problem with Sulphur atoms

[upper-polariton]

I am having difficulties running std2 (version 2025-2-6 10:30:41.979) when the molecule contains sulfur atoms. This could be related to issue #8.

As the simplest example, i took water, and replaced the central oxygen with sulfur.

For water everything seemingly works fine. I run xtb (version 6.7.1), create the molden input file, with which i can run std2 without (technical) problems. I did not validate the resulting excitation energies yet though.

For H2S, running xtb goes fine and the molden file looks OK. However, running std2 gives an “internal MO norm error”. Running the std2 program with the -chk flag i get a discrepancy between the mulliken populations, and there is a crash. This is as in issue #8.

Optimization of the H2S prior to running the std2 -check does not alter the situation, although the number of electrons from the Mulliken population analysis is different.

I compiled both programs with the intel oneapi 2022.1.0 compilers and MKL library.

The problem seems related to the integral computation with the libcint, as I can run std2 on both water and H2S without it (-libcintOFF). Perhaps i should also report the issue there?

[mdewergi]

Dear Gerrit,
Can you give us your molden file to perfom tests?
Normally you should use xtb4stda to provide a xtb ground state to std2 to perform sTD-DFT-xTB calculations.
Using GFN2-xTB with the xtb program should be avoided because it is a minimal basis set.
Nonetheless, I see no reason it should not work but are orbitals cartesian with xtb?

[upper-polariton]

Sure, in this comment I copied the molden file for water. In the next I copied the one for H2S. Concerning the usage of std2, thanks for the tip. I used the xtb4stda, but ran into an IO problem when reading the generated wnf.xtb with std2. I still need to look into that more carefully.

[Molden Format]
[Title]
[Atoms] AU
O 1 8 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
H 2 1 0.00000000000000E+00 0.00000000000000E+00 0.17952398183894E+01
H 3 1 0.16925709980388E+01 0.00000000000000E+00 -0.59840634380068E+00
[GTO]
1 0
s 4 1.0000000000000000
69.137961906196551 -0.20478756370077797
11.906129132707308 -0.24997023136827334
0.95670827744340703 0.40025880240639616
0.36462520496073686 0.15952206667693555
p 4 1.0000000000000000
8.2124193257781641 1.1321556799186829
2.1293576997098116 1.0476840782254817
0.75066448202360914 0.54956508217158984
0.29885246543283073 8.2908486592766617E-002

       2 0

s 3 1.0000000000000000
3.3702276975336001 0.27359110588908298
0.61389118221497996 0.26460540653860526
0.16614291148415999 8.2465947534082318E-002

       3 0

s 3 1.0000000000000000
3.3702276975336001 0.27359110588908298
0.61389118221497996 0.26460540653860526
0.16614291148415999 8.2465947534082318E-002

[MO]
Sym= 1a
Ene= -0.68031601181311863
Spin= Alpha
Occup= 2.00000000
1 -0.79696813682285073
2 -6.2001356325238316E-002
3 -3.3733997019716053E-016
4 -4.3841783562875603E-002
5 -0.18302392722445154
6 -0.18302388611855053
Sym= 2a
Ene= -0.57061511807816878
Spin= Alpha
Occup= 2.00000000
1 3.5656154083807340E-008
2 0.39777143361554551
3 -3.8388638911436575E-016
4 -0.56253128735324132
5 -0.35521338846823303
6 0.35521342046843180
Sym= 3a
Ene= -0.50791255962360238
Spin= Alpha
Occup= 2.00000000
1 0.43311941007154897
2 -0.67043471347518224
3 4.4100912682265785E-016
4 -0.47407102737094808
5 -0.23299590567442779
6 -0.23299592495538654
Sym= 4a
Ene= -0.44592705532728250
Spin= Alpha
Occup= 2.00000000
1 3.4859613474845227E-016
2 -2.5466930243571403E-016
3 -0.99999999999999989
4 9.9538184328788003E-017
5 2.4797058545291726E-017
6 -1.4846111948561575E-016
Sym= 5a
Ene= 9.2535560943533574E-002
Spin= Alpha
Occup= 0.00000000
1 -0.85888227741228651
2 -0.56660250245774657
3 -2.3967236714820113E-017
4 -0.40064960150517254
5 0.77780605223707966
6 0.77780696203955091
Sym= 6a
Ene= 0.27848612737127859
Spin= Alpha
Occup= 0.00000000
1 5.7249143211503837E-007
2 -0.56873703247846474
3 7.1601910081855270E-018
4 0.80431277969904169
5 -0.90997808796473256
6 0.90997716613252844

[upper-polariton]

For H2S

[Molden Format]
[Title]
[Atoms] AU
S 1 16 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
H 2 1 0.00000000000000E+00 0.00000000000000E+00 0.17952398183894E+01
H 3 1 0.16925709980388E+01 0.00000000000000E+00 -0.59840634380068E+00
[GTO]
1 0
s 4 1.0000000000000000
5.9405971566712825 -8.9372417311598049E-002
1.6733203164693664 -0.18082641609838965
0.30005235337611069 0.21723996338879178
0.14762698261069515 6.0930362386553291E-002
p 4 1.0000000000000000
7.6040239430642842 -0.25814820324554671
0.78579953064441499 0.29055569447587165
0.35515453993277829 0.22849483671210347
0.17168954147534055 3.3790487300818996E-002
d 3 1.0000000000000000
1.5157593763923909 0.57480891956705049
0.47526859543376815 0.26185396196292493
0.18512883107762873 3.4887549426725117E-002

       2 0

s 3 1.0000000000000000
3.3702276975336001 0.27359110588908298
0.61389118221497996 0.26460540653860526
0.16614291148415999 8.2465947534082318E-002

       3 0

s 3 1.0000000000000000
3.3702276975336001 0.27359110588908298
0.61389118221497996 0.26460540653860526
0.16614291148415999 8.2465947534082318E-002

[MO]
Sym= 1a
Ene= -0.75515859016115972
Spin= Alpha
Occup= 2.00000000
1 -0.82770803077940180
2 -2.2387856696177044E-002
3 9.6747827003584322E-018
4 -1.5830677739070667E-002
5 -2.3036798735921408E-003
6 5.8368257455935994E-003
7 -3.5331458720014586E-003
8 7.2799726135141061E-018
9 2.0077439688818248E-003
10 2.4935670033241497E-016
11 -0.13070733182859406
12 -0.13070729953732604
Sym= 2a
Ene= -0.55186148845959460
Spin= Alpha
Occup= 2.00000000
1 -8.0379771765564804E-009
2 -0.35453841551198501
3 -1.8112926788272010E-017
4 0.50139080983477868
5 -4.4402015336127134E-003
6 1.0886108394933536E-009
7 4.4402004450018739E-003
8 1.7582930243289365E-018
9 1.8126803275607117E-003
10 6.0989020689122361E-016
11 0.36747664544475961
12 -0.36747668711789871
Sym= 3a
Ene= -0.47448415692100532
Spin= Alpha
Occup= 2.00000000
1 0.42862671592242230
2 -0.66644968735592180
3 2.5948525079918485E-016
4 -0.47125319809477684
5 -8.2624695727772646E-003
6 1.0455465381829364E-002
7 -2.1929958090520993E-003
8 -3.5189467856593576E-018
9 -9.9115354972969597E-003
10 3.8780520923142506E-016
11 -0.24307866053845523
12 -0.24307865899178635
Sym= 4a
Ene= -0.40285662431650437
Spin= Alpha
Occup= 2.00000000
1 1.1829876593712477E-016
2 -1.6950429943368899E-016
3 -0.99988905566548658
4 -1.1468443995531984E-016
5 3.1065878482993980E-018
6 9.1882695905307985E-018
7 -1.2294857438830196E-017
8 -1.2162118659953180E-002
9 -6.6915819381995044E-019
10 -8.5999552372644124E-003
11 -9.0144655120330472E-017
12 -6.5692678546053152E-017
Sym= 5a
Ene= -0.12827029904885082
Spin= Alpha
Occup= 0.00000000
1 7.0246240804210988E-008
2 0.26971497384551962
3 -2.3618544899007179E-017
4 -0.38143276161337680
5 -0.66813491208316500
6 1.1266001614940180E-007
7 0.66813479942314891
8 -1.0557972549575127E-016
9 0.27276142934537384
10 1.2625021834130975E-015
11 0.22532015436594155
12 -0.22532027237047966
Sym= 6a
Ene= -8.9426190279511181E-002
Spin= Alpha
Occup= 0.00000000
1 -0.27214265957953526
2 -0.19611983051247711
3 -5.9946666322205098E-018
4 -0.13867834135511081
5 9.5585678539015645E-002
6 -0.59144960771457866
7 0.49586392917556305
8 7.5040007604539868E-016
9 -0.65365973138715250
10 -1.9146230484205890E-015
11 0.17726204002689805
12 0.17726198817668060
Sym= 7a
Ene= -4.7084986386856494E-002
Spin= Alpha
Occup= 0.00000000
1 5.4387303151876673E-016
2 1.2733460146157008E-016
3 8.3600623253726057E-010
4 -1.7988538623739843E-017
5 -7.9803478262327396E-017
6 1.1645150433164719E-016
7 -3.6648026069319791E-017
8 0.57735195360754632
9 2.5368636631983562E-015
10 -0.81649538986178616
11 -9.3621706703607917E-018
12 -9.3996152761930468E-016
Sym= 8a
Ene= -4.2913614733572893E-002
Spin= Alpha
Occup= 0.00000000
1 9.1339377235016769E-002
2 7.7453179080569590E-002
3 -4.6100727284128384E-017
4 5.4767912202430678E-002
5 -0.55430648695934592
6 0.71059685463066824
7 -0.15629036767132232
8 3.5621223600490198E-015
9 -0.64996624335856301
10 8.3249432408441969E-016
11 -6.0658158496147273E-002
12 -6.0658157231520113E-002
Sym= 9a
Ene= -3.4973822443502320E-002
Spin= Alpha
Occup= 0.00000000
1 5.4785975380804521E-016
2 2.7938721207097597E-016
3 1.4895514773975788E-002
4 2.3517885796482324E-016
5 -2.2795907263704454E-015
6 2.5748014419422230E-015
7 -2.9521071557177771E-016
8 -0.81640480433131435
9 -1.5868417795498019E-015
10 -0.57728789966910565
11 -2.6007339453134852E-016
12 -7.5896961073458210E-016

[mdewergi]

For xtb4stda, check that both are compiled either 32 bits or 64 bits for integer. If you mix this, they are not compatible.

I will check this when I will have the time.
Best wishes,
Marc

[mdewergi]

What -sty option did you used? I suppose that it is -sty 0 that should be used here.

[upper-polariton]

indeed -sty 0. This is what running the std2 -check suggested. Concerning the xtb4stda, that could indeed be the problem. I will check.

[mdewergi]

(Also they are no default parameters for GFN2-xTB ground state with sTD-DFT.)

[mdewergi]

So this is a normalization problem with d orbitals using libcint and sty 0 format. For the moment, you can use -libcintOFF keyword. I am looking at it.

[mdewergi]

The fix has been applied to account correctly for -sty 0 option with libcint.