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MOLCAS geometry optimisation (Read 5884 times)
Gerrit-Jan Linker
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MOLCAS geometry optimisation
21.02.08 at 12:19:03
 
MOLCAS geometry optimisation
 
A geometry optimisation is specified in MOLCAS in the input file. Above the SEWARD and SCF input the following is specified:

> SET MAXITER 50
> Do While

 
At the end of the input file, below the SCF input,  the following is added just before the !exit:

 &ALASKA &END
End of Input
 
 &SLAPAF &END
End of Input
 
> ENDDO

 
See also:
Slapaf
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1251489595
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« Last Edit: 03.03.12 at 10:40:42 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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Posts: 75
Geometry optimisation constraints
Reply #1 - 29.05.08 at 07:34:09
 
Geometry optimisation constraints
 
To fix part of the molecule and let the rest be optimised, constraints can be specified in the SLAPAF input. Constraints can be set on all sorts of things such as angles, bond lengths and dihedral angles.  
 
I have used the fixing of cartesian coordinates. The points in the constraints are left at their original xyz coordinates and all other atom positions are allowed to change:
 
 &SLAPAF &END
Constraints
S3x = Cartesian x S3
S3y = Cartesian y S3
S3z = Cartesian z S3
Values
S3x = 2.315041 Angstrom
S3y = 3.912737 Angstrom
S3z = 5.246721 Angstrom
End of Constraints
End of Input
 
See also:
Another example of constraint optimisation with slapaf
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1251489595#2
SLAPAF
http://www.teokem.lu.se/molcas/documentation/manual/node77.html#UG:sec:definitio n_of_internal_coordinates
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« Last Edit: 25.01.15 at 10:32:43 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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Geometry optimisation: convergence but minimum?
Reply #2 - 08.10.09 at 08:17:49
 
Geometry optimisation: convergence but minimum?
 
When doing geometry optimisations in MOLCAS, be sure to check whether the found optimal geometry is indeed the lowest in energy. I find often that after convergence the found structure is not minimal in energy.  
 
The geometry convergence can be viewed graphically in molden. Run the command below and press the Geom. conv. button in the molden control.
molden project.geo.molden
 
Example:
 
********************************************************************************
*********************************
*                                  Energy Statistics for Geometry Optimization                                  *
********************************************************************************
*********************************
                      Energy     Grad     Grad              Step                 Estimated   Geom     Hessian
Iter      Energy       Change     Norm     Max    Element    Max     Element     Final Energy Update Update Index
  1  -2051.56142401  0.00000000 0.083964-0.066459 nrc005  -0.114133  nrc005    -2051.56699800 RS-RFO  None    0
  2  -2051.56997153 -0.00854751 0.048321-0.033952 nrc004  -0.110539  nrc004    -2051.57316644 RS-RFO  BFGS    0
  3  -2051.57342531 -0.00345378 0.016056-0.007256 nrc002  -0.013382  nrc002    -2051.57353874 RS-RFO  BFGS    0
  4  -2051.57360565 -0.00018034 0.012248-0.005030 nrc002  -0.030860  nrc002    -2051.57380449 RS-RFO  BFGS    0
...
 30  -2051.57420782 -0.00019313 0.002383-0.000717 nrc030  -0.029446  nrc030    -2051.57426462 RS-RFO  BFGS    0
 31  -2051.57420873 -0.00000091 0.002154 0.000507 nrc033   0.023807  nrc027    -2051.57421290 RS-RFO  BFGS    0
 32  -2051.57421208 -0.00000335 0.002219-0.000712 nrc030  -0.006074  nrc030    -2051.57421587 RS-RFO  BFGS    0
33  -2051.57421538 -0.00000330 0.002105-0.000699 nrc030  -0.010540  nrc030    -2051.57421590 RS-RFO  BFGS    0
34  -2051.57421093  0.00000444 0.002129-0.000541 nrc030  -0.081886  nrc027    -2051.57427830 RS-RFO  BFGS    0
 35  -2051.57418141  0.00002952 0.002743-0.000709 nrc001   0.042811  nrc027    -2051.57419273 RS-RFO  BFGS    0
 36  -2051.57420345 -0.00002204 0.001603-0.000387 nrc027  -0.062326  nrc027    -2051.57422681 RS-RFO  BFGS    0
...
 53  -2051.57413206  0.00001112 0.001172 0.000101 nrc052   0.011896  nrc027    -2051.57414357 RS-RFO  BFGS    0
 54  -2051.57414143 -0.00000937 0.001160 0.000091 nrc052  -0.004405  nrc030    -2051.57414165 RS-RFO  BFGS    0
 55  -2051.57413572  0.00000571 0.001154 0.000086 nrc052  -0.008189  nrc027    -2051.57414183 RS-RFO  BFGS    0
 56  -2051.57413560  0.00000013 0.001159 0.000092 nrc052  -0.005692  nrc030    -2051.57413580 RS-RFO  BFGS    0
 57  -2051.57412848  0.00000712 0.001150 0.000084 nrc052  -0.005343  nrc026    -2051.57413565 RS-RFO  BFGS    0
 58  -2051.57413367 -0.00000519 0.001157 0.000089 nrc052  -0.002565  nrc027    -2051.57413373 RS-RFO  BFGS    0
 59  -2051.57413078  0.00000289 0.001156 0.000085 nrc052   0.005824  nrc027    -2051.57413387 RS-RFO  BFGS    0
 60  -2051.57413098 -0.00000020 0.001150 0.000082 nrc052  -0.003281  nrc027    -2051.57413109 RS-RFO  BFGS    0
 61  -2051.57412599  0.00000499 0.001141 0.000072 nrc052   0.002948  nrc027    -2051.57413100 RS-RFO  BFGS    0
 62  -2051.57413117 -0.00000518 0.001148 0.000078 nrc052  -0.000449  nrc027    -2051.57413119 RS-RFO  BFGS    0
 
      +----------------------------------+----------------------------------+
      +    Cartesian Displacements       +    Gradient in internals         +
      +  Value      Threshold Converged? +  Value      Threshold Converged? +
 +-----+----------------------------------+----------------------------------+
 + RMS + 0.2348E-03  0.1200E-02     Yes   + 0.1675E-03  0.3000E-03     Yes   +
 +-----+----------------------------------+----------------------------------+
 + Max + 0.4131E-03  0.1800E-02     Yes   + 0.7836E-04  0.4500E-03     Yes   +
 +-----+----------------------------------+----------------------------------+
 
 Geometry is converged in  62 iterations to a Minimum Structure
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« Last Edit: 08.10.09 at 08:18:47 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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Posts: 75
MOLCAS geometry optimisation
Reply #3 - 21.05.15 at 09:00:46
 
MOLCAS geometry optimisation: convergence
 
When there are convergence problems, the following settings can help.
 
When calculating with CHOLESKI integral decomposition, try to use HIGH CHOLESKI (default is LOW CHOLESKI) in the seward/gateway input.
 
Try to improve the calculated gradient by using a higher (than the default 1.0d-7) cutoff value in alaska. Use e.g. 1.0d-10.
 
Switch off hessian updating in slapaf: noupdate.
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