Examples¶

Introduction¶

The AMS package contains a series of sample runs. They consists of UNIX scripts (to run the calculations) and the resulting output files.

The examples serve:

• To demonstrate how to do calculations. The number of options available in AMS is substantial and the sample runs do not cover all of them. They should be sufficient, however, to get a feeling for how to explore the possibilities.

• To work out special applications that do not fit well in the User’s Guide.

Note: Most of the provided samples have been devised to be short and simple, at the expense of physical or chemical relevance and precision or general quality of results. They serve primarily to illustrate the use of input, necessary files, and type of results. The descriptions have been kept brief. Extensive information about using keywords in input and their implications is given in the User’s Manual.

Where references are made to the operating system (OS) and to the file system on your computer, the terminology of a UNIX type OS is used.

All sample files are stored in subdirectories under $AMSHOME/examples/, where $AMSHOME is the main directory of the AMS package. There are many subdirectories in $AMSHOME/examples/: the examples presented in this section are located in $AMSHOME/examples/adf/. Each sample run has its own directory. For instance, $AMSHOME/examples/adf/HCN/ contains an ADF calculation on the HCN molecule.

Each sample subdirectory contains:

• A file TestName.run: the UNIX script to execute the calculation(s). A sample may involve several calculations, for instance a molecular AMS calculation (using ADF engine) followed by NMR calculation (using the NMR program) to compute chemical shifts.

• A file TestName_orig.out.gz: the resulting output(s) against which you can compare the outcome of your own calculation. Note: the files are compressed using gzip.

• Zero or more files with a .ams extension. These files, if present, are intended for AMSinput and demonstrate the same functionality as the two files above. However, there are also differences between the .ams and the TestName.run files so the results obtained with the .ams files cannot be compared directly with TestName_orig.out. Also, the TestName.run file usually contains more than one calculation, for which more than one .ams file is required. That’s why in some directories you may find more than one .ams file.

Technical notes:

• Running the examples on Windows: You can run an example calculation by double-clicking on the appropriate .run file. After the calculation has finished, you can compare the TestName.out file with the reference TestName_orig.out file. See remarks about comparing output files below.

• The UNIX scripts make use of the rm (remove) command. Some UNIX users may have aliased the rm command. They should accordingly adapt these commands in the sample scripts so as to make sure that the scripts will remove the files. New users may get stuck initially because of files that are lingering around after an earlier attempt to run one of the examples. In a subsequent run, when the program tries to open a similar (temporary or result) file again, an error may occur if such a file already exists. Always make sure that no files are left in the run-directory except those that are required specifically.

• It is a good idea to run each example in a separate directory that contains no other important files.

• The run-scripts use the environment variables AMSBIN and AMSRESOURCES. They stand respectively for the directory that contains the program executables and the main directory of the basis set files. To use the scripts as they are you must have defined the variables AMSBIN and AMSRESOURCES in your environment. If a parallel version has been installed, it is preferable to have also the environment variable NSCM. This defines the default number of parallel processes that the program will try to use. Consult the Installation Manual for details.

• As you will note the sample run scripts refer to the programs by names like ‘ams’, ‘nmr’, and so on. When you inspect your $AMSBIN directory, however, you may find that the program executables have names ‘ams.exe’, ‘nmr.exe’. There are also files in $AMSBIN with names ‘ams’, ‘nmr’, but these are in fact scripts to execute the binaries. We strongly recommend that you use these scripts in your calculations, in particular when running parallel jobs: the scripts take care of some aspects that you have to do otherwise yourself in each calculation.

• You need a license file to run any calculations successfully. If you have troubles with your license file, consult the Installation manual. If that doesn’t help contact us at support@scm.com

When you compare your own results with the sample outputs, you should check in particular (as far as applicable):

• Occupation numbers and energies of the one-electron orbitals;

• The optimized geometry;

• Vibrational frequencies;

• The bonding energy and the various terms in which it has been decomposed;

• The dipole moment;

• The logfile. At the end of a calculation the logfile is automatically appended (by the program itself) to the standard output.

General remarks about comparisons:

• For technical reasons, the discussion of which is beyond the scope of this document, differences between results obtained on different machines (or with different numbers of parallel processes) may be much larger than you would expect. They may significantly exceed the machine precision. What you should check is that they fall well (by at least an order of magnitude) within the numerical integration precision used in the calculation.

• For similar reasons the orientation of the molecule used by the program may be different on different machines, even when the same input is supplied. In such cases the different orientations should be related and only differ in some trivial way, such as by a simple rotation of all coordinates by 90 degrees around the z-axis. When in doubt, contact an SCM representative.

Model Hamiltonians¶

Structure and Reactivity¶

Spectroscopic Properties¶

Transport properties¶

Analysis¶

Accuracy and Efficiency¶

Restarts¶

Scripting¶

List of Examples¶