Visualization and printing

ORCA4 note: Examples below use the ORCA4 def2/J auxiliary keyword. In ORCA3, use def2-SVP/J instead.

Various GUI programs that can visualize results from ORCA output and/or create inputfiles are available:

Chemcraft: Good molecular builder. Can create ORCA input files. Opens ORCA output directly and show optimization steps and frequencies. Allows visualization of orbitals from outputfile. Visualization of orbitals and densities through Cube files. Can render orbitals from MO coefficients if present in output. Generally recommended. (Mac/Linux versions work via Wine e.g. Winebottler or WineHQ)
Avogadro: Good molecular builder. Can create ORCA input files. Visualization of orbitals and densities through Cube files. Opens xyz coordinate and trajectory files. Recent version with extended ORCA support: ORCA input generator, vibration visualization, direct visualization of orbitals from output and spectra display. See ORCA forum post.
GabEdit: Can create ORCA input files. Opens ORCA output directly. Can even submit job through GUI.
VMD: Visualization of xyz coordinates and MD trajectories. Visualization of orbitals and densities through Cube files. See the script page for a nice script to automate visualization of Cube files (can be created by ORCA).
Chimera:  Visualization of xyz coordinates. Visualization of orbitals and densities through Cube files and PLT files.
Molden: Molecular builder. Convenient for opening up Molden files that can be created by ORCA and be used for visualization of orbitals, geometries, frequencies etc. Use:
 "orca_2mkl basename -molden"
to create a Molden file (where basename is the calculation name without file extension).
IboView: Visualization of orbitals and densities. Can read ORCA output via Molden file. Can produce very high quality graphics. 
Also note that ORCA includes a number of other command-line helper programs that prepares ORCA output for later visualization (see below).



Controlling printing in ORCA output
Controlling what and how much information ORCA prints to the outputfile. Printing too much leads to too large outputfiles, affecting disk space over time, while sometimes it is useful to have ORCA print output that it normally does not print.

General printing keywords
For minimal printing use !MiniPrint . This will only print coordinates, grid information, SCF iterations, orbital energies and property output.
The default printing setting in ORCA (Smallprint) will in addition print some basis set information, SCF settings, minimal Mulliken, Löwdin and Mayer population analysis. 
The !NormalPrint option will in addition to Smallprint, print a Löwdin orbital analysis (useful to analyze the MOs) and more detailed SCF iteration output.
The !LargePrint option will in addition to Normalprint print the full basis set, composition of the guess orbitals, the final molecular orbitals and density (these outputfiles can easily become very large in filesize).

Specific printing options (see manual for a full list)
To print the basis set, use: 
!Printbasis

To print the molecular orbitals: 
%scf print[p_mos] 1 end 


ORCA reduces printing in geometry optimization steps by default (prints full output in the first and last steps only). If more information is needed in each optimization step (for example to monitor the electronic structure through the population analysis during the optimization) use this: 

%geom ReducePrint false end



Visualizing Vibrational Frequencies

Some molecular viewers like Chemcraft can visualize the frequencies directly from an ORCA outputfile. 
The orca_pltvib program (part of the distributed ORCA binaries) can also create xyz trajectories for each vibrational mode using the calculated Hessian.
$ orca_pltvib
usage: orca_pltvib Output-file vibrations
 vibrations are: all - all vibrations
             or: a list like 1 34 19 26


Example: 
orca_pltvib jobname.out 6 7   # This will create vibrational mode no. 6 and no. 7 as xyz trajectory files.


The Hessian file jobname.hess can also be used.
orca_pltvib jobname.hess 6 7   # This will create vibrational mode no. 6 and no. 7 as xyz trajectory files.


This will create XYZ trajectory files jobname.out.v006.xyz and jobname.out.v007.xyz that can be animated in programs such as Chemcraft, Avogadro, VMD etc.


Creating spectra using orca_mapspc

The orca_mapspc program (part of the ORCA package) can be used to create spectra from an ORCA spectroscopy calculation. The program creates simple text files containing energies and intensities that can then be plotted using any plotting program ( e.g. GnuPlot, Origin, Excel, Mjograph).

$ orca_mapspc
usage: orca_mapspc Output-file {ABS, ABSV, ABSQ, CD, IR, RAMAN, NRVS, VDOS, MCD, SOCABS, XES, XESV, XESQ, XAS, XASV, XASQ, XESSOC, XASSOC} -options
  -o  output file
  -cm use cm**-1 (default)
  -eV use eV (default cm**-1)
  -g  use Gaussian lineshape default
  -l  use Lorentz  lineshape
  -x0 initial point of spectrum
  -x1 final   point of spectrum
  -w  line width
  -kw coeffitient for the line width calculated as kw*sqrt(energy)
  -n  number of points


Examples:
-Plotting an IR spectrum in the region 300-4000 cm-1 using default broadening (requires ORCA outputfile from a NumFreq job)
orca_mapspc jobname.out IR -x0300 -x14000    # Note the x0 and x1 symbols before the 300 and 4000 values.  
      
This will create two files jobname.out.ir.dat and  jobname.out.ir.stk. The jobname.out.ir.stk file will contain the calculated frequencies and intensities. The dat file contains a broadened spectrum.

-Plotting a UV-VIS spectrum in the 10000-30000 cm-1 region using 1000 cm-1 broadening (requires ORCA outputfile from an excited-state job, e.g. TDDFT)
orca_mapspc jobname.out ABS -x010000 -x130000 -w1000

Will create jobname.out.abs.dat (broadened spectrum) and jobname.out.abs.stk (energies and intensities of calculated transitions).

- Plotting an Fe K-edge XAS spectrum (with quadrupole contributions) in the 3000-9000 eV range, 1 eV broadening and 5000 points.
orca_mapspc jobname.out ABSQ -eV -x03000 -x19000 -w1.0 -n5000


- Plotting an Fe XES spectrum (with quadrupole contributions) in the 100-7100 eV range, 1 eV broadening and 5000 points.
orca_mapspc jobname.out XESQ -eV -x0100 -x17100 -w1.0 -n5000



Visualizing Molecular Orbitals from ORCA

Molecular orbitals from an SCF calculation are always available from the GBW file. The orca_plot program (in the same directory as the main orca program) can print the orbitals if the standard GBW file is available. 
orca_plot file.gbw -i 


Also note that other orbitals  that are created by ORCA (such as UNOs, QROs, UCOs, localized orbitals etc.,  see Orbital and density analysis) also have their own GBW files that can be read in the same way:
orca_plot file.uno -i # To read in UNOs
orca_plot file.qro -i  # To read in QROs
orca_plot file.uco -i # To read in corresponding orbitals
orca_plot file.loc -i  # To read in localized orbitals
orca_plot file.s1.nto -i  # To read in NTOs


The orca_plot program will show you a menu with options to plot different types of orbitals, densities etc. If you enter 1 and press Enter, you will get to a new menu where you can select what type of plot you want, press 5 to change output file format, press 4 to change resolution, 2 and 3 to change the orbital to plot and press to generate the selected plot.

PlotType       ... MO-PLOT
MO/Operator    ... 0 0
Format         ... Grid3D/Binary
Resolution     ... 40 40 40
Boundaries     ...   -13.572248    13.572248 (x direction)
                     -13.463043    13.463043 (y direction)
                     -13.278247    13.278247 (z direction)

       1 - Enter type of plot
       2 - Enter no of orbital to plot
       3 - Enter operator of orbital (0=alpha,1=beta)
       4 - Enter number of grid intervals
       5 - Select output file format
       6 - Plot CIS/TD-DFT difference densities
       7 - Plot CIS/TD-DFT transition densities
       8 - Set AO(=1) vs MO(=1) to plot

      10 - Generate the plot
      11 - exit this program
Enter a number:



You can also tell ORCA to print specific orbitals in the inputfile directly. The Cube file format is used here which can be opened in programs such as VMDAvogadro, JMol, ChemcraftSee the script page for a nice script to automate visualization of Cube files in VMD.
! UKS BP86 def2-SVP def2/J
%plots
Format CUBE
MO("Orbital-4.cube",4,0); #This would print orbital 4 of operator 0 (alpha spinorbital)
MO("Orbital-8.cube”,8,1); #This would print orbital 8 of operator 1 (beta spinorbital)
end


You can also tell ORCA to print all the necessary information (basis set and MO coefficients) in the outputfile so that a software such as Chemcraft can later render the orbitals. This is convenient but also increases the size of the outputfile.

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


One can even use this approach for visualizing previously calculated orbitals, localized orbitals, UNOs, QROs (see Orbital and density analysis) etc. This requires a separate inputfile. In the input below, previously calculated localized orbitals are read in and printed out (without iterations using the Noiter keyword; make sure to specify the same basis set as before to prevent basis set projection). Chemcraft can then later render the orbitals from the outputfile alone. Make sure to remember to remove any %scf Maxiter keyword, because this overrides the Noiter keyword.

!  Normalprint MOREAD NoIter def2-SVP
%moinp "localizedorbitals.loc" # Here reading in a previously calculated .loc file for visualization of the localized orbitals. 
%output
Print[ P_Basis ] 2
Print[ P_MOs ] 1
end



Visualizing Electron Density or Spin Density

There are two ways of visualizing electron densities or spin densities. One is to tell ORCA in the inputfile to plot the densities once the calculation is done:

! UKS BP86 def2-SVP def2/J
%plots
dim1 100
dim2 100
dim3 100
Format Gaussian_Cube
SpinDens("spindensity");
ElDens("electrondensity");
end


The other way is to use orca_plot after the calculation is done plot density/spin density plots from the files. Here shown for a broken-symmetry solution of H2 (alpha spin localized on H1 and beta spin localized on H2) :
! BP def2-SVP def2/J KeepDens
# KeepDens keyword preserves the electron and spin density files.
%scf
Flipspin 0
FinalMs 0.0
end
*xyz 0 3
H 0.0 0.0 0.0
H 0.0 0.0 3.0
*


then:

orca_plot job.gbw -i  

(select file format, resolution, type of plot, give the name of the job.scfp or job.scfr file (if available) and then generate the plot). If the Cube File Format is chosen, the file can be open in programs like JMol, Chemcraft, Chimera, VMD. If electron density/spin density files (job.scfr or job.scfp) are not available (if KeepDens keyword was not used) then orca_plot will recalculate the density matrices.

Note: Spin and electron density plots can also be generated for excited states, e.g. from a TDDFT calculation. See TDDFT page for more information about this.

Figure 1. Upper: H2 at 3.0 Å. Middle: Electron density Lower: Spin density

Comments