Output Files

In addition to the information printed to the screen, TeraChem writes several output files to the scratch directory. The scratch directory is called scr by default; if the jobname keyword is set it is called scr.jobname instead.

All calculations

File	Description
scr/c0	Converged wavefunction (binary): MO coefficients C[i][j], where row i is the MO and column j is the AO basis-function index. Can be reused as an initial guess (guess) in later calculations.
scr/ca0, scr/cb0	As c0, but the alpha- and beta-spin orbital coefficients for UHF/UKS jobs.
scr/charge_mull.xls	Tab-separated Mulliken atomic charges.
scr/mullpop	Detailed Mulliken population analysis, including atomic spin densities.
scr/bo.csv	Mulliken overlap populations (akin to bond orders).
scr/results.dat	Summary of results: final energy, center-of-mass coordinates, and dipole moment.
scr/jobname.basis	Normalized basis-set information for the current run.
scr/jobname.geometry	Geometry information for the current run (XYZ coordinates and masses in AMU). For MD this is the starting structure.
scr/jobname.molden	Geometry and MO information for the current run (Molden format).
scr/bond_order.mat	Mayer bond-order matrix, written if bond_order_mat is set.
scr/bond_order.list	Mayer bond orders as a thresholded list, written if bond_order_list is set.

Project jobs

File	Description
scr/prjct	Converged wavefunction projected onto another (usually larger) basis set. Generated by run project jobs and used as an efficient initial guess.
scr/prjcta, scr/prjctb	As prjct, for the alpha and beta orbitals in UHF/UKS jobs.

Geometry optimization / transition-state search

File	Description
scr/charge.xls	Atomic charges at each optimization step (atoms in columns, steps in rows).
scr/optlog.xls	Tab-separated file of 7 columns; only the first is currently used — the SCF energy along the optimization or transition-state search.
scr/optim.xyz / scr/optim.pdb	Optimization/TS-search trajectory in XMol or PDB format (visualize with VMD; XYZ also works in Molden). For an NEB calculation this holds a single frame: the putative transition state (the climbing image).
scr/spin.xls	Excess spin per atom, same format as charge.xls. Only produced for unrestricted (UHF/UKS) calculations.

Transition-state search (NEB)

File	Description
scr/neb_n.xyz	XMol trajectory of the n-th NEB image. The last image (e.g. neb_10.xyz when min_image is 10) is the transition state, also stored in optim.xyz.
scr/nebinfo	Energies of all (min_image−1) NEB images along the converged path.
scr/nebpath.xyz	XYZ coordinates of all (min_image−1) NEB images along the converged path.
scr/img_n.molden	Molden file with coordinates and MO coefficients for the n-th NEB image.

Frequency calculation

File	Description
scr/Hessian.restart	Binary checkpoint for restarting frequency calculations.
scr/Hessian.bin	Binary Hessian (force-constant) matrix. If present, it is reused for subsequent frequency calculations — e.g. to run the thermochemical analysis at a different temperature (or with different atomic masses) without recomputing the Hessian.
scr/Frequencies.dat	Normal modes (Cartesian) and their frequencies, after removal of rotation and translation (normally \(3N_\text{atoms}-6\) vectors). Also used as input for FMS90.

Initial-condition generation

File	Description
scr/Hessian.restart	See Frequency calculation.
scr/Hessian.bin	See Frequency calculation.
scr/CentralGeometry.initcond.xyz	XMol file with the reference geometry used for sampling.
scr/Geometry.initcond.xyz	XMol file with a geometry drawn from initial-condition sampling — use as the starting geometry in a subsequent MD run.
scr/Velocities.initcond.xyz	XMol file with the matching sampled velocities — use together with Geometry.initcond.xyz.
scr/Frequencies.initcond.dat	Reference geometry and atomic masses; not of general interest but serves as input for the quantum-dynamics code FMS90.

MD simulation

File	Description
scr/log.xls	Tab-separated, 8 columns: (1) time, (2) SCF energy, (3) unused, (4) kinetic energy, (5) temperature, (6) total energy (SCF + kinetic), (7) HOMO energy, (8) LUMO energy. Energies in Hartree, temperature in K. In NVT dynamics the total energy excludes the damping-force contribution and is not conserved.
scr/coors.xyz	MD trajectory geometry in XMol format (Å); visualize with VMD. Not created if MDBinaryOutput is true.
scr/vel.log	Atomic velocities along the trajectory, formatted like coors.xyz but with a blank line between sets. Units are AMBER's — Angstroms/(1/20.455 ps). Not created if MDBinaryOutput is true.
scr/coors.dcd	MD trajectory geometry in binary DCD format (VMD-readable). Only created if MDBinaryOutput is true.
scr/vel.dcd	Atomic velocities in binary DCD format. Only created if MDBinaryOutput is true.
scr/restart.md	Binary MD restart file (wavefunction, coordinates, velocities, etc.). Written every 100th MD iteration by default; change the interval with restartmdfreq.
scr/restart.mdRnd	Binary state of the random-number generator, so a restarted run exactly reproduces a single longer run with the same seed (relevant e.g. for Langevin dynamics). Used automatically on restart — both restart.md and restart.mdRnd are needed.

PCM

File	Description
scr/ratom.txt	Actual radii used for each PCM cavity sphere (reflecting the cavity-radii scaling factor). One row per atom, in input-geometry order.
scr/sas.xyz	All PCM grid points as an .xyz file (the element name in column 1 is a placeholder for visualization). Only created if print_ms is true.

ESP / RESP

File	Description
scr/esp.xyz	ESP grid points (Å) and the electrostatic potential at each. Column 1: element type of the originating atom; columns 2–4: grid-point coordinates; column 5: ESP at the point; column 6: index of the originating atom (same order as the input deck). Visualization software reads the first 4 columns (and sometimes column 5 as a label, e.g. Molden). See RESP.