225
Hall_symbol: "-F 4 2 3"
primitive_matrix:
- [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
- [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
- [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
supercell_matrix:
- [ 2, 0, 0 ]
- [ 0, 2, 0 ]
- [ 0, 0, 2 ]
primitive_cell:
lattice:
- [ 0.000000000000000, 3.821343698739000, 3.821343698739000 ] # a
- [ 3.821343698739000, 0.000000000000000, 3.821343698739000 ] # b
- [ 3.821343698739000, 3.821343698739000, 0.000000000000000 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
reciprocal_lattice: # without 2pi
- [ -0.130844027498755, 0.130844027498755, 0.130844027498755 ] # a*
- [ 0.130844027498755, -0.130844027498755, 0.130844027498755 ] # b*
- [ 0.130844027498755, 0.130844027498755, -0.130844027498755 ] # c*
unit_cell:
lattice:
- [ 7.642687397478000, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 7.642687397478000, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 7.642687397478000 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
supercell:
lattice:
- [ 15.285374794956001, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 15.285374794956001, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 15.285374794956001 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 5
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 6
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 7
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 8
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 9
coordinates: [ 0.000000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 10
coordinates: [ 0.500000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 11
coordinates: [ 0.000000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 12
coordinates: [ 0.500000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 13
coordinates: [ 0.000000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 14
coordinates: [ 0.500000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 15
coordinates: [ 0.000000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 16
coordinates: [ 0.500000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 17
coordinates: [ 0.250000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 18
coordinates: [ 0.750000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 19
coordinates: [ 0.250000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 20
coordinates: [ 0.750000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 21
coordinates: [ 0.250000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 22
coordinates: [ 0.750000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 23
coordinates: [ 0.250000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 24
coordinates: [ 0.750000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 25
coordinates: [ 0.250000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 26
coordinates: [ 0.750000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 27
coordinates: [ 0.250000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 28
coordinates: [ 0.750000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 29
coordinates: [ 0.250000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 30
coordinates: [ 0.750000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 31
coordinates: [ 0.250000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 32
coordinates: [ 0.750000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000

251
example/Al-ABACUS/abacus-pw/reference/phonopy_disp.yaml Normal file
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@ -0,0 +1,251 @@
phonopy:
version: 2.15.1
calculator: abacus
frequency_unit_conversion_factor: 15.633302
symmetry_tolerance: 1.00000e-05
configuration:
dim: "2 2 2"
atom_name: "Al"
create_displacements: ".true."
calculator: "abacus"
physical_unit:
atomic_mass: "AMU"
length: "au"
force_constants: "eV/angstrom.au"
space_group:
type: "Fm-3m"
number: 225
Hall_symbol: "-F 4 2 3"
supercell_matrix:
- [ 2, 0, 0 ]
- [ 0, 2, 0 ]
- [ 0, 0, 2 ]
primitive_cell:
lattice:
- [ 7.642687397478000, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 7.642687397478000, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 7.642687397478000 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
magnetic_moment: 0.00000000
reciprocal_lattice: # without 2pi
- [ 0.130844027498755, 0.000000000000000, 0.000000000000000 ] # a*
- [ 0.000000000000000, 0.130844027498755, 0.000000000000000 ] # b*
- [ 0.000000000000000, 0.000000000000000, 0.130844027498755 ] # c*
unit_cell:
lattice:
- [ 7.642687397478000, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 7.642687397478000, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 7.642687397478000 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 2
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 3
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 4
magnetic_moment: 0.00000000
supercell:
lattice:
- [ 15.285374794956001, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 15.285374794956001, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 15.285374794956001 ] # c
points:
- symbol: Al # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 2
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 3
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 5
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 6
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 7
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 8
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 1
magnetic_moment: 0.00000000
- symbol: Al # 9
coordinates: [ 0.000000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 10
coordinates: [ 0.500000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 11
coordinates: [ 0.000000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 12
coordinates: [ 0.500000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 13
coordinates: [ 0.000000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 14
coordinates: [ 0.500000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 15
coordinates: [ 0.000000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 16
coordinates: [ 0.500000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 9
magnetic_moment: 0.00000000
- symbol: Al # 17
coordinates: [ 0.250000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 18
coordinates: [ 0.750000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 19
coordinates: [ 0.250000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 20
coordinates: [ 0.750000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 21
coordinates: [ 0.250000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 22
coordinates: [ 0.750000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 23
coordinates: [ 0.250000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 24
coordinates: [ 0.750000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 26.981539
reduced_to: 17
magnetic_moment: 0.00000000
- symbol: Al # 25
coordinates: [ 0.250000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 26
coordinates: [ 0.750000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 27
coordinates: [ 0.250000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 28
coordinates: [ 0.750000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 29
coordinates: [ 0.250000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 30
coordinates: [ 0.750000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 31
coordinates: [ 0.250000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
- symbol: Al # 32
coordinates: [ 0.750000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 26.981539
reduced_to: 25
magnetic_moment: 0.00000000
displacements:
- atom: 1
displacement:
[ 0.0200000000000000, 0.0000000000000000, 0.0000000000000000 ]

2
example/Al-ABACUS/abacus-pw/reference/setting.conf Normal file
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@ -0,0 +1,2 @@
DIM=2 2 2
ATOM_NAME = Al

290
phonopy/interface/abacus.py Normal file
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@ -0,0 +1,290 @@
"""ABACUS calculator interface"""
# Copyright (C) 2022 Yuyang Ji
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in
# the documentation and/or other materials provided with the
# distribution.
#
# * Neither the name of the phonopy project nor the names of its
# contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import re
import sys
import string
import numpy as np
from collections import Counter
from phonopy.units import Bohr
from phonopy.interface.vasp import check_forces, get_drift_forces
from phonopy.structure.atoms import PhonopyAtoms, atom_data, symbol_map
#
# read ABACUS STRU
#
def read_abacus(filename, elements=[]):
"""
Parse ABACUS structure, distance in unit au (bohr)
"""
pps = []
orbitals = None
cell = []
magmoms = []
numbers = []
positions = []
with open(filename, "r") as file:
if _search_sentence(file, "ATOMIC_SPECIES"):
for it, elem in enumerate(elements):
line = _skip_notes(file.readline())
_, _, pseudo = line.split()
pps.append(pseudo)
if _search_sentence(file, "NUMERICAL_ORBITAL"):
orbitals = []
for elem in elements:
orbitals.append(_skip_notes(file.readline()))
if _search_sentence(file, "LATTICE_CONSTANT"):
lat0 = float(_skip_notes(file.readline()).split()[0])
if _search_sentence(file, "LATTICE_VECTORS"):
for i in range(3):
cell.append(_list_elem_2float(
_skip_notes(file.readline()).split()))
cell = np.array(cell)*lat0
if _search_sentence(file, "ATOMIC_POSITIONS"):
ctype = _skip_notes(file.readline())
for elem in elements:
if _search_sentence(file, elem):
magmoms.append(float(_skip_notes(file.readline()).split()[0]))
na = int(_skip_notes(file.readline()).split()[0])
numbers.append(na)
for i in range(na):
line = _skip_notes(file.readline())
positions.append(_list_elem_2float(line.split()[:3]))
expanded_symbols = _expand(numbers, elements)
magnetic_moments = _expand(numbers, magmoms)
if ctype == "Direct":
atoms = PhonopyAtoms(symbols=expanded_symbols,
cell=cell, scaled_positions=positions, magnetic_moments=magnetic_moments)
elif ctype == "Cartesian":
atoms = PhonopyAtoms(symbols=expanded_symbols,
cell=cell, positions=positions, magnetic_moments=magnetic_moments)
elif ctype == "Cartesian_angstrom":
atoms = PhonopyAtoms(symbols=expanded_symbols,
cell=cell, positions=np.array(positions)/Bohr, magnetic_moments=magnetic_moments)
return atoms, pps, orbitals
#
# write ABACUS STRU
#
def write_abacus(filename, atoms, pps, orbitals=None):
"""Write structure to file"""
with open(filename, 'w') as f:
f.write(get_abacus_structure(atoms, pps, orbitals))
def write_supercells_with_displacements(
supercell,
cells_with_displacements,
ids,
pps,
orbitals,
pre_filename="STRU",
width=3,
):
"""Write supercells with displacements to files."""
write_abacus("%s.in" % pre_filename, supercell, pps)
for i, cell in zip(ids, cells_with_displacements):
filename = "{pre_filename}-{0:0{width}}".format(
i, pre_filename=pre_filename, width=width
)
write_abacus(filename, cell, pps, orbitals)
def get_abacus_structure(atoms, pps, orbitals=None):
"""Return ABACUS structure in text"""
empty_line = ''
line = []
line.append("ATOMIC_SPECIES")
elements = list(Counter(atoms.symbols).keys())
numbers = list(Counter(atoms.symbols).values())
for i, elem in enumerate(elements):
line.append(f"{elem}\t{atom_data[symbol_map[elem]][3]}\t{pps[i]}")
line.append(empty_line)
if orbitals:
line.append("NUMERICAL_ORBITAL")
for i in range(len(elements)):
line.append(f"{orbitals[i]}")
line.append(empty_line)
line.append("LATTICE_CONSTANT")
line.append(str(1.0))
line.append(empty_line)
line.append("LATTICE_VECTORS")
for i in range(3):
line.append(" ".join(_list_elem2str(atoms.cell[i])))
line.append(empty_line)
line.append("ATOMIC_POSITIONS")
line.append("Direct")
line.append(empty_line)
index = 0
for i, elem in enumerate(elements):
line.append(f"{elem}\n{atoms.magnetic_moments[index]}\n{numbers[i]}")
for j in range(index, index+numbers[i]):
line.append(" ".join(_list_elem2str(
atoms.scaled_positions[j]))+" "+"1 1 1")
line.append(empty_line)
index += numbers[i]
return '\n'.join(line)
#
# set Force
#
def read_abacus_output(filename):
"""Read abacus output.
Read ABACUS forces from last self-consistency iteration.
"""
with open(filename, 'r') as file:
for line in file:
if re.search(r"TOTAL ATOM NUMBER = [0-9]+", line):
natom = int(re.search("[0-9]+", line).group())
force = np.zeros((natom, 3))
if re.search("TOTAL-FORCE \(eV/Angstrom\)", line):
for i in range(4):
file.readline()
for i in range(natom):
_, fx, fy, fz = file.readline().split()
force[i] = (float(fx), float(fy), float(fz))
return force
def parse_set_of_forces(num_atoms, forces_filenames, verbose=True):
"""Parse forces from output files."""
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
abacus_forces = read_abacus_output(filename)
if check_forces(abacus_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(
abacus_forces, filename=filename, verbose=verbose
)
force_sets.append(np.array(abacus_forces) - drift_force)
else:
is_parsed = False
if is_parsed:
return force_sets
else:
return []
#
# tools
#
def _expand(num_atoms, attr):
expanded_attr = []
for s, num in zip(attr, num_atoms):
expanded_attr += [s] * num
return expanded_attr
def _search_sentence(file, sentence):
"""Search sentence in file
:params file: file descriptor
:params sentence: sentence will be searched
"""
if isinstance(sentence, str):
sentence = sentence.strip()
for line in file:
line = _skip_notes(line).strip()
if line == sentence:
return line
elif isinstance(sentence, list):
sentence = _list_elem2strip(sentence)
for line in file:
line = _skip_notes(line).strip()
if line in sentence:
return line
file.seek(0, 0)
return False
def _skip_notes(line):
"""Delete comments lines with '#' or '//'
:params line: line will be handled
"""
line = re.compile(r"#.*").sub("", line)
line = re.compile(r"//.*").sub("", line)
line = line.strip()
return line
def _list_elem2strip(a, ds=string.whitespace):
"""Strip element of list with `str` type"""
def list_strip(s):
return s.strip(ds)
return list(map(list_strip, a))
def _list_elem_2float(a):
"""Convert type of list element to float
:params a: 1-D list
"""
return list(map(float, a))
def _list_elem2str(a):
"""Convert type of list element to str
:params a: 1-D list
"""
return list(map(str, a))

29
phonopy/interface/calculator.py
View File

@ -63,6 +63,7 @@ from phonopy.units import (
)
calculator_info = {
"abacus":{"option": {"name": "--abacus", "help": "Invoke ABACUS mode"}},
"abinit": {"option": {"name": "--abinit", "help": "Invoke Abinit mode"}},
"aims": {"option": {"name": "--aims", "help": "Invoke FHI-aims mode"}},
"cp2k": {"option": {"name": "--cp2k", "help": "Invoke CP2K mode"}},
@ -193,6 +194,12 @@ def write_crystal_structure(
speci, restlines = optional_structure_info
fleur.write_fleur(filename, cell, speci, 1, restlines)
elif interface_mode == "abacus":
import phonopy.interface.abacus as abacus
pps = optional_structure_info[1]
orbitals = optional_structure_info[2]
abacus.write_abacus(filename, cell, pps, orbitals)
else:
raise RuntimeError("No calculator interface was found.")
@ -316,6 +323,13 @@ def write_supercells_with_displacements(
N = abs(determinant(additional_info["supercell_matrix"]))
fleur_args = args + (speci, N, restlines)
fleur.write_supercells_with_displacements(*fleur_args, **kwargs)
elif interface_mode == "abacus":
import phonopy.interface.abacus as abacus
pps = optional_structure_info[1]
orbitals = optional_structure_info[2]
abacus_args = args + (pps, orbitals)
abacus.write_supercells_with_displacements(*abacus_args, **kwargs)
else:
raise RuntimeError("No calculator interface was found.")
@ -453,6 +467,11 @@ def read_crystal_structure(
unitcell, speci, restlines = read_fleur(cell_filename)
return unitcell, (cell_filename, speci, restlines)
elif interface_mode == "abacus":
from phonopy.interface.abacus import read_abacus
unitcell, pps, orbitals = read_abacus(cell_filename, elements=chemical_symbols)
return unitcell, (cell_filename, pps, orbitals)
else:
raise RuntimeError("No calculator interface was found.")
@ -483,6 +502,8 @@ def get_default_cell_filename(interface_mode):
return "unitcell.cell"
elif interface_mode == "fleur":
return "fleur.in"
elif interface_mode == "abacus":
return "STRU"
else:
return None
@ -512,6 +533,8 @@ def get_default_supercell_filename(interface_mode):
return "geometry.in.supercell"
elif interface_mode in ("castep"):
return "supercell.cell"
elif interface_mode in ("abacus"):
return "sSTRU"
else:
return None
@ -526,6 +549,7 @@ def get_default_displacement_distance(interface_mode):
"siesta",
"turbomole",
"fleur",
"abacus"
):
displacement_distance = 0.02
else: # default or vasp, crystal, cp2k
@ -550,6 +574,7 @@ def get_default_physical_units(interface_mode=None):
FHI-aims : eV, angstrom, AMU, eV/angstrom, eV/angstrom^2
castep : eV, angstrom, AMU, eV/angstrom, eV/angstrom^2
fleur : hartree, au, AMU, hartree/au, hartree/au^2
abacus : eV, au, AMU, eV/angstrom, eV/angstrom.au
units['force_constants_unit'] is used in
the 'get_force_constant_conversion_factor' method.
@ -595,7 +620,7 @@ def get_default_physical_units(interface_mode=None):
units["distance_to_A"] = Bohr
units["force_constants_unit"] = "hartree/au^2"
units["length_unit"] = "au"
elif interface_mode == "siesta":
elif interface_mode in ["siesta", "abacus"]:
units["factor"] = SiestaToTHz
units["nac_factor"] = Hartree / Bohr
units["distance_to_A"] = Bohr
@ -679,6 +704,8 @@ def get_force_sets(
from phonopy.interface.castep import parse_set_of_forces
elif interface_mode == "fleur":
from phonopy.interface.fleur import parse_set_of_forces
elif interface_mode == "abacus":
from phonopy.interface.abacus import parse_set_of_forces
else:
return []

33
test/interface/NaCl-abacus.stru Normal file
View File

@ -0,0 +1,33 @@
ATOMIC_SPECIES
Na 22.98976928 Na_ONCV_PBE-1.0.upf
Cl 35.453 Cl_ONCV_PBE-1.0.upf
NUMERICAL_ORBITAL
Na_gga_9au_100Ry_4s2p1d.orb
Cl_gga_8au_100Ry_2s2p1d.orb
LATTICE_CONSTANT
1.8897261254578281
LATTICE_VECTORS
5.6903014761756712 0.0000000000000000 0.0000000000000000
0.0000000000000000 5.6903014761756712 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.6903014761756712
ATOMIC_POSITIONS
Direct
Na
0.0
4
0.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
Cl
0.0
4
0.5000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 0.5000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 0.5000000000000000

0
test/interface/NaCl-abinit-pwscf.yaml → test/interface/NaCl-abinit-pwscf-abacus.yaml
View File

22
test/interface/test_abacus.py Normal file
View File

@ -0,0 +1,22 @@
"""Tests for ABACUS calculater interface."""
import os
import numpy as np
from phonopy.interface.phonopy_yaml import read_cell_yaml
from phonopy.interface.abacus import read_abacus
data_dir = os.path.dirname(os.path.abspath(__file__))
def test_read_abacus():
"""Test of read_ABACUS."""
cell, pps, orbitals = read_abacus(os.path.join(data_dir, "NaCl-abacus.stru"), elements=['Na', 'Cl'])
filename = os.path.join(data_dir, "NaCl-abinit-pwscf-abacus.yaml")
cell_ref = read_cell_yaml(filename)
assert (np.abs(cell.cell - cell_ref.cell) < 1e-5).all()
diff_pos = cell.scaled_positions - cell_ref.scaled_positions
diff_pos -= np.rint(diff_pos)
assert (np.abs(diff_pos) < 1e-5).all()
for s, s_r in zip(cell.symbols, cell_ref.symbols):
assert s == s_r