Bader analysis of quartz slab

[Leonardo2]

Dear Colleagues,

I have taken the structure of a simple quartz slab model from a publication, re-optimized it with VASP, and attempted to perform a Bader analysis to obtain the charges of all involved atoms. While the resulting ACF.dat file appears to be accurate for the oxygen atoms, the charges of all silicon atoms showed strictly zero charges.

Considering the advice for VASP users, I then added "LAECHG=.TRUE." to my INCAR file and, using the command chgsum.pl AECCAR0 AECCAR2, I found a charge of approximately 0.8 for all silicon atoms and about 7.6 for all oxygen atoms. To me, this result seems unusual. Typically, for silicon in a tetrahedral coordination, the charge should be closer to 4, reflecting its four valence electrons.

If you have an idea and would like to help, please find below my POSCAR and INCAR files.

With many thanks for any hint in advance, I send you my very best wishes,

Leo

O Si
1.000000000000000
10.0988837574330006 0.0393839052360000 -0.0049363979610000
-10.0306688294989996 17.3360464343490008 -0.0006390735130000
-0.0488672307220000 -0.0318660707160000 97.2222421060200048
O Si
144 72
Selective dynamics
Direct
0.4616669413140002 0.0886269987690014 0.1533611471740031 T T T
0.4619254622650004 0.5884086904960029 0.1533258834779971 T T T
0.0601304843119976 0.2390905532409988 0.1550130831779981 T T T
0.0607960513640009 0.7389643852240013 0.1548322063930030 T T T
0.2614740024099973 0.1372306931699967 0.1559824965819985 T T T
0.2612597516969970 0.6368968816999967 0.1560113897149975 T T T
0.4161948010370011 0.1630927416940011 0.1322409453259965 T T T
0.4159624182670001 0.6631809725150006 0.1322793682530019 T T T
0.2333042256059983 0.1973934529749997 0.1164968179819965 T T T
0.2337319991380014 0.6974431107139978 0.1165084391460027 T T T
0.3810892196240019 0.1578641025880003 0.0782405184300003 T T T
0.3810894546540027 0.6578643376169993 0.0782405184300003 T T T
0.4357620732560008 0.0209378870899997 0.0967482324499969 T T T
0.4356325105550027 0.5207858396749998 0.0967733767590033 T T T
0.1389278156930018 0.2225231000469989 0.0919240052590027 T T T
0.1387676766999988 0.7225260323579974 0.0919598823140007 T T T
0.1158552691929984 0.0744735088220025 0.1320369155169985 T T T
0.1155893298330000 0.5745647112649976 0.1320536212880015 T T T
0.2918893336980020 0.0873869440790003 0.1092556124020021 T T T
0.2914351215910003 0.5871338224839988 0.1092856081399987 T T T
0.0827253459969981 0.0580388000989984 0.0732063465150006 T T T
0.0827255810269989 0.5580390351279974 0.0732063465150006 T T T
0.2310449428030026 0.2001259523689995 0.0609300523880023 T T T
0.2310451778330034 0.7001261873990003 0.0609300523880023 T T T
0.2867798291740016 0.0890045391269965 0.0532070067920003 T T T
0.2867800642030005 0.5890047741569973 0.0532070067920003 T T T
0.1056527400300027 0.2090752924409998 0.0376069132000012 T T T
0.1056529750590016 0.7090755274710006 0.0376069132000012 T T T
0.4104652104750031 0.0245482554569989 0.0379321892970026 T T T
0.4104654455040020 0.5245484904869997 0.0379321892970026 T T T
0.0709927441539975 0.1135451561220009 0.0165823986200024 T T T
0.0709929791830035 0.6135453911520017 0.0165823986200024 T T T
0.2631178471189983 0.0163745131070030 0.0142696896810008 T T T
0.2631174945739971 0.5163741605620018 0.0142696896810008 T T T
0.4546597410819970 0.2098826191610002 0.0152408917319988 T T T
0.4546599761119978 0.7098828541899991 0.0152408917319988 T T T
0.9622225777579985 0.0892021629490003 0.1534269220230016 T T T
0.9619616779230000 0.5890656127300034 0.1534114578440011 T T T
0.5607774748210019 0.2387422145709976 0.1549423101900018 T T T
0.5601945401500004 0.7386369778630026 0.1550144786899992 T T T
0.7611475544330020 0.1373784324820022 0.1559374886560008 T T T
0.7616293725990033 0.6383129618250010 0.1555231516650011 T T T
0.9164852090200029 0.1631845070980020 0.1322453194459996 T T T
0.9173691291570023 0.6625243062679971 0.1320390128209965 T T T
0.7338305808579975 0.1974408523269986 0.1164966406020014 T T T
0.7345759452449983 0.6977581899550032 0.1164950239969968 T T T
0.8810892196240019 0.1578641025880003 0.0782405184300003 T T T
0.8810894546540027 0.6578643376169993 0.0782405184300003 T T T
0.9355695125340020 0.0207234163449996 0.0967701202860027 T T T
0.9356748111529996 0.5208282192520031 0.0967454689609966 T T T
0.6388541612870000 0.2225598012580008 0.0919601820629978 T T T
0.6388074827600008 0.7224956932779989 0.0919487418649965 T T T
0.6161053752109993 0.0744568264950018 0.1320103481809980 T T T
0.6153305089770029 0.5742180251950018 0.1318093006520016 T T T
0.7917931277640022 0.0871887469379971 0.1092621734269983 T T T
0.7913648044159984 0.5872128579609992 0.1091126880009980 T T T
0.5827253459969981 0.0580388000989984 0.0732063465150006 T T T
0.5827255810269989 0.5580390351279974 0.0732063465150006 T T T
0.7310449428030026 0.2001259523689995 0.0609300523880023 T T T
0.7310451778330034 0.7001261873990003 0.0609300523880023 T T T
0.7867798291740016 0.0890045391269965 0.0532070067920003 T T T
0.7867800642030005 0.5890047741569973 0.0532070067920003 T T T
0.6056527400300027 0.2090752924409998 0.0376069132000012 T T T
0.6056529750590016 0.7090755274710006 0.0376069132000012 T T T
0.9104652104750031 0.0245482554569989 0.0379321892970026 T T T
0.9104654455040020 0.5245484904869997 0.0379321892970026 T T T
0.5709927441539975 0.1135451561220009 0.0165823986200024 T T T
0.5709929791830035 0.6135453911520017 0.0165823986200024 T T T
0.7631178471189983 0.0163745131070030 0.0142696896810008 T T T
0.7631174945739971 0.5163741605620018 0.0142696896810008 T T T
0.9546597410819970 0.2098826191610002 0.0152408917319988 T T T
0.9546599761119978 0.7098828541899991 0.0152408917319988 T T T
0.4603918690919997 0.3378224485060031 0.1530921303549988 T T T
0.4620814099110007 0.8388101315879979 0.1533573912070025 T T T
0.0595799748840022 0.4889142774379991 0.1550540736869976 T T T
0.0600727970340031 0.9889663932310029 0.1549982818009994 T T T
0.2616085494410001 0.3875959613510034 0.1559403086830002 T T T
0.2615226193919966 0.8873853695779985 0.1559008550799987 T T T
0.4157506081750029 0.4132154835579982 0.1322158845259978 T T T
0.4162971475710009 0.9131719274399970 0.1322218048689976 T T T
0.2328049664610035 0.4472181471319985 0.1164759510259969 T T T
0.2337878213180034 0.9475854611799974 0.1164829240030016 T T T
0.3810896309259988 0.4078645138890025 0.0782405184300003 T T T
0.3810892783809976 0.9078641613450031 0.0782405184300003 T T T
0.4355517777749967 0.2707769899890025 0.0967581893299965 T T T
0.4356344304099977 0.7707921034970013 0.0967612549889978 T T T
0.1390791278859993 0.4726033689229965 0.0919098631780031 T T T
0.1389869558620020 0.9726328995250029 0.0919384525040030 T T T
0.1154648674979981 0.3244210049000031 0.1320357671329973 T T T
0.1154665924330018 0.8246079861520030 0.1319519575200019 T T T
0.2913751729030025 0.3371584390639981 0.1092533917620031 T T T
0.2920930468890006 0.8373056758649966 0.1092463004330000 T T T
0.0827251697250020 0.3080386238260004 0.0732063465150006 T T T
0.0827254047550028 0.8080388588560012 0.0732063465150006 T T T
0.2310453541049995 0.4501263636710036 0.0609300523880023 T T T
0.2310450015599983 0.9501260111269971 0.0609300523880023 T T T
0.2867796529019984 0.3390043628550004 0.0532070067920003 T T T
0.2867798879309973 0.8390045978839993 0.0532070067920003 T T T
0.1056525637569976 0.4590751161689965 0.0376069132000012 T T T
0.1056527987869984 0.9590753511989973 0.0376069132000012 T T T
0.4104656217770000 0.2745486667590029 0.0379321892970026 T T T
0.4104652692319988 0.7745483142149965 0.0379321892970026 T T T
0.0709931554560015 0.3635455674239978 0.0165823986200024 T T T
0.0709928029110003 0.8635452148789966 0.0165823986200024 T T T
0.2631176708460004 0.2663743368349998 0.0142696896810008 T T T
0.2631173183020010 0.7663739842899986 0.0142696896810008 T T T
0.4546595648100009 0.4598824428880022 0.0152408917319988 T T T
0.4546597998389998 0.9598826779180030 0.0152408917319988 T T T
0.9620765260429991 0.3391104162000005 0.1534357158479978 T T T
0.9624222922530024 0.8390691303839972 0.1534019938659981 T T T
0.5619747658880030 0.4888266904340028 0.1547149412689990 T T T
0.5605661040870018 0.9889014956569966 0.1549672237970015 T T T
0.7606786115339972 0.3872781471810001 0.1559013384390013 T T T
0.7611717017979984 0.8870624345779987 0.1559458384580026 T T T
0.9168956100790027 0.4133608381140021 0.1322546934190001 T T T
0.9164166837740026 0.9131712869349968 0.1322423473050023 T T T
0.7341071969269990 0.4474696375479965 0.1164910527609990 T T T
0.7335896987509969 0.9473825823390030 0.1165136635000010 T T T
0.8810896309259988 0.4078645138890025 0.0782405184300003 T T T
0.8810892783809976 0.9078641613450031 0.0782405184300003 T T T
0.9357482916179976 0.2707406493610023 0.0967712890520005 T T T
0.9358442758749987 0.7710741482289976 0.0967252752050030 T T T
0.6386967729049999 0.4723056927079980 0.0919159014650006 T T T
0.6386984183929982 0.9724293971650013 0.0919526741249967 T T T
0.6165896054089970 0.3240820708750007 0.1319503511370002 T T T
0.6160690162219993 0.8241093700270028 0.1320013727319989 T T T
0.7929858751910004 0.3375393494349979 0.1092384376580000 T T T
0.7920345626409997 0.8374293712699981 0.1092204849090024 T T T
0.5827251697250020 0.3080386238260004 0.0732063465150006 T T T
0.5827254047550028 0.8080388588560012 0.0732063465150006 T T T
0.7310453541049995 0.4501263636710036 0.0609300523880023 T T T
0.7310450015599983 0.9501260111269971 0.0609300523880023 T T T
0.7867796529019984 0.3390043628550004 0.0532070067920003 T T T
0.7867798879309973 0.8390045978839993 0.0532070067920003 T T T
0.6056535814649990 0.4590751161689965 0.0376069132000012 T T T
0.6056538164949998 0.9590753511989973 0.0376069132000012 T T T
0.9104656217770000 0.2745486667590029 0.0379321892970026 T T T
0.9104652692319988 0.7745483142149965 0.0379321892970026 T T T
0.5709931554560015 0.3635455674239978 0.0165823986200024 T T T
0.5709928029110003 0.8635452148789966 0.0165823986200024 T T T
0.7631176708460004 0.2663743368349998 0.0142696896810008 T T T
0.7631173183020010 0.7663739842899986 0.0142696896810008 T T T
0.9546595648100009 0.4598824428880022 0.0152408917319988 T T T
0.9546597998389998 0.9598826779180030 0.0152408917319988 T T T
0.2453125736969994 0.1258865610770030 0.0664408298610013 T T T
0.2453128087259984 0.6258867961069967 0.0664408298610013 T T T
0.2589232057369983 0.0052106065099977 0.0475811901429992 T T T
0.2589228531919971 0.5052102539659984 0.0475811901429992 T T T
0.4252616527990014 0.1567943472290025 0.1490890883530014 T T T
0.4251124362389973 0.6565268922599969 0.1491218738489977 T T T
0.0997095530710013 0.0731843235610015 0.1489757085889991 T T T
0.0994331590500011 0.5730174096609986 0.1489884240629991 T T T
0.2642447946180013 0.1299239970979968 0.1223850045389980 T T T
0.2641151955370020 0.6298044033350010 0.1224070396459993 T T T
0.0116286472419986 0.2406638599429982 0.0851040085750014 T T T
0.0116288822719994 0.7406640949729990 0.0851040085750014 T T T
0.2755395853920035 0.0067670846249968 0.1035342479859978 T T T
0.2752598060169973 0.5065402593940007 0.1035456443930016 T T T
0.0975883522989989 0.1990894717780023 0.0208459417030014 T T T
0.0975879997549995 0.6990891192340030 0.0208459417030014 T T T
0.4255527924009996 0.0290191062619982 0.0210610104750018 T T T
0.4255530274310004 0.5290193412919990 0.0210610104750018 T T T
0.7453125736969994 0.1258865610770030 0.0664408298610013 T T T
0.7453128087259984 0.6258867961069967 0.0664408298610013 T T T
0.7589232057369983 0.0052106065099977 0.0475811901429992 T T T
0.7589228531919971 0.5052102539659984 0.0475811901429992 T T T
0.9253244870510002 0.1571218778230019 0.1491006336390015 T T T
0.9258909318600033 0.6570063493999996 0.1489074529719971 T T T
0.5996605022110018 0.0730147125609975 0.1489359441000033 T T T
0.5997554450740026 0.5728370858279987 0.1487601291689984 T T T
0.7645811759639969 0.1299153459129982 0.1223765791550022 T T T
0.7646235436349968 0.6297805787069990 0.1222798180150022 T T T
0.5116286472419986 0.2406638599429982 0.0851040085750014 T T T
0.5116288822719994 0.7406640949729990 0.0851040085750014 T T T
0.7752903744869997 0.0064995871450009 0.1035516422680018 T T T
0.7752424176440016 0.5064577904470013 0.1035119039960009 T T T
0.5975883522989989 0.1990894717780023 0.0208459417030014 T T T
0.5975879997549995 0.6990891192340030 0.0208459417030014 T T T
0.9255527924009996 0.0290191062619982 0.0210610104750018 T T T
0.9255530274310004 0.5290193412919990 0.0210610104750018 T T T
0.2453129849990034 0.3758869723789999 0.0664408298610013 T T T
0.2453126324540023 0.8758866198350006 0.0664408298610013 T T T
0.2589230294650022 0.2552104302380016 0.0475811901429992 T T T
0.2589232644940012 0.7552106652680024 0.0475811901429992 T T T
0.4252041532580009 0.4065986931139989 0.1490719617990024 T T T
0.4255520348930020 0.9068861988009971 0.1490667159750032 T T T
0.0998832680250032 0.3233247812610003 0.1489789198870000 T T T
0.0998672709630029 0.8232047704640024 0.1488925754149975 T T T
0.2638837228549988 0.3797995684570026 0.1223825402360035 T T T
0.2643755160929970 0.8799566126750022 0.1223504032549982 T T T
0.0116284709700025 0.4906636836710021 0.0851040085750014 T T T
0.0116287059990015 0.9906639187000010 0.0851040085750014 T T T
0.2752863495840003 0.2566010707639990 0.1035406040959970 T T T
0.2753792745279995 0.7565465108160012 0.1035511455210028 T T T
0.0975881760270028 0.4490892955059991 0.0208459417030014 T T T
0.0975884110560017 0.9490895305349980 0.0208459417030014 T T T
0.4255526161290035 0.2790189299900021 0.0210610104750018 T T T
0.4255528511589972 0.7790191650200029 0.0210610104750018 T T T
0.7453129849990034 0.3758869723789999 0.0664408298610013 T T T
0.7453126324540023 0.8758866198350006 0.0664408298610013 T T T
0.7589230294650022 0.2552104302380016 0.0475811901429992 T T T
0.7589232644940012 0.7552106652680024 0.0475811901429992 T T T
0.9249082793620005 0.4069094668030004 0.1491111663830011 T T T
0.9252773148679978 0.9069115291010021 0.1490901557040019 T T T
0.5993730788069982 0.3227543306879994 0.1488850763619993 T T T
0.5996279319159967 0.8227316486269984 0.1489372666489999 T T T
0.7650633660569994 0.3799512873249995 0.1223694841820020 T T T
0.7644868684590023 0.8798188304060020 0.1223741135439980 T T T
0.5116284709700025 0.4906636836710021 0.0851040085750014 T T T
0.5116287059990015 0.9906639187000010 0.0851040085750014 T T T
0.7755817784950025 0.2566445704820026 0.1035463900480025 T T T
0.7755899668810002 0.7567144015180034 0.1035275667490012 T T T
0.5975881760270028 0.4490892955059991 0.0208459417030014 T T T
0.5975884110560017 0.9490895305349980 0.0208459417030014 T T T
0.9255526161289964 0.2790189299900021 0.0210610104750018 T T T
0.9255528511589972 0.7790191650200029 0.0210610104750018 T T T


For my INCAR file, I have used:

# Basic Setup
SYSTEM= WF RQ2 by itself
ISTART = 0
ICHARG = 2
ENMAX = 900
ISPIN = 1

LAECHG=.TRUE.

AMIN = 0.02

# Accuracy controls:
PREC = ACCURATE
ENCUT = 900

# Electronic loop controls:
ALGO = Fast
EDIFF = 0.00000100
EDIFFG = -0.0010
NELMIN = 8
NELM = 800
ISMEAR = 0
SIGMA = 0.05

[graeme]

I think these results reflect polar covalent bonds where charge has moved from Si to the more electronegative O atoms.