Implement a new BFGS optimizer, used for geometry relaxation #5467
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| INPUT_PARAMETERS | ||
| # Created by Atomic Simulation Enviroment | ||
| suffix abacus | ||
| calculation relax | ||
| relax_method bfgs_trad | ||
| relax_nmax 50 | ||
| nspin 2 | ||
| nupdown 2 | ||
| symmetry 0 | ||
| dft_functional PBE | ||
| basis_type pw | ||
| ecutwfc 100 | ||
| scf_thr 1e-07 | ||
| scf_nmax 50 | ||
| gamma_only True | ||
| smearing_method gauss | ||
| smearing_sigma 0.01 | ||
| mixing_type broyden | ||
| mixing_beta 0.2 | ||
| mixing_beta_mag 0.8 | ||
| mixing_gg0 1.5 | ||
| mixing_gg0_mag 0 | ||
| ks_solver dav | ||
| cal_force 1 | ||
| ntype 2 | ||
| orbital_dir . |
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| K_POINTS | ||
| 0 | ||
| Gamma | ||
| 1 1 1 0 0 0 |
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| conda create -n ase-abacus python=3.10 | ||
| conda activate ase-abacus | ||
| git clone https://gitlab.com/1041176461/ase-abacus.git | ||
| cd ase-abacus | ||
| pip install . |
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| ATOMIC_SPECIES | ||
| Si 28.085 Si.ccECP.upf | ||
| H 1.008 H.ccECP.upf | ||
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| NUMERICAL_ORBITAL | ||
| Si_gga_7au_100Ry_2s2p1d.orb | ||
| H_gga_6au_100Ry_2s1p.orb | ||
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| LATTICE_CONSTANT | ||
| 1.8897261258369282 | ||
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| LATTICE_VECTORS | ||
| 21.167088000 0.0000000000 0.0000000000 | ||
| 0.0000000000 21.167088000 0.0000000000 | ||
| 0.0000000000 0.0000000000 21.167088000 | ||
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| ATOMIC_POSITIONS | ||
| Direct | ||
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| Si | ||
| 0.0000000000 | ||
| 1 | ||
| 0.5000000000 0.4999990000 0.5047030000 1 1 1 v 0.0 0.0 0.0 mag 0.0 | ||
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| H | ||
| 0.0000000000 | ||
| 2 | ||
| 0.5000000000 0.5610460000 0.4685160000 1 1 1 v 0.0 0.0 0.0 mag 0.0 | ||
| 0.5000000000 0.4389560000 0.4685160000 1 1 1 v 0.0 0.0 0.0 mag 0.0 | ||
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| data_image0 | ||
| _chemical_formula_structural SiH2 | ||
| _chemical_formula_sum "Si1 H2" | ||
| _cell_length_a 21.16708843 | ||
| _cell_length_b 21.16708843 | ||
| _cell_length_c 21.16708843 | ||
| _cell_angle_alpha 90.0 | ||
| _cell_angle_beta 90.0 | ||
| _cell_angle_gamma 90.0 | ||
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| _space_group_name_H-M_alt "P 1" | ||
| _space_group_IT_number 1 | ||
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| loop_ | ||
| _space_group_symop_operation_xyz | ||
| 'x, y, z' | ||
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| loop_ | ||
| _atom_site_type_symbol | ||
| _atom_site_label | ||
| _atom_site_symmetry_multiplicity | ||
| _atom_site_fract_x | ||
| _atom_site_fract_y | ||
| _atom_site_fract_z | ||
| _atom_site_occupancy | ||
| Si Si1 1.0 0.49999992 0.49999894409649426 0.5047026224112832 1.0000 | ||
| H H1 1.0 0.5000000400000001 0.5610455426063221 0.46851619853432114 1.0000 | ||
| H H2 1.0 0.5000000400000001 0.4389555032963629 0.4685163190552164 1.0000 |
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| # Generated by ABACUS ModuleIO::CifParser | ||
| data_? | ||
| _symmetry_space_group_name_H-M 'P 1' | ||
| _cell_length_a 21.16708843 | ||
| _cell_length_b 21.16708843 | ||
| _cell_length_c 21.16708843 | ||
| _cell_angle_alpha 90.00000000 | ||
| _cell_angle_beta 90.00000000 | ||
| _cell_angle_gamma 90.00000000 | ||
| _symmetry_Int_Tables_number 1 | ||
| _chemical_formula_structural SiH | ||
| _chemical_formula_sum SiH2 | ||
| _cell_volume 9483.82152169 | ||
| _cell_formula_units_Z 1 | ||
| loop_ | ||
| _symmetry_equiv_pos_site_id | ||
| _symmetry_equiv_pos_as_xyz | ||
| 1 'x, y, z' | ||
| loop_ | ||
| _atom_site_type_symbol | ||
| _atom_site_label | ||
| _atom_site_symmetry_multiplicity | ||
| _atom_site_fract_x | ||
| _atom_site_fract_y | ||
| _atom_site_fract_z | ||
| _atom_site_occupancy | ||
| Si Si0 1 0.49999992 0.49999980 0.50526114 1.0 | ||
| H H1 1 0.50000004 0.56098905 0.46823705 1.0 | ||
| H H2 1 0.50000004 0.43901114 0.46823695 1.0 |
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| ABACUS v3.8.1 | ||
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| Atomic-orbital Based Ab-initio Computation at UStc | ||
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| Website: http://abacus.ustc.edu.cn/ | ||
| Documentation: https://abacus.deepmodeling.com/ | ||
| Repository: https://github.com/abacusmodeling/abacus-develop | ||
| https://github.com/deepmodeling/abacus-develop | ||
| Commit: 146a50931 (Mon Oct 21 16:41:35 2024 +0800) | ||
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| Thu Oct 24 12:09:59 2024 | ||
| MAKE THE DIR : OUT.abacus/ | ||
| RUNNING WITH DEVICE : CPU / Intel(R) Xeon(R) Platinum | ||
| UNIFORM GRID DIM : 256 * 256 * 256 | ||
| UNIFORM GRID DIM(BIG) : 256 * 256 * 256 | ||
| DONE(0.28622 SEC) : SETUP UNITCELL | ||
| DONE(0.286508 SEC) : INIT K-POINTS | ||
| --------------------------------------------------------- | ||
| Self-consistent calculations for electrons | ||
| --------------------------------------------------------- | ||
| SPIN KPOINTS PROCESSORS | ||
| 2 2 16 | ||
| --------------------------------------------------------- | ||
| Use plane wave basis | ||
| --------------------------------------------------------- | ||
| ELEMENT NATOM XC | ||
| Si 1 | ||
| H 2 | ||
| --------------------------------------------------------- | ||
| Initial plane wave basis and FFT box | ||
| --------------------------------------------------------- | ||
| DONE(0.373599 SEC) : INIT PLANEWAVE | ||
| DONE(0.725854 SEC) : LOCAL POTENTIAL | ||
| DONE(0.825578 SEC) : NON-LOCAL POTENTIAL | ||
| MEMORY FOR PSI (MB) : 30.921 | ||
| DONE(0.914662 SEC) : INIT BASIS | ||
| ------------------------------------------- | ||
| SELF-CONSISTENT : | ||
| ------------------------------------------- | ||
| START CHARGE : atomic | ||
| DONE(3.68617 SEC) : INIT SCF | ||
| * * * * * * | ||
| << Start SCF iteration. | ||
| ITER TMAG AMAG ETOT/eV EDIFF/eV DRHO TIME/s | ||
| DS1 2.00e+00 2.03e+00 -1.34430231e+02 0.00000000e+00 3.9191e-01 14.62 | ||
| DS2 2.00e+00 2.02e+00 -1.34775372e+02 -3.45141827e-01 9.7737e-02 10.50 | ||
| DS3 2.00e+00 2.02e+00 -1.35111314e+02 -3.35941751e-01 6.5112e-03 15.38 | ||
| DS4 2.00e+00 2.02e+00 -1.35170475e+02 -5.91607382e-02 1.5503e-03 26.84 | ||
| DS5 2.00e+00 2.02e+00 -1.35186232e+02 -1.57568707e-02 1.7038e-04 20.76 | ||
| DS6 2.00e+00 2.02e+00 -1.35188302e+02 -2.07018353e-03 1.5779e-05 26.53 | ||
| DS7 2.00e+00 2.02e+00 -1.35188101e+02 2.01251562e-04 5.6585e-06 13.65 | ||
| DS8 2.00e+00 2.02e+00 -1.35188148e+02 -4.72056440e-05 2.2478e-07 14.42 | ||
| DS9 2.00e+00 2.02e+00 -1.35188152e+02 -4.09432453e-06 7.8883e-08 12.36 | ||
| DS10 2.00e+00 2.02e+00 -1.35188153e+02 -1.47620397e-06 4.3864e-09 9.45 | ||
| >> Leave SCF iteration. | ||
| * * * * * * | ||
| TIME STATISTICS | ||
| ----------------------------------------------------------------------------- | ||
| CLASS_NAME NAME TIME/s CALLS AVG/s PER/% | ||
| ----------------------------------------------------------------------------- | ||
| total 170.93 15 11.40 100.00 | ||
| Driver reading 0.02 1 0.02 0.01 | ||
| Input_Conv Convert 0.00 1 0.00 0.00 | ||
| Driver driver_line 170.91 1 170.91 99.99 | ||
| UnitCell check_tau 0.00 1 0.00 0.00 | ||
| PW_Basis_Sup setuptransform 0.06 1 0.06 0.03 | ||
| PW_Basis_Sup distributeg 0.05 1 0.05 0.03 | ||
| mymath heapsort 0.10 3 0.03 0.06 | ||
| PW_Basis_K setuptransform 0.04 1 0.04 0.03 | ||
| PW_Basis_K distributeg 0.04 1 0.04 0.02 | ||
| PW_Basis setup_struc_factor 0.06 1 0.06 0.03 | ||
| ppcell_vnl init 0.01 1 0.01 0.01 | ||
| ppcell_vl init_vloc 0.21 1 0.21 0.12 | ||
| ppcell_vnl init_vnl 0.10 1 0.10 0.06 | ||
| WF_atomic init_at_1 0.09 1 0.09 0.05 | ||
| wavefunc wfcinit 0.00 1 0.00 0.00 | ||
| Ions opt_ions 169.89 1 169.89 99.39 | ||
| ESolver_KS_PW runner 169.22 1 169.22 99.00 | ||
| ESolver_KS_PW before_scf 2.77 1 2.77 1.62 | ||
| H_Ewald_pw compute_ewald 0.02 1 0.02 0.01 | ||
| Charge set_rho_core 0.00 1 0.00 0.00 | ||
| Charge atomic_rho 1.18 2 0.59 0.69 | ||
| PW_Basis_Sup recip2real 9.56 122 0.08 5.59 | ||
| PW_Basis_Sup gathers_scatterp 4.46 122 0.04 2.61 | ||
| Potential init_pot 2.27 1 2.27 1.33 | ||
| Potential update_from_charge 23.35 11 2.12 13.66 | ||
| Potential cal_fixed_v 0.09 1 0.09 0.05 | ||
| PotLocal cal_fixed_v 0.09 1 0.09 0.05 | ||
| Potential cal_v_eff 23.18 11 2.11 13.56 | ||
| H_Hartree_pw v_hartree 2.15 11 0.20 1.26 | ||
| PW_Basis_Sup real2recip 11.37 154 0.07 6.65 | ||
| PW_Basis_Sup gatherp_scatters 5.94 154 0.04 3.48 | ||
| PotXC cal_v_eff 20.80 11 1.89 12.17 | ||
| XC_Functional v_xc 20.70 11 1.88 12.11 | ||
| Potential interpolate_vrs 0.08 11 0.01 0.05 | ||
| Charge_Mixing init_mixing 0.00 1 0.00 0.00 | ||
| ESolver_KS_PW hamilt2density 136.57 10 13.66 79.90 | ||
| HSolverPW solve 136.42 10 13.64 79.81 | ||
| Nonlocal getvnl 0.47 20 0.02 0.28 | ||
| pp_cell_vnl getvnl 0.47 20 0.02 0.28 | ||
| Structure_Factor get_sk 0.07 28 0.00 0.04 | ||
| WF_atomic atomic_wfc 0.08 2 0.04 0.05 | ||
| Diago_DavSubspace diag_once 122.67 20 6.13 71.76 | ||
| Diago_DavSubspace first 24.52 20 1.23 14.34 | ||
| DavSubspace hpsi_func 110.08 186 0.59 64.40 | ||
| Operator hPsi 109.69 186 0.59 64.17 | ||
| Operator EkineticPW 0.87 186 0.00 0.51 | ||
| Operator VeffPW 106.68 186 0.57 62.41 | ||
| PW_Basis_K recip2real 61.85 1675 0.04 36.19 | ||
| PW_Basis_K gathers_scatterp 21.52 1675 0.01 12.59 | ||
| PW_Basis_K real2recip 45.62 1375 0.03 26.69 | ||
| PW_Basis_K gatherp_scatters 12.75 1375 0.01 7.46 | ||
| Operator NonlocalPW 2.14 186 0.01 1.25 | ||
| Nonlocal add_nonlocal_pp 1.19 186 0.01 0.70 | ||
| Diago_DavSubspace cal_elem 3.69 186 0.02 2.16 | ||
| Diago_DavSubspace diag_zhegvx 0.13 186 0.00 0.08 | ||
| Diago_DavSubspace cal_grad 93.08 166 0.56 54.46 | ||
| Diago_DavSubspace check_update 0.00 166 0.00 0.00 | ||
| Diago_DavSubspace last 1.52 34 0.04 0.89 | ||
| Diago_DavSubspace refresh 0.48 14 0.03 0.28 | ||
| ElecStatePW psiToRho 12.04 10 1.20 7.04 | ||
| Charge_Mixing get_drho 2.91 10 0.29 1.70 | ||
| Charge_Mixing inner_product_recip_rho 0.09 10 0.01 0.05 | ||
| Charge mix_rho 3.61 9 0.40 2.11 | ||
| Charge Broyden_mixing 0.58 9 0.06 0.34 | ||
| Charge_Mixing inner_product_recip_hartree 0.48 72 0.01 0.28 | ||
| ESolver_KS_PW after_scf 1.94 1 1.94 1.14 | ||
| ModuleIO write_rhog 1.06 1 1.06 0.62 | ||
| Forces cal_force_loc 0.12 1 0.12 0.07 | ||
| Forces cal_force_ew 0.05 1 0.05 0.03 | ||
| Forces cal_force_nl 0.12 1 0.12 0.07 | ||
| FS_Nonlocal_tools cal_becp 0.06 2 0.03 0.04 | ||
| FS_Nonlocal_tools cal_dbecp_f 0.06 6 0.01 0.03 | ||
| Forces cal_force_cc 0.00 1 0.00 0.00 | ||
| Forces cal_force_scc 0.38 1 0.38 0.22 | ||
| ModuleIO write_istate_info 0.00 1 0.00 0.00 | ||
| ----------------------------------------------------------------------------- | ||
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| START Time : Thu Oct 24 12:09:59 2024 | ||
| FINISH Time : Thu Oct 24 12:12:50 2024 | ||
| TOTAL Time : 171 | ||
| SEE INFORMATION IN : OUT.abacus/ |
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| ABACUS v3.8.2 | ||
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| Atomic-orbital Based Ab-initio Computation at UStc | ||
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| Website: http://abacus.ustc.edu.cn/ | ||
| Documentation: https://abacus.deepmodeling.com/ | ||
| Repository: https://github.com/abacusmodeling/abacus-develop | ||
| https://github.com/deepmodeling/abacus-develop | ||
| Commit: unknown | ||
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| Fri Nov 15 08:05:02 2024 | ||
| MAKE THE DIR : OUT.abacus/ | ||
| RUNNING WITH DEVICE : CPU / 13th Gen Intel(R) Core(TM) i7-13700KF | ||
| UNIFORM GRID DIM : 256 * 256 * 256 | ||
| UNIFORM GRID DIM(BIG) : 256 * 256 * 256 | ||
| DONE(2.46674 SEC) : SETUP UNITCELL | ||
| DONE(2.71952 SEC) : INIT K-POINTS | ||
| --------------------------------------------------------- | ||
| Ion relaxation calculations | ||
| --------------------------------------------------------- | ||
| SPIN KPOINTS PROCESSORS THREADS | ||
| 2 2 8 8 | ||
| --------------------------------------------------------- | ||
| Use plane wave basis | ||
| --------------------------------------------------------- | ||
| ELEMENT NATOM XC | ||
| Si 1 | ||
| H 2 | ||
| --------------------------------------------------------- | ||
| Initial plane wave basis and FFT box | ||
| --------------------------------------------------------- | ||
| DONE(3.80033 SEC) : INIT PLANEWAVE | ||
| DONE(5.7434 SEC) : LOCAL POTENTIAL | ||
| DONE(5.97613 SEC) : NON-LOCAL POTENTIAL | ||
| MEMORY FOR PSI (MB) : 61.8411 | ||
| DONE(6.25469 SEC) : INIT BASIS | ||
| ------------------------------------------- | ||
| STEP OF ION RELAXATION : 1 | ||
| ------------------------------------------- | ||
| START CHARGE : atomic | ||
| DONE(26.3435 SEC) : INIT SCF | ||
| ITER TMAG AMAG ETOT/eV EDIFF/eV DRHO TIME/s | ||
| DA1 2.00e+00 2.03e+00 -1.36488047e+02 0.00000000e+00 3.9185e-01 67.66 |
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| Step Time Energy fmax | ||
| BFGS: 0 12:01:24 -135.186543 0.192194 | ||
| BFGS: 1 12:04:16 -135.187369 0.131104 | ||
| BFGS: 2 12:07:10 -135.188012 0.025128 | ||
| BFGS: 3 12:09:58 -135.188032 0.023977 | ||
| BFGS: 4 12:12:50 -135.188153 0.001422 | ||
| Final structure is saved in SiH2-pos-fin.cif |
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| from ase.calculators.abacus import Abacus | ||
| from ase.calculators.abacus import AbacusProfile | ||
| from ase.io import read, write | ||
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| def abacus_init(fname, profile, **kwargs): | ||
| '''instantiate a instance of Abacus calculator (and bind) with | ||
| specific structures and ABACUS parameters | ||
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| Parameters | ||
| ---------- | ||
| fname : str | ||
| The filename of the structure, can be any format that ASE supports. | ||
| For a complete list of supported formats, see: | ||
| https://wiki.fysik.dtu.dk/ase/ase/io/io.html#module-ase.io | ||
| profile : AbacusProfile | ||
| The command to run ABACUS | ||
| **kwargs : dict | ||
| The ABACUS parameters, e.g. pp, basis, etc. | ||
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| Returns | ||
| ------- | ||
| a : Atoms | ||
| The Atoms object with the attached ABACUS calculator | ||
| ''' | ||
| a = read(fname) | ||
| pp = kwargs.pop('pp', {}) | ||
| # if there is no data in pp, pops an warning | ||
| if not pp: | ||
| print('WARNING: No pseudopotential data is provided') | ||
| a.calc = Abacus(pp=pp, profile=profile, **kwargs) | ||
| return a | ||
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| def relax(a, method='BFGS', fmax=0.05, max_steps=100, **kwargs): | ||
| '''relax the structure using the given method''' | ||
| if method == 'BFGS': | ||
| from ase.optimize import BFGS | ||
| dyn = BFGS(a, trajectory=None, **kwargs) | ||
| dyn.run(fmax=fmax, steps=max_steps) | ||
| else: | ||
| raise NotImplementedError(f'{method} is not supported by ASE') | ||
| return a | ||
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| if __name__ == '__main__': | ||
| pp={'Si': 'Si.ccECP.upf', 'H': 'H.ccECP.upf'} | ||
| env = AbacusProfile('mpirun -np 16 /usr/local/bin/abacus') | ||
| recipe = {'suffix': 'abacus', | ||
| 'pseudo_dir': '.', | ||
| 'orbital_dir': '.', | ||
| 'nspin': 2, | ||
| 'nupdown': 2, | ||
| 'symmetry': 0, | ||
| 'dft_functional': 'PBE', | ||
| 'ecutwfc': 100, | ||
| 'scf_thr': 1e-8, | ||
| 'scf_nmax': 50, | ||
| 'basis_type': 'pw', | ||
| 'gamma_only': True, | ||
| 'smearing_method': 'fixed', | ||
| 'mixing_type': 'broyden', | ||
| 'mixing_beta': 0.4, | ||
| 'mixing_beta_mag': 0.4, | ||
| 'mixing_gg0': 0, | ||
| 'mixing_gg0_mag': 0, | ||
| 'ks_solver': 'dav_subspace', | ||
| 'out_chg': -1} | ||
| ini = 'SiH2-pos-ini.cif' | ||
| fin = 'SiH2-pos-fin.cif' | ||
| a = abacus_init(ini, profile=env, pp=pp, **recipe) | ||
| a = relax(a, fmax=0.01, max_steps=100) | ||
| write(fin, a) | ||
| print(f'Final structure is saved in {fin}') |
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do not add new file, this file is too large
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@19hello
for SiH2 example, you can attach it as zip file under the corresponding issue, but not in source-code
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I've delete SiH2-3et-relax
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@19hello After you resolve this comment, please mark them as resolved