Structure of the Output¶
AMS produces two ASCII files: standard output and the ams.log file. ADF writes part of these files. See also
The ams.log file is a very concise summary of the calculation’s progress during the run. Furthermore, ADF produces and reads binary data files. Most of these files have the so-called KF format. KF stands for Keyed File: KF files are keyword oriented, which makes them easy to process by simple procedures. KF files are Direct Access binary files. Consult the Scripting Section for information about how to use some standard utilities for processing KF files.
The graphical user interface ADF-GUI provides graphical representations of calculated data fields:
Job Characteristics on standard Output¶
Input Echo, Output Header
- Header with the program name, the release number and a copyright statement.
- AMS part of the output file with the geometry
- Copy of the ADF engine part of the input file
- Title and any comments that may have been supplied via input (key COMMENT).
Main Job Characteristics
- The Model Parameters such as the Density Functional and relativistic options.
- A list of attached files: restart data files and fragment files.
- (Initial) geometric data: atomic positions, atom types, defined fragments, and the inter-atomic distance matrix.
- The point group symmetry, with a list of the irreducible representations and subspecies.
- The electronic configuration: occupation numbers (if specified), their distribution over spin-\(\alpha\) and spin-\(\beta\), and the net charge of the molecule.
Build Info: Fragments and Function Sets
- Correspondence between fragments in the molecule and the corresponding master fragments on the pertaining fragment file. (This output is by default off)
- SFOs: the Symmetry combinations of Fragment Orbitals. The SFOs are the basic conceptual entities for the analysis of MOs and other results.
- The elementary basis functions and the frozen-core levels of the atoms.
- Parallelization and vectorization characteristics.
- Update strategy parameters for the SCF procedure.
- General precision settings for numerical integration and neglect-of-small function values (in integral evaluations).
- Numerical integration parameter(s) and the number of generated (symmetry unique) integration points, and partitioning of the points in blocks.
- SCF procedure, at each cycle: for each irreducible representation: the one-electron orbital energies and the occupation numbers for a contiguous sequence of orbitals.
- Gross atomic charges, computed from a Mulliken population analysis.
- Property specific output, like spectroscopic properties.
- AMS part of the output
- Normal termination or an error message.
Log file, adf.rkf, TAPE13¶
The ams.log file (logfile) is generated during the calculation and flushed after (almost) each message that is sent to it by the program. Consequently, the user can inspect it and see what is going on without being delayed by potentially large system I/O buffers. Each message contains date and time of the message plus additional info.
A major part of the messages simply states the name of a procedure. Such messages are sent when the procedure is entered. During the SCF procedure, the SCF errors, which are a measure for non-self-consistency, are written at every cycle. In calculations where the geometry is changing (optimization, frequencies…) each set of new coordinates is sent to the log file (Cartesian, in angstrom and also Z-matrix, if a Z-matrix structure was provided in the input file). Other messages should be self-explanatory.
Be alert on error messages. Take them seriously: inspect the standard output carefully and try to understand what has gone wrong. Be also alert to warnings. They are not necessarily fatal but you should understand what they are about before being satisfied with the results of the calculation. Do not ignore them just because the program has not aborted: in some cases the program may not be able to determine whether or not you really want to do what appears to be wrong or suspicious. If you believe that the program displays erratic behavior, then the standard output file may contain more detailed information. Therefore, in such case save the complete standard output file, together with the logfile, in case we need these files for further analysis.
adf.rkf is the general result file of an ADF calculation. It is a KF file: Direct-Access, binary, and keyword driven. It contains information about the calculation. You can use it as a fragment file in a subsequent calculation on a bigger molecule, where the current one may be a part, or in an analysis or property program. For more information on adf.rkf, see Appendix on adf.rkf.
TAPE13 is the checkpoint file for restarts after a crash. It is a concise version of adf.rkf, containing only the data the program uses for restarting the calculation. See the RESTART keyword. Like adf.rkf, TAPE13 is a binary, keyword driven KF file, see Appendix on TAPE13.