welcome to somewhereville (.com)
est. 2001, pop. 1 ~ Damian G. Allis Ph.D., residing
Title says it all (A&S Article | Local PDF). As to the "Resistance Is Futile" subheading, we can ponder the futility of a material trying to not manifest an intrinsic property under stimulus, but you’d get many more visits to your site debating the relevance of anthropomorphizing members of The Collective.
With thanks to Daniel Bernardi of the (and my) College of Arts and Sciences for the article and for keeping the science behind the original article understandable.
In press, in Chemistry of Materials (doi.org/10.1021/acs.chemmater.9b03644).
The theory that underlies the reason for this article is addressed in "Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential," then the history of the material is exhaustively reviewed in "Polyacetylene: Myth and Reality" (open access, so you've no excuse to not read it). The preparation of the starting material, di-iodo-butadiene, C4H4I2, in urea, is published in "Commensurate Urea Inclusion Crystals With The Guest (E,E)-1,4-Diiodo-1,3-Butadiene."
I'm also very happy to be able to officially acknowledge my use of the Syracuse University Academic Virtual Hosting Environment (AVHE) as part of this work, which was involved in everything from periodic DFT calculations and the anharmonic treatment of polyacetylene on the electronic structure side, to cleaning up crystal cells of the polyacetylene-urea complexes for the generation of images in VMD and UberPOV – why just make a picture when you can, at least, make a method-consistent one?
As an aside, this is also my first experience using GIMP for a production-quality graphic – in this case, in the form of a proposed journal cover image (below. We'll see if it gets accepted in the coming month or so).
This GIMP use was instigated by originally formatting my MPB post-repair to Case-sensitive APFS three years ago, for which Photoshop refused to install with a widely-posted but little-addressed "Case-sensitive drives not supported" error (for which the Adobe solution remains "don't do that"). After a small learning curve, I'm pleased to say that GIMP is a hell of a program, well worth the price, and is just as pleasant an experience in Ubuntu 18.04 as it is in OS X 10.15 – a tidy sum saved each year for the 0.2% of features actually needed in either program to do the above.
Steluta A. Dinca, Damian G. Allis, Michael D. Moskowitz, Michael B. Sponsler, Bruce S. Hudson
Abstract: We report a novel, highly effective strategy for controlling the synthesis of polyacetylene as a guest in an organic host crystal by monitoring in situ an elimination–condensation polymerization reaction. Specifically, in this process, the polymer material is forced to have its chains extended and aligned such that translational periodicity applies, producing a bond alternation potential that has a symmetric double minimum. The synthetic approach used is photochemical elimination of iodine from a conjugated diene, (E,E)-1,4-diiodo-1,3-butadiene, which forms a commensurate and fully ordered urea inclusion compound. Photochemical cleavage of the terminal C–I bonds results in elimination of iodine from the single crystal and formation of C–C bonds between adjacent radicals to produce the conjugated 1,8-diiodo-1,3,5,7-octatetraene and subsequent longer polyene species. The combination of in situ crystal mass-loss measurements and vibrational Raman spectroscopy demonstrates clearly the presence of new polyene chains and loss of iodine from the urea substructure. The first few product oligopolyenes exhibit very strong Raman scattering with the most intense vibrational features decreasing in frequency for longer chains approaching an asymptotic limiting frequency that mimics the behavior of conjugated polyenes of known lengths from previous vibrational Raman studies. With extensive irradiation, the mass loss approaches that anticipated from the crystal stoichiometry and, at the same time of irradiation, the Raman intensity largely disappears. These results demonstrate that the reaction reported here proceeds to completion, leading to a quasi-one-dimensional array of isolated polyacetylene chains that are constrained to be in a continuous extended, all-trans conformation within the tunnels formed by the urea crystal lattice.
And Happy Leap Day (a first after nearly 20 years of this domain existing).
UPDATE 5 March 2025: The parameter sets have been moved since this post was published over seven years ago. To spare me from having to redo the linking in the future, please instead go right to the source at https://dftb.org/ (current link being https://dftb.org/downloads/parameters.html).
Addressing the conversion of the 3ob-3-1, matsci-0-3, mio-1-1, and pbc-0-3 parameter sets (with fixes transferable to others).
While there is some information available online about converting dftb.org Slater-Koster (.skf) files for use in Gaussian 09/16, the simple procedures you might see for set A might not work for set B because of subtle formatting issues between the different sets.
As is often the case, some of the issues below would not have been confirmed/remedied without the kind assistance of feedback from Gaussian Technical Support. Also as usual for this site, error messages are provided for each stage of the conversion process for relevant parameter sets, with the searches for these errors likely being the way you found this page in the first place.
Because it behooves you to keep up to date with DFTB developments, including staying up-to-date with new and corrected parameter sets. "Parameter sets downloaded from a personal website that are converted parameter sets from a research website with several relevant citations listed." is a lousy-looking reference.
For each of the four sets converted, I provide the dry-run error out of Gaussian 16, then work through the series of steps used to make the .skf files G16/G09-compatible (the versions behave the same in terms of reading the files, while G16 does a much better job of completing SCF cycles with DFTB). The presentation order goes:
#p DFTB opt [empty line] comment line [empty line] 0 1 R1 X1 Y1 Z1 ... Rn Xn Yn Zn [empty line] @parameter_set_R1-R1.skf @parameter_set_R1-Rn.skf ... @parameter_set_Rn-R1.skf @parameter_set_Rn-Rn.skf [empty line]
Final note – some files may have extra blank lines or other features that will throw errors out. Judicious use of comment markers (!) or block deletion should fix issues. More often than not, your error will be not counting the same number of grid point lines as Gaussian expects to see for a given parameter set.
Download: http://www.dftb.org/parameters/download/mio/mio-1-1-cc/
The easy search-for is the "Missing values on 1st line of a parameter block." line.
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx 000014e3168f9187
...
r15 00000000000003e6
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x14e31705b890]
/lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x14e3168f9187]
/opt/g16/l302.exe() [0x4266e0]
...
/opt/g16/l302.exe() [0x40381d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x14e3168dbb97]
/opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729]
Aborted (core dumped)
(Enter /opt/g16/l302.exe)
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
Generate DFT-SCTB integrals.
Missing values on 1st line of a parameter block.
Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 20:24:45 2018.
Job cpu time: 0 days 0 hours 0 minutes 2.7 seconds.
Elapsed time: 0 days 0 hours 0 minutes 0.6 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
As reported on the Gaussian Support page, the first lines of these files must include the atom R1 and atom R2 atomic numbers for the combination in order. Commas were removed to keep the formatting standard.
C-C.skf original: 0.02, 500 ,2 modified: 0.02 500 6 6 C-H.skf original: 0.02, 500, modified: 0.02 500 6 1 H-C.skf original: 0.02, 500, modified: 0.02 500 1 6 H-H.skf original: 0.02, 500,1 modified: 0.02 500 1 1
Addressing the second fix Gaussian reports must be done.
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx 00001539c3c12187
...
r12 00007ffd67a516d8, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x1539c4374890]
/lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x1539c3c12187]
/opt/g16/l302.exe() [0x4266e0]
...
/opt/g16/l302.exe() [0x40381d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x1539c3bf4b97]
/opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729]
Aborted (core dumped)
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
Generate DFT-SCTB integrals.
Parameters for element pair 0 0 have already been read.
Duplicate DFTB parameters read in.
Error termination via Ln
k1e in /opt/g16/l302.exe at Mon Sep 3 20:30:01 2018.
Job cpu time: 0 days 0 hours 0 minutes 3.7 seconds.
Elapsed time: 0 days 0 hours 0 minutes 0.7 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
Also as follows from the Gaussian website, the second number of the first line must reflect the number of lines of values before the line containing the word "Spline" in the .skf file. As Gaussian words it under Modifying Slater-Koster Files:
The second field in the first line of each file should contain the number of lines in the file containing grid points for the Hamiltonian and overlap integrals.
C-C.skf original: 0.02 500 6 6 modified: 0.02 521 6 6 C-H.skf original: 0.02 500 6 1 modified: 0.02 520 6 1 H-C.skf original: 0.02 500 1 6 modified: 0.02 520 1 6 H-H.skf original: 0.02 500 1 1 modified: 0.02 521 1 1
There are several times in several parameter sets (and maybe even between different files of the same sets) where the treatment of the R1-R1.skf and R2-R2.skf files is different from that of R1-R2.skf and R2-R1.skf files.
Error: segmentation violation rax 0000000000000000, rbx ffffffffffffffff, rcx 000014ffe79ef187 ... r12 00007ffde2862268, r13 0000000000000000, r14 0000000000000000 r15 00000000000003e6 /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x14ffe8151890] /lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x14ffe79ef187] /opt/g16/l302.exe() [0x4266e0] ... /opt/g16/l302.exe() [0x40381d] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x14ffe79d1b97] /opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729] Aborted (core dumped) One-electron integrals computed using PRISM. Generate DFT-SCTB integrals. Wanted a floating point number as input. Found a string as input. Spline ? Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 20:43:44 2018. Job cpu time: 0 days 0 hours 0 minutes 10.1 seconds. Elapsed time: 0 days 0 hours 0 minutes 1.8 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
Seeing the "Found a string as input. Spline ?" block at the bottom is a sure sign that your .skf file pre-"Spline" second number is off by 1. As it happens, Gaussian includes an extra read for an additional line in the Atom R1 – Atom R1 series (C-C, H-H). For the mio-1-1 series, the Atom R1 – Atom R1 (same element) combinations need to be reduced by 1 (then brought in to correspondence with the R1-R2 combinations).
C-C.skf original: 0.02 521 6 6 modified: 0.02 520 6 6 H-H.skf original: 0.02 521 1 1 modified: 0.02 520 1 1
With luck, Tom Waits…
THE LARGE PRINT GIVETH,
AND THE SMALL PRINT TAKETH AWAY.
-- TOM WAITS
Job cpu time: 0 days 0 hours 1 minutes 28.9 seconds.
Elapsed time: 0 days 0 hours 0 minutes 17.9 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 3 Scr= 1
Normal termination of Gaussian 16 at Mon Sep 3 20:48:26 2018.
Download: http://www.dftb.org/parameters/download/3ob/3ob-3-1-cc/
By far the easiest one to convert.
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx 0000149226329187
...
r15 00000000000003e6
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x149226a8b890]
/lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x149226329187]
/opt/g16/l302.exe() [0x4266e0]
...
/opt/g16/l302.exe() [0x40381d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x14922630bb97]
/opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729]
Aborted (core dumped)
(Enter /opt/g16/l302.exe)
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
Generate DFT-SCTB integrals.
Missing values on 1st line of a parameter block.
Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 19:32:38 2018.
Job cpu time: 0 days 0 hours 0 minutes 3.0 seconds.
Elapsed time: 0 days 0 hours 0 minutes 0.7 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
C-C.skf original: 2.000000000000E-02, 650, 2 modified: 2.000000000000E-02 650 6 6 H-H.skf original: 2.000000000000E-02, 550, 2 modified: 2.000000000000E-02 550 1 1 C-H.skf original: 2.000000000000E-02, 600 modified: 2.000000000000E-02 600 6 1 H-C.skf original: 2.000000000000E-02, 600 modified: 2.000000000000E-02 600 1 6
Error: segmentation violation rax 0000000000000000, rbx ffffffffffffffff, rcx 000014ed48f53187 ... r12 00007ffc0b6d2fe8, r13 0000000000000000, r14 0000000000000000 r15 00000000000003e6 /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x14ed496b5890] /lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x14ed48f53187] /opt/g16/l302.exe() [0x4266e0] ... /opt/g16/l302.exe() [0x40381d] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x14ed48f35b97] /opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729] Aborted (core dumped) One-electron integrals computed using PRISM. Generate DFT-SCTB integrals. Wanted a floating point number as input. Found a string as input. Spline ? Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 19:38:31 2018. Job cpu time: 0 days 0 hours 0 minutes 4.3 seconds. Elapsed time: 0 days 0 hours 0 minutes 0.9 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
C-C.skf original: 2.000000000000E-02 650 6 6 modified: 2.000000000000E-02 651 6 6 H-H.skf original: 2.000000000000E-02 550 1 1 modified: 2.000000000000E-02 551 1 1 C-H.skf original: 2.000000000000E-02 600 6 1 modified: 2.000000000000E-02 601 6 1 H-C.skf original: 2.000000000000E-02 600 1 6 modified: 2.000000000000E-02 601 1 6
And just those two fixes are needed for the 3ob-3-1 parameter set.
Download: http://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/
Another simple conversion, with the exception of just one problematic file (for the C/H combination, anyway. Your conversion efforts may vary) and the presence of blank lines some (not all) .skf files.
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx 000015368de33187
...
r12 00007ffd8ac2b2a8, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x15368e595890]
/lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x15368de33187]
/opt/g16/l302.exe() [0x4266e0]
...
/opt/g16/l302.exe() [0x40381d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x15368de15b97]
/opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729]
Aborted (core dumped)
damianallis@prime:~/dftb/pbc-0-3$
(Enter /opt/g16/l302.exe)
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
Generate DFT-SCTB integrals.
Missing values on 1st line of a parameter block.
Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 20:54:58 2018.
Job cpu time: 0 days 0 hours 0 minutes 2.8 seconds.
Elapsed time: 0 days 0 hours 0 minutes 0.7 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
The usual.
C-C.skf original: 0.02, 520 modified: 0.02 520 6 6 C-H.skf original: 0.02, 520, modified: 0.02 520 6 1 H-C.skf original: 0.02, 520, modified: 0.02 520 1 6 H-H.skf original: 0.02, 500,1 modified: 0.02 500 1 1
This (simple issue) stumped me for hours and didn't get resolves without Gaussian. The problem is the existence of an extra blank line at the bottom of -some- of the .skf files.
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx 0000149d301e7187
...
r12 00007fff0460a188, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x149d30949890]
/lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x149d301e7187]
/opt/g16/l302.exe() [0x4266e0]
...
/opt/g16/l302.exe() [0x40381d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x149d301c9b97]
/opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729]
Aborted (core dumped)
damianallis@prime:~/dftb/pbc-0-3$ tail -n 10 *.log
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
Generate DFT-SCTB integrals.
Element pair 8 1 not in DFTB parameters.
Pair not found in DFTBHS.
Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 21:00:21 2018.
Job cpu time: 0 days 0 hours 0 minutes 4.1 seconds.
Elapsed time: 0 days 0 hours 0 minutes 0.9 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
Just remove'em if they're present.
C-C.skf - delete the bottom blank line C-H.skf - delete the bottom blank line H-C.skf - delete the bottom blank line H-H.skf - no blank line at bottom to delete
Back to familiar errors, but this time for only one case (H-H).
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx 000014ff73e9f187
...
r12 00007ffcc1c9b598, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x14ff74601890]
/lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x14ff73e9f187]
/opt/g16/l302.exe() [0x4266e0]
...
/opt/g16/l302.exe() [0x40381d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x14ff73e81b97]
/opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729]
Aborted (core dumped)
damianallis@prime:~/dftb/pbc-0-3$ tail -n 10 *.log
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
Generate DFT-SCTB integrals.
Parameters for element pair 0 0 have already been read.
Duplicate DFTB parameters read in.
Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 21:02:16 2018.
Job cpu time: 0 days 0 hours 0 minutes 11.6 seconds.
Elapsed time: 0 days 0 hours 0 minutes 2.1 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
The H-H.skf file value at top for the grid lines is 500, but there are, like the others, 520 lines.
H-H.skf original: 0.02 500 1 1 modified: 0.02 520 1 1
That should be it for the pbc-0-3 parameter set, but note that blank lines may or may not be in those files.
Download: http://www.dftb.org/parameters/download/matsci/matsci-0-3-cc/
Combining all of the issues above and adding a new one, the matsci-0-3 conversion involves the most adjusting, which is just as easily fixed by selective deletion of blocks of text for some cases.
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx 0000154c100f5187
...
r12 00007ffdfd928ea8, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x154c10857890]
/lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x154c100f5187]
/opt/g16/l302.exe() [0x4266e0]
...
/opt/g16/l302.exe() [0x40381d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x154c100d7b97]
/opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729]
Aborted (core dumped)
(Enter /opt/g16/l302.exe)
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
Generate DFT-SCTB integrals.
Missing values on 1st line of a parameter block.
Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 19:59:34 2018.
Job cpu time: 0 days 0 hours 0 minutes 2.5 seconds.
Elapsed time: 0 days 0 hours 0 minutes 0.5 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
C-C.skf original: 0.05 400 modified: 0.05 400 6 6 C-H.skf original: 0.05 400 modified: 0.05 400 6 1 H-C.skf original: 0.05 400 modified: 0.05 400 1 6 H-H.skf original: 0.05 400 modified: 0.05 400 1 1
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx 0000149fb6976187
...
r15 00000000000003e6
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x149fb70d8890]
/lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x149fb6976187]
/opt/g16/l302.exe() [0x4266e0]
...
/opt/g16/l302.exe() [0x40381d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x149fb6958b97]
/opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729]
Aborted (core dumped)
One-electron integrals computed using PRISM.
Generate DFT-SCTB integrals.
Wanted a floating point number as input.
Found a string as input.
0.0000 -0.1939 -0.4955 -0.0439 0.3647 0.3647 0.3647 0.00 2.00 2.00 T 1 0.341975 0.387425
?
Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 20:02:29 2018.
Job cpu time: 0 days 0 hours 0 minutes 2.5 seconds.
Elapsed time: 0 days 0 hours 0 minutes 0.5 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
Gaussian wasn't aware of the existence of non-numeric characters in the R1-R1 block of this parameter set, but found that commenting the section to the right didn't affect the run. Checking with DFTB developers, it turns out only the first 10 numbers on this line are used and the T and beyond is ignored. So, safe to comment out.
Using the .skf comment character (!).
C-C.skf original: 0.0000 -0.1939 -0.4955 -0.0439 0.3647 0.3647 0.3647 0.00 2.00 2.00 T 1 0.341975 0.387425 modified: 0.0000 -0.1939 -0.4955 -0.0439 0.3647 0.3647 0.3647 0.00 2.00 2.00 !T 1 0.341975 0.387425 H-H.skf original: 0.0000 0.0000 -0.2284 -0.0330 0.0000 0.0000 0.4195 0.00 0.00 1.00 T 0 0.3471 0.4919 modified: 0.0000 0.0000 -0.2284 -0.0330 0.0000 0.0000 0.4195 0.00 0.00 1.00 !T 0 0.3471 0.4919
Back to familiar territory.
Error: segmentation violation rax 0000000000000000, rbx ffffffffffffffff, rcx 000014c62f39c187 ... r12 00007ffdaa3d4e08, r13 0000000000000000, r14 0000000000000000 r15 00000000000003e6 /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x14c62fafe890] /lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x14c62f39c187] /opt/g16/l302.exe() [0x4266e0] ... /opt/g16/l302.exe() [0x40381d] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x14c62f37eb97] /opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729] Aborted (core dumped) One-electron integrals computed using PRISM. Generate DFT-SCTB integrals. Wanted a floating point number as input. Found a string as input. Spline ? Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 20:03:58 2018. Job cpu time: 0 days 0 hours 0 minutes 3.3 seconds. Elapsed time: 0 days 0 hours 0 minutes 0.6 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
Note that the H-H.skf is different than the others (no scripting of global changes without an if/then statement).
C-C.skf 15*0.0 -0.00000001 4*0.0 [blank line - delete me] Spline C-H.skf 8*0.0 0.00000024 -0.00000029 8*0.0 -0.00000042 0.00000042 [blank line - delete me] Spline H-C.skf 8*0.0 0.00000024 -0.00000029 8*0.0 -0.00000042 0.00000042 [blank line - delete me] Spline H-H.skf Fine as is.
The "Potential in Slaters" blocks of these files are the culprit, plus the existence of blank lines in some files right before this block.
Error: segmentation violation rax 0000000000000000, rbx ffffffffffffffff, rcx 0000148e48e8d187 ... r12 00007fff480d5328, r13 0000000000000000, r14 0000000000000000 r15 00000000000003e6 /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890) [0x148e495ef890] /lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x148e48e8d187] /opt/g16/l302.exe() [0x4266e0] ... /opt/g16/l302.exe() [0x40381d] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x148e48e6fb97] /opt/g16/l302.exe(sched_setaffinity+0xa1) [0x403729] Aborted (core dumped) One-electron integrals computed using PRISM. Generate DFT-SCTB integrals. Wanted a floating point number as input. Found a string as input. Potential in Slaters #Next line: Z, nExponent, nCoeff #following lines as i=[1:nCoeff]: coeff[1:nExponent,iCoeff] ? Error termination via Lnk1e in /opt/g16/l302.exe at Mon Sep 3 20:06:47 2018. Job cpu time: 0 days 0 hours 0 minutes 3.4 seconds. Elapsed time: 0 days 0 hours 0 minutes 0.6 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
Commenting out and deleting blank lines in the R1-R1.skf files is the final trick.
C-C.skf – original
... 4.2 4.3 6.019814129663628e-06 -0.0005674033746491677 0.008895585140284115 -0.038235328067588 4.3 4.34 0 6.465381138001741e-05 -0.002575013279992242 -0.04932579667564679 3.253576522516708 -35.53160271107893 Potential in Slaters #Next line: Z, nExponent, nCoeff #following lines as i=[1:nCoeff]: coeff[1:nExponent,iCoeff] 6 3 3 6.00000000 3.00000000 1.50000000 -2.12442360e+02 5.59079360e+02 -3.40637000e+02 -3.01560830e+02 2.61267120e+01 1.55803120e+02 -1.60453960e+02 3.78116880e+02 -1.54975130e+01 Density in Slaters #Next line: Z, nExponent, nCoeff #following lines as i=(1:nCoeff): coeff[1:nExponent,iCoeff] 6 4 4 12.00000000 6.00000000 3.00000000 1.50000000 1.59823070e+03 1.88015110e+03 -1.85962620e+03 -1.57991220e+01 -5.04092550e+02 3.99692480e+03 2.04191460e+03 5.28198730e+00 1.55375210e+03 1.91344500e+03 -7.06812390e+02 -5.97730740e-01 -3.77811200e+03 3.00641870e+03 9.60074820e+01 2.28013400e-02 Wave function in Slaters #Next line: Z, nExponent, nCoeff, lMax #following lines as bloks of (l=1:lMax+1): with block lines (i=1:nCoeff, l): with line entries of coeff[1:nExponent, iCoeff, l] 6 3 3 1 6.00000000 3.00000000 1.50000000 8.88439570e+00 -5.29071630e+01 3.69269320e+01 1.68873640e+01 -1.13153240e+01 -1.27781290e+01 2.13469890e+00 -3.29673710e+01 1.12025690e+00 -1.89810030e+01 2.04379200e+01 6.34324680e+00 -3.49566390e+01 -2.71222760e+01 -2.20425860e+00 -3.38020070e+01 8.49032790e+00 1.91079440e-01
C-C.skf – modified
... 4.2 4.3 6.019814129663628e-06 -0.0005674033746491677 0.008895585140284115 -0.038235328067588 4.3 4.34 0 6.465381138001741e-05 -0.002575013279992242 -0.04932579667564679 3.253576522516708 -35.53160271107893 !Potential in Slaters #Next line: Z, nExponent, nCoeff #following lines as i=[1:nCoeff]: coeff[1:nExponent,iCoeff] ! 6 3 3 ! 6.00000000 3.00000000 1.50000000 !-2.12442360e+02 5.59079360e+02 -3.40637000e+02 !-3.01560830e+02 2.61267120e+01 1.55803120e+02 !-1.60453960e+02 3.78116880e+02 -1.54975130e+01 !Density in Slaters #Next line: Z, nExponent, nCoeff #following lines as i=(1:nCoeff): coeff[1:nExponent,iCoeff] ! 6 4 4 ! 12.00000000 6.00000000 3.00000000 1.50000000 ! 1.59823070e+03 1.88015110e+03 -1.85962620e+03 -1.57991220e+01 !-5.04092550e+02 3.99692480e+03 2.04191460e+03 5.28198730e+00 ! 1.55375210e+03 1.91344500e+03 -7.06812390e+02 -5.97730740e-01 !-3.77811200e+03 3.00641870e+03 9.60074820e+01 2.28013400e-02 !Wave function in Slaters #Next line: Z, nExponent, nCoeff, lMax #following lines as bloks of (l=1:lMax+1): with block lines (i=1:nCoeff, l): with line entries of !coeff[1:nExponent, iCoeff, l] ! 6 3 3 1 ! 6.00000000 3.00000000 1.50000000 ! 8.88439570e+00 -5.29071630e+01 3.69269320e+01 ! 1.68873640e+01 -1.13153240e+01 -1.27781290e+01 ! 2.13469890e+00 -3.29673710e+01 1.12025690e+00 !-1.89810030e+01 2.04379200e+01 6.34324680e+00 !-3.49566390e+01 -2.71222760e+01 -2.20425860e+00 !-3.38020070e+01 8.49032790e+00 1.91079440e-01
H-H.skf – original
... 1.85000001639128 1.93000000149012 0 -0.001039722277270741 -0.02024810718864866 1.734044159065938 -25.7369734407929 115.698697168618 ----------------[blank line - delete me]---------------- Potential in Slaters #Next line: Z, nExponent, nCoeff #following lines as i=[1:nCoeff]: coeff[1:nExponent,iCoeff] 1 2 3 2.00000000 1.00000000 -9.24055790e+01 9.34055790e+01 -5.82200230e+01 -3.35996430e+01 -1.69769380e+01 3.27773210e+00 Density in Slaters #Next line: Z, nExponent, nCoeff #following lines as i=(1:nCoeff): coeff[1:nExponent,iCoeff] 1 3 4 4.00000000 2.00000000 1.00000000 1.06902450e+02 -9.30819650e+01 -4.15847960e+00 1.47002580e+02 7.52926390e+01 1.04675560e+00 8.59204060e+01 -1.88496570e+01 -8.98345500e-02 1.90775940e+01 2.50292100e+00 2.61437050e-03 Wave function in Slaters #Next line: Z, nExponent, nCoeff, lMax #following lines as bloks of (l=1:lMax+1): with block lines (i=1:nCoeff, l): with line entries of coeff[1:nExponent, iCoeff, l] 1 2 3 0 2.00000000 1.00000000 -1.50471540e+01 1.19407670e+01 -1.23858090e+01 -3.54954100e+00 -2.61484850e+00 2.66724870e-01
H-H.skf – modified
... 1.85000001639128 1.93000000149012 0 -0.001039722277270741 -0.02024810718864866 1.734044159065938 -25.7369734407929 115.698697168618 !Potential in Slaters #Next line: Z, nExponent, nCoeff #following lines as i=[1:nCoeff]: coeff[1:nExponent,iCoeff] ! 1 2 3 ! 2.00000000 1.00000000 !-9.24055790e+01 9.34055790e+01 !-5.82200230e+01 -3.35996430e+01 !-1.69769380e+01 3.27773210e+00 !Density in Slaters #Next line: Z, nExponent, nCoeff #following lines as i=(1:nCoeff): coeff[1:nExponent,iCoeff] ! 1 3 4 ! 4.00000000 2.00000000 1.00000000 ! 1.06902450e+02 -9.30819650e+01 -4.15847960e+00 ! 1.47002580e+02 7.52926390e+01 1.04675560e+00 ! 8.59204060e+01 -1.88496570e+01 -8.98345500e-02 ! 1.90775940e+01 2.50292100e+00 2.61437050e-03 !Wave function in Slaters #Next line: Z, nExponent, nCoeff, lMax #following lines as bloks of (l=1:lMax+1): with block lines (i=1:nCoeff, l): with line entries of !coeff[1:nExponent, iCoeff, l] ! 1 2 3 0 ! 2.00000000 1.00000000 !-1.50471540e+01 1.19407670e+01 !-1.23858090e+01 -3.54954100e+00 !-2.61484850e+00 2.66724870e-01