Viewing MOs from ORCA output files

General Discussion Support
1

Hi, I am currently using the Avogadro version 1.2.0 with ORCA support. I am having trouble viewing the orbitals from an ORCA output file.

The input files looks like the following:

! NOITER UKS NormalPrint def2-TZVPP def2-TZVPP/J MOREAD
%pal nprocs 6 end
%maxcore 2000
%moinp “SPE.gbw”
%output
Print[P_MOs] 1
Print[P_Basis] 2
end

  • xyzfile 1 2 SPE.xyz

I know that the keywords “NormalPrint” and the %output block containing “Print[P_MOs] 1” and “Print[P_Basis] 2” were necessary for some other users to get Avogadro to show the MOs for their molecule, but I don’t know which version they are using.

Please let me know what I need to add to my input file in order to utilize this feature of Avogadro for calculations from ORCA. The molecule that I’m trying to visualize the MOs for is quite large (~ 800 Da). Does the size of the molecule matter?

2

What would help more than the input file is the output files.

I admit I don’t use ORCA much at the moment, but I think the important questions are:

  • Can you visualize orbitals from other ORCA calculations (e.g., methane or water)?
  • Can you post the output files?
3

Hi,

The problem lies in the extension of the output file generated by the cluster. We just have to change the output file from ***.log to ***.out in order for Avogadro to recognize the file for rendering.

There shouldn’t be anymore trouble.

Thank you for your time.
Phan

4

That’s kinda weird. I’ll take a look at that part of the code to make sure it looks for both *.log and *.out files.

5

Hi,
I’m having a similar problem: Avogadro seems to generate the MOs from .out files of HF computations but not for .out files of Semi-Empirical jobs. I want to use the semi-empirical calculations because I’m teaching my students a pretty basic intro to MO theory. The matix showing the LCAO = MO for a semi-empirical calculation accords well with what they see in their intro texts. Having the visuals to relate to the linear combinations is pretty important.

6

At the moment, I don’t have any example files from ORCA semiempirical calculations.

The code was contributed by the ORCA developers, so it’s worth asking on their forum too - for example, I don’t know if the semiempirical calculations use Slater orbitals for output (likely) in which case there’s some work needed to either read STOs for those calculations or transcribe for GTOs.

In order to fix the problem though, I’d need some example files and some feedback from the ORCA team.

Thanks!

7

Hi, i’m having a similar problem using Avogadro 1.2 on Ubuntu 18.04 LTS. I’m trying to opening Orca’s output files to get the MOs and every time the process fails. Using the terminal the i received the following message:

rochajcs@rochajcs:/media/rochajcs/HD/rochajcs/Exercícios/nh3#opt#freq#1$ avogadro nh3#1.out
"Avogadro version: 1.2.0 Git:
LibAvogadro version: 1.2.0 Git: "
Locale: “C”
Libavogadro translations not found.
System has OpenGL support.
About to test OpenGL capabilities.
OpenGL capabilities found:
Double Buffering.
Direct Rendering.
Antialiasing.
Loading plugins: “/usr/bin/…/lib/avogadro/1_2”
Searching for plugins in “/usr/lib/avogadro/1_2”
Searching for plugins in “/usr/lib/avogadro/1_2/colors”
Searching for plugins in “/usr/lib/avogadro/1_2/engines”
Searching for plugins in “/usr/lib/avogadro/1_2/extensions”

*** Open Babel Error in ReadMolecule
Problems reading an output file: Could not determine the format of this file. Please report it to the openbabel-discuss @ lists.sourceforge.net mailing list.
Searching for plugins in “/usr/lib/avogadro/1_2/tools”
Loading plugins: “/home/rochajcs/.avogadro/1_2/plugins”
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x557c46271300 not contained in stack
dev warning: Extension “GAMESS” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Orbitals” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
Could not find python module…
dev warning: Extension “Python Terminal” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Vibration” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
HOMO at: -1
GLWidget initialisation…
GLSL support enabled, OpenGL 2.0 support confirmed.
GLWidget initialised…
createObjects()
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: cHRM: invalid chromaticities

The input file was written as follow:

! HF TZVP Opt numfreq UseSym Normalprint tightSCF

%scf
MaxIter 500
end

%maxcore 4000

%output
Print [P_Basis] 1
Print [P_Basis] 2
Print [P_MOs] 1
end

  • xyz 0 1
    N 0.099 -0.0024 0.223
    H -0.366 -0.807 -0.176
    H 1.033 -0.0010 -0.171
    H -0.365 0.808 -0.175

Can someone help me?

Regards

8

Today, 16 July 19, I tried Avogadro from Source Forge and also Avogadro from Orca Download Portal. With both, I only get 4 Display settings: Axes, Ball and Stick, Label, Stick. So I cannot use most of the utilities and cannot view orbitals. Can anyone advise? I use Orca output in a Carbon ThinkPad.

9

OK, my fault - I see that I can add display types in “Settings”. Sorry about that.

10

I don’t know what version of Open Babel is installed on your system. I believe there’s an Avogadro version through orca - which should definitely work.

11

Thaks for the answerd. The Open Babel version installed is 2.3.2.

12

You definitely need a newer version of Open Babel. Try 2.4.x.

13

Actually the current version installed is 2.4.1. I’m gonna try to recompile Open Babel and use Avogadro 1.2.0 again