TURBOMOLE Modules > Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools
plt tool mislabelling atoms with ECPs
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Dempsey:
Dear Developers,
I have come across a minor problem with the plt tool. For calculations using ECP basis sets the plt tool presents any atoms as Z - Nelectrons in the ECP. For example, my molecule has 94Pu and I am using the Dolg 60 electron ECP so the cub file created by the plt tool presents the 94Pu as 34Se. I double-checked and 93Np becomes 33As in the cub file confirming my suspicions about the interaction of plt with the ECP.
I compared the wavefunctions generated by both plt and tm2molden and they appear to be the same. The ECP atoms can be fixed manually by editing the cub file e.g. changing 34 to 94 but maybe you could implement a fix for this?
I should also note that I am using Turbomole 7.3, this may be fixed in newer versions?
--- Code: ---$title
$operating system unix
$symmetry c1
$redundant file=coord
$user-defined bonds file=coord
$coord file=coord
$optimize
internal on
redundant on
cartesian off
global off
basis off
$atoms
pu 1 \
basis =pu def-SV(P) \
ecp =pu def-ecp \
jbas =pu def-SV(P)
o 2,5,8,11,14,17,20,23 \
basis =o def2-SVP \
jbas =o def2-SVP
h 3-4,6-7,9-10,12-13,15-16,18-19,21-22,24-25 \
basis =h def2-SVP \
jbas =h def2-SVP
$basis file=basis
$ecp file=basis
$newecp
$rundimensions
dim(fock,dens)=52606
natoms=25
nshell=125
nbf(CAO)=322
dim(trafo[SAO<-->AO/CAO])=385
rhfshells=2
nbf(AO)=291
$uhfmo_alpha file=alpha
$uhfmo_beta file=beta
$uhf
$scfiterlimit 3000
$thize 0.10000000E-04
$thime 5
$scfdump
$scfintunit
unit=30 size=0 file=twoint
$scfdiis
$maxcor 500 MiB per_core
$drvopt
cartesian on
basis off
global off
hessian on
dipole on
nuclear polarizability
$interconversion off
qconv=1.d-7
maxiter=25
$coordinateupdate
dqmax=0.3
interpolate on
statistics 5
$forceupdate
ahlrichs numgeo=0 mingeo=3 maxgeo=4 modus=<g|dq> dynamic fail=0.3
threig=0.005 reseig=0.005 thrbig=3.0 scale=1.00 damping=0.0
$forceinit on
diag=default
$energy file=energy
$grad file=gradient
$forceapprox file=forceapprox
$dft
functional pbe0
gridsize m4
$disp3 -bj
$scfconv 8
$scfdamp start=0.700 step=0.050 min=0.050
$scforbitalshift automatic=.1
$ricore 500
$rij
$jbas file=auxbasis
$marij
$last SCF energy change = -.40488317E-06
$ssquare from ridft
6.025 (not to be modified here)
$charge from ridft
4.000 (not to be modified here)
$dipole from ridft
x 0.12195769945513 y 0.00426054814190 z 0.06652229715999 a.u.
| dipole | = 0.3532693012 debye
$alpha shells
a 1-57 ( 1 )
$beta shells
a 1-53 ( 1 )
$pointval fmt=cub mo 110
$last step ridft
$orbital_max_rnorm 0.27147188038346E-04
$subenergy Etot E1 Ej Ex Ec En Disp
-1161.602293901 -3945.264799283 1745.918486321 -77.06141850395 -4.307684619003 1119.137232935 -.2411075074845E-01
$end
--- End code ---
--- Code: ---amplitude of MO 57a a -1.06731a.u.
OUTER/INNER/MIDDLE LOOP: X,Y,Z
25 -7.163758 -8.035522 -8.200891
72 0.203215 0.000000 0.000000
81 0.000000 0.202709 0.000000
81 0.000000 0.000000 0.202628
34 0.000000 0.040324 0.008193 0.009549
8 0.000000 3.146616 -2.432724 -2.180174
1 0.000000 2.745017 -2.158459 -3.593451
1 0.000000 2.635920 -3.810491 -1.906671
8 0.000000 3.076968 2.296790 2.447402
1 0.000000 2.549683 2.045558 3.823159
1 0.000000 2.658780 3.697589 2.136379
8 0.000000 3.264512 2.244631 -2.227628
1 0.000000 2.824009 3.651637 -1.982379
1 0.000000 2.848885 1.962346 -3.635260
8 0.000000 2.623040 -2.448840 2.415281
1 0.000000 2.134659 -3.832814 2.132511
1 0.000000 2.109782 -2.143523 3.785392
8 0.000000 -3.163758 0.121235 3.191230
1 0.000000 -2.760680 -1.062833 4.009380
1 0.000000 -2.701127 1.299839 3.985409
8 0.000000 -3.114510 -3.223036 -0.080960
1 0.000000 -2.622558 -4.035522 -1.234956
1 0.000000 -2.717292 -4.009175 1.126541
8 0.000000 -2.898531 0.047471 -3.420261
1 0.000000 -2.372725 1.208506 -4.200891
1 0.000000 -2.432278 -1.154166 -4.176920
8 0.000000 -2.947779 3.391742 -0.148071
1 0.000000 -2.416113 4.154849 -1.318053
1 0.000000 -2.510847 4.181195 1.043445
--- End code ---
Best,
Dempsey
uwe:
Hello,
you are right, cub files generated directly by the keyword
$pointval fmt=cub ...
do add the charge of the nuclei which in case of ECPs is not correct. Should be fixed in the next major release.
You could write standard plt format instead (just remove the fmt=cub option) and then use 'plt2cub' from here:
https://www.turbomole.org/turbomole/utilities/
to do the conversion. plt2cub should write the correct element identifiers also in case of ECPs.
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