search

zorkzou / Molden2AIM

Molden2AIM is a utility program which can be used to create AIM-WFN, AIM-WFX, and NBO-47 files from a Molden file.
MIT License
52 stars 15 forks source link

Normalization Check Failed when generating .wfn/.wfx file from NWChem 6.8 molden file output #6

Open ghost opened 6 years ago

ghost commented 6 years ago

As the title says, taking a molden file from NWChem 6.8 and running through molden2AIM. The file was created using the JANPA normalization in NWChem with the molden keyword in the DFT section. The calculation uses an ECP and the core electrons were specified in the [Core] section of the output molden file prior to submission to the program.

When using molden2aim, both the WFN and WFX files fail the normalization check, and using the normalized molden files or wfn/wfx files give strange results in Multifn. Is this an NWChem issue or an input issue from me?

zorkzou commented 6 years ago

Dear Saranethavora,

Yes, there are some problems in the default molden file by NWChem. Please check the two examples and readme file in m2a/examples/NWChem6.8

Best regards, Wenli

On Wed, Nov 28, 2018 at 4:04 AM saranethavora notifications@github.com wrote:

As the title says, taking a molden file from NWChem 6.8 and running through molden2AIM. The file was created using the JANPA normalization in NWChem with the molden keyword in the DFT section. The calculation uses an ECP and the core electrons were specified in the [Core] section of the output molden file prior to submission to the program.

When using molden2aim, both the WFN and WFX files fail the normalization check, and using the normalized molden files or wfn/wfx files give strange results in Multifn. Is this an NWChem issue or an input issue from me?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/zorkzou/Molden2AIM/issues/6, or mute the thread https://github.com/notifications/unsubscribe-auth/AOKChyFjbGtpCu3AYPNypt0r_xlybT9Hks5uzZrBgaJpZM4Y2PUX .

ghost commented 6 years ago

Wenli,

I set the parameters as directed and added a [Core] section to the output molden files. Molden2aim correctly identifies the electron counts before processing, but then the normalization checks fail.

zorkzou commented 5 years ago

Would you please send me your nwchem input file?

On Fri, Nov 30, 2018 at 10:49 PM saranethavora notifications@github.com wrote:

Wenli,

I set the parameters as directed and added a [Core] section to the output molden files. Molden2aim correctly identifies the electron counts before processing, but then the normalization checks fail.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/zorkzou/Molden2AIM/issues/6#issuecomment-443226047, or mute the thread https://github.com/notifications/unsubscribe-auth/AOKCh-2BjruPpZmJoX3GIN0nmE60suReks5u0UVugaJpZM4Y2PUX .

ghost commented 5 years ago

start brettphos_lanl2dz_spe_2 title "SPE of BrettPhos-Pd-4-tolyl cationic complex in gas phase" memory total 1024 mb geometry noautoz Pd -0.39260 0.74580 -0.10260 P 1.78990 -0.04490 0.18040 C 1.63080 -1.89510 0.19060 C 2.75500 -2.73970 0.39590 C 2.60520 -4.12440 0.42690 H 3.46010 -4.77240 0.57650 C 1.34470 -4.69700 0.27550 H 1.25240 -5.77580 0.31000 C 0.22430 -3.88970 0.09630 C 0.35240 -2.47540 0.04510 O 3.96180 -2.12970 0.56990 C 5.11880 -2.93120 0.80490 H 5.01340 -3.52450 1.72120 H 5.94480 -2.22770 0.92300 H 5.32690 -3.59560 -0.04220 C -0.96310 -1.74150 -0.13870 C -1.56790 -1.72410 -1.44340 C -3.78660 -1.40340 -0.43580 C -3.18620 -1.36160 0.82270 H -3.80560 -1.24820 1.70550 C -1.80360 -1.54170 1.00240 C -0.76970 -1.99590 -2.71820 H 0.29170 -1.99190 -2.45750 C -1.09840 -3.38460 -3.30440 H -0.92690 -4.18230 -2.57670 H -0.47200 -3.57960 -4.18330 H -2.14690 -3.43850 -3.62180 C -0.99470 -0.91430 -3.79240 H -2.01710 -0.94480 -4.18700 H -0.31340 -1.07640 -4.63610 H -0.81730 0.09370 -3.40120 C -5.29860 -1.37900 -0.64160 H -5.49030 -0.76800 -1.53500 C -5.80490 -2.80450 -0.95080 H -5.29550 -3.23420 -1.82040 H -6.88110 -2.78980 -1.16080 H -5.63440 -3.47090 -0.09610 C -6.09560 -0.77320 0.52140 H -6.03120 -1.39240 1.42410 H -7.15500 -0.70600 0.24930 H -5.75140 0.23560 0.77570 C -1.28390 -1.66200 2.43490 H -0.19530 -1.73880 2.39230 C -1.81060 -2.94620 3.10770 H -2.89980 -2.91230 3.23060 H -1.36460 -3.05940 4.10330 H -1.56670 -3.83630 2.51970 C -1.62900 -0.43010 3.29210 H -1.25030 0.49290 2.83740 H -1.17880 -0.52850 4.28710 H -2.71090 -0.32080 3.43290 N -2.36040 1.58210 -0.49140 H -2.94970 0.80710 -0.80460 H -2.24130 2.19300 -1.30160 C -3.07620 2.33830 0.56980 H -3.30470 1.63420 1.37530 H -2.38500 3.08520 0.96760 C -4.35230 3.01720 0.06410 H -5.03750 2.25550 -0.33400 H -4.09610 3.68210 -0.77380 C -5.06230 3.82580 1.15860 H -5.30740 3.16210 1.99990 H -4.37010 4.58240 1.55360 C 0.23430 2.64650 -0.38660 C 0.17960 3.60620 0.63520 H -0.09810 3.32080 1.64660 C 0.47000 4.94990 0.37340 H 0.42220 5.67030 1.18840 C 0.81650 5.38530 -0.91380 C 0.85320 4.42630 -1.93400 H 1.10660 4.73190 -2.94770 C 0.56810 3.07800 -1.67890 H 0.61300 2.37160 -2.50400 C 1.15340 6.83330 -1.18290 H 1.08400 7.06830 -2.25050 H 2.17630 7.07200 -0.86090 H 0.48160 7.50990 -0.64160 C -6.33820 4.51100 0.66130 H -6.81980 5.08240 1.46360 H -6.12160 5.20630 -0.15960 H -7.06600 3.77720 0.29200 C 2.75070 0.39180 1.74190 C 3.00160 1.90560 1.89460 C 2.13030 -0.18180 3.02990 H 3.71630 -0.10130 1.59520 C 3.91600 2.18250 3.10120 H 2.04850 2.42320 2.04290 H 3.44960 2.32540 0.98700 C 3.03390 0.10160 4.24350 H 1.14550 0.27220 3.19910 H 1.97560 -1.26240 2.93460 C 3.33400 1.59900 4.39600 H 4.06670 3.26490 3.20360 H 4.90680 1.74240 2.91550 H 2.55750 -0.28750 5.15260 H 3.97860 -0.44840 4.12300 H 4.02510 1.76430 5.23260 H 2.40420 2.13160 4.64620 C 2.90400 0.52110 -1.23790 C 4.43250 0.35980 -1.10140 C 2.42250 -0.04760 -2.58640 H 2.69150 1.59810 -1.24300 C 5.14860 1.05550 -2.27340 H 4.69430 -0.70180 -1.09990 H 4.78970 0.77730 -0.15440 C 3.15960 0.60600 -3.76850 H 2.59060 -1.13340 -2.60430 H 1.34510 0.11120 -2.69460 C 4.68340 0.49980 -3.62580 H 6.23320 0.92800 -2.16170 H 4.95320 2.13740 -2.23460 H 2.82880 0.14200 -4.70690 H 2.87580 1.66700 -3.82320 H 5.17870 1.03070 -4.44900 H 4.98400 -0.55560 -3.70490 O -1.04320 -4.38810 -0.03010 C -1.22710 -5.80160 0.01320 H -2.30010 -5.96240 -0.10730 H -0.69230 -6.30360 -0.80260 H -0.90320 -6.22030 0.97390 C -2.94600 -1.53950 -1.55420 H -3.40010 -1.55420 -2.54210 end basis

zorkzou commented 5 years ago

I checked your input file (without any modifications) using the latest version of nwchem (6.8.1). There is no problem in the molden file.

On Tue, Dec 4, 2018 at 1:09 AM saranethavora notifications@github.com wrote:

start brettphos_lanl2dz_spe_2 title "SPE of BrettPhos-Pd-4-tolyl cationic complex in gas phase" memory total 1024 mb geometry noautoz Pd -0.39260 0.74580 -0.10260 P 1.78990 -0.04490 0.18040 C 1.63080 -1.89510 0.19060 C 2.75500 -2.73970 0.39590 C 2.60520 -4.12440 0.42690 H 3.46010 -4.77240 0.57650 C 1.34470 -4.69700 0.27550 H 1.25240 -5.77580 0.31000 C 0.22430 -3.88970 0.09630 C 0.35240 -2.47540 0.04510 O 3.96180 -2.12970 0.56990 C 5.11880 -2.93120 0.80490 H 5.01340 -3.52450 1.72120 H 5.94480 -2.22770 0.92300 H 5.32690 -3.59560 -0.04220 C -0.96310 -1.74150 -0.13870 C -1.56790 -1.72410 -1.44340 C -3.78660 -1.40340 -0.43580 C -3.18620 -1.36160 0.82270 H -3.80560 -1.24820 1.70550 C -1.80360 -1.54170 1.00240 C -0.76970 -1.99590 -2.71820 H 0.29170 -1.99190 -2.45750 C -1.09840 -3.38460 -3.30440 H -0.92690 -4.18230 -2.57670 H -0.47200 -3.57960 -4.18330 H -2.14690 -3.43850 -3.62180 C -0.99470 -0.91430 -3.79240 H -2.01710 -0.94480 -4.18700 H -0.31340 -1.07640 -4.63610 H -0.81730 0.09370 -3.40120 C -5.29860 -1.37900 -0.64160 H -5.49030 -0.76800 -1.53500 C -5.80490 -2.80450 -0.95080 H -5.29550 -3.23420 -1.82040 H -6.88110 -2.78980 -1.16080 H -5.63440 -3.47090 -0.09610 C -6.09560 -0.77320 0.52140 H -6.03120 -1.39240 1.42410 H -7.15500 -0.70600 0.24930 H -5.75140 0.23560 0.77570 C -1.28390 -1.66200 2.43490 H -0.19530 -1.73880 2.39230 C -1.81060 -2.94620 3.10770 H -2.89980 -2.91230 3.23060 H -1.36460 -3.05940 4.10330 H -1.56670 -3.83630 2.51970 C -1.62900 -0.43010 3.29210 H -1.25030 0.49290 2.83740 H -1.17880 -0.52850 4.28710 H -2.71090 -0.32080 3.43290 N -2.36040 1.58210 -0.49140 H -2.94970 0.80710 -0.80460 H -2.24130 2.19300 -1.30160 C -3.07620 2.33830 0.56980 H -3.30470 1.63420 1.37530 H -2.38500 3.08520 0.96760 C -4.35230 3.01720 0.06410 H -5.03750 2.25550 -0.33400 H -4.09610 3.68210 -0.77380 C -5.06230 3.82580 1.15860 H -5.30740 3.16210 1.99990 H -4.37010 4.58240 1.55360 C 0.23430 2.64650 -0.38660 C 0.17960 3.60620 0.63520 H -0.09810 3.32080 1.64660 C 0.47000 4.94990 0.37340 H 0.42220 5.67030 1.18840 C 0.81650 5.38530 -0.91380 C 0.85320 4.42630 -1.93400 H 1.10660 4.73190 -2.94770 C 0.56810 3.07800 -1.67890 H 0.61300 2.37160 -2.50400 C 1.15340 6.83330 -1.18290 H 1.08400 7.06830 -2.25050 H 2.17630 7.07200 -0.86090 H 0.48160 7.50990 -0.64160 C -6.33820 4.51100 0.66130 H -6.81980 5.08240 1.46360 H -6.12160 5.20630 -0.15960 H -7.06600 3.77720 0.29200 C 2.75070 0.39180 1.74190 C 3.00160 1.90560 1.89460 C 2.13030 -0.18180 3.02990 H 3.71630 -0.10130 1.59520 C 3.91600 2.18250 3.10120 H 2.04850 2.42320 2.04290 H 3.44960 2.32540 0.98700 C 3.03390 0.10160 4.24350 H 1.14550 0.27220 3.19910 H 1.97560 -1.26240 2.93460 C 3.33400 1.59900 4.39600 H 4.06670 3.26490 3.20360 H 4.90680 1.74240 2.91550 H 2.55750 -0.28750 5.15260 H 3.97860 -0.44840 4.12300 H 4.02510 1.76430 5.23260 H 2.40420 2.13160 4.64620 C 2.90400 0.52110 -1.23790 C 4.43250 0.35980 -1.10140 C 2.42250 -0.04760 -2.58640 H 2.69150 1.59810 -1.24300 C 5.14860 1.05550 -2.27340 H 4.69430 -0.70180 -1.09990 H 4.78970 0.77730 -0.15440 C 3.15960 0.60600 -3.76850 H 2.59060 -1.13340 -2.60430 H 1.34510 0.11120 -2.69460 C 4.68340 0.49980 -3.62580 H 6.23320 0.92800 -2.16170 H 4.95320 2.13740 -2.23460 H 2.82880 0.14200 -4.70690 H 2.87580 1.66700 -3.82320 H 5.17870 1.03070 -4.44900 H 4.98400 -0.55560 -3.70490 O -1.04320 -4.38810 -0.03010 C -1.22710 -5.80160 0.01320 H -2.30010 -5.96240 -0.10730 H -0.69230 -6.30360 -0.80260 H -0.90320 -6.22030 0.97390 C -2.94600 -1.53950 -1.55420 H -3.40010 -1.55420 -2.54210 end basis

  • library 6-31G* except Pd Pd library "LANL2DZ ECP" end ecp Pd library "LANL2DZ ECP" end charge 1 dft xc b3lyp direct vectors output 2.movecs molden end set molden:do_norm_janpa t task dft

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/zorkzou/Molden2AIM/issues/6#issuecomment-443788595, or mute the thread https://github.com/notifications/unsubscribe-auth/AOKChx-nKBhFymX7jGo1Q2rsnLHWpafAks5u1VrmgaJpZM4Y2PUX .

ghost commented 5 years ago

It must be an issue with nwchem 6.8 (the previous version) then. I'll see if I can get it updated and try again.

ghost commented 5 years ago

Did the normalization check succeed for the wfn and wfx files as well?

zorkzou commented 5 years ago

Yes.

On Wed, Dec 5, 2018 at 12:22 AM saranethavora notifications@github.com wrote:

Did the normalization check succeed for the wfn and wfx files as well?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/zorkzou/Molden2AIM/issues/6#issuecomment-444161011, or mute the thread https://github.com/notifications/unsubscribe-auth/AOKChxFswxqqgRhRdoN4sF5NNxrQioHBks5u1qEpgaJpZM4Y2PUX .