Linker IT Software
Google
Web www.oraxcel.com
menubar-top-links menubar-top-rechts
Home Help Search Login
Welcome, Guest. Please Login.
SQL*XL: Database to Excel bridge litLIB: Excel power functions pack ExcelLock: Locking and securing your valuable Excel spreadsheets encOffice: Protect your Excel file easy and safe encOffice: Protect your Excel file easy and safe
Pages: 1
SLAPAF (Read 6645 times)
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
SLAPAF
28.08.09 at 21:59:55
 
SLAPAF
 
Slapaf is a molcas program that is used for geometry optimisations. It needs gradients as input.
 
Example:
Geometry optimisation of PF6- (Octaedral symmetry)
 
copy $PBS_O_WORKDIR/INPORB INPORB
 
> SET MAXITER 150
> Do While
 
 &SEWARD &END
Title
PF6
SYMMETRY
xyz
Basis set
P.6-31G..16s10p.4s3p.
P 0.0 0.0 0.0    Angstrom
End of basis
Basis set
F.6-31G..10s4p.3s2p.
F1 1.59 0 0   Angstrom
F2 0 1.59 0   Angstrom  
F3 0 0 1.59   Angstrom  
End of basis
End of input
 
 &SCF &END
Title
PF6
UHF
*LUMORB
Charge
-1
End of input
 
 &ALASKA &END
End of Input
 
 &SLAPAF &END
Internal coordinates
a1 = Bond P F1
a2 = Bond P F2
a3 = Bond P F3
t1 = Angle F1 P F2
t2 = Angle F1 P F3
t3 = Angle F2 P F3
Vary
r1 = 1.0 a1 + 1.0 a2 + 1.0 a3
Fix
r2 = 1.0 a1 - 1.0 a2
r3 = 1.0 a1 - 1.0 a3
t1
t2
t3
End of Internal
End of Input
 
> ENDDO
 
 &GRID_IT &END
End of Input
 
A few notes:
  • There are 3N-6 degrees of freedom so 3.4-3 = 6 internal coordinates must be defined.
  • From a Z-matrix representation of the geometry of the molecule, internal coordinates can be taken as bonds, angles and dihedrals.
  • We vary r1 = 1.0 a1 + 1.0 a2 + 1.0 a3 and to keep all bonds the same we fix
    r2 = 1.0 a1 - 1.0 a2 and r3 = 1.0 a1 - 1.0 a3 both to zero.

 
 
 
Reference:
MOLCAS - SLAPAF
http://www.teokem.lu.se/molcas/documentation/manual/node77.html#UG:sec:definitio n_of_internal_coordinates
http://www.teokem.lu.se/molcas/documentation/manual/node77.html
 
See also:
Geometry optimisation in MOLCAS
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1203592743/0#1
Back to top
 
« Last Edit: 05.11.09 at 13:13:15 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
SLAPAF thresholds
Reply #1 - 12.04.11 at 12:47:03
 
SLAPAF thresholds
 
Convergence thresholds can be set with regards to the energy change and the norm of the gradient. The defaults are specified in the input below.
 
 &SLAPAF &END
THRS
1.0E-6 3.0E-4
End of Input
 
Source:
http://www.teokem.lu.se/molcas/documentation/manual72/node70.html
Back to top
 
« Last Edit: 13.04.11 at 07:41:15 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
SLAPAF: using geometry constraints
Reply #2 - 22.04.11 at 11:43:06
 
SLAPAF: using geometry constraints
 
Using constraints certain bonds, angles or dihedral angles can be kept fixed.
 
In the example below angles a1 to a4 are defined and fixed to a value of 115.
 
 &SLAPAF &END
THRS
1E-8 1E-5
Constraints
a1 = Angle C1 O7 C4
a2 = Angle C1 O9 C6
a3 = Angle C2 O8 C3
a4 = Angle C2 O10 C5
Values
a1 = 115.0 degrees
a2 = 115.0 degrees
a3 = 115.0 degrees
a4 = 115.0 degrees
End of constraints
End of Input
 
In the next example of a 3 atomic molecule, the bond angle is varied, the bond lengths also but they are kept equal. The sum of the bonds b1 and b2 is varied while the difference of b1 and b2 is kept fixed.
 
Internal coordinates
a1 = Angle BR2 SE1 BR3
b1 = Bond  SE1 BR2
b2 = Bond  SE1 BR3
Vary
 r1 = 1.0 b1 + 1.0 b2
 a1
Fix
 r2 = 1.0 b1 - 1.0 b2
End of internal
 
Back to top
 
« Last Edit: 19.07.15 at 19:59:24 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
SLAPAF convergence
Reply #3 - 16.05.11 at 21:37:20
 
SLAPAF convergence
 
If convergence in the geometry optimisation is a problem the following may help.
 
In alaska a more detailed hessian can be calculated by reducing the cutoff parameter.
 
Also the maxstep in SLAPAF may help to reduce the change of the coordinates.
Back to top
 
 

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
SLAPAF: Constraint optimisation
Reply #4 - 10.01.15 at 10:57:12
 
SLAPAF: Constraint optimisation
 
To optimise a geometry using gometry constraints, internal coordinates can be used. First internal coordinates must be defined (how many?) and then using vary and fix some of the internal coordinates can be fixed.
 
In the example below we optimise O=C=C=C=O for the first excited singlet state. We keep C2v symmetry by keeping angles and bond lengths and dihedral angles on both sides of the molecule the same while optimising.
 
&GATEWAY &END
Basis set
C.ANO-S
 C1   1.26731251  0.41939613  0.00848501 Angstrom
 C2  -0.07196864  0.04744371 -0.00031372 Angstrom
 C3  -1.23846656  0.80294613  0.02415440 Angstrom
End of basis
Basis set
O.ANO-S
 O4   2.38638895  0.02389535 -0.00521604 Angstrom
 O5  -2.42469826  0.76033568  0.02394735 Angstrom
End of basis
End of input
 
> SET MAXITER 50
> Do While
 
 &SEWARD &END
End of Input
 
 &RASSCF &END
NACTEL
12 0 0
INAC
11
RAS2
10
SPIN
1
CIROOT
1 2
2
RLXROOT
2
End of input
 
 &SLAPAF &END
Internal coordinates
b1 = Bond C1 C2
b2 = Bond C2 C3
b3 = Bond O4 C1
b4 = Bond O5 C3
a1 = Angle O4 C1 C2
a2 = Angle O5 C3 C2
a3 = Angle C1 C2 C3
d1 = Dihedral O5 C3 C2 C1
d2 = Dihedral O4 C1 C2 C3
Vary
a = 1.0 b1 + 1.0 b2
b = 1.0 b3 + 1.0 b4
c = 1.0 a1 + 1.0 a2
d = 1.0 d1 + 1.0 d2
a3
Fix
a = 1.0 b1 + -1.0 b2
b = 1.0 b3 + -1.0 b4
c = 1.0 a1 + -1.0 a2
d = 1.0 d1 + -1.0 d2
End of internal
End of Input
 
> ENDDO
Back to top
 
 

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Pages: 1