[QE-users] More Questions About SCF "Atom Charges"
Victor Bermudez
bermudez at alum.mit.edu
Thu Feb 20 16:03:34 CET 2020
Greetings All,
This question concerns the "atom charge" values that are printed upon convergence of an SCF cycle. I understand from previous exchanges that these are highly approximate results that are obtained by integrating charge densities over a sphere of radius "r_m" (given at the start of the calculation) and are indicative only of trends in the "true" atom charges (as would be obtained in a Bader analysis, for example).
However, I have been doing Born-Oppenheimer molecular dynamics (MD) calculations for NO2 interacting with a monolayer of MoS2. The free, isolated NO2 molecule gives a total of about 7.8 for the sum of the N and O "atom charges" upon convergence of the SCF in a static (i.e., not MD) calculation. For a neutral molecule, this sum should be 17 (5 valence electrons on N and 6 on O), but as noted above the "atom charges" are crude values. At the start of an MD run, the sum of NO2 "atom charges" is always close to 7.8 but then decreases and goes through cycles as the run progresses. At some stages of the run the sum of NO2 charges can decrease to well below 1.0 before turning around and increasing (but never getting back to anything like 7.8). At all points in the trajectory the NO2 is interacting only weakly with the MoS2 and never gets any closer than about 4.0 Angstroms. On the other hand, the Mo and S "atom charges" remain roughly constant.
My question is this: How can the NO2 "charge" decrease from 7.8 to <1.0, and what sense (if any) can be made of these results ? This strange behavior seems to have something to do with the use of MD since, in a static calculation, the NO2 charge is always close to 7.8 even when starting from a configuration that gave a much smaller charge during MD.
I'm inserting here a typical MD input file and 2 typical sections of output, one from early in the run and one from later. I've followed the MD trajectory, step-by-step, using Xcrysden and tried to correlate what I'm seeing with the "atom charge" behavior, but I can't identify any consistent connection. Just as a comment, the MD is using a time step of 1.45 fsec, which should be OK because the period of the highest-energy vibrational mode (the NO2 asym. stretch) is about 20 fsec. I've checked, and there is essentially no drift in the sum of kinetic and potential energies.
I've been struggling to work this out on my own for quite some time now, so any help would be greatly appreciated.
Vic Bermudez
US Naval Research Laboratory (retired)
********* START MD Input ************************
&CONTROL
calculation='md',
restart_mode='from_scratch',
title='MoS2 slab-(2x2) cell (TS relaxed) + 1 NO2 - restart with #257444 converged structure',
pseudo_dir="/p/home/bermudvm/Pseudo",
outdir="/p/work1/workspace/bermudvm/2811142.THUNDER/tmp",
! outdir='/p/work1/workspace/bermudvm/2669600.THUNDER/tmp/',
nstep=100000,
dt=30.0D0, ! dt in atomic units - 1 au = 0.0484 fsec (Rydberg a.u.)
verbosity='default',
etot_conv_thr=1.0D-4,
forc_conv_thr=1.0D-3,
tefield=.TRUE.,
dipfield=.TRUE.,
max_seconds=431500.0,
wf_collect=.true.
/
&SYSTEM
ibrav=4,
A=6.3397233, B=6.3404242, C=30.0, cosAB=-0.499864, cosAC=0.0, cosBC=0.0,
nat=15,
ntyp=4,
ecutwfc=100.0,
ecutrho=400.0,
occupations='smearing',
smearing='gaussian',
degauss=0.001,
nspin=2,
starting_magnetization(1)=0.0,
starting_magnetization(2)=0.0,
starting_magnetization(3)=0.2,
starting_magnetization(4)=0.0,
vdw_corr='TS',
report=100,
edir=3,
eamp=0.0,
emaxpos=0.5,
eopreg=0.1
/
&ELECTRONS
electron_maxstep=200,
conv_thr=1.0D-7,
mixing_mode='local-TF',
mixing_beta=0.7
/
&IONS
ion_dynamics='verlet',
ion_temperature='rescaling',
tempw=200.0D0,
tolp=5.0D0
/
ATOMIC_SPECIES
Mo 95.94 Mo_ONCV_PBE-1.0.upf
S 32.06 S_ONCV_PBE-1.1.upf
N 14.0067 N_ONCV_PBE-1.0.upf
O 15.9994 O_ONCV_PBE-1.0.upf
ATOMIC_POSITIONS crystal
S -0.013004927 -0.243981414 0.053754468
S -0.013575765 0.255146374 0.053470059
S -0.513243717 -0.243986201 0.053739861
S -0.513199512 0.255546936 0.053736255
Mo -0.346747611 0.089055052 0.001394036
Mo -0.346554368 -0.410928077 0.001535756
Mo 0.153652403 0.089087479 0.001415542
Mo 0.153389860 -0.410958008 0.001505248
S -0.013344102 -0.244420134 -0.050785020
S -0.013163404 0.255849062 -0.050859957
S -0.513325356 -0.244474152 -0.050790473
S -0.513056598 0.256093904 -0.050850410
N 0.093057852 0.418910530 0.170162509
O -0.075905400 0.433824119 0.155238223
O -0.739300868 -0.590384479 0.153081270
K_POINTS automatic
6 6 1 0 0 0
********** END MD Input ****************
********** After MD Step #13 *************
Magnetic moment per site:
atom: 1 charge: 4.1248 magn: 0.0028 constr: 0.0000
atom: 2 charge: 4.1206 magn: 0.0141 constr: 0.0000
atom: 3 charge: 4.1232 magn: 0.0038 constr: 0.0000
atom: 4 charge: 4.1428 magn: 0.0039 constr: 0.0000
atom: 5 charge: 10.6980 magn: 0.0075 constr: 0.0000
atom: 6 charge: 10.7161 magn: 0.0010 constr: 0.0000
atom: 7 charge: 10.6863 magn: 0.0076 constr: 0.0000
atom: 8 charge: 10.7068 magn: -0.0001 constr: 0.0000
atom: 9 charge: 4.1440 magn: -0.0001 constr: 0.0000
atom: 10 charge: 4.1083 magn: 0.0006 constr: 0.0000
atom: 11 charge: 4.1241 magn: -0.0000 constr: 0.0000
atom: 12 charge: 4.1270 magn: -0.0001 constr: 0.0000
atom: 13 charge: 1.9079 magn: 0.1609 constr: 0.0000
atom: 14 charge: 2.8714 magn: 0.1639 constr: 0.0000
atom: 15 charge: 2.9303 magn: 0.1636 constr: 0.0000
*********** After MD Step #973 **********
Magnetic moment per site:
atom: 1 charge: 4.1054 magn: 0.0003 constr: 0.0000
atom: 2 charge: 3.9798 magn: 0.0006 constr: 0.0000
atom: 3 charge: 4.0230 magn: 0.0004 constr: 0.0000
atom: 4 charge: 3.9807 magn: 0.0002 constr: 0.0000
atom: 5 charge: 10.5898 magn: 0.0004 constr: 0.0000
atom: 6 charge: 10.7102 magn: 0.0002 constr: 0.0000
atom: 7 charge: 10.6883 magn: 0.0003 constr: 0.0000
atom: 8 charge: 10.7106 magn: 0.0001 constr: 0.0000
atom: 9 charge: 4.1648 magn: -0.0000 constr: 0.0000
atom: 10 charge: 4.1637 magn: 0.0000 constr: 0.0000
atom: 11 charge: 4.1616 magn: -0.0000 constr: 0.0000
atom: 12 charge: 4.1410 magn: -0.0000 constr: 0.0000
atom: 13 charge: 0.1334 magn: 0.0032 constr: 0.0000
atom: 14 charge: 0.0284 magn: 0.0005 constr: 0.0000
atom: 15 charge: 0.0024 magn: 0.0010 constr: 0.0000
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