[DFTB-Plus-User] Old/New Version of Modes Output
Gabriel Phun
gphun at ucr.edu
Thu Mar 28 17:39:36 CET 2024
Hello Ben,
Thank you for your email. I appreciate the reply. I will check out the
changes.
Thank you,
Gabriel
On Thu, Mar 28, 2024 at 9:34 AM Benjamin Hourahine <
benjamin.hourahine at strath.ac.uk> wrote:
> Hello Gabriel,
>
> The difference was due to an internal change to re-use the same code for
> xyz file writing. Unfortunately the mode vectors were then scaled by the
> conversion factor for velocities. This is corrected in the changes at
> https://github.com/dftbplus/dftbplus/pull/1426 which will be incorporated
> in the next release.
>
> I noticed that there is a small change in the vibrational mode energy in
> your output:
>
> Eigenmode 78 1633.0007897800006 cm-1
> Eigenmode 77 1632.7251246441465 cm-1
>
> but also that the mode number is different, which probably explains that
> change.
>
> Regards,
>
> Ben
>
> Dr. B. Hourahine
> Senior Lecturer and Director of Student Support
> Department of Physics, SUPA
> University of Strathclyde, John Anderson Building,
> 107 Rottenrow, Glasgow G4 0NG, UK
> <https://www.google.com/maps/search/107+Rottenrow,+Glasgow+G4+0NG,+UK?entry=gmail&source=g>
> .
> +44 141 548 2325, benjamin.hourahine at strath.ac.uk
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> ------------------------------
> *From:* DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
> on behalf of Gabriel Phun <gabriel.phun1 at ucr.edu>
> *Sent:* 21 March 2024 16:31
> *To:* dftb-plus-user at mailman.zfn.uni-bremen.de <
> dftb-plus-user at mailman.zfn.uni-bremen.de>
> *Subject:* [DFTB-Plus-User] Old/New Version of Modes Output
>
> *CAUTION: This email originated outside the University. Check before
> clicking links or attachments.*
> Hello,
>
> I am trying to use the Newton-X & DFTB+ codes together through the
> Newton-X provided interface.
>
> They have provided a test case which used:
> dftbplus-1.3.0.x86_64-linux/dftb+ Feb 20 17:17:25 CET 2018
>
> I have done a modes calculation using the current DFTB+ code and the
> numbers that I am getting are orders of magnitude different.
>
> For example using the same geometry current DFTB+ code doing a hessian
> calculation followed by a modes calculation yields:
>
> 30
> * NEW DFTB+ CODE:* Eigenmode 78 1633.0007897800006 cm-1
> S 5.94579600 -1.10777300 -0.12001500 -81.01137682
> -367.19447690 -17.10234889
> C 7.15513400 0.02269300 -0.00168600 1461.23807917
> 1804.55578411 175.90079125
> C 6.66129000 1.32178900 -0.08465300 -10217.06942626
> 14.89298898 -685.44985895
> C 5.29886400 1.40394400 -0.15737600 11059.55783528
> 422.02202910 588.41589040
> C 4.71199400 0.08284500 -0.20536700 -1393.30711465
> 1102.31829239 25.46289111
> C 3.25884600 -0.17660600 -0.12560100 -406.42733121
> -832.27235191 -48.62665245
> S 2.00487300 0.95538600 -0.09073300 60.86586900
> -44.58583207 2.37095245
> C 0.69429800 -0.19885200 -0.16596300 -1999.03754184
> 1267.08288404 151.63567634
> C 1.22238000 -1.49843700 -0.33355200 206.63271889
> -840.55265973 -100.78489127
> C 2.61933200 -1.50824500 -0.16920200 589.26634316
> 575.95974739 43.53752709
> H 0.50531200 -2.31896800 -0.41132000 -1272.00046658
> 77.08021259 -103.15357197
> H 3.15404700 -2.39352700 -0.37257900 -781.31469417
> -336.30800489 -17.96433897
> H 8.25501000 -0.28466100 0.16729400 -632.31053512
> -6345.88175585 -32.63247120
> H 7.20710700 2.05661200 0.03228500 -5470.65537754
> -4419.79589737 7.87889622
> H 4.64624500 2.22346300 -0.21519000 -721.42935001
> -11398.22500230 -115.44363780
> C -0.66577900 0.14042000 -0.11440300 1912.79428117
> -817.19155764 -43.55825858
> C -1.28915400 1.42942300 -0.13449200 286.14910460
> 412.40234945 42.92262482
> C -2.65408600 1.49537800 -0.26995900 -956.94682567
> -361.90156459 15.33544646
> C -3.19665000 0.21159100 0.06469800 331.29672267
> 244.78504571 -51.72246720
> S -1.92834700 -1.01148900 -0.17380600 -61.29632775
> -6.35789232 5.92745426
> C -4.61729200 -0.09147400 -0.12926700 -222.99896623
> -29.00719252 -19.10093768
> C -5.26535600 -1.39496900 -0.14623500 133.93134302
> 18.13059096 -5.82562329
> C -6.64143700 -1.38373900 -0.01063200 -101.62885588
> -21.82603289 2.91869553
> C -7.18801200 -0.00689700 -0.01880800 0.70555359
> 26.79130902 0.84542026
> S -5.86053500 1.14215800 -0.20056300 7.16711859
> -4.57083612 1.18445312
> H -0.52982000 2.40410900 0.00599800 1602.41576580
> 121.37646883 -3.30583259
> H -3.33682300 2.45238700 -0.22871000 1139.19768944
> 1224.38968570 -10.61295412
> H -4.71596700 -2.23298200 -0.04406900 -96.44284009
> -136.76879959 -10.46313785
> H -7.21492700 -2.30422900 0.19275700 -17.47261890
> -91.49724151 0.23924985
> H -8.19334700 0.19947700 0.22757500 1.64629568
> -13.84281451 -46.68024450
>
>
> 30
> *OLD DFTB+ CODE*: Eigenmode 77 1632.7251246441465 cm-1
> S 5.909384 -1.137258 -0.130090 0.000473 0.002463 0.000084
> C 7.174790 0.015817 -0.072753 0.035766 -0.157952 -0.003826
> C 6.666004 1.308322 -0.044473 -0.026231 0.167299 0.004270
> C 5.249767 1.347010 -0.069373 -0.123539 -0.153392 -0.006560
> C 4.662169 0.075170 -0.117388 0.041003 0.115715 0.004095
> C 3.240719 -0.236156 -0.148925 0.104605 0.161045 0.005450
> S 1.996126 0.979211 -0.136975 -0.000832 0.001385 0.000021
> C 0.702599 -0.184275 -0.182138 0.050598 -0.130951 -0.002628
> C 1.240700 -1.480187 -0.206464 -0.060584 0.155498 0.002905
> C 2.651525 -1.508441 -0.188642 -0.114296 -0.183668 -0.005954
> H 0.626613 -2.391342 -0.237940 0.229234 -0.002464 0.002596
> H 3.229103 -2.443733 -0.203431 0.265564 0.016733 0.004118
> H 8.235147 -0.255698 -0.060780 0.130771 0.074691 0.004546
> H 7.297625 2.205738 -0.006504 0.209416 0.047312 0.005296
> H 4.674999 2.283861 -0.051607 0.229215 0.038465 0.005216
> C -0.702593 0.184273 -0.182124 0.052752 -0.133725 0.002576
> C -1.240694 1.480188 -0.206403 -0.062187 0.156690 -0.002919
> C -2.651518 1.508433 -0.188564 -0.112990 -0.183608 0.005936
> C -3.240711 0.236158 -0.148880 0.102320 0.158725 -0.005412
> S -1.996119 -0.979214 -0.136982 -0.000584 0.001207 0.000004
> C -4.662161 -0.075179 -0.117337 0.045456 0.122718 -0.004344
> C -5.249760 -1.347010 -0.069353 -0.123004 -0.159359 0.006834
> C -6.665995 -1.308334 -0.044436 -0.033028 0.173575 -0.004426
> C -7.174780 -0.015820 -0.072673 0.039790 -0.161280 0.003910
> S -5.909378 1.137254 -0.129990 0.000511 0.002277 -0.000092
> H -0.626607 2.391342 -0.237857 0.241795 -0.006593 -0.002626
> H -3.229098 2.443734 -0.203317 0.266369 0.019495 -0.004183
> H -4.674989 -2.283870 -0.051620 0.250165 0.041758 -0.005735
> H -7.297614 -2.205744 -0.006488 0.219164 0.039934 -0.005226
> H -8.235140 0.255691 -0.060680 0.131450 0.067166 -0.004334
>
> I wouldn't be surprised to see differences but I am wondering why the last
> 3 columns are so different. Did DFTB+ change units or use a different
> definition of the modes?
>
> Here are the input files that I used.
>
> *dftb_in.hsd*
> Geometry = GenFormat {
> <<< "geom.gen"
> }
> SlaterKosterFiles = Type2FileNames {
> Prefix =
> "/rhome/gphun/bigdata/dftbplus-24.1.x86_64-linux/slako/3ob/3ob-3-1/"
> Separator = "-"
> Suffix = ".skf"
> }
> Hessian = {
> <<< "hessian.out"
> }
> DisplayModes {
> PlotModes = -90:-1
> Animate = No
> XMakeMol = No
> }
>
>
> *modes_in.hsd*
> Geometry = GenFormat {
> <<< "geom.gen"
> }
> SlaterKosterFiles = Type2FileNames {
> Prefix =
> "/rhome/gphun/bigdata/dftbplus-24.1.x86_64-linux/slako/3ob/3ob-3-1/"
> Separator = "-"
> Suffix = ".skf"
> }
> Hessian = {
> <<< "hessian.out"
> }
> DisplayModes {
> PlotModes = -90:-1
> Animate = No
> XMakeMol = No
> }
>
> *geom.gen*
> 30 C
> S C H
> 1 1 5.9457960000E+00 -1.1077730000E+00 -1.2001500000E-01
> 2 2 7.1551340000E+00 2.2693000000E-02 -1.6860000000E-03
> 3 2 6.6612900000E+00 1.3217890000E+00 -8.4653000000E-02
> 4 2 5.2988640000E+00 1.4039440000E+00 -1.5737600000E-01
> 5 2 4.7119940000E+00 8.2845000000E-02 -2.0536700000E-01
> 6 2 3.2588460000E+00 -1.7660600000E-01 -1.2560100000E-01
> 7 1 2.0048730000E+00 9.5538600000E-01 -9.0733000000E-02
> 8 2 6.9429800000E-01 -1.9885200000E-01 -1.6596300000E-01
> 9 2 1.2223800000E+00 -1.4984370000E+00 -3.3355200000E-01
> 10 2 2.6193320000E+00 -1.5082450000E+00 -1.6920200000E-01
> 11 3 5.0531200000E-01 -2.3189680000E+00 -4.1132000000E-01
> 12 3 3.1540470000E+00 -2.3935270000E+00 -3.7257900000E-01
> 13 3 8.2550100000E+00 -2.8466100000E-01 1.6729400000E-01
> 14 3 7.2071070000E+00 2.0566120000E+00 3.2285000000E-02
> 15 3 4.6462450000E+00 2.2234630000E+00 -2.1519000000E-01
> 16 2 -6.6577900000E-01 1.4042000000E-01 -1.1440300000E-01
> 17 2 -1.2891540000E+00 1.4294230000E+00 -1.3449200000E-01
> 18 2 -2.6540860000E+00 1.4953780000E+00 -2.6995900000E-01
> 19 2 -3.1966500000E+00 2.1159100000E-01 6.4698000000E-02
> 20 1 -1.9283470000E+00 -1.0114890000E+00 -1.7380600000E-01
> 21 2 -4.6172920000E+00 -9.1474000000E-02 -1.2926700000E-01
> 22 2 -5.2653560000E+00 -1.3949690000E+00 -1.4623500000E-01
> 23 2 -6.6414370000E+00 -1.3837390000E+00 -1.0632000000E-02
> 24 2 -7.1880120000E+00 -6.8970000000E-03 -1.8808000000E-02
> 25 1 -5.8605350000E+00 1.1421580000E+00 -2.0056300000E-01
> 26 3 -5.2982000000E-01 2.4041090000E+00 5.9980000000E-03
> 27 3 -3.3368230000E+00 2.4523870000E+00 -2.2871000000E-01
> 28 3 -4.7159670000E+00 -2.2329820000E+00 -4.4069000000E-02
> 29 3 -7.2149270000E+00 -2.3042290000E+00 1.9275700000E-01
> 30 3 -8.1933470000E+00 1.9947700000E-01 2.2757500000E-01
>
> Please let me know what you all think about this!
>
> Thank you,
> Gabriel
>
>
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