[QE-users] GC-SCF_calculation of adsoprtion energy using GC_SCF method
Saroj Kumari, Dr
saroj.kumari at mcgill.ca
Fri Oct 3 19:52:15 CEST 2025
Hi All,
I am trying to calculate adsoprtion energy of OH over Cu(111) using GC-SCF method as per the link:- https://gitlab.com/QEF/qe/-/blob/master/PW/examples/ESM_example/run_example_GCSCF
As I am a beginner to GC-SCF DFT using Quantum Espresso, kindly help me in knowing the procedure of calculating the adsorption energy., what is formula used to calculate it.
Below attached my input file :
&CONTROL
calculation='scf'
title='Optimization of bulk of Cu(4x4)'
restart_mode='from_scratch',
prefix='gc_dft_cu_111_scf'
etot_conv_thr=1.0D-06
forc_conv_thr=1.0D-03
nstep=1000
pseudo_dir = '/home/saroj3/scratch/cu_111_acet',
outdir = '/home/saroj3/scratch/cu_111_acet/gc_dft_oh_cu_111/gc_dft_cu_111_scf',
tprnfor = .true.,
/
&SYSTEM
ibrav=14
celldm(1)=19.4774
celldm(2)=1
celldm(3)=2.75696
celldm(4)=0
celldm(5)=0
celldm(6)=0.5
nat=64,
ntyp=1,
nspin=2,
vdw_corr='DFT-D',
starting_magnetization(1)=0.5,
ecutwfc=50,
ecutrho=500,
occupations='smearing',
smearing='mp',
degauss=0.02
nosym=.TRUE.,
lda_plus_u=.false.,
assume_isolated='esm', esm_bc='bc2'
lgcscf = .TRUE.
gcscf_mu = -4.4
gcscf_conv_thr = 1.d-2
/
&ELECTRONS
diagonalization='david'
conv_thr=1.0d-6
mixing_mode='local-TF'
mixing_beta=0.7
electron_maxstep=1000,
/
&IONS
ion_dynamics='bfgs'
/
ATOMIC_SPECIES
Cu 63.546 Cu.pbe-dn-kjpaw_psl.0.2.UPF
ATOMIC_POSITIONS (angstrom)
Cu 0.0000000000 0.0000000000 2.1039000000 0 0 0
Cu 2.5767800000 0.0000000000 2.1039000000 0 0 0
Cu 5.1535500000 0.0000000000 2.1039000000 0 0 0
Cu 7.7303300000 0.0000000000 2.1039000000 0 0 0
Cu 1.2883900000 2.2315500000 2.1039000000 0 0 0
Cu 3.8651700000 2.2315500000 2.1039000000 0 0 0
Cu 6.4419500000 2.2315500000 2.1039000000 0 0 0
Cu 9.0187200000 2.2315500000 2.1039000000 0 0 0
Cu 2.5767800000 4.4631100000 2.1039000000 0 0 0
Cu 5.1535600000 4.4631100000 2.1039000000 0 0 0
Cu 7.7303400000 4.4631100000 2.1039000000 0 0 0
Cu 10.3071100000 4.4631100000 2.1039000000 0 0 0
Cu 3.8651700000 6.6946600000 2.1039000000 0 0 0
Cu 6.4419500000 6.6946600000 2.1039000000 0 0 0
Cu 9.0187200000 6.6946600000 2.1039000000 0 0 0
Cu 11.5955000000 6.6946600000 2.1039000000 0 0 0
Cu 1.2883400000 0.7438200000 4.2078000000 0 0 0
Cu 3.8651200000 0.7438200000 4.2078000000 0 0 0
Cu 6.4418900000 0.7438200000 4.2078000000 0 0 0
Cu 9.0186700000 0.7438200000 4.2078000000 0 0 0
Cu 2.5767300000 2.9753800000 4.2078000000 0 0 0
Cu 5.1535100000 2.9753800000 4.2078000000 0 0 0
Cu 7.7302800000 2.9753800000 4.2078000000 0 0 0
Cu 10.3070600000 2.9753800000 4.2078000000 0 0 0
Cu 3.8651200000 5.2069300000 4.2078000000 0 0 0
Cu 6.4419000000 5.2069300000 4.2078000000 0 0 0
Cu 9.0186700000 5.2069300000 4.2078000000 0 0 0
Cu 11.5954500000 5.2069300000 4.2078000000 0 0 0
Cu 5.1535100000 7.4384900000 4.2078000000 0 0 0
Cu 7.7302900000 7.4384900000 4.2078000000 0 0 0
Cu 10.3070600000 7.4384900000 4.2078000000 0 0 0
Cu 12.8838400000 7.4384900000 4.2078000000 0 0 0
Cu 10.3054809557 1.4884138076 6.2366103369
Cu 2.5754608211 1.4888633271 6.2366647976
Cu 5.1523330640 1.4888548480 6.2365555119
Cu 7.7289978720 1.4883941504 6.2366230851
Cu 11.5941907913 3.7202323416 6.2362172708
Cu 3.8639148278 3.7204193199 6.2368356979
Cu 6.4402638906 3.7198969875 6.2363993776
Cu 9.0170880805 3.7213000663 6.2366440344
Cu 12.8827843912 5.9517581935 6.2362016854
Cu 5.1516881418 5.9515206673 6.2364437378
Cu 7.7292790683 5.9518983520 6.2360975291
Cu 10.3053763756 5.9520624367 6.2370569907
Cu 14.1709160346 8.1830767046 6.2364933512
Cu 6.4412579689 8.1827129098 6.2364756331
Cu 9.0173595498 8.1828108455 6.2361940415
Cu 11.5930669210 8.1827530538 6.2368039560
Cu 10.3052332856 0.0012485255 8.2885146185
Cu 2.5749867059 0.0013809359 8.2879532443
Cu 5.1513109127 0.0013437366 8.2878944074
Cu 7.7277679778 0.0013458659 8.2885540421
Cu 11.5933252102 2.2327754985 8.2888289720
Cu 3.8632113504 2.2327620564 8.2881936345
Cu 6.4398492158 2.2328001619 8.2889274190
Cu 9.0162878727 2.2332534469 8.2884698603
Cu 12.8814921082 4.4649105840 8.2883393039
Cu 5.1516088814 4.4646635549 8.2885195826
Cu 7.7278892087 4.4646743673 8.2876200818
Cu 10.3051308532 4.4648191406 8.2875640879
Cu 14.1702399736 6.6958976303 8.2887636689
Cu 6.4399789215 6.6957019165 8.2878080215
Cu 9.0159991774 6.6966752539 8.2883993164
Cu 11.5933091198 6.6957798706 8.2876979446
K_POINTS (AUTOMATIC)
3 3 1 0 0 0
Output file :
the Fermi energy is -4.4391 ev
! total energy = -13638.31732234 Ry
total all-electron energy = -211838.622488 Ry
estimated scf accuracy < 0.00000073 Ry
! total charge of GC-SCF = -0.05882073 e
smearing contrib. (-TS) = 0.00372527 Ry
internal energy E=F+TS = -13638.32104760 Ry
The total energy is F=E-TS. E is the sum of the following terms:
one-electron contribution = -346263.68516746 Ry
hartree contribution = 172813.58540239 Ry
xc contribution = -2353.75959543 Ry
ewald contribution = 167474.63352712 Ry
Dispersion Correction = -1.37689157 Ry
one-center paw contrib. = -5307.73751786 Ry
pot.stat. contrib. (-muN) = 0.01919520 Ry
total magnetization = -0.00 Bohr mag/cell
absolute magnetization = 0.00 Bohr mag/cell
convergence has been achieved in 22 iterations
negative rho (up, down): 7.518E-03 7.517E-03
Forces acting on atoms (cartesian axes, Ry/au):
atom 1 type 1 force = 0.00014342 -0.00009992 0.00840612
atom 2 type 1 force = -0.00014372 -0.00015093 0.00842556
atom 3 type 1 force = -0.00015506 0.00000209 0.00828089
atom 4 type 1 force = 0.00000675 0.00003835 0.00832202
atom 5 type 1 force = -0.00010847 -0.00005012 0.00850644
atom 6 type 1 force = -0.00002170 -0.00003893 0.00839349
atom 7 type 1 force = -0.00004116 0.00017441 0.00832134
atom 8 type 1 force = 0.00001303 0.00015433 0.00840733
atom 9 type 1 force = -0.00009631 0.00004252 0.00843721
atom 10 type 1 force = 0.00023201 0.00020694 0.00841253
atom 11 type 1 force = -0.00012013 0.00021758 0.00842564
atom 12 type 1 force = -0.00017361 0.00006927 0.00837141
atom 13 type 1 force = 0.00026535 0.00001130 0.00839467
atom 14 type 1 force = 0.00001337 -0.00006545 0.00842554
atom 15 type 1 force = -0.00025396 -0.00006849 0.00837088
atom 16 type 1 force = -0.00017878 -0.00005618 0.00834987
atom 17 type 1 force = -0.00008101 -0.00000647 -0.00861555
atom 18 type 1 force = -0.00028878 0.00005644 -0.00880369
atom 19 type 1 force = 0.00000992 0.00015753 -0.00878367
atom 20 type 1 force = 0.00014552 0.00007517 -0.00866451
atom 21 type 1 force = -0.00018647 0.00001231 -0.00860024
atom 22 type 1 force = 0.00002230 0.00028309 -0.00869603
atom 23 type 1 force = -0.00002371 0.00033602 -0.00854939
atom 24 type 1 force = -0.00005049 0.00010314 -0.00860427
atom 25 type 1 force = 0.00019185 0.00008622 -0.00869784
atom 26 type 1 force = 0.00005294 0.00024658 -0.00854455
atom 27 type 1 force = -0.00027288 0.00004437 -0.00864677
atom 28 type 1 force = -0.00019597 -0.00007584 -0.00866439
atom 29 type 1 force = 0.00024582 -0.00013414 -0.00869185
atom 30 type 1 force = -0.00033763 -0.00025512 -0.00879414
atom 31 type 1 force = -0.00022003 -0.00020459 -0.00893200
atom 32 type 1 force = 0.00006479 -0.00008271 -0.00870877
atom 33 type 1 force = 0.00017815 0.00011955 0.00024281
atom 34 type 1 force = -0.00027764 -0.00002804 0.00016984
atom 35 type 1 force = -0.00005800 0.00015870 0.00016924
atom 36 type 1 force = 0.00024578 0.00029579 0.00020272
atom 37 type 1 force = -0.00010406 -0.00020047 0.00019297
atom 38 type 1 force = 0.00002600 0.00000651 0.00008586
atom 39 type 1 force = 0.00029334 0.00046431 0.00013556
atom 40 type 1 force = -0.00007213 -0.00015705 0.00011242
atom 41 type 1 force = 0.00009226 -0.00012464 0.00021559
atom 42 type 1 force = 0.00054325 -0.00000444 0.00012530
atom 43 type 1 force = -0.00036066 -0.00024217 0.00019041
atom 44 type 1 force = -0.00017235 -0.00040780 -0.00011283
atom 45 type 1 force = 0.00029378 -0.00008761 0.00030599
atom 46 type 1 force = -0.00011994 -0.00009477 0.00004061
atom 47 type 1 force = -0.00041570 -0.00007685 0.00019748
atom 48 type 1 force = 0.00038071 0.00002762 0.00004643
atom 49 type 1 force = 0.00007691 -0.00003041 -0.00129787
atom 50 type 1 force = -0.00016124 -0.00001591 -0.00119907
atom 51 type 1 force = -0.00004253 -0.00001063 -0.00100993
atom 52 type 1 force = 0.00035061 -0.00003792 -0.00117775
atom 53 type 1 force = -0.00000356 -0.00004094 -0.00147452
atom 54 type 1 force = -0.00011019 0.00004064 -0.00116365
atom 55 type 1 force = 0.00017040 0.00015990 -0.00132902
atom 56 type 1 force = 0.00021823 0.00000292 -0.00142644
atom 57 type 1 force = 0.00011733 -0.00016442 -0.00120496
atom 58 type 1 force = 0.00016228 0.00005152 -0.00143901
atom 59 type 1 force = 0.00011421 0.00007590 -0.00133791
atom 60 type 1 force = -0.00011538 -0.00018004 -0.00117105
atom 61 type 1 force = 0.00019287 0.00000451 -0.00134817
atom 62 type 1 force = 0.00006613 -0.00007634 -0.00143254
atom 63 type 1 force = -0.00006675 -0.00034756 -0.00127342
atom 64 type 1 force = 0.00010067 -0.00010864 -0.00092342
Total force = 0.005367 Total SCF correction = 0.003287
SCF correction compared to forces is large: reduce conv_thr to get better values
Writing all to output data dir /home/saroj3/scratch/cu_111_acet/gc_dft_oh_cu_111/0V_gc_dft_cu_111_scf/0V_gc_dft_cu_111_scf.save/ :
XML data file, charge density, pseudopotentials, collected wavefunctions
init_run : 11.63s CPU 11.86s WALL ( 1 calls)
electrons : 4721.43s CPU 4821.87s WALL ( 1 calls)
forces : 5.14s CPU 5.29s WALL ( 1 calls)
force_london : 0.01s CPU 0.01s WALL ( 1 calls)
Called by init_run:
wfcinit : 7.69s CPU 7.86s WALL ( 1 calls)
potinit : 0.87s CPU 0.89s WALL ( 1 calls)
hinit0 : 2.20s CPU 2.23s WALL ( 1 calls)
Called by electrons:
c_bands : 4656.64s CPU 4754.97s WALL ( 22 calls)
sum_band : 48.44s CPU 49.79s WALL ( 22 calls)
v_of_rho : 4.45s CPU 4.61s WALL ( 23 calls)
newd : 2.71s CPU 2.92s WALL ( 23 calls)
PAW_pot : 4.22s CPU 4.35s WALL ( 23 calls)
mix_rho : 4.31s CPU 4.41s WALL ( 22 calls)
energy_londo : 0.01s CPU 0.01s WALL ( 1 calls)
Called by c_bands:
init_us_2 : 0.72s CPU 0.75s WALL ( 460 calls)
cegterg : 4649.72s CPU 4747.71s WALL ( 1055 calls)
Called by *egterg:
cdiaghg : 1802.25s CPU 1837.96s WALL ( 19288 calls)
h_psi : 1523.16s CPU 1557.74s WALL ( 19361 calls)
s_psi : 166.83s CPU 170.66s WALL ( 19361 calls)
g_psi : 1.85s CPU 1.88s WALL ( 18296 calls)
Called by h_psi:
h_psi:calbec : 311.23s CPU 319.44s WALL ( 19361 calls)
vloc_psi : 1041.56s CPU 1063.87s WALL ( 19361 calls)
add_vuspsi : 169.05s CPU 173.08s WALL ( 19361 calls)
General routines
calbec : 328.14s CPU 336.83s WALL ( 19621 calls)
fft : 7.27s CPU 7.47s WALL ( 588 calls)
ffts : 1.75s CPU 1.80s WALL ( 2673 calls)
fftw : 1022.43s CPU 1044.36s WALL ( 3460208 calls)
interpolate : 0.96s CPU 0.99s WALL ( 46 calls)
Parallel routines
PWSCF : 1h19m CPU 1h21m WALL
This run was terminated on: 16:56:50 30Sep2025
=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
Warm regards,
Saroj
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