# Running the program¶

When ADF has been installed you can run it by supplying appropriate input and starting the ‘adf’ script, located in $ADFBIN. This script sets up some environment variables and parses the input to see if anything special needs to be done (for example, if the BASIS key is used the adf script will also execute commands to make the appropriate fragment files). You can use this run script both for the serial and parallel versions of the program. For other programs in the package, there are similar run scripts (‘band’, ‘dirac’, and so on). Running the program using the run script involves the following steps: • Construct an ASCII input file, say “in”. • Run the program by typing (under UNIX): $ADFBIN/adf {-n nproc} < in > out

The part between curly brackets is optional, so the shortest application has the format

$ADFBIN/adf < in > out Note that the run files in the$ADFHOME/examples directory are UNIX scripts which are executed with:

run > out

• Move / copy relevant result files (in particular TAPE21) to the directory where you want to save them, and give them appropriate names.

• Inspect the standard output file out to verify that all has gone well.

During the run you may inspect the logfile, to see how far the program has proceeded, or whether you should interrupt the calculation.

In the above scheme adf is the name of the run script that invokes the adf.exe program executable. During the installation the script has been put in the same directory where the program executables are generated: $ADFBIN. You may have moved it to another place, or renamed it. We recommend that you adjust your$PATH variable so that you can omit $ADFBIN from the execution command. To run another program from the ADF suite, just use the appropriate program run script. The input for the program is read from standard input, and output is written to standard output, redirected in the example above to in and out, respectively. The part between square brackets is optional and is only meaningful for a parallel program version. The -n flag specifies the number of parallel processes (nproc) to use. If omitted the default applies, which is the value of the environment variable$NSCM, if such variable exist, otherwise it is defined by installation parameters (in the $ADFHOME/settings file, see the Installation Manuals). The program run scripts have, in fact, more flags and arguments, for special usage. You can get a survey by typing $ADFBIN/adf -h

If a parallel version of ADF has been installed you should be aware of a few special aspects of running ADF in parallel. Partially this depends on the platform and on the installation settings.

First of all, you may specify (by command-line options in the run-script and/or by defining suitable environment variables) explicitly how many parallel processes are to be used. Secondly, you should realize that most of the files that you would have in a single-node run are in a parallel run distributed over the parallel processes. Some parts of the file may be identical across the processes while other parts are not and would only after a recombination yield the data of the corresponding single-node file. The normal result files, (standard output, the logfile and the binary result file TAPE21) are complete at the master process.

How to set up a parallel calculation can be found in the Installation Manual.

## Files¶

The ADF program may generate several output / result files, along with the standard output file. The most important one is TAPE21 (.t21 file), the general result file. TAPE21 contains relevant information about the outcome of the calculation. You may want to store this file somewhere under an appropriate name, for future usage. The meaning of any other files that are produced are explained later in this User’s Guide.

Any files produced by the program are generated in the local (working) directory where the calculation runs. If you want to keep them, make sure to move them after the calculation has finished to wherever you want to store them.

Files attached to the job, such as fragment files, are by default also assumed to exist in the local directory. You must take care to move or copy required files to that directory before starting the calculation, or to provide via input adequate information to the program where to find the files. In many cases you can specify a complete path to the file.

Most files that are generated by the program, in particular the standard result file that can be used as a fragment file in other calculations, are binary files. A binary file should usually not be moved from one machine to another, i.e. it may not be readable by another machine than the one that generated the file, unless the two machines are of the same type. The ADF package provides utilities to convert the ADF binary result files from binary to ASCII, and vice versa, so that you don’t have to regenerate your fragment libraries when going to another machine. See the Scripting Section for further details regarding such aspects.

### TAPE21 and logfile¶

Two of the files that are produced by ADF deserve special attention. The first is the general result file TAPE21 (.t21 files). It is a binary file that contains a lot of information about the calculation, such as the one-electron orbitals expressed in the basis functions. It can be used as a fragment file for subsequent calculations (although only TAPE21 files from spin-restricted calculations can be used as fragment files). Like all files produced by the program, it is generated in the directory where the job runs. Having done a calculation, you will usually store TAPE21 somewhere under a suitable name so that you can later reuse it, as a fragment file, for a restart, to feed it to an analysis program, and so on.

The second is an ASCII log file, called logfile. It accumulates messages from ADF into a (brief) summary of the run. You can inspect it during the calculation to check how far the calculation has proceeded, whether there are important warnings and so on. At the end of the run this file is copied to the tail of the normal standard output file.

### Standard output¶

ADF is a program that lends itself particularly well for chemical analysis. This is a direct result of the fragment-based approach, where properties of the molecule are related to the properties of the constituent fragments, which is precisely how the chemist thinks. Molecular Orbitals are (optionally) analyzed extensively as how they are composed from occupied and virtual fragment orbitals. This inherently implies a large amount of output. Even computations on small molecules may produce startlingly many pages of output. This is not necessarily so because you can regulate the production of output in detail. Obviously, some kind of default production of output had to be implemented. The field of ADF users is so wide and diverse that it is hard to satisfy everybody as regards this default level of output. Depending on your purposes the automatic settings, which determine how much output is generated without instructions to the contrary, may yield boringly many numbers that you just skip through in search for the one value you’re interested in, or it may be widely insufficient. Therefore, take notice of the possibilities to regulate output.

Above all, however get familiar with the analysis tools that ADF provides to see in what ways these may help to interpret your results. In a later chapter a global description of output is given as it is normally produced. The chapter below gives an introduction in some of the essential features of ADF, which may be sufficiently different from what you are used to in other Quantum Chemistry codes to deserve your attention.

### File names during parallel runs¶

The adf process of a kid normally runs in a separate directory.

Standard output is a special: the parent writes its normal (‘print’) output to standard output while the kids each write to a file KidOutput.