The VCTRANS program reads the output from quantum chemistry calculations at a number of points in coordinate space (conveniently created by the VCPNT program) and transforms the information into a database that can be used by the fitting program VCHFIT . The name is a contraction of VibronicCouplingTRANSformation.

Input data is specified in an input file. Output is written to an info file .

To run the program type
vctrans input
or
vctrans input.inp
where input (or input.inp) denotes the input file. The input format uses, like all the Quantics package input files, keywords that are for the most part free format and case insensitive. See Quantics input file structure

for further information on the general use of keywords, noting that there are no sections in the VCHAM input files. The input file ends with the keyword end-input

Defining the system and input data files
Keyword Description
file0 = S S is name of file containing normal modes and Q0 geometry
nmodes = I (, I1) System contains I normal modes and I1 trivial degrees of
freedom (default 6).
all_eigenvectors Use all Hessian eigenvectors, including those corresponding
to translations and infinitesimal rotations. NOT IN USE.
nstates = I System contains I states. This needs to be the number included in the quantum chemistry calculations, i.e. the number of states in the output files.
Defining the point files to be read
Keyword Argument
datadir = S Files are contained in the directory S. Default is "."
files
file.log I [options]
....
end-files		 Read the data for state I from file.log.
The files and end-files keywords must be alone on a line.
Various options can be used
Option Description
orient = S select orientation to be read if different
from default (see orientation keyword below)
root = I read data for Ith root. This is used if
the calculated state to be read is different from the
state label given in the states keyword. This
if useful if, for example, an intruder state changes the
ordering.
orbital = I read data for Ith orbital. This is to
select the orbital of origin defining the
state in OVGF calculations, and is analogous
to the root=I keyword above
abintype = S select ab initio type if different
from default (see abinitiotype keyword below)
gndfile = S read the ground-state energy from file S
rather than the data-file.
gndabtype = S select ab initio type of ground-state
file if different from default (see gndabtype
keyword below)
gndorient = S select input orientation to be read in
ground-state file if different from default (see
orient keyword below)
eshift = S applies a positive energy shift of S to the value
read in in eV

If I is given as 0, all state energies for a given point are read
from the file specified and sorted energetically. This can be useful
to avoid problems associated with root flipping. If I=0 is specified,
the following options may be used

Option Description
extra = S An extra S states were included in the
calculation and the corresponding energies are
to be read and sorted
ignore = S Ignore the Sth state, were the label S is
determined after sorting
remove = S Do not read in the Sth state energy

datasets
data.set
....
end-datasets		 Read the set of files listed in the file data.set. The list uses
the same format as the files ... end-files keywords.
The datasets and end-datasets keywords must be alone on a line.
Defining the input data to be read from a GAUSSIAN output file.
abinitiotype = S Define the ab initio method used in the calculations to be read
S Method
RHF
OVGF
CIS
MP2
MP3
MP4
DFT
CAS
Defining the input data to be read from a MOLPRO output file.
abinitiotype = S Define the ab initio method used in the calculations to be read
S Method
CAS CASSCF
PT2 CASPT2
SOC Spin orbit coupling read and put into soc.gnu
MRCI MRCI
EOM EOM-CCSD
molpro_reorder If states reorder between CAS and CAS-PT2 calculation this will read in derivative couplings and assign them to correct state. If used the CAS ordering of states must be given with the states keyword. The ordering of the states given in the info file is then written out in numerical order
Defining the input data to be read from a GAMMES-US output file.
abinitiotype = S Define the ab initio method used in the calculations to be read
EOM EOM-CCSD
CR-EOM CR-EOM-CCSD
DELTA-CR-EOM DELTA-CR-EOM-CCSD
Defining the input data to be read from a TURBOMOLE output file.
abinitiotype = S Define the ab initio method used in the calculations to be read
RICC2 RI-CC2
Defining the input data to be read from a DD-vMCG QC database.
abinitiotype = DB The database from a direct dynamics calculation will be transformed into an info file for fitting. The following options must be set in addition:
datadir = S the string S is the path of the QC DB. The frequency file specified by file0 must be in this directory.
file0abtype = S the string S specifies the calculation type used in file0 using the usual options for abinitiotype.
DB0 Only the first DB dataset is read and output. An analysis of the gradients and couplings will be made, ordering the modes in terms of coupling strengths.
file0abtype = S S is the calculation type used for file0. If not used, type is that
defined by the abinitiotype keyword. See abinitiotype
keyword above for options
gndabtype = S If ground-state energies are read from separate files
(see data file options above) S is the calculation type used in these
files. See abinitiotype keyword above for options
order = I I=0 only energies read at each point
I=1 energies and gradients read if present in file
Gradient Difference and Derivative coupling too.
I=2 energies, gradients, and hessians read if present in file.
orient = S S is a string defining the input orientation to be read
S Orientation
input Input orientation
standard Standard orientation
z-matrix Z-matrix orientation
Default = input
file0orient = S Orientation to be read from file. This is used to select the
geometry in output from GAUSSIAN. See orient keyword for
options. If not set, file0orient = orient
Defining the input data to be read from a MOLCAS output file.
abinitiotype = S Define the ab initio method used in the calculations to be read
S Method
RHF Restricted Hartree Fock
PT2 CASPT2

e.g. file0 = geometry0.log
will read the file geometry0.log for the information. If using GAUSSIAN, this file should be created using the freq=hpmodes keyword

The following keywords make the program write additional data to the info file. This can be useful for analysis.
Defining the output
Keyword Argument
title
line 1
....
end-title		 Add title to info file. The title keyword must be alone on a line and up to five lines can be written before the end-title keyword - which must also be alone on a line.
derivatives_in_q If the first derivatives have been read for a dataset they are written out in normal mode coordinates as well as cartesian
second_derivatives_in_q If the second derivatives (Hessian) have been read for a dataset they are written out in normal mode coordinates as well as cartesian
gradient_difference If the derivative coupling and gradient difference are read for a dataset, both are written out. Otherwise only the derivative coupling is given. If derivative_in_q is also set these vectors are given in both cartesian and normal mode coordiantes
transition_dipoles If the transition dipole moment between the ground-state and the state of interest has been read it is written out.
nmode_trafos Output the cartesian to mass-frequency scaled normal mode transformation matrix.
units_au Atomic units (Hartree and Bohr) used in place of the default eV and Angstrom.

Defining the system
Keyword Argument
energy0 = R The zero of energy is taken as R. Input can can be in a variety of units
states = I, I1, ... The database will include information from states I, I1, ... By convention I = 1 is the ground-state. E.g. states = 1,3,4 will read the ground-state, and the second- and third-excited states. If this keyword is not used, the database will read information for all states from 1,..., nstates as defined by the nstates keyword.
frequencies
I LAB R
....
end-frequencies		 for the Ith mode with label LAB use the frequency R instead of that read in the file0. Default is frequency in eV, but units can be used.
nm2curv dihed = M transforms the normal mode to the dihedral angle defined by the atoms in dihed-section (see note 1 below).

Note 1: Defining a dihedral
If the nm2curv dihedral keyword is used the atoms to be kept fixed and those that are to be rotated are specified in the dihed-section. Each atom is listed in the same order as in the file0, followed by a letter denoting its place. In the digram below a,b and c are frozen and each of the atoms labeled d are rotated.

The atom denoted a is not rotated but used as the reference for the dihedral angle. A is connected to b which forms part of the b-c bond which the dihedral angle is rotated about. The above digram would require the following example input section.

dihed-section
H a
O b
C c
H d
H d
H d
end-dihed-section

Any other atoms in the molecule which are not to be rotated and do not form part of the dihedral bond must be frozen using the flag f.

Is also worth mentioning that in the output database (.info) this normal mode will no longer be expressed in normal mode coordinates, but in torsional degrees.

Example: Cr(CO)5

The vibonic coupling model Hamiltonian has been calculated for the lowest three states of Cr(CO)5. At the D3h trigonal bipyramid geometry, these form an (Exe)+A pseudo-Jahn-Teller system with a doubly degenerate state coupled to a singly degenerate state. See Worth et al. Mol. Phys. (2006) 104: 1095. In the fit the following 2 datadases of points were used.

crco5_trans0.info is a zero-order info file for Cr(CO)5. It was created using the input crco5_trans0.inp . According to this input, the file CrCO5_D3h.log is the result of a GAUSSIAN calculation containing the normal modes and frequencies. The frequencies for the model, both for the mass-frequency scaled coordinates and the zero-order Hamiltonian, are taken from the input file rather than the GAUSSIAN calculation. The system contains 27 normal modes. Information about the surfaces is read up to second order (energy, first and second serivatives, and gradient difference and derivative coupling) from the files crco5_d3h_72.log and crco5_d3h_73.log which are both stored in the directory points. The calculations have been done using a CAS method, and the system will include information from for 3 states, labelled 1,2 and 3 in the files. Information about states 1 and 2 is read from crco5_d3h_72.log and information about state 3 is read from crco5_d3h_73.log. Energies in the .info file are taken relative to -650.1354407439 and the derivative coupling vectors, as well as the derivatives in the dimensionless normal mode coordinate system are also written out.

A second database was then set up with the energies of the various states at a number of points along the most important vibrational modes: crco5_trans1.info The input file was crco5_trans1.inp . In contrast to the crco5_trans0 the order is set to 0, which means that only energies are read in. In addition to the files at Q0 read before, the files listed in crco5_1.set crco5_2.set crco5_8.set are to be read. These are the points along modes 1, 2, and 8 respectively.