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Gamess-UK (Read 14182 times)
Gerrit-Jan Linker
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Gamess-UK
28.05.13 at 11:02:01
 
Gamess-UK
 
GAMESS-UK is the general purpose ab initio molecular electronic structure program for performing SCF-, DFT- and MCSCF-gradient calculations, together with a variety of techniques for post Hartree Fock calculations.
 
website: http://www.cfs.dl.ac.uk/
documentation: http://www.cfs.dl.ac.uk/docs/index.shtml
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Gamess-UK: RHF
Reply #1 - 28.05.13 at 11:06:00
 
Gamess-UK: RHF
 
Example RHF calculation on H2:
 
#!/bin/bash
export ed3=ed3
 
mpirun -n 8 -machinefile $PBS_NODEFILE /usr/local/b
in/gamess-uk<<EOF
core 64000000
adapt off
title
mijn molecuul
charge 0
mult 1
geom ang
0.0 0.0 0.0 1.0 h
0.0 0.0 1.4 1.0 h
end
basis 6-31g**
scftype direct
vectors atdens
enter 1
EOF

 
Explanation:
geom ang/bohr: geometry in angstrom/bohr. Following lines: x y z nuclear_charge atom_symbol.  
adapt off: no symmetry adapted orbitals.
mult: multiplicity
charge: molecular charge
scftype direct: direct SCF
vectors atdens: uses atomic densities as start vectors
enter 1: optimised vectors will be stored in position 1 on file ed3
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« Last Edit: 28.05.13 at 21:38:30 by Gerrit-Jan Linker »  

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Gamess-UK: manual entry of basis set
Reply #2 - 28.05.13 at 11:26:45
 
Gamess-UK: manual entry of basis set
 
Manual entry of the basis set is possible by entering a basis section after the geometry section.
In the example below the 3-21G basis set for H2 is manually specified. It can be copied and pasted from the basis set exchange at https://bse.pnl.gov/bse/portal.
 
core 64000000
charge 0
mult 1
geom ang
0.0 0.0 0.0 1.0 h
0.0 0.0 1.4 1.0 h
end
basis  
# HYDROGEN
S   H
     0.1562850              5.4471780        
     0.9046910              0.8245470        
S   H
     1.0000000              0.1831920    
end
scftype direct
vectors atdens
enter 1
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« Last Edit: 28.05.13 at 11:29:27 by Gerrit-Jan Linker »  

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Gamess-UK vectors
Reply #3 - 01.06.13 at 11:46:40
 
Gamess-UK vectors
 
With the keyword vectors, vectors can be retrieved.
vectors atdens ; creates vectors on the basis of atomic densities
vectors 1 ; retrieves vectors from section 1 of the vectors file
 
Note: when a UHF calculation is restarted both section 1 and 2 must be read in: vectors 1, 2
 
With the enter keyword, vectors can be written to the dump file that in default is routed to ED3. This file is crucial to the program and controls all restart activities.
enter 1 ; sets the vectors to section 1 of the file, overwriting what was already there
enter 2 3 ; writes vectors to sections 2 and 3.
 
Printing of vectors (for plotting). This can be handy to verify vectors that are read in or ones that are modified:
vectors 1 print
 
Vectors can be interchanged using the swap keyword, e.g. to swap vectors 100 and 101 use:
vectors 1
swap  
100 101
end
 
Interchanging vectors in UHF can be done in both alpha and beta orbital sets by using the swap alpha or swap beta keyword:
 
swap alpha
10 11
end
 
Source:
Dump file
http://www.cfs.dl.ac.uk/docs/html/part2/node2.html#SECTION00022000000000000000
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« Last Edit: 09.10.14 at 11:15:36 by Gerrit-Jan Linker »  

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Gamess-UK max cycles
Reply #4 - 07.06.13 at 23:27:36
 
Gamess-UK max cycles
 
To extend the maximum number of SCF cycles, the maxcycles keyword can be used.  
Example:
 
scftype direct
open 1 1 1 1
vectors 1
maxcyc 150
enter 2 3
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Gamess-UK: level shifter
Reply #5 - 11.06.13 at 16:23:14
 
Gamess-UK: level shifter
 
A level shifter can be specified by using the level keyword. E.g.
level 0.5 1.0
 
Two values for the level shifter can be given. The first will be used up to a certain iteration number and from there the second value will be used.
 
Source:
http://www.cfs.dl.ac.uk/docs/pdf/chap4.pdf
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Gamess-UK increased accuracy
Reply #6 - 01.07.13 at 13:18:29
 
Gamess-UK increased accuracy
 
To increase the accuracy of a Gamess-UK calculation the integrals can be calculated with high precision.  
Keywords:
integral high
accuracy 40 40
 
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« Last Edit: 15.09.13 at 19:15:00 by Gerrit-Jan Linker »  

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Gamess-UK : convergance options
Reply #7 - 13.07.13 at 21:20:57
 
Gamess-UK : convergence options
 
If convergence cannot be obtained it is recommended to first play with a level shifter. If that also doesn't help you can try the conv keyword. Iterate a few steps using this keyword and save the ed3 orbitals file. Restart using different parameter from that until it converges.
 
Add the keyword:
conv n
 
Where n is
    0........use Pople's extrapolation
    1........do NOT use damping, extrapolation or level shifting
    2........use damping and Pople's extrapolation
    3........use Davidson's damping
    4........use level shifting and extrapolation
    5........use level shifting (default)
    6........use damping, extrapolation and level shifting
    7........use level shifting and damping
   10........use damping, extrapolation and restrict orbital
            mixing in GVB or open shell calculations.
   11........use damping and restrict orbital mixing
   14........use damping, extrapolation, level shifting and
             restrict orbital mixing
   15........use level shifting, damping and restrict orbital
            mixing
 
Source:
http://www.cfs.dl.ac.uk/docs/html/part4/node7.html#SECTION00074000000000000000
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« Last Edit: 14.07.13 at 17:00:49 by Gerrit-Jan Linker »  

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Gamess-UK: print analysed coordinates
Reply #8 - 02.09.13 at 13:28:59
 
Gamess-UK: print analysed coordinates
 
Gamess-UK can print the coordinates in high precision after analysis of the geometry. In the output the coordinates are printed with few decimals. A file can be created using the following input in which the coordinates are displayed in high precision.
 
Add the following line to the input:
punch high coordinates
 
It will dump the coordinates in a file called ftn058.
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Gamess-UK: Spin-unrestricted
Reply #9 - 27.10.13 at 16:06:32
 
Gamess-UK: Spin-unrestricted
 
For spin-unrestricted calculations, use the SCFTYPE UHF or SCFTYPE DIRECT UHF.
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« Last Edit: 28.10.13 at 10:14:06 by Gerrit-Jan Linker »  

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Gamess-UK: orbitals localisation
Reply #10 - 28.10.13 at 10:17:27
 
Gamess-UK: orbitals localisation
 
In gamess-uk orbitals can be localised with the following procedure.
 
Start a new calculation (restart new) reading in old vectors with runtype analyze. Use the local overlap keyword to localise particular orbitals.
 
Example:
core 64000000
restart new
title
mijn molecuul
<<snip>>
runtype analyse
local overlap
337 338 end
maxcyc 1500
vectors 2
enter 1
 
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Gamess-UK: Plot orbitals
Reply #11 - 04.04.14 at 14:50:46
 
Gamess-UK: Plot orbitals
 
Orbitals can be viewed with molden. Simply open the output file with molden to view the orbitals:
molden mycalculation.output
 
To view ROHF orbitals the output should be edited so it looks like RHF output. The required edits are:
  • Replace SCF TYPE gvb to rhf
  • Replace the title of the section that contains the orbitals from "gvb natural orbitals..." to "eigenvectors"
  • Below this title and above the table with eigenvalues, remove one line.
     
    See also:
    molden
    http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1219308111
     
     
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    « Last Edit: 04.04.14 at 14:51:00 by Gerrit-Jan Linker »  

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    Gamess-UK: geometry optimisation
    Reply #12 - 21.09.14 at 12:34:19
     
    Gamess-UK: geometry optimisation
     
    Geometry optimisations are indicated with the keyword "runtype optimize" or "runtype optxyz". Using "runtype optimize" the geometry should be given in a z-matrix which is easily created in molden. Export it from molden using variables. The zmatrix file can be loaded in directly in the gamess-uk input. With "runtype optxyz" the input should be given in cartesian coordinates.
     
    Example input
     
             TITLE
             HCN  
             ZMAT ANGSTROM
             C
             BQ 1 RCN2
             X 2 1.0 1 90.0
             N 2 RCN2 3 90.0 1 180.0
             X 1 1.0 2 90.0 3 0.0
             H 1 RCH 5 90.0 4 180.0
             VARIABLES
             RCN2 0.580
             RCH 1.056
             END
             BASIS 6-31G**
             RUNTYPE OPTIMIZE
             ENTER
     
    The convergence threshold is 0.001 but it can be specified in the input using the XTOL keyword.
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    « Last Edit: 13.10.14 at 22:09:36 by Gerrit-Jan Linker »  

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    Gamess-UK: external field
    Reply #13 - 06.10.14 at 08:11:40
     
    Gamess-UK: external field
     
    Using the keyword field, a static electric field can be switched on:
    field x y z
     
    X,y and z are the components of the field in the respective directions.
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    Gamess-UK: calculate polarisability
    Reply #14 - 06.10.14 at 08:12:47
     
    Gamess-UK: calculate polarisability
     
    To calculate the polarisability or other response properties, use: runtype polarisability.
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