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mpjohans

Member

Registered: 2020-02-19

Posts: 2

Reading in XTB Molden file with gold atoms

Hello there,

I have some problems reading in a Molden file created by Grimme's XTB code. If I use the Molden file as created directly by XTB, it assumes gold has 54 core electrons and gives the error:

Au( 1) Core electrons: 54 EDF primitive GTFs: 0
Warning: Unable to find proper EDF information for this atom!

If I edit the Molden file so that the third column gives the correct number of active electrons (11 for Au, 6 for oxygen), MultiWFN still adds the 58 core electrons to Au, giving in total 122 core electrons...

I got MultiWFN to read in the Molden without complaints, by specifying a net charge of 65 to gold, and leaving the charge of oxygen as 8. A quick test indicates that the results produced by MultiWFN are reasonable using this procedure.

The question is: is MultiWFN actually reading in the data properly with this odd setting of charges in the Molden file?

I have copy pasted the entire modified Molden file to the end of this message. The test system is Au-H2O, with the following XYZ coordinates:

Au -3.1613340 -0.2396687 4.1142669
O -3.1238195 -1.0529979 6.5122043
H -3.6543341 -0.7098369 7.2463837
H -3.2163609 -2.0167627 6.5464291

The xtb command used to create the Molden file:
xtb coord --molden --chrg -0 --acc 0.1 --gfn 1

Using MultiWFN 3.7(dev) release date: 2020-Jan-30

Cheers,
Mikael

[Molden Format] [Title] [Atoms] AU AU 1 65 -0.59740554745799E+01 -0.45290820562473E+00 0.77748376785964E+01 O 2 8 -0.59031633435678E+01 -0.19898776495037E+01 0.12306282648400E+02 H 3 1 -0.69056906470651E+01 -0.13413973400165E+01 0.13693680646807E+02 H 4 1 -0.60780412455216E+01 -0.38111291780190E+01 0.12370958147353E+02 [GTO] 1 0 d 4 1.00000000000000 4.11227012495660 -0.473324940844010 0.806185037858737 0.444535854258023 0.446191616580503 0.220093041100352 0.255520804275981 1.799334157976449E-002 s 6 1.00000000000000 3.13574168248545 7.648787779934786E-003 1.46954105694718 5.028748904572377E-002 0.429170727024132 -0.285734603859830 0.268962144785663 -6.041806113357730E-002 0.161301092388156 0.241714969909251 0.101964157764926 4.658609754208300E-002 p 6 1.00000000000000 2.05081467491250 9.734601823274501E-003 0.427246249106250 -6.316501149654702E-002 0.250019283150000 -5.711049520372285E-002 0.140456333955000 5.738814902734826E-002 9.068998265250000E-002 4.789881971164786E-002 5.764302795562500E-002 4.394514711933854E-003 2 0 s 6 1.00000000000000 152.287696607881 -0.128259784124054 27.9280152159731 -0.178972249529991 7.84837479238452 -0.172118558938750 1.12233502027056 0.260053743770140 0.509384658790786 0.241553208010412 0.242922665325103 4.224420474647501E-002 p 6 1.00000000000000 27.2034214871677 0.701740873673413 7.09409912597673 0.848929183574319 2.53833626053460 0.866990360869820 1.06107307678439 0.621673076410288 0.485194891641043 0.231598405185667 0.229383025506425 2.380113334610014E-002 3 0 s 4 1.00000000000000 7.61199720705997 0.185361036261688 1.39290170588020 0.237716782231063 0.386963346250483 0.186322055973239 0.128429655926973 4.458969372625468E-002 s 7 1.00000000000000 10.2562860703149 -1.31865446782543 0.622796532587539 1.60387770076958 0.239100766785391 0.601323010177280 7.61199720705997 -0.980904319863310 1.39290170588020 -1.25796350353405 0.386963346250483 -0.985989899905078 0.128429655926973 -0.235962336419595 4 0 s 4 1.00000000000000 7.61199720705997 0.185361036261688 1.39290170588020 0.237716782231063 0.386963346250483 0.186322055973239 0.128429655926973 4.458969372625468E-002 s 7 1.00000000000000 10.2562860703149 -1.31865446782543 0.622796532587539 1.60387770076958 0.239100766785391 0.601323010177280 7.61199720705997 -0.980904319863310 1.39290170588020 -1.25796350353405 0.386963346250483 -0.985989899905078 0.128429655926973 -0.235962336419595 [MO] Sym= 1a Ene= -0.791630682436142 Spin= Alpha Occup= 2.00000000 1 7.459435263705037E-004 2 7.493458840687124E-004 3 -1.495289410439216E-003 4 3.632901882264507E-005 5 -1.637332545088016E-004 6 6.851808929658977E-004 7 1.742969947380617E-002 8 -2.211161953316562E-003 9 -9.326738648627297E-003 10 2.002990785224640E-002 11 -0.813224576390345 12 3.530103155183657E-002 13 3.502954213152983E-002 14 -4.266784400957112E-002 15 -0.174010453264092 16 -1.062375405843982E-002 17 -0.174749271407527 18 -1.035080278014656E-002 Sym= 2a Ene= -0.642484901464492 Spin= Alpha Occup= 2.00000000 1 -3.128343398256299E-003 2 3.451759267524019E-003 3 -3.234158692677199E-004 4 -1.113184802510753E-003 5 3.064596981844156E-003 6 -1.153236936286695E-002 7 3.154040652008243E-003 8 2.670073395718736E-003 9 -7.958310236471908E-003 10 5.059228373848420E-005 11 9.838231971994679E-004 12 0.202398306492168 13 -0.600307952211927 14 -0.324459400521450 15 -0.326551768570101 16 -4.443765211850183E-002 17 0.324666908871009 18 4.501661200324258E-002 Sym= 3a Ene= -0.587604186881679 Spin= Alpha Occup= 2.00000000 1 -3.610403821619260E-002 2 -2.864094167779696E-002 3 6.474497989398956E-002 4 -3.665807357576578E-003 5 1.122683650171988E-002 6 -3.357046650585227E-002 7 6.233036854855723E-002 8 1.344079930378323E-002 9 -2.470464492185759E-002 10 9.430662999086262E-002 11 0.338862874131528 12 0.396481745099506 13 0.446225545114538 14 -0.572497334410804 15 -0.183941424006226 16 -3.461911969575203E-002 17 -0.191400799984350 18 -3.546647950751426E-002 Sym= 4a Ene= -0.538456348890254 Spin= Alpha Occup= 2.00000000 1 -3.736549549087398E-002 2 -2.194536786184258E-002 3 5.931086335271656E-002 4 9.275535582690692E-003 5 -2.765866208881454E-002 6 -4.363667401206977E-002 7 5.455718591432374E-002 8 -3.478578990592702E-002 9 -2.251258304731657E-002 10 4.455815199183038E-002 11 -4.387434727694108E-002 12 -0.822613131417877 13 1.358643440258028E-002 14 -0.534317565913066 15 1.250820266437535E-002 16 1.129235763944909E-002 17 8.613081208338057E-003 18 1.072399244349440E-002 Sym= 5a Ene= -0.414603864801457 Spin= Alpha Occup= 2.00000000 1 -0.834351916777958 2 0.736623880363021 3 9.772803641493698E-002 4 0.252020289562204 5 9.833091997441487E-002 6 0.307574140090862 7 -1.042866576764573E-004 8 1.652951517948396E-006 9 9.462739156072865E-005 10 -1.860187828731585E-004 11 -6.849856399792029E-004 12 3.341006901581453E-005 13 6.756756722112140E-004 14 9.526392763059735E-005 15 -2.364969796659597E-004 16 -1.687855145218044E-005 17 1.263430286988538E-003 18 -7.932704406607211E-004 Sym= 6a Ene= -0.414603356107506 Spin= Alpha Occup= 2.00000000 1 -0.234874623434089 2 0.206038054256848 3 2.883656917724140E-002 4 -0.915015282636082 5 -0.299613280128508 6 8.569319559936464E-002 7 -8.445089798949816E-005 8 6.133050695640027E-006 9 4.859322246019998E-005 10 -1.489790040342671E-004 11 -4.614769130843715E-004 12 1.360745742799759E-004 13 -5.567098124235617E-005 14 -1.603581824329877E-004 15 6.250485127861243E-004 16 -4.407701851226682E-004 17 2.154017023786449E-005 18 -1.435147930138982E-004 Sym= 7a Ene= -0.414495302441312 Spin= Alpha Occup= 2.00000000 1 2.414469334671199E-002 2 -0.507198776529808 3 0.483054083183097 4 9.349256310609605E-002 5 -0.281017854648589 6 0.764481073561522 7 6.446755595879677E-004 8 6.759015240855080E-004 9 -2.434898747293111E-003 10 5.919134700827981E-005 11 1.595468595619644E-003 12 4.074774884313097E-003 13 -1.214248614994350E-002 14 -3.268232389418115E-003 15 -1.096427070338828E-002 16 -5.796390746669296E-003 17 9.751741906363518E-003 18 8.389715181664485E-003 Sym= 8a Ene= -0.414323552862566 Spin= Alpha Occup= 2.00000000 1 -1.669348956262254E-003 2 0.182401503524587 3 -0.180732154568325 4 0.300407543743557 5 -0.905365079593277 6 -0.212701106525525 7 6.574367594876330E-004 8 4.554105237172425E-003 9 6.814145086260231E-004 10 2.471797851589443E-003 11 1.164930852318209E-002 12 3.996782234741740E-002 13 9.989740564894508E-003 14 7.632768136325121E-003 15 -7.262856573884634E-003 16 -3.237816747500939E-003 17 -5.949327580221616E-003 18 -3.710684090464159E-003 Sym= 9a Ene= -0.411152527691183 Spin= Alpha Occup= 2.00000000 1 0.494215522838914 2 0.350153064863933 3 -0.844368587702847 4 -1.250773891475894E-002 5 3.293360642183491E-002 6 0.513534928333139 7 6.906823382765487E-002 8 -2.674262766089689E-003 9 -1.617254432508677E-002 10 4.906204543135567E-002 11 5.504692375952659E-002 12 -3.917659205469266E-002 13 3.846835771301018E-002 14 -0.104921786648143 15 -3.095416904905818E-002 16 2.091948679735608E-003 17 -1.959646155411654E-002 18 5.132724898709618E-003 Sym= 10a Ene= -0.326769979516112 Spin= Alpha Occup= 1.00000000 1 -2.743020359935016E-002 2 -2.001546259246835E-002 3 4.744566619181851E-002 4 2.621369492957128E-004 5 -4.333125704373928E-004 6 -2.828146202223753E-002 7 0.984798212807540 8 2.630667772186727E-003 9 4.463121928087532E-002 10 -0.136867596028075 11 -0.101986453603023 12 3.571916593103407E-002 13 -4.081042066654863E-002 14 0.115410486115169 15 4.826476445599266E-002 16 -1.116950167403070E-002 17 3.533217912489275E-002 18 -2.276382738258570E-002 Sym= 11a Ene= -0.199476683707863 Spin= Alpha Occup= 0.00000000 1 4.992345266803993E-003 2 1.004974056601383E-003 3 -5.997319323405375E-003 4 -1.391970150539552E-005 5 1.277806568496397E-004 6 5.644901559326934E-003 7 -2.961629508963231E-002 8 -4.496723051021111E-002 9 -0.919090613967178 10 -0.247126511041866 11 -0.100792291654207 12 3.372808995029564E-002 13 7.190329535038283E-002 14 4.198263621373055E-003 15 7.771050441053545E-002 16 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sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,773

Website

Re: Reading in XTB Molden file with gold atoms

Thank you very much for reporting this issue. I checked the code and found that the code used to determine the number of core electrons for molden file generated by xtb is not completely correct. I have fixed this bug and updated the latest version on Multiwfn website, please download it. Now the molden file generated by xtb can be directly loaded without any manual modification.

Since Multiwfn automatically applies special treatment for molden file generated by xtb, you do not need to manually edit any content in this file.

mpjohans

Member

Registered: 2020-02-19

Posts: 2

Re: Reading in XTB Molden file with gold atoms

Works now, many thanks for the fix and of course for the whole wonderful package!