[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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