diff --git a/ABACUS-DeePKS/H2O-deepks-pw/H_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/H2O-deepks-pw/H_ONCV_PBE-1.0.upf new file mode 100644 index 0000000000000000000000000000000000000000..f8b1ebb63c87d413e9291f7c0b9fd8707f9c8256 --- /dev/null +++ b/ABACUS-DeePKS/H2O-deepks-pw/H_ONCV_PBE-1.0.upf @@ -0,0 +1,897 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + H 1.00 0 1 4 upf +# +# n l f energy (Ha) + 1 0 1.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 0 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.13748 -0.23860 5 8 9.72141 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.49352 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.27464 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 0.0800 0.0900 0.1000 0.1100 0.1200 0.1300 0.1400 0.1500 + 0.1600 0.1700 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3.785767743619e-04 + 1.983765869872e-04 8.519893699498e-05 2.556086363756e-05 3.217573100688e-06 + 0.000000000000e+00 \ No newline at end of file diff --git a/ABACUS-DeePKS/H2O-deepks-pw/INPUT b/ABACUS-DeePKS/H2O-deepks-pw/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..e167aa7fd56c22a07e75b29bd950fef5a0817445 --- /dev/null +++ b/ABACUS-DeePKS/H2O-deepks-pw/INPUT @@ -0,0 +1,29 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix abacus +calculation scf +ntype 2 +nbands 6 +symmetry 0 + +#Parameters (2.Iteration) +ecutwfc 50 +scf_thr 1e-8 +scf_nmax 50 + +#Parameters (3.Basis) +basis_type pw +gamma_only 1 + +#Parameters (4.Smearing) +smearing_method gaussian +smearing_sigma 0.02 + +#Parameters (5.Mixing) +mixing_type pulay +mixing_beta 0.4 + +#Parameters (6.File) +out_band 0 +deepks_out_labels 1 +deepks_descriptor_lmax 2 diff --git a/ABACUS-DeePKS/H2O-deepks-pw/INPUTs b/ABACUS-DeePKS/H2O-deepks-pw/INPUTs new file mode 100644 index 0000000000000000000000000000000000000000..44ca6c0838a223e9ddea4635bac971e5b8e9b1bc --- /dev/null +++ b/ABACUS-DeePKS/H2O-deepks-pw/INPUTs @@ -0,0 +1,8 @@ +INPUT_ORBITAL_INFORMATION + +1 // smooth or not +0.1 // smearing_sigma +20 // energy cutoff for spherical bessel functions(Ry) +2 // cutoff of wavefunctions(a.u.) +1.0e-12 // tolerence + diff --git a/ABACUS-DeePKS/H2O-deepks-pw/KPT b/ABACUS-DeePKS/H2O-deepks-pw/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/H2O-deepks-pw/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/H2O-deepks-pw/O_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/H2O-deepks-pw/O_ONCV_PBE-1.0.upf new file mode 100644 index 0000000000000000000000000000000000000000..7e7db6d66f69ceb7e960ade73fd5d8885fb5ffb8 --- /dev/null +++ b/ABACUS-DeePKS/H2O-deepks-pw/O_ONCV_PBE-1.0.upf @@ -0,0 +1,1224 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + O 8.00 1 2 4 upf +# +# n l f energy (Ha) + 1 0 2.00 + 2 0 2.00 + 2 1 4.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 1 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.29195 -0.88057 5 8 8.98916 + 1 1.47310 -0.33187 5 8 9.14990 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.90330 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.51851 + 1 2 1.53631 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 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H_ONCV_PBE-1.0.upf +O 15.9994 O_ONCV_PBE-1.0.upf + +NUMERICAL_ORBITAL +H_gga_6au_60Ry_2s1p.orb +O_gga_6au_60Ry_2s2p1d.orb + +LATTICE_CONSTANT +10 + +LATTICE_VECTORS +1 0 0 +0 1 0 +0 0 1 + +ATOMIC_POSITIONS +Cartesian + +H +0 +2 +0.2336137046291667 0.8630016418166666 0.7271997623458333 1 1 1 +0.23417266949166665 0.9245341895916668 0.7207232227333333 1 1 1 +O +0 +1 +0.20910677665833333 0.894927691625 0.7301984601833333 1 1 1 diff --git a/ABACUS-DeePKS/H2O-deepks-pw/descriptor.dat b/ABACUS-DeePKS/H2O-deepks-pw/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..843547ef0cc0d477e09d0a61e61f5475ba8a1f4d --- /dev/null +++ b/ABACUS-DeePKS/H2O-deepks-pw/descriptor.dat @@ -0,0 +1,48 @@ +H atom_index 1 n_descriptor 117 +8.6337 1.64286 0.335071 0.131771 0.0476684 0.0225226 0.0116164 0.00588298 +0.00324368 0.00153789 0.000798237 0.000364279 0.000169084 0.405463 0.774783 3.17103 +0.320238 0.401018 0.416599 0.14597 0.167703 0.171042 0.0557152 0.0694168 +0.0828051 0.0175949 0.0286645 0.0360523 0.0056741 0.0115018 0.0162086 0.00148592 +0.00484878 0.00673434 0.00040785 0.00193997 0.00298168 9.45225e-05 0.000774866 0.00111817 +4.80692e-05 0.000284433 0.00046522 3.31228e-05 9.92706e-05 0.000144674 2.49332e-05 3.36781e-05 +6.29598e-05 3.55959e-06 3.76563e-06 9.19828e-06 1.86463e-05 0.000495479 0.0158654 0.0164122 +0.131167 1.21854e-06 0.000498166 0.0170361 0.0182622 0.0229838 2.37349e-06 9.79136e-05 +0.0136992 0.0149038 0.0194728 1.80217e-06 5.19709e-05 0.00925381 0.0100169 0.0128096 +1.06341e-06 2.84027e-05 0.00556941 0.00600754 0.00883919 7.26986e-07 1.36759e-05 0.00323978 +0.00348365 0.00503592 3.53711e-07 8.26414e-06 0.0018024 0.00181919 0.00317192 2.11246e-07 +4.17861e-06 0.000941667 0.00095985 0.00160115 8.42441e-08 2.41634e-06 0.000409661 0.000474298 +0.000895715 3.5565e-08 1.34604e-06 0.000179148 0.000214292 0.000381697 8.8433e-09 7.5638e-07 +6.30949e-05 9.13342e-05 0.000190989 1.63448e-09 4.21859e-07 2.09944e-05 2.95453e-05 5.76515e-05 +2.52811e-11 1.59956e-08 9.63818e-08 1.87631e-07 3.57585e-06 +H atom_index 2 n_descriptor 117 +8.58629 1.64279 0.333321 0.131436 0.0468976 0.0222956 0.0113884 0.00582681 +0.00319229 0.00153173 0.000789979 0.000365163 0.000168024 0.428327 0.774951 3.22546 +0.323387 0.400148 0.416881 0.146513 0.167956 0.171337 0.055514 0.0696468 +0.084421 0.017907 0.0288043 0.0363163 0.0057377 0.0115866 0.0166051 0.00156437 +0.0048947 0.00681812 0.000422159 0.0019657 0.00307941 0.000100246 0.00078749 0.00113914 +4.58591e-05 0.00029052 0.000486945 2.9619e-05 0.000101678 0.000148827 2.33115e-05 3.48065e-05 +6.73526e-05 3.39956e-06 3.69115e-06 9.03414e-06 1.10973e-05 0.000561533 0.0158827 0.0160544 +0.10203 6.96469e-07 0.000543107 0.0165868 0.0179468 0.0209534 1.26938e-06 9.31636e-05 +0.0134988 0.0147624 0.0188412 3.49364e-07 5.21841e-05 0.00908559 0.00980599 0.0124494 +4.8741e-07 2.80017e-05 0.00548797 0.00595887 0.00872226 1.47042e-07 1.40112e-05 0.00319001 +0.00341412 0.00497452 1.55652e-07 8.11539e-06 0.00178868 0.00181172 0.00315219 4.1026e-08 +4.25747e-06 0.000928262 0.000949085 0.00159341 4.33366e-08 2.31115e-06 0.000414829 0.000471228 +0.000894336 6.82658e-09 1.32567e-06 0.000177523 0.00021326 0.000381831 8.50005e-09 6.9477e-07 +6.49545e-05 9.12906e-05 0.000191355 1.17968e-09 4.23974e-07 2.02826e-05 2.98077e-05 5.78414e-05 +1.08748e-09 1.83654e-08 6.91167e-08 2.28524e-07 2.85146e-06 +O atom_index 1 n_descriptor 117 +8.39927 1.74924 0.320158 0.112639 0.0233291 0.00835168 0.00230151 0.0010965 +0.000685832 0.000358311 0.000283113 0.000141987 0.000102514 0.382931 0.785038 3.18816 +0.325464 0.403513 0.435225 0.17871 0.182868 0.186876 0.081024 0.0943096 +0.0978905 0.0362042 0.0431748 0.0474245 0.0161162 0.0227891 0.0232373 0.00758905 +0.0103734 0.0116325 0.00351414 0.00558713 0.00573454 0.00161866 0.00241805 0.00274659 +0.000718772 0.00125817 0.00128576 0.000294225 0.000473332 0.000545205 0.000127139 0.00025082 +0.000258046 1.45077e-05 2.71564e-05 2.99321e-05 5.9403e-06 0.000288006 0.000502287 0.000630795 +0.184366 1.39968e-06 0.000332439 0.000510098 0.000734575 0.00738666 1.21917e-06 0.000269666 +0.000294478 0.000627856 0.00317448 8.51215e-07 0.000146432 0.000184091 0.000469511 0.000989314 +5.24365e-07 8.09823e-05 0.000142 0.000310221 0.000470881 2.93804e-07 4.30581e-05 8.14991e-05 +0.000204871 0.000233799 1.7751e-07 2.40895e-05 6.00404e-05 0.0001152 0.000138208 9.21282e-08 +1.2903e-05 3.32158e-05 6.96494e-05 8.43918e-05 5.36017e-08 7.13565e-06 2.17522e-05 3.78762e-05 +5.14935e-05 2.54311e-08 3.67034e-06 1.15774e-05 2.31958e-05 2.95982e-05 1.37544e-08 1.98643e-06 +6.89745e-06 1.34907e-05 1.75484e-05 5.01753e-09 8.71328e-07 3.17905e-06 8.07677e-06 8.7924e-06 +3.33246e-11 5.102e-09 4.27705e-08 5.0544e-08 4.80027e-06 diff --git a/ABACUS-DeePKS/H2O-deepks-pw/descriptor.dat.bak b/ABACUS-DeePKS/H2O-deepks-pw/descriptor.dat.bak new file mode 100644 index 0000000000000000000000000000000000000000..843547ef0cc0d477e09d0a61e61f5475ba8a1f4d --- /dev/null +++ b/ABACUS-DeePKS/H2O-deepks-pw/descriptor.dat.bak @@ -0,0 +1,48 @@ +H atom_index 1 n_descriptor 117 +8.6337 1.64286 0.335071 0.131771 0.0476684 0.0225226 0.0116164 0.00588298 +0.00324368 0.00153789 0.000798237 0.000364279 0.000169084 0.405463 0.774783 3.17103 +0.320238 0.401018 0.416599 0.14597 0.167703 0.171042 0.0557152 0.0694168 +0.0828051 0.0175949 0.0286645 0.0360523 0.0056741 0.0115018 0.0162086 0.00148592 +0.00484878 0.00673434 0.00040785 0.00193997 0.00298168 9.45225e-05 0.000774866 0.00111817 +4.80692e-05 0.000284433 0.00046522 3.31228e-05 9.92706e-05 0.000144674 2.49332e-05 3.36781e-05 +6.29598e-05 3.55959e-06 3.76563e-06 9.19828e-06 1.86463e-05 0.000495479 0.0158654 0.0164122 +0.131167 1.21854e-06 0.000498166 0.0170361 0.0182622 0.0229838 2.37349e-06 9.79136e-05 +0.0136992 0.0149038 0.0194728 1.80217e-06 5.19709e-05 0.00925381 0.0100169 0.0128096 +1.06341e-06 2.84027e-05 0.00556941 0.00600754 0.00883919 7.26986e-07 1.36759e-05 0.00323978 +0.00348365 0.00503592 3.53711e-07 8.26414e-06 0.0018024 0.00181919 0.00317192 2.11246e-07 +4.17861e-06 0.000941667 0.00095985 0.00160115 8.42441e-08 2.41634e-06 0.000409661 0.000474298 +0.000895715 3.5565e-08 1.34604e-06 0.000179148 0.000214292 0.000381697 8.8433e-09 7.5638e-07 +6.30949e-05 9.13342e-05 0.000190989 1.63448e-09 4.21859e-07 2.09944e-05 2.95453e-05 5.76515e-05 +2.52811e-11 1.59956e-08 9.63818e-08 1.87631e-07 3.57585e-06 +H atom_index 2 n_descriptor 117 +8.58629 1.64279 0.333321 0.131436 0.0468976 0.0222956 0.0113884 0.00582681 +0.00319229 0.00153173 0.000789979 0.000365163 0.000168024 0.428327 0.774951 3.22546 +0.323387 0.400148 0.416881 0.146513 0.167956 0.171337 0.055514 0.0696468 +0.084421 0.017907 0.0288043 0.0363163 0.0057377 0.0115866 0.0166051 0.00156437 +0.0048947 0.00681812 0.000422159 0.0019657 0.00307941 0.000100246 0.00078749 0.00113914 +4.58591e-05 0.00029052 0.000486945 2.9619e-05 0.000101678 0.000148827 2.33115e-05 3.48065e-05 +6.73526e-05 3.39956e-06 3.69115e-06 9.03414e-06 1.10973e-05 0.000561533 0.0158827 0.0160544 +0.10203 6.96469e-07 0.000543107 0.0165868 0.0179468 0.0209534 1.26938e-06 9.31636e-05 +0.0134988 0.0147624 0.0188412 3.49364e-07 5.21841e-05 0.00908559 0.00980599 0.0124494 +4.8741e-07 2.80017e-05 0.00548797 0.00595887 0.00872226 1.47042e-07 1.40112e-05 0.00319001 +0.00341412 0.00497452 1.55652e-07 8.11539e-06 0.00178868 0.00181172 0.00315219 4.1026e-08 +4.25747e-06 0.000928262 0.000949085 0.00159341 4.33366e-08 2.31115e-06 0.000414829 0.000471228 +0.000894336 6.82658e-09 1.32567e-06 0.000177523 0.00021326 0.000381831 8.50005e-09 6.9477e-07 +6.49545e-05 9.12906e-05 0.000191355 1.17968e-09 4.23974e-07 2.02826e-05 2.98077e-05 5.78414e-05 +1.08748e-09 1.83654e-08 6.91167e-08 2.28524e-07 2.85146e-06 +O atom_index 1 n_descriptor 117 +8.39927 1.74924 0.320158 0.112639 0.0233291 0.00835168 0.00230151 0.0010965 +0.000685832 0.000358311 0.000283113 0.000141987 0.000102514 0.382931 0.785038 3.18816 +0.325464 0.403513 0.435225 0.17871 0.182868 0.186876 0.081024 0.0943096 +0.0978905 0.0362042 0.0431748 0.0474245 0.0161162 0.0227891 0.0232373 0.00758905 +0.0103734 0.0116325 0.00351414 0.00558713 0.00573454 0.00161866 0.00241805 0.00274659 +0.000718772 0.00125817 0.00128576 0.000294225 0.000473332 0.000545205 0.000127139 0.00025082 +0.000258046 1.45077e-05 2.71564e-05 2.99321e-05 5.9403e-06 0.000288006 0.000502287 0.000630795 +0.184366 1.39968e-06 0.000332439 0.000510098 0.000734575 0.00738666 1.21917e-06 0.000269666 +0.000294478 0.000627856 0.00317448 8.51215e-07 0.000146432 0.000184091 0.000469511 0.000989314 +5.24365e-07 8.09823e-05 0.000142 0.000310221 0.000470881 2.93804e-07 4.30581e-05 8.14991e-05 +0.000204871 0.000233799 1.7751e-07 2.40895e-05 6.00404e-05 0.0001152 0.000138208 9.21282e-08 +1.2903e-05 3.32158e-05 6.96494e-05 8.43918e-05 5.36017e-08 7.13565e-06 2.17522e-05 3.78762e-05 +5.14935e-05 2.54311e-08 3.67034e-06 1.15774e-05 2.31958e-05 2.95982e-05 1.37544e-08 1.98643e-06 +6.89745e-06 1.34907e-05 1.75484e-05 5.01753e-09 8.71328e-07 3.17905e-06 8.07677e-06 8.7924e-06 +3.33246e-11 5.102e-09 4.27705e-08 5.0544e-08 4.80027e-06 diff --git a/ABACUS-DeePKS/H2O-deepks-pw/logout.bak b/ABACUS-DeePKS/H2O-deepks-pw/logout.bak new file mode 100644 index 0000000000000000000000000000000000000000..964c4479015fc1c5dd0fa4fe9dbaf9867ccff8c6 --- /dev/null +++ b/ABACUS-DeePKS/H2O-deepks-pw/logout.bak @@ -0,0 +1,73 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Sat Jan 30 16:21:16 2021 + MAKE THE DIR : OUT.abacus/ + DONE(0.0508616 SEC) : SETUP UNITCELL + DONE(0.0510054 SEC) : INIT K-POINTS + --------------------------------------------------------- + This calculation is self-consistent + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS + 1 1 1 + --------------------------------------------------------- + Use plane wave basis + --------------------------------------------------------- + ELEMENT NATOM XC + H 2 PBE + O 1 PBE + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.128295 SEC) : INIT PLANEWAVE + UNIFORM GRID DIM : 48 * 48 * 48 + UNIFORM GRID DIM(BIG): 48 * 48 * 48 + MEMORY FOR PSI (MB) : 0.552155 + DONE(0.142381 SEC) : LOCAL POTENTIAL + DONE(0.147029 SEC) : NON-LOCAL POTENTIAL + START POTENTIAL : atomic + DONE(0.220855 SEC) : INIT POTENTIAL + DONE(0.25472 SEC) : INIT BASIS + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) SCF_THR CG_ITER TIME(S) + CG1 -2.835018e+01 0.000000e+00 5.192e+00 1.000e+01 3.332e-01 + CG2 -2.718276e+01 1.167415e+00 6.586e-01 3.000e+00 1.672e-01 + CG3 -2.922537e+01 -2.042603e+00 3.547e-02 2.667e+00 1.576e-01 + CG4 -2.927314e+01 -4.777474e-02 5.820e-02 4.000e+00 1.858e-01 + CG5 -2.937300e+01 -9.986165e-02 1.613e-03 2.667e+00 1.610e-01 + CG6 -2.937923e+01 -6.231003e-03 1.783e-05 5.500e+00 2.225e-01 + CG7 -2.937924e+01 -3.778364e-06 8.821e-06 5.000e+00 2.062e-01 + CG8 -2.937925e+01 -9.245653e-06 6.311e-07 2.667e+00 1.563e-01 + CG9 -2.937925e+01 -1.147022e-06 5.296e-08 4.667e+00 2.033e-01 + CG10 -2.937925e+01 -1.211570e-07 9.727e-09 5.167e+00 2.038e-01 + DONE(2.398e+00 SEC) : jlq3d_overlap + DONE(2.399e+00 SEC) : GENERATE DESCRIPTOR FOR DEEPKS + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + A DC_Driv solve_eachf 2.3 1 2.3 95 % + B Run_Frag frag_pw_line 2.3 1 2.3 95 % + X FFT FFT3D 1.2 879 0.0014 50 % + E potential v_of_rho 0.56 11 0.051 23 % + G Hamilt_PW cinitcgg 0.26 11 0.023 11 % + H Hamilt_PW h_psi 1.1 338 0.0034 47 % + C Ions opt_ions_pw 2 1 2 83 % + D electrons self_consistent 2 1 2 83 % + E electrons c_bands 1.2 10 0.12 51 % + F Hamilt diago 1.2 10 0.12 51 % + G Diago_CG diag 0.98 10 0.098 41 % + E Charge mix_rho 0.13 10 0.013 5.5 % + ---------------------------------------------------------------------------------------- + + START Time : Sat Jan 30 16:21:16 2021 + FINISH Time : Sat Jan 30 16:21:18 2021 + TOTAL Time : 2 + SEE INFORMATION IN : OUT.abacus/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/README.md b/ABACUS-DeePKS/water_single_lda2pbe_abacus/README.md new file mode 100644 index 0000000000000000000000000000000000000000..2bf06ed5f8c8cc47a390dc6df177f780c3c0af7e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/README.md @@ -0,0 +1,105 @@ +# Example for water (LDA to PBE) : using ABACUS in scf iteration + +This is an example on how to use `deepks` library to train a **LDA-to-PBE** model for water molecules, with SCF calculation done by **[ABACUS](https://github.com/deepmodeling/abacus-develop)**. + +The sub-folders are grouped as following: + +- `systems` contains atom data with PBE energy and force. +- `iter` contains input files used to train a self consistent model iteratively (DeePKS). + +## Running this example locally + +To train a self-consistant model with ABACUS, you can `cd iter` and run: + +`python -u -m deepks iterate machines.yaml params.yaml systems.yaml scf_abacus.yaml >> log.iter 2> err.iter` + +or directly + +`cd iter && bash run.sh` + +## Running this example with DPDispatcher + +If you want the jobs submitted to supercomputer platforms by **[DPDispatcher](https://github.com/deepmodeling/dpdispatcher)** , you need to set `dispatcher` as `"dpdispatcher"`and set `dpdispatcher_machine` and `dpdispatcher_resources` according to [DPDispatcher docs](https://dpdispatcher.readthedocs.io/) (see `machines_bohrium.yaml`). Remember to set the remote `abacus_path` (see `scf_abacus_bohrium.yaml`). Taking **[Bohrium](https://bohrium.dp.tech/)** as an example, `cd iter` and run: + +`python -u -m deepks iterate machines_bohrium.yaml params.yaml systems.yaml scf_abacus_bohrium.yaml >> log.iter 2> err.iter` + +or directly + +`cd iter && bash run.sh` + +## Prameters for ABACUS +ABACUS parameters are specified in `scf_abacus.yaml`. These parameters can be divided into 3 categories: + +- Paras for running ABACUS: + - `abacus_path`: the path of ABACUS binary executable file (ABACUS) + - `run_cmd`: command to run ABACUS, usually `mpirun` + +- Paras for `INPUT` file: + - `ntype`: number of atom types + - `nbands`: total number of bands to calculate + - `ecutwfc`: energy cutoff for plane wave functions + - `scf_thr`: the charge density error threshold between two sequential density from electronic iterations to judge convergence + - `scf_nmax`: max scf steps + - `dft_functional`: Exchange-Correlation functional, which can be 'lda', 'gga', 'pbe', etc + - `gamma_only`: 1 for gamma-point, 0 for multi-kpoints + - `cal_force`: set 1 to calculate force, default 0 + - `cal_stress`: set 1 to calculate stress, default 0 + +- Paras for `STRU` file: + - `orb_files`: paths of atom orbitals, a list of str with the order same as the order of atom types in `atoms.npy` + - `pp_files`: paths of pseudo potential files, a list of str with the order same as the order of atom types in `atoms.npy` + - `proj_file`: path of orbital file for descripor basis + - `lattice_constant`: spacial period, in Bohr + - `lattice_vector`: spacial period of x,y and z, in Bohr +tips: you can set different STRU parasmeters for each data group, by adding a `stru_abacus.yaml`in systems/group.xx. + +There are some other important parameters for using ABACUS in `params.yaml ` and `machines.yaml`: +- `use_abacus`: set `true` to calculate SCF by ABACUS, `false` for using PySCF +- `cpus_per_task`: how many cpu cores are used for calculating each frame in using ABACUS +- `sub_size`: how many frames are calculated simultaneously + +**Caution**: The meanings of `cpus_per_task` and `sub_size` when using ABACUS are kind of different to using PySCF, because ABACUS supports parallel calculation in **each single frame (configuration)** while PySCF not. Each frame's calculation is an "ABACUS task" with a unique workdir. + + +## Data units +`deepks` accept `.npy` data in following units: +Property | Unit +--- | :---: +Length | Bohr (Å if from xyz) +Energy | $E_h$ (Hartree) +Force | $E_h$/Bohr ($E_h$/Å if from xyz) + +In this example, each grouped folder contain an `atom.npy` that has shape `n_frames x n_atoms x 4` and the four elements correspond to the nuclear charge of the atom and its three spacial coordinates. +Other properties can be provided as separate files like `energy.npy` and `force.npy`. + + +## Train a model: DeePHF or DeePKS + +Set `n_iter = 0` to train a perturbative energy model, which is a pure machine learning task. Please see [DeePHF paper](https://arxiv.org/pdf/2005.00169.pdf) for a detailed explanation of the construction of the descriptors. + +After SCF calculation, the following result files will be saved in `iter.init/00.scf/data_train(test)` prepared to training: + +- descriptor (`dm_eig`) +- energy labels (`l_e_delta`) +- force labels (`l_f_delta`) , only when `cal_force = 1 ` + +Set `n_iter` to a positive integer to train a self consistent model, following the iterative approach described in [DeePKS paper](https://arxiv.org/pdf/2008.00167.pdf). In scf calculation , a trained model file `model.pth` will be loaded into ABACUS. And beside above result files, a `grad_vx` file will appear in `iter.xx/00.scf/data_train(test)` when force label is used in training. + + +## Explaination for output files + +### RECORD file + +For each iteration, each sub-step would correspond to a row in `RECORD` file, used to indicate which steps have finished. It would have three numbers. The first one correspond to the iteration number. The second one correspond to the sub-folder in the iteration and the third correspond to step in that folder. + +- (`X 0 0`): pre process of SCF, generate ABACUS work direcotry and input files in each group of `systems` +- (`X 0 1`): run SCF calculation with given model by ABACUS +- (`X 0 2`): concatenate and check the SCF result and print convergence and accuracy +- (`X 1 0`): train a new model using the old one as starting point +- (`X 1 1`): test the model on all data to see the pure fitting error + +### log file + +One can check `iter.*/00.scf/log.data` for stats of SCF results, `iter*/01.train/log.train` for training curve and `iter*/01.train/log.test` for model prediction of $E_\delta$ (e_delta). + + \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/H_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/H_ONCV_PBE-1.0.upf new file mode 100644 index 0000000000000000000000000000000000000000..f8b1ebb63c87d413e9291f7c0b9fd8707f9c8256 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/H_ONCV_PBE-1.0.upf @@ -0,0 +1,897 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + H 1.00 0 1 4 upf +# +# n l f energy (Ha) + 1 0 1.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 0 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.13748 -0.23860 5 8 9.72141 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.49352 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.27464 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 0.0800 0.0900 0.1000 0.1100 0.1200 0.1300 0.1400 0.1500 + 0.1600 0.1700 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0000000000000000000000000000000000000000..7e7db6d66f69ceb7e960ade73fd5d8885fb5ffb8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/O_ONCV_PBE-1.0.upf @@ -0,0 +1,1224 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + O 8.00 1 2 4 upf +# +# n l f energy (Ha) + 1 0 2.00 + 2 0 2.00 + 2 1 4.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 1 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.29195 -0.88057 5 8 8.98916 + 1 1.47310 -0.33187 5 8 9.14990 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.90330 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.51851 + 1 2 1.53631 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 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-6.463966570746e-02 +-5.983213508908e-02 -5.496252350283e-02 -5.004030907345e-02 -4.507498543086e-02 +-4.007604502571e-02 -3.505296252697e-02 -3.001517833094e-02 -2.497208221092e-02 +-1.993299713613e-02 -1.490716328841e-02 -9.903722304457e-03 -4.931701771028e-03 +4.773444701199e-14 4.882628890872e-03 9.707589564902e-03 1.446645969794e-02 +1.915100382853e-02 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/machines.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/machines.yaml new file mode 100644 index 0000000000000000000000000000000000000000..e415c3b70aec57ce522c4de607a71e8ab9c0555a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/machines.yaml @@ -0,0 +1,25 @@ +# this is only part of input settings. +# should be used together with systems.yaml and params.yaml +scf_machine: + group_size: 125 + resources: + cpus_per_task: 1 + sub_size: 4 + dispatcher: + context: local + batch: shell # set to shell to run on local machine, you can also use `slurm` + +train_machine: + dispatcher: + context: local + batch: shell # same as above, use shell to run on local machine + remote_profile: null # use lazy local + python: "python" # use python in path + # resources are no longer needed, and the task will use gpu automatically if there is one + +# other settings (these are default, can be omitted) +cleanup: false # whether to delete slurm and err files +strict: true # do not allow undefined machine parameters + +#paras for abacus +use_abacus: true # use abacus in scf calculation \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/machines_bohrium.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/machines_bohrium.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1be8f40ff272af1d0ee81b0b7de96271b14d5e4d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/machines_bohrium.yaml @@ -0,0 +1,66 @@ +# this is only part of input settings. +# should be used together with systems.yaml and params.yaml +scf_machine: + resources: + cpus_per_task: 4 + dispatcher: dpdispatcher + dpdispatcher_resources: + number_node: 1 + cpu_per_node: 8 + group_size: 100 + source_list: [/opt/intel/oneapi/setvars.sh] + sub_size: 1 + dpdispatcher_machine: + context_type: lebesguecontext + batch_type: lebesgue + local_root: ./ + remote_profile: + email: (your-account-email) + password: (your-passward) + program_id: (your-program-id) + input_data: + log_file: log.scf + err_file: err.scf + job_type: indicate + grouped: true + job_name: deepks-scf + disk_size: 100 + scass_type: c8_m8_cpu + platform: ali + image_name: abacus-workshop + on_demand: 0 +train_machine: + dispatcher: dpdispatcher + dpdispatcher_machine: + context_type: lebesguecontext + batch_type: lebesgue + local_root: ./ + remote_profile: + email: (your-account-email) + password: (your-passward) + program_id: (your-program-id) + input_data: + log_file: log.train + err_file: err.train + job_type: indicate + grouped: true + job_name: deepks-train + disk_size: 100 + scass_type: c16_m32_cpu + platform: ali + image_name: abacus-workshop + on_demand: 0 + dpdispatcher_resources: + number_node: 1 + cpu_per_node: 8 + group_size: 1 + source_list: [~/.bashrc] + python: "/usr/bin/python3" # use python in path + # resources are no longer needed, and the task will use gpu automatically if there is one + +# other settings (these are default, can be omitted) +cleanup: false # whether to delete slurm and err files +strict: true # do not allow undefined machine parameters + +#paras for abacus +use_abacus: true # use abacus in scf calculation diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/params.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/params.yaml new file mode 100644 index 0000000000000000000000000000000000000000..fdec6e98479671bc533c6103c3714451b3db8f3e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/params.yaml @@ -0,0 +1,62 @@ +# this is only part of input settings. +# should be used together with systems.yaml and machines.yaml + +# number of iterations to do, can be set to zero for DeePHF training +n_iter: 1 + +# directory setting (these are default choices, can be omitted) +workdir: "." +share_folder: "share" # folder that stores all other settings + +# scf settings, set to false when n_iter = 0 to skip checking +scf_input: false + + +# train settings, set to false when n_iter = 0 to skip checking +train_input: + # model_args is ignored, since this is used as restart + data_args: + batch_size: 16 + group_batch: 1 + extra_label: true + conv_filter: true + conv_name: conv + preprocess_args: + preshift: false # restarting model already shifted. Will not recompute shift value + prescale: false # same as above + prefit_ridge: 1e1 + prefit_trainable: false + train_args: + decay_rate: 0.5 + decay_steps: 1000 + display_epoch: 100 + force_factor: 1 + n_epoch: 5000 + start_lr: 0.0001 + +# init settings, these are for DeePHF task +init_model: false # do not use existing model to restart from + +init_scf: True + +init_train: # parameters for nn training + model_args: + hidden_sizes: [100, 100, 100] # neurons in hidden layers + output_scale: 100 # the output will be divided by 100 before compare with label + use_resnet: true # skip connection + actv_fn: mygelu # same as gelu, support force calculation + data_args: + batch_size: 16 + group_batch: 1 # can collect multiple system in one batch + preprocess_args: + preshift: true # shift the descriptor by its mean + prescale: false # scale the descriptor by its variance (can cause convergence problem) + prefit_ridge: 1e1 # do a ridge regression as prefitting + prefit_trainable: false + train_args: + decay_rate: 0.96 # learning rate decay factor + decay_steps: 500 # decay the learning rate every this steps + display_epoch: 100 + n_epoch: 5000 + start_lr: 0.0003 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/run.sh b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/run.sh new file mode 100644 index 0000000000000000000000000000000000000000..96bcd43fedc7f25918517cd53af402fea13b07fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/run.sh @@ -0,0 +1 @@ +nohup python -u -m deepks iterate machines.yaml params.yaml systems.yaml scf_abacus.yaml >> log.iter 2> err.iter & diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/run_bohrium.sh b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/run_bohrium.sh new file mode 100755 index 0000000000000000000000000000000000000000..206dfcdf7f1dbcfe40a546edd82fef8b369dafb5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/run_bohrium.sh @@ -0,0 +1,2 @@ +nohup python -u -m deepks iterate machines_bohrium.yaml params.yaml systems.yaml scf_abacus_bohrium.yaml >> log.iter 2> err.iter & +echo $! > PID diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/scf_abacus.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/scf_abacus.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ad654e82f3e6fd059bce835c1a1ed4b60050b784 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/scf_abacus.yaml @@ -0,0 +1,38 @@ +scf_abacus: + #INPUT args + ntype: 2 + nbands: 8 + ecutwfc: 50 + scf_thr: 1e-7 + scf_nmax: 50 + dft_functional: "lda" + gamma_only: 1 + cal_force: 1 + #STRU args ( Here are default STRU args, you can set for each group in ../systems/group.xx/stru_abacus.yaml ) + orb_files: ["O_gga_6au_60Ry_2s2p1d.orb", "H_gga_6au_60Ry_2s1p.orb"] + pp_files: ["O_ONCV_PBE-1.0.upf", "H_ONCV_PBE-1.0.upf"] + proj_file: ["jle.orb"] + deepks_descriptor_lmax: 2 + lattice_constant: 1 + lattice_vector: [[28, 0, 0], [0, 28, 0], [0, 0, 28]] + #cmd args + run_cmd : "mpirun" + abacus_path: "/usr/local/bin/abacus" +init_scf_abacus: + orb_files: ["O_gga_6au_60Ry_2s2p1d.orb", "H_gga_6au_60Ry_2s1p.orb"] + pp_files: ["O_ONCV_PBE-1.0.upf", "H_ONCV_PBE-1.0.upf"] + proj_file: ["jle.orb"] + ntype: 2 + nbands: 8 + ecutwfc: 50 + scf_thr: 1e-7 + scf_nmax: 50 + dft_functional: "lda" + gamma_only: 1 + cal_force: 0 + deepks_descriptor_lmax: 2 + lattice_constant: 1 + lattice_vector: [[28, 0, 0], [0, 28, 0], [0, 0, 28]] + #cmd args + run_cmd : "mpirun" + abacus_path: "/usr/local/bin/abacus" \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/scf_abacus_bohrium.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/scf_abacus_bohrium.yaml new file mode 100644 index 0000000000000000000000000000000000000000..aa261193fa3337c791d1e984dce7bec08625b8ff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/scf_abacus_bohrium.yaml @@ -0,0 +1,38 @@ +scf_abacus: + #INPUT args + ntype: 2 + nbands: 8 + ecutwfc: 50 + scf_thr: 1e-7 + scf_nmax: 50 + dft_functional: "lda" + gamma_only: 1 + cal_force: 1 + #STRU args ( Here are default STRU args, you can set for each group in ../systems/group.xx/stru_abacus.yaml ) + orb_files: ["O_gga_6au_60Ry_2s2p1d.orb", "H_gga_6au_60Ry_2s1p.orb"] + pp_files: ["O_ONCV_PBE-1.0.upf", "H_ONCV_PBE-1.0.upf"] + proj_file: ["jle.orb"] + deepks_descriptor_lmax: 2 + lattice_constant: 1 + lattice_vector: [[28, 0, 0], [0, 28, 0], [0, 0, 28]] + #cmd args + run_cmd : "mpirun" + abacus_path: "/root/abacus-develop/build/abacus" +init_scf_abacus: + orb_files: ["O_gga_6au_60Ry_2s2p1d.orb", "H_gga_6au_60Ry_2s1p.orb"] + pp_files: ["O_ONCV_PBE-1.0.upf", "H_ONCV_PBE-1.0.upf"] + proj_file: ["jle.orb"] + ntype: 2 + nbands: 8 + ecutwfc: 50 + scf_thr: 1e-7 + scf_nmax: 50 + dft_functional: "lda" + gamma_only: 1 + cal_force: 0 + deepks_descriptor_lmax: 2 + lattice_constant: 1 + lattice_vector: [[28, 0, 0], [0, 28, 0], [0, 0, 28]] + #cmd args + run_cmd : "mpirun" + abacus_path: "/root/abacus-develop/build/abacus" diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/systems.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/systems.yaml new file mode 100644 index 0000000000000000000000000000000000000000..068710dc231bb801032353f77f4d3ab83db8c10e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus/iter/systems.yaml @@ -0,0 +1,9 @@ +# this is only part of input settings. +# should be used together with params.yaml and machines.yaml + +# training and testing systems +systems_train: # can also be files that containing system paths + - ../systems/group.00 # support glob + +systems_test: # if empty, use the last system of training set + - ../systems/group.03 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.00/atom.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.00/atom.npy new file mode 100644 index 0000000000000000000000000000000000000000..6a230754a34b936523b3d5b9f232fa34d7fca78e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.00/atom.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.00/energy.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.00/energy.npy new file mode 100644 index 0000000000000000000000000000000000000000..e27c7758cde78ffa2953c23c6f99c50af32e0db6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.00/energy.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.00/force.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.00/force.npy new file mode 100644 index 0000000000000000000000000000000000000000..efa55d25dc2a3909a21b909ab18ae8bc8ee70919 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.00/force.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.01/atom.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.01/atom.npy new file mode 100644 index 0000000000000000000000000000000000000000..904d9b34c16e784419ee1ed7bb41b9bfea5545ae Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.01/atom.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.01/energy.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.01/energy.npy new file mode 100644 index 0000000000000000000000000000000000000000..abd20527ba350a8cc10f75a904398aef1815c0d5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.01/energy.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.01/force.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.01/force.npy new file mode 100644 index 0000000000000000000000000000000000000000..e664ec83e4c36274f0017821ee7e154d89424aa8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.01/force.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.02/atom.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.02/atom.npy new file mode 100644 index 0000000000000000000000000000000000000000..498bf3bc5bc9df01fe86d4509dfce2ab745973fb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.02/atom.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.02/energy.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.02/energy.npy new file mode 100644 index 0000000000000000000000000000000000000000..087e0341b0b5ee60dfe9f809507f354b7089cc0c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.02/energy.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.02/force.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.02/force.npy new file mode 100644 index 0000000000000000000000000000000000000000..6dc34004157af3b98b95ad421638639e8a7da85d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.02/force.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.03/atom.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.03/atom.npy new file mode 100644 index 0000000000000000000000000000000000000000..f92999c9eb81456a1ba83faca9a193609aa1b984 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.03/atom.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.03/energy.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.03/energy.npy new file mode 100644 index 0000000000000000000000000000000000000000..05263d2801917c0a8e79fc98469f3c684aaa51cd Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.03/energy.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.03/force.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.03/force.npy new file mode 100644 index 0000000000000000000000000000000000000000..5d6e764aad09f134ce52be39e593194ccca2568f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus/systems/group.03/force.npy differ