CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian



 Sent to CCL by: Zeljko Vitnik [zvitnik[]chem.bg.ac.rs]
 Hello Grigoriy,
 
In your case, I would first adapt the geometry. I would put Cartesians part on the front of list and Z-Matrix part will be defined on the three atoms from Cartesians part. This will at the same time cancel the need for Dummy atom and prevents movement of large Cartesians part due to small changes in geometry parameters of Z-Matrix part.
 
Next, Gaussian 09 has the option for freezing the any part of geometry on the basis of provided list. See OPT=ReadFreeze option. It must be followed by the list of frozen atoms after the geometry list. It must be separated by one empty line and in a form of: atoms=list [notatoms=list], where each list is a comma or space-separated list of atom numbers, atom number ranges and/or atom types after the geometry list separated with one separated by one empty line.
 
I think that this option can be combined with ModRedundant option, too. This allows you to do the simply scan of any parameter defined in Z-Matrix part.
 If you must to use Dummy atom, use Bq instead of X.
 Greeting,
 Z Vitnik
 
On 2017-12-18 15:34, Grigoriy Zhurko reg_zhurko||chemcraftprog.com wrote:
 Sent to CCL by: Grigoriy Zhurko [reg_zhurko]~[chemcraftprog.com]
 Hello,
 I need to perform a PES scan in Gaussian, so that the distance
 between an atom and the center between two other atoms will be
 scanned.
 When I need to simply scan an iteratomic distance, I use
 OPT(MODREDUNDANT). But in current case I have to use a z-matrix and
 add a dummy atom (the center between two real atoms).
 It is possible to use only Z-matrix for this job, but the result
 becomes rather bad: the optimization starts with evident bugs
 (probably because this geometry has rings).
 I tried to combine the Z-matrix with the Cartesians. I created the
 following input file:
 %NPROCSHARED=3
  #P uwB97XD/6-31G(D,P) OPT(Z-Matrix,LOOSE)
  NOSYMM
  Silicon
  0 1
  X
  N 1 R12
  X 1 1.400000 2 90.000000
  N 1 R12 3 90.000000 2 180.000000
  N 1 R15 2 A215 3 -90.000000
  N 1 R16 3 A316 5 D5316
  Zn 1 R17 2 A217 5 -D5217
  6 0.000000000 2.863016000 1.101006000
  6 0.000000000 2.425840000 2.425840000
  6 0.000000000 1.101006000 2.863016000
  1 0.000000000 3.193595000 3.193595000
  6 0.000000000 2.863016000 -1.101006000
  6 0.000000000 2.425840000 -2.425840000
  6 0.000000000 1.101006000 -2.863016000
  1 0.000000000 3.193595000 -3.193595000
  6 0.000000000 -1.101006000 -2.863016000
  6 0.000000000 -2.425840000 -2.425840000
  6 0.000000000 -2.863016000 -1.101006000
  1 0.000000000 -3.193595000 -3.193595000
  6 0.000000000 -2.863016000 1.101006000
  6 0.000000000 -2.425840000 2.425840000
  6 0.000000000 -1.101006000 2.863016000
  1 0.000000000 -3.193595000 3.193595000
  6 0.000000000 -4.245855000 0.681548000
  6 0.000000000 -4.245855000 -0.681548000
  6 0.000000000 -0.681548000 -4.245855000
  6 0.000000000 0.681548000 -4.245855000
  6 0.000000000 -0.681548000 4.245855000
  6 0.000000000 0.681548000 4.245855000
  6 0.000000000 4.245855000 0.681548000
  6 0.000000000 4.245855000 -0.681548000
  1 0.000000000 -5.096481000 1.350466000
  1 0.000000000 -5.096481000 -1.350466000
  1 0.000000000 -1.350466000 -5.096481000
  1 0.000000000 1.350466000 -5.096481000
  1 0.000000000 5.096481000 -1.350466000
  1 0.000000000 5.096481000 1.350466000
  1 0.000000000 -1.350466000 5.096481000
  1 0.000000000 1.350466000 5.096481000
  Variables:
  R12 = 2.04198300
  R15 = 2.04198300
  A215 = 90.00000000
  R16 = 2.04198300
  A316 = 90.00000000
  D5316 = 180.00000000
  A217 = 90.00000000
  D5217 = 90.00000000
  constants
  R17 = 0.40000000 s 20 0.2
 This job constructs a valid geometry, the optimization starts, but it
 starts incorrectly: during the optimization, only the Z-matrix
 parameters are varied, while the coordinates of most atoms are fixed.
 Can I do something to make Gaussian optimize these atomic coordinates
 as well?
 
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 ************************************************************
 Dr Željko Vitnik
 Senior research associate
 IChTM-Department of Chemistry, University of Belgrade
 Studentski trg 12-16, 11000 Belgrade (Serbia)
 Phone: (+381) 11-3336-735; Mobile: (+381) 64-1272-051
 E-mail: zvitnik:_:chem.bg.ac.rs
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