Hints for Using Spartan 04

Shusterman Research Group

This page is a compilation of hints and tricks for using Spartan 04 and some of its ancestors as provided over the years by the Wavefunction support staff (support@wavefun.com). These folks also maintain a modest FAQ page.

Alan Shusterman, January 2004

(The tech staff at Wavefunction recently sent me two more FAQ pages for Sp04 (Windows): Memory | Properties June 2005)

How do I use Jaguar with Sp04(Windows)? (Aug 9, 04)

1. Build your model with Sp04 and save it as job.spinput
2. Transfer job.spinput file to a Linux computer
3. Open job.spinput with Jaguar. Rename the job. Setup the job and, in the setup, ask Jaguar to create a Spartan archive file
 
After Jaguar job has run, you have several options for getting the results back in to Sp04. It all depends on how much data you want to bring back with you.
 
4A. (keep Jaguar geometry only) Rename job.arc to 'job.sparchive'. Transfer job.sparchive to a Windows computer and open with Sp04. You will be prompted that this is an old/incomplete file. Accept all of Sp04's recommendations and voila!
 
4B. (keep Jaguar geometry and wave function)
- Copy (do not rename) job.spinput, job.arc, and job.out to 'input', 'archive', and 'output', respectively.
- Copy input + archive + output to 'c:\unixMolecules' folder on Windows computer
- Use Wordpad or Notepad to create a text file named 'proparc' (no suffix). Enter the following 8 lines:
 
PROP STRING INITIAL_KEYWORDS 6 BEGIN
 "OPT"
 "BLYP"
 "6-31G**"
 "STDECP"
 "CONVERGE"
 "NOSYMTRY"
END
 
Ideally, the keywords entered into 'proparc' should reflect the settings actually used in the Jaguar job (and it is not necessary to have 6 keywords, just adjust the number in the first line to match the number of keywords), but it is strictly required that the keywords match those in 'input'. So consult 'input' before setting up 'proparc'. BTW - the 6 keywords shown above are for a geometry optimization with BLYP/LACVP** (6-31G** + LANL eff core potential for transition metals) using "converge" (a standard DFT setting in Sp04) and not using symmetry constraints.
 
Some warnings about setting up 'proparc':
>> first line must be a comment
>> keywords must match those in 'input' (always consult 'input' before creating 'proparc')
>> use a basis set and method that Sp04 recognizes. You can test your basis/method by opening the Setup Calculations window and typing the basis or method in the Options box and pressing Enter. If you have typed a Sp04-recognized term, it will disappear from the Options box and reappear in the appropriate setup menu (if Sp04 doesn't recognize your term, it will substitute a default term: HF for method and 3-21G(*) for basis set). Note: Sp04 recognizes LACVP*, but it doesn't know that this is the same as 6-31G* + STDECP (the latter is preferred?).
 
- use Spartan's file converter to Convert Unix to PC (this creates several moleculeName.spxxx files in c:\Molecules)
- open moleculeName.spinput with Sp04 (accept the 'old to new' model conversion that is requested and save the new moleculeName.spartan model)
- setup and submit a graphics calculation (the Jaguar-generated geometry and wave function will be used without any add'l SCF calculations)

4C. (shortcut for 4B that avoids using the file converter)
- copy 'input', 'archive', 'output' and '_spartan' to a dedicated folder on your Windows computer ('_spartan' can be an empty text file)
- select New with Sp04 and open the spreadsheet for this unbuilt model ('M001')
- adjust window sizes so you can see the spreadsheet and the window that contains your (Unix) model folder. Left-click on the model folder and drag it onto the spreadsheet
- select the cell that says 'M001', then right-click on it and select Delete Selected
- save your new model and proceed with graphics calculations
 

How do I use Jaguar with Sp(Linux)? (Aug 9, 04)

1. Build your model with Sp(Linux) and save it
2. Open your model's 'input' file with Jaguar. Rename the job. Setup the job and, in the setup, ask Jaguar to create a Spartan archive file
3. After the job runs, there will be a 'job.arc' and a 'job.out' file (and a bunch of other files) in your model directory Copy (don't rename) these files to 'archive' and 'output', respectively
4. Re-open your model with Sp(Linux) and setup/calculate your surfaces and maps
 
If all goes well in step 4, Sp(Linux) will see that you have a (Jaguar-generated) geometry and wavefunction in your 'archive' and will not attempt to recalculate these items.
 

How do I calculate excitation energies using TDDFT? (Aug 9, 04)

If your model geometry has already been optimized, setup 'Single Point Energy at Ground State' with 'Density Functional' and so on. Check the UV/Vis box.
 
Note: it may seem logical to calculate excitation energies by setting up 'Single Point Energy at First Excited State' but this is a bad way to go. This calc will give you only the energy of the model and will not provide information about the nature of the excited state, other excited states, etc. Only use 'at First Excited State' when you are trying to locate a stationary point on the excited surface.
 

 

Geometry optimization of Cr(CO)₆ with B3LYP/6-31G* and symmetry (Oh) fails (in addition, graphical image is a mess and the molecule opens with an error message that atom numbers in input file don't match archive). What gives? (Aug 9, 04)

(from Spartan help email...) This is an unfortunate and long standing bug in the qchem backends.
They cannot handle Ih and Oh symmetry, and just do terribly wrong things, as you've reported.
To make matters worse .... we can't really turn off symmetry in qchem
In the newest (read next) update of qchem we do a better job of turning off symmetry
but that was surprisingly hard to do ;(
 
For now breaking the symmetry by hand should work. (AJS note: after receiving this message, I tried lengthening a CO bond to reduce symmetry, but job failed again. Then I tried bending a CO bond to reduce symmetry to Cs, left Symmetry checked and added check for Pseudopotential, but job failed again.)

You might want to try the following set of keywords:
 SYMMETRY=FALSE SYM_IGNORE GEOM_OPT_SYMFLAG=FALSE GEOM_OPT_COORDS=0  ONEEXE_SPAR
 

What "submital logic" keywords will be available in v. 102 (roughly 6 months from now)? (Jan 25, 04)

A tentative list of keywords for controlling "submital logic" are listed in this document.
 

What happens if I type "RERUN" in the Options box? (Jan 19, 04)

This keyword discards the current "archive" (wave function + Hessian) before attempting a new calculation. The "archive" does not appear as a separate file in Sp04(Windows), but it does appear as a standalone file in the scratch directory and at all times in Sp(Linux). Note: RESTART is not a recognized keyword yet (but it will be in v.1.02).
 

How do I build an isolated atom? (Jan 19, 04)

To build an atom, select the atom you want from the Expert builder and click anywhere in the workspace. Then use the Delete Atom button to remove all of the free valences.
 

How do I build a hydrogen atom? (Jan 19, 04)

Follow the same procedure as above. Note: You must use a POLYvalent hydrogen atom in the Expert builder for this to work. If you use a MONOvalent hydrogen atom, deleting the free valence will also delete the atom.
 

Is it safe to log out while a calculation is in progress? (Jan 19, 04)

It depends on your operating system. If you use Windows 98 or Windows 2000, you should not log out until your Spartan calculation is finished. If you log out before the calculation is finished, it will stop.
 
If you use Windows XP, you should not log out either. However, you can SWITCH USER without interrupting your job.
 

How do I restart an interrupted job? (Jan 19, 04)

When a calculation is running it creates temporary scratch files in the X:\Documents and Settings\Username\Local Settings\Temp folder (the italicized items will vary from one computer to the next). The scratch files all have the same prefix, WFxxxxx, ('xxxxx' is a numeric string), but different suffixes. Open the WFxxxxx.spinput file and check Display: Output for useful info. In the best of all possible worlds, the output will show the contents of WFxxxxx.archive, and the contents of the archive file will allow a good restart.
 
To restart, use File: Save As to create a new model, setup the calculation, and submit. Good luck.

 

How can I change the MMFF94 force field to the MMFF94s force field? (May 4, 99)

Spartan is sticking with the MMFF94 force field because MMFF94s makes certain RNH2 groups too flat.
 
To change Spartan's force field, modify the parameters in the params.MMFF94 file (UNIX's xdiff utility is useful here; download the 94s parameters and use xdiff to compare the new and old parameter files). Fortunately, there aren't many differences.
 

How can I enter the correct SpartanView file types on a Macintosh? (Feb 15, 99)

molecule collections are Type: Sani and Creator: SpVi
Spartan exchanges are Type: Sstp and Creator: SpVi
 
Note: Capitalization is important
 

 

What does 'BP86' mean? (Oct 15, 97)

This is the GGA functional that combines Becke88 exchange with Perdew86 correlation corrections to the local spin density (LSD) xc functionals. The latter contains an X-alpha (= 1) exchange term and a VWN correlation term (SVWN in Gaussian's terminology)