2
$\begingroup$

I want to plot a magnetic shielding isosurface around benzene molecule, for that, I prepared a 100 atom grid keeping benzene at the center.

At each grid point there is a dummy atom (X with charge=0.0). Now I want to set a magnetic shielding calculation on this molecular cluster (here by cluster I mean benzene molecule surrounded by 100 dummy atoms). The moment I'm putting up my .mol and .dal file for calculation,

I'm receiving an error that says the basis set doesn't support element with charge 0. Surprisingly I tried other basis sets too but they all ended up with giving same error somehow. I think somehow I have to edit the basis set to incorporate X atom too but I'm clearly lacking the knowledge for same.

I'm attaching all three things, the .mol file, .dal file and the error message I received (the supplied files I'm attaching only contain 9 dummy atoms to keep my question concise).

I suspect if I can plot magnetic shielding isosurfaces directly using Multiwfn but I'm not sure how to do it, as dalton output cannot be converted into .wfn file.

.mol file

BASIS
SV+DoubleRydberg(Dunning-Hay)
 Benzene using the SV+DoubleRydberg(Dunning-Hay) Basis set
 Using automatic symmetry detection.
Atomtypes=3
Charge=6.0 Atoms=6
C        1.209256425      0.698164522      0.000000000
C       -1.209256425      0.698164522      0.000000000
C        1.209256425     -0.698164522      0.000000000
C       -1.209256425     -0.698164522      0.000000000
C        0.000000000      1.396329044      0.000000000
C        0.000000000     -1.396329044      0.000000000
Charge=1.0 Atoms=6
H        2.150060899      1.241338238      0.000000000
H       -2.150060899      1.241338238      0.000000000
H        2.150060899     -1.241338238      0.000000000
H       -2.150060899     -1.241338238      0.000000000
H        0.000000000      2.482676477      0.000000000
H        0.000000000     -2.482676477      0.000000000
Charge=0.0 Atoms=9
X       -0.398701210     -0.101689719      1.433969427
X        1.274720770      0.101689719     -1.433969427
X       -1.027638330      0.104867522     -1.478780971
X        1.510572190     -0.096128562      1.355549224
X       -2.802139491     -0.073883936      1.041868412
X        3.318766411     -0.050050408      0.705781827
X        3.026759891      0.080239544     -1.131491501
X       -2.779677451      0.081033995     -1.142694387
X       -4.048782711      0.011916764     -0.168043292

.dal file

**DALTON INPUT
.RUN PROPERTIES
**WAVE FUNCTIONS
.HF
**PROPERTIES
.SHIELD
.SPIN-S
**END OF DALTON INPUT

Error Message is

Output from 'grep -n ERROR' :
302: ERROR: Nuclear charge    0 is an unsupported element for basis SV+DoubleRydberg(Dunning-Hay)
303: ERROR: You must choose another basis set, or enter it manually.
307:  --- SEVERE ERROR, PROGRAM WILL BE ABORTED ---
Improve this question
$\endgroup$
4
  • $\begingroup$ +1 Welcome to our forum. $\endgroup$
    – Camps ♦
    Commented Jan 5 at 16:56
  • $\begingroup$ About plotting wave function from DALTON, take a look here. $\endgroup$
    – Camps ♦
    Commented Jan 5 at 17:00
  • $\begingroup$ Also, I found the following in the DALTON manual (v2020.1, page 247): The charge of the ion-core is determined by the keyword .ZCMVAL (default: +1), not by a charge specified for X; use Charge=0.0. $\endgroup$
    – Camps ♦
    Commented Jan 5 at 17:08
  • $\begingroup$ @Camps Thank you so much for your comment. I already tried this way but unfortunately its not working in my case , so i was really expecting if someone who has already done some dummy atom calculations can share there inputs for me to get a better idea on where I'm going wrong. $\endgroup$
    – MeliodusSama
    Commented Jan 10 at 13:53

1 Answer 1

Reset to default
1
$\begingroup$

Kinda late but give this basis set to the other atom types and for the dummy atoms give "Basis=pointcharge"

ps. if you managed to get grids and stuff I have some questions as well.

Improve this answer
$\endgroup$
1
  • $\begingroup$ As it’s currently written, your answer is unclear. Please edit to add additional details that will help others understand how this addresses the question asked. You can find more information on how to write good answers in the help center. $\endgroup$
    – Community Bot
    Commented Jun 21 at 3:31

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .