The file ufftopology

The topology file ufftopology contains the blocks nxtnei12, nxtenei13, nxtnei14, connectivity, angle, torsion, inversion, nonbond and qpartial. It starts with $ufftopology and ends with $end. The first three blocks (nxtnei12, nxtnei13, nxtnei14) have the same form: they start with the atom number and the number of its neighbours, in the next line are the numbers of the neighbour atoms. Then the connectivity-block follows starting with the number of bond terms. Each line contains one bond term:

$$I \qquad J .$$

Here are $I$ and $J$ the number of the atoms, d the distance in a.u. and BO is the bond order.

The angle terms follow, starting with the number of the angle terms. In each line is one angle term:

$$J \qquad I \qquad K \qquad \theta \qquad nr_{JI} \qquad nr_{IK}.$$

Here are $J, I$ and $K$ the atoms number, where atom $I$ is in the apex. ``wtyp'' is the angle type and has the following values:

wtyp = 1

linear case

wtyp = 2

trigonal planar case

wtyp = 3

quadratic planar case

wtyp = 6

octahedral case

wtyp = 9

all other cases.

$\theta$ is the angle value in degree. $nr_{JI}$ and $nr_{IK}$ are the number of the bonds between $J$ and $I$ and the bond between $I$ and $K$. The hybridization of atom $I$ determines ``wtyp''.

Then the torsion terms follow, starting with the number of the torsion terms. Each line contains one torsion term:

$$I \qquad J \qquad K \qquad L \qquad nr_{JK} \qquad \phi \qquad \theta_{IJK} \qquad \theta_{JKL}.$$

Here are $I, J, K$ and $L$ the atom numbers. $nr_{JK}$ is the number of the bond between $J$ and $K$. ``ttyp'' is the torsion type:

ttyp = 1

$J$ (sp$^3$)-K (sp$^3$)

ttyp = 11

like ttyp=1, but one or both atoms are in Group 16

ttyp = 2

$J$ (sp$^2$)-K (sp$^3$) or vice versa

ttyp = 21

like ttyp=2, but one or both atoms are in Group 16

ttyp = 22

like ttyp=2, but $J$ or $K$ is next a sp$^2$ atom

ttyp = 3

$J$ (sp$^2$)-K (sp$^2$)

ttyp = 9

all other cases.

$\phi$ is the value of the torsion angle in degree. $\theta_{IJK}$ is the angle value of ($I-J-K$) and $\theta_{JKL}$ is the cwone for $J-K-L$. The hybridizations of $J$ and $K$ determine ``ttyp''.

The inversion terms follow starting with the number of inversion terms (e.g. the pyramidalisation of NH$_3$). In each line is one inversion term:

$$I \qquad J \qquad K \qquad L \qquad \omega_1 \qquad \omega_2 \qquad \omega_3.$$

$I, J, K$ and $L$ are the atom numbers. Atom $I$ is the central one. ityp1, ityp2, ityp3 are the types of the inversions:

ityp = 10

atom $I$ is C and atom $L$ is O

ityp = 11

like ityp=10, but $L$ is any atom

ityp = 2

$I$ is P

ityp = 3

$I$ is As

ityp = 4

$I$ is Sb

ityp = 5

$I$ is Bi

ityp = 9

all other cases.

$\omega_1, \omega_2$ and $\omega_3$ are the values of the inversion angles in degree.

The nonbond terms follow starting with the number of the non-bonded terms. In each line is one nonbond term:

$$I \qquad J .$$

Here $I$ and $J$ are the atom numbers, d the distance in a.u. Then the partial charges follow.

If the determination of the molecule connectivity failed, you can specify the block nxtnei12 in the file ufftopology. Then the program calculates the other blocks.

Based on the numbers of the next neighbours (block nxtnei12 in the file ufftopology) the program tries to determine the UFF type of an atom. The following rules are implemented: If the atom has three next neighbours and it is in the nitrogen group, then it has a hybridization three. If it is not in the nitrogen group, it has hybridization two. If the atom has four next neighbours and it is in the carbon group, it has hybridization three. If it is not in the carbon group, it becomes hybridization four. If the number of next neighbours is six, then it gets the hybridization six.

Since the smallest eigenvalues $\lambda_i$ of the Hessian has the greatest influence on the convergence of the geometry optimization, one can shift these values with

$$\tilde{\lambda}_i = \lambda_i \cdot \left( \alpha + \beta \cdot e^{-\gamma x} \right)$$

and calculates a new Hessian with these modified eigenvalues.