internal coordinates problem

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Hi,

I have been having some troubles trying to run some calculations. Most of them die with the following message


         ------
auto-z
------
!! There are insufficient internal variables: expected 124 got 126
!! Either AUTOZ failed or your geometry has changed so much that the
!! coordinates should be regenerated.
------------------------------------------------------------------------
geom_binvr: #indep variables incorrect 12400126
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
52: end
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error related to the specified geometry
------------------------------------------------------------------------


it doesn't matter if I use cartesians or z-matrix (I have built several z-matrices for the same molecules), they always die in the same way. My molecules are slightly linear (if you could say so). Please find below an input file for a similar
molecule (it is not exactly the same I am interested in) which also crashes with the same error. Could anyone please shed some light on what is the problem or what I am doing wrong?

Of course I want to optimize the geometries in internal coordinates for obvious reasons.

Thanks a lot!!!

Cheers

start TEST
title "TEST"

memory total 400 mw

geometry units angstroms
 C         -8.38039    -1.34197    -0.07227
C -6.98548 -1.34307 -0.06413
C -6.26690 -0.12573 -0.06674
C -6.99151 1.08746 -0.07813
C -8.38665 1.07946 -0.08614
C -9.08696 -0.13298 -0.08335
H -8.92264 -2.29323 -0.06970
H -6.43106 -2.28559 -0.05541
H -6.44439 2.03445 -0.08045
H -8.93360 2.02796 -0.09433
H -10.18162 -0.13576 -0.09004
C -4.83982 -0.12908 -0.05719
C -3.61950 -0.15553 -0.04725
C -2.19739 -0.16932 -0.03376
C -1.46971 1.04023 -0.03500
C -1.48786 -1.40039 -0.01682
C -0.07376 1.05458 -0.01879
H -2.03685 1.97082 -0.04838
C -0.09192 -1.38602 -0.00054
C 0.63577 -0.17642 -0.00087
H 0.47526 -2.31659 0.01339
O -2.24104 -2.52743 -0.01725
C -1.60694 -3.78482 0.00064
H -0.96821 -3.93596 -0.89213
H -0.99014 -3.92131 0.91102
H -2.41196 -4.53665 -0.00306
O 0.67946 2.18160 -0.01781
C 0.04543 3.43902 -0.03588
H 0.85049 4.19081 -0.03211
H -0.57123 3.57548 -0.94636
H -0.59342 3.59026 0.85679
C 2.05785 -0.19076 0.01738
C 3.27804 -0.21961 0.03421
C 4.70498 -0.22706 0.05370
C 5.42552 -1.44253 0.07588
C 5.42754 0.98790 0.05106
C 6.82056 -1.43902 0.09476
H 4.87532 -2.38773 0.07796
C 6.82235 0.98232 0.07009
H 4.87635 1.93218 0.03361
C 7.52486 -0.22888 0.09187
H 7.36432 -2.38925 0.11193
H 8.61945 -0.22966 0.10653
H 7.36769 1.93180 0.06800
symmetry c1
end

basis spherical
 * library Def2-SV(P)
end

basis "cd basis" spherical
 * library "Ahlrichs Coulomb Fitting"
end

dft
 xc xcamb88 1.00 lyp 0.81 vwn_5 0.19 hfexch 1.00
cam 0.33 cam_alpha 0.19 cam_beta 0.46
direct
iterations 100
end

driver
 tight
maxiter 200
end

task dft optimize

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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You have two options:

1. Not using internal coordinates by specifying "noautoz" on the geometry line.

2. Use the zcoord block (http://www.nwchem-sw.org/index.php/Geometry#ZCOORD_--_Forcing_internal_coordinates) to
a. Define a slightly larger cvr_scaling value , which would lead to more internal coordinates.
or b. Manually define some additional internal coordinates.

Bert



Quote:Ccamacho Nov 28th 2:15 pm
Hi,

I have been having some troubles trying to run some calculations. Most of them die with the following message


         ------
auto-z
------
!! There are insufficient internal variables: expected 124 got 126
!! Either AUTOZ failed or your geometry has changed so much that the
!! coordinates should be regenerated.
------------------------------------------------------------------------
geom_binvr: #indep variables incorrect 12400126
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
52: end
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error related to the specified geometry
------------------------------------------------------------------------


it doesn't matter if I use cartesians or z-matrix (I have built several z-matrices for the same molecules), they always die in the same way. My molecules are slightly linear (if you could say so). Please find below an input file for a similar
molecule (it is not exactly the same I am interested in) which also crashes with the same error. Could anyone please shed some light on what is the problem or what I am doing wrong?

Of course I want to optimize the geometries in internal coordinates for obvious reasons.

Thanks a lot!!!

Cheers

start TEST
title "TEST"

memory total 400 mw

geometry units angstroms
 C         -8.38039    -1.34197    -0.07227
C -6.98548 -1.34307 -0.06413
C -6.26690 -0.12573 -0.06674
C -6.99151 1.08746 -0.07813
C -8.38665 1.07946 -0.08614
C -9.08696 -0.13298 -0.08335
H -8.92264 -2.29323 -0.06970
H -6.43106 -2.28559 -0.05541
H -6.44439 2.03445 -0.08045
H -8.93360 2.02796 -0.09433
H -10.18162 -0.13576 -0.09004
C -4.83982 -0.12908 -0.05719
C -3.61950 -0.15553 -0.04725
C -2.19739 -0.16932 -0.03376
C -1.46971 1.04023 -0.03500
C -1.48786 -1.40039 -0.01682
C -0.07376 1.05458 -0.01879
H -2.03685 1.97082 -0.04838
C -0.09192 -1.38602 -0.00054
C 0.63577 -0.17642 -0.00087
H 0.47526 -2.31659 0.01339
O -2.24104 -2.52743 -0.01725
C -1.60694 -3.78482 0.00064
H -0.96821 -3.93596 -0.89213
H -0.99014 -3.92131 0.91102
H -2.41196 -4.53665 -0.00306
O 0.67946 2.18160 -0.01781
C 0.04543 3.43902 -0.03588
H 0.85049 4.19081 -0.03211
H -0.57123 3.57548 -0.94636
H -0.59342 3.59026 0.85679
C 2.05785 -0.19076 0.01738
C 3.27804 -0.21961 0.03421
C 4.70498 -0.22706 0.05370
C 5.42552 -1.44253 0.07588
C 5.42754 0.98790 0.05106
C 6.82056 -1.43902 0.09476
H 4.87532 -2.38773 0.07796
C 6.82235 0.98232 0.07009
H 4.87635 1.93218 0.03361
C 7.52486 -0.22888 0.09187
H 7.36432 -2.38925 0.11193
H 8.61945 -0.22966 0.10653
H 7.36769 1.93180 0.06800
symmetry c1
end

basis spherical
 * library Def2-SV(P)
end

basis "cd basis" spherical
 * library "Ahlrichs Coulomb Fitting"
end

dft
 xc xcamb88 1.00 lyp 0.81 vwn_5 0.19 hfexch 1.00
cam 0.33 cam_alpha 0.19 cam_beta 0.46
direct
iterations 100
end

driver
 tight
maxiter 200
end

task dft optimize

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HI ,
i am having the same kind of problem even after using internal coordinates by specifying "noautoz" on the geometry line.

Please suggest me how to define internal coordinates manually

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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See option 2. that I gave above.

Bert


Quote: Dec 22nd 1:51 pm
HI ,
i am having the same kind of problem even after using internal coordinates by specifying "noautoz" on the geometry line.

Please suggest me how to define internal coordinates manually

  • Guest -
    Send PM
Hi

i tried with option 2 as given above but for some input files i am getting the following error and for some it is fine can anybody tell me what is the problem
!!! You are using internal coordinates for the optimization but applying
!!! constraints on the Cartesian coordinates by only computing gradients
!!! for a subset of the atoms (via geometry:actlist). This does not
!!! currently work. Either,
!!!
!!! 1) Retain the Cartesian constraints and perform the optimization
!!! entirely in Cartesians by specifying the coordinates in
!!! cartesians and using the NOAUTOZ keyword on the GEOMETRY directive
!!!
!!! or
!!!
!!! 2) Remove the Cartesian constraints and perform the optimization
!!! in redundant internal coordinates. To remove the Cartesian
!!! constraints remove the "set geometry:actlist ..." directive from
!!! startup jobs, or use "unset geometry:actlist" in restart jobs.

------------------------------------------------------------------------

my input file is given below
geometry autosym units angstrom noautoz
C     0.000000     0.000000     0.000000
C 0.000000 0.000000 1.422685
C 1.243222 0.000000 2.106095
C 2.462344 0.000000 1.367711
C 2.432584 0.000000 -0.050656
C 1.171749 0.000000 -0.709693
C -1.201159 0.000000 2.185082
C -1.172423 0.000000 3.554679
C 0.059659 0.000000 4.266022
C 1.273120 0.000000 3.531065
C 2.522142 0.000000 4.217664
C 2.551902 0.000000 5.636031
C 1.319820 0.000000 6.347373
C 0.119346 0.000000 5.687461
C 3.741264 0.000000 3.479279
C 3.711365 0.000000 2.054295
C 3.664665 0.000000 -0.761999
C 4.865140 0.000000 -0.102087
C 4.924815 0.000000 1.319346
C 6.156896 0.000000 2.030689
C 6.185633 0.000000 3.400286
C 4.984474 0.000000 4.162683
C 4.984474 0.000000 5.585368
C 3.812736 0.000000 6.295053
H -0.952031 0.000000 -0.520488
H -2.150791 0.000000 1.660229
H 1.151488 0.000000 -1.794524
H 3.639405 0.000000 -1.846726
H 5.794501 0.000000 -0.662050
H 7.083677 0.000000 1.466466
H 7.135256 0.000000 3.925155
H 5.936496 0.000000 6.105872
H 3.833007 0.000000 7.379885
H 1.345080 0.000000 7.432100
H -0.810011 0.000000 6.247432
H -2.099194 0.000000 4.118918
XX 2.492246 0.000000 2.792692
O     2.492246     4.000000     2.792692
XX 1.615920 4.000000 2.310974
C     2.492246     5.220000     2.792692
H 3.318711 5.764500 3.247001
H 1.665781 5.764500 2.338383
end


geometry adjust
zcoord
bond 38 39 1.0 xxo constant
angle 39 38 37 90.0 xxoxx constant
torsion 39 38 37 15 180.0 xxoxxc constant
angle 40 38 39 90.0 coxx constant
torsion 40 38 39 37 180 coxxxx constant
end
end

constraints
fix atom 1:38
end

task dft optimize

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Try setting the zcoord internal coordinates without setting the optional "constant" keyword. You are trying to force the optimizer NOT to change these internals AND are trying to limit optimization to a few atoms only. This doesn't work.

Bert


Quote: Dec 26th 8:11 am
Hi

i tried with option 2 as given above but for some input files i am getting the following error and for some it is fine can anybody tell me what is the problem
!!! You are using internal coordinates for the optimization but applying
!!! constraints on the Cartesian coordinates by only computing gradients
!!! for a subset of the atoms (via geometry:actlist). This does not
!!! currently work. Either,
!!!
!!! 1) Retain the Cartesian constraints and perform the optimization
!!! entirely in Cartesians by specifying the coordinates in
!!! cartesians and using the NOAUTOZ keyword on the GEOMETRY directive
!!!
!!! or
!!!
!!! 2) Remove the Cartesian constraints and perform the optimization
!!! in redundant internal coordinates. To remove the Cartesian
!!! constraints remove the "set geometry:actlist ..." directive from
!!! startup jobs, or use "unset geometry:actlist" in restart jobs.

------------------------------------------------------------------------

my input file is given below
geometry autosym units angstrom noautoz
C     0.000000     0.000000     0.000000
C 0.000000 0.000000 1.422685
C 1.243222 0.000000 2.106095
C 2.462344 0.000000 1.367711
C 2.432584 0.000000 -0.050656
C 1.171749 0.000000 -0.709693
C -1.201159 0.000000 2.185082
C -1.172423 0.000000 3.554679
C 0.059659 0.000000 4.266022
C 1.273120 0.000000 3.531065
C 2.522142 0.000000 4.217664
C 2.551902 0.000000 5.636031
C 1.319820 0.000000 6.347373
C 0.119346 0.000000 5.687461
C 3.741264 0.000000 3.479279
C 3.711365 0.000000 2.054295
C 3.664665 0.000000 -0.761999
C 4.865140 0.000000 -0.102087
C 4.924815 0.000000 1.319346
C 6.156896 0.000000 2.030689
C 6.185633 0.000000 3.400286
C 4.984474 0.000000 4.162683
C 4.984474 0.000000 5.585368
C 3.812736 0.000000 6.295053
H -0.952031 0.000000 -0.520488
H -2.150791 0.000000 1.660229
H 1.151488 0.000000 -1.794524
H 3.639405 0.000000 -1.846726
H 5.794501 0.000000 -0.662050
H 7.083677 0.000000 1.466466
H 7.135256 0.000000 3.925155
H 5.936496 0.000000 6.105872
H 3.833007 0.000000 7.379885
H 1.345080 0.000000 7.432100
H -0.810011 0.000000 6.247432
H -2.099194 0.000000 4.118918
XX 2.492246 0.000000 2.792692
O     2.492246     4.000000     2.792692
XX 1.615920 4.000000 2.310974
C     2.492246     5.220000     2.792692
H 3.318711 5.764500 3.247001
H 1.665781 5.764500 2.338383
end


geometry adjust
zcoord
bond 38 39 1.0 xxo constant
angle 39 38 37 90.0 xxoxx constant
torsion 39 38 37 15 180.0 xxoxxc constant
angle 40 38 39 90.0 coxx constant
torsion 40 38 39 37 180 coxxxx constant
end
end

constraints
fix atom 1:38
end

task dft optimize


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