Output description

Output description#

In URVA, results are all written to external files instead of standard output. All output files have the suffix of “.csv” or “.dat”. The execution of URVA will abort if a result file with a duplicated name is found in the current folder. Make sure that current directory is cleaned up before execution.

Energy and derivatives#

Usually the Self-Consistent Field(SCF) energy is calculated and used to construct the potential energy surface along the reaction path.

In order to check this value, the @DATAFILETYPE must be set to old or new and @ENERGY must be set to on.

The unit of SCF energy is Hartree as one of the atomic units(a.u.). In order to calculate first and second derivatives of SCF energy against reaction coordinate/parameter \(\mathbf{s}\), cubic spline fitting is used. For the second derivative of SCF energy, the region between \(\mathbf{s}=-0.1\) and \(\mathbf{s}=+0.1\) is predicted via cubic spline fitting from the information outside this region.

NOTE: 1 Hartree = 627.509 474 kcal/mol

Output files:

  • energy.csv

    SCF energy vs. \(\mathbf{s}\)

  • energy_1_d.csv

    First derivative of SCF energy vs. \(\mathbf{s}\)

  • energy_2_d.csv

    Second derivative of SCF energy vs. \(\mathbf{s}\)

Internal coordinates#

The value of user-defined internal coordinates could be calculated. All types of internal coordinates described in section 2.2.2 are supported.

In order to have this result, @PARM must be set to GeomOnly or All.

The unit of printed internal coordinates is atomic unit with bohr for distance and radian for angles.

NOTE: 1 Bohr = 0.529177 :math:`AA`; 1 rad = 57.295 8 :math:`^{circ}`

Output file:

  • q\(\_\)n.csv

Decomposition of reaction path direction and curvature into internal coordinates#

In order to have this result, @PARM must be set to All.

Output files:

  • eta-q_n.csv

    Decomposition of reaction path direction into internal coordinates

  • kappa-q_n.csv

    Decomposition of reaction path curvature into internal coordinates

Generalized vibrational frequency#

For any point on reaction path, we could have \(3N - K - 1\) vibrations, in which \(K\) is the total number of translations and rotations. In URVA, \(K\) takes the value of 6 which excludes the possibility of analysis of reactions like H\(_2\) + H \(\rightarrow\) H + H\(_2\) where the whole reaction complex stays in a linear geometry.

In order to have this result, @VIBRATION must be set to on.

Output file:

  • freq_dmo.csv

    Generalized vibrational frequencies vs. \(\mathbf{s}\)

NOTE: Unit of frequencies is :math:`cm^{-1}`.

Scalar curvature#

The original scalar curvature calculated without correction around the TS region and spike removal will be written to file originalkappa.dat.

In order to have this result, @DIRCURV must be set to on.

If the CURVCOR and AUTOSMTH modules are used, the corrected curvature data will be written to merged.dat.

If RMSPK module is also used, the curvature data after spike removal will be written to merged-nospk.dat.

Adiabatic force constant#

The adiabatic force constant of chemical bonds between two atoms along the reaction path will be written to adiabfc-ka.csv.

In order to have this result, @ADIABFC must be set to on.

In some situations, there might be noise in the result. These noise regions could be nicely removed via cubic spline fitting.

NOTE: Only result of bond length between 2 atoms could make sense.

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