Text Files in PSI3

Psi uses several text files to store certain types of information. Storing information in text files makes it much easier for users to inspect and manipulate that information, provided that the user understands the format of that file. In the following file format descriptions, I will use the notation ${ x_i, y_i,}$ and ${z_i}$ to denote the x, y and z coordinates of nucleus i, respectively, ${\eta_{ i}}$ will denote the ${i^{\rm th}}$ internal coordinate, and E will denote the sum of the electronic energy and nuclear repulsion energy.

	geom.dat

A vectorized format which is appropriate for the routines in libipv1 or iomr is employed in geom.dat Generally, the first line of geom.dat is

%%

Though this does not affect the parsing routines in libipv1, or any of the common programs which read geom.dat (i.e. rgeom or ugeom), some PSI2 modules (bmat, etc.) expected this line and would muddle up geom.dat if it is not present. geom.dat will frequently have several entries, with the topmost being the most recent addition by bmat.

format: n = number of atoms.

$$\begin{array}{lcccr} {\tt geometry = (}\\ {\tt (} &x_1 \hspace{0... ...n} &y_n \hspace{0.8in} &z_n \hspace{0.8in} &{\tt )} \\ \ \ {\tt )} \end{array}$$ (1)

Other geometries of the same format may follow.

	fconst.dat

This file contains the force constant matrix produced by optking or intder95. Because the force constant matrix is symmetric, only the lower diagonal is stored here. The force constant matrix may be represented in either cartesian or internal coordinates, depending upon what flags were used when intder95 was run to produce fconst.dat. optking is the program which uses fconst.dat most frequently, and it assumes that the force constant matrix will be in terms of the internal coordinates as defined in input.dat or intco.dat. For this reason, it is best to have intder95 produce a fconst.dat in internal coordinates. The order of internal coordinates is determined by the order set up in input.dat or intco.dat. The totally symmetric coordinates always come first, followed by all asymmetric coordinates.

In the following format, ${f_{\eta_i}}$ is the force constant for internal coordinate ${\eta_i}$ and ${f_{\eta_i,\eta_j}}$ is the force constant for the mixed displacement of internal coordinates i and j.

format: n = total number of internal coordinates in intco.dat or input.dat.

$$\begin{array}{lllll} f_{\eta_1} \\ f_{\eta_2,\eta_1} & f_{\eta_2... ...{\eta_{n},\eta_2} & f_{\eta_{n},\eta_3} & \cdots & f_{\eta_{n}} \\ \end{array}$$ (2)

If the force constant matrix is stored in cartesian coordinates, however, the format, using a similar notation, with n now equal to the total number of atoms, is as follows:

$$\begin{array}{llllll} f_{x_1} \\ f_{y_1,x_1} & f_{y_1} \\ f_{z_... ...1} & f_{z_n,y_1} & f_{z_n,z_1} & f_{z_n,x_2} & \cdots & f_{z_n} \\ \end{array}$$ (3)

	file11.dat

The number of atoms (n), total energy as predicted by the final wavefunction, cartesian geometry, cartesian gradients, atomic charges (Z$_i$) and a label are all contained in file11. The exact nature of the label depends upon the type of wavefunction for which the gradient was calculated. The first part of the label is determined by the label keyword in input.dat. If an SCF gradient is run, then the calculation type (calctype), and derivative type (dertype) will also appear. If a correlated gradient has been run, calctype [CI, CCSD, or CCSD(T)] and derivative type (FIRST) appear. file11 will frequently have several entries, with the last entry being the latest addition by cints -deriv1.

format:

$$\begin{array}{l} label\hspace{0.5in} calctype \hspace{0.5in} dert... ...{\delta E}{\delta y_n} & \frac{\delta E}{\delta z_n} \\ \end{array}\end{array}$$ (4)

	file12.dat

Internal coordinate values and gradients, the number of atoms (n), and the total energy (E) may be found in file12. file12 is produced by intder95, which can convert cartesian gradients into internal gradients. Generally, file12 will have several entries, with each entry corresponding to an entry in the file11 of interest.

format:

$$\begin{array}{l} n\hspace{1.5in} E \\ \begin{array}{cc} \v... ...lta E}{\delta \eta_n} \hspace{1.2in}\\ \end{array}\end{array}$$ (5)

	file12a.dat

In order to calculate second derivatives from gradients taken at geometries finitely displaced from a particular geometry, intdif requires a file12a. This file contains essentially the same information as file12, but each entry also has information concerning which internal coordinate (numintco) was displaced in the gradient calculation and by how much (disp) it was displaced.

format:

$$\begin{array}{l} numintco\hspace{0.5in}disp\hspace{1.5in}E \... ...elta E}{\delta \eta_n} \hspace{0.8in}\\ \end{array}\end{array}$$ (6)

	file15.dat

The cartesian Hessian matrix is found in file15. The first line of this file gives the number of atoms (n) and, in case you are curious, six times the number of atoms (sixtimesn).

format:

$$\begin{array}{l} n\hspace{0.4in}sixtimesn \\ \begin{array}{... ...2 E}{\delta^2 z_n} \hspace{0.3in}\\ \par\end{array}\end{array}$$ (7)

	file16.dat

The second derivatives of the total energy with respect to the internal coordinates are found in file16. As in file15, the number of atoms (n) and six times that number (sixtimesn) are given.

format:

$$\begin{array}{l} n\hspace{0.4in}sixtimesn \\ \begin{array}{... ...}{\delta^2 \eta_n} \hspace{0.3in}\\ \par\end{array}\end{array}$$ (8)

	file17.dat

First derivatives of the cartesian dipole moments ( ${\mu_x,\mu_y,\mu_z}$) with respect to the cartesian nuclear coordinates may be found in file17. The first line and subsequent format are similar to that of file15.

format:

$$\begin{array}{l} n\hspace{0.4in}threetimesn \\ \begin{array... ...lta \mu_z}{\delta z_n} \hspace{0.3in}\\ \end{array}\end{array}$$ (9)

	file18.dat

First derivatives of the cartesian dipole moments ( ${\mu_x,\mu_y,\mu_z}$) with respect to the internal nuclear coordinates may be found in file18.

format:

$$\begin{array}{l} n\hspace{0.4in}threetimesn \\ \begin{array... ...mu_z}{\delta \eta_{n}} \hspace{0.3in}\\ \end{array}\end{array}$$ (10)