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Hints and tips

  • The main cde input file is CASE SENSITIVE.

Warning

Everything in the input file should be lower-case, except for chemical element symbols.

  • If you are running a calculation which does not use some of the input parameters, they will be read in but then simply ignored. However, their formatting still needs to be correct.

Tips for bonding definitions.

  • In cde, bonds between atoms are based on a cutoff distance given by

    \(R = (CovRad(i) + CovRad(j)) * bondingsf\)

The factors CovRad(:) are the covalent radii of each species, and can be found in constants.f90. The factor bondingsf is also found in constants.f90 - it is a scale-factor, usually with a value of 1.1.

  • The CovRad(:) and bondingsf are defined as Fortran constants - if you want to change them, you need to recompile the code.

  • The Covrad(:) and bondingsf values do not need to be extremely accurate - they are used to define what is bonded to what, so as long as they adequately capture typical bonds they should be fine.

Tips on external executables

  • The input parameters pesexecutable and pesoptexecutable define the external executables which are run when evaluating energy or performing geometry optimizations.

  • The CDE code uses the Fortran implicit EXECUTE_COMMAND_LINE to run these executables.

  • It is often easiest to define an alias for executables like ORCA and DFTB+. For example, if the ORCA executable is in a directory /user/test/code/orca/bin, then setting an alias so that the command orca actually executes the command /user/test/code/orca/bin/orca is a useful way of simplifying the input file.

Warning

If the executables can't be found when run by EXECUTE_COMMAND_LINE, the code will just give up and crash!

  • If you want to use pesopttype UFF (that is, the Universal Force-Field), you need to install OpenBabel.

  • When using pesopttype UFF, the executables babel and obminimize are called directly from withing cde. As a result, both of these executables need to be in your PATH variable before running cde.

Other pro-tips...

Hint

In several types of calculations (e.g. double-ended reaction-path finding, NEB), the first step that the CDE code performs is to evaluate the connectivity matrix of the input molecular structures. Depending on the calculation type, this connectivity matrix is then used to define the graph-restraining potential (GRP) for structure optimization and checking. However, if the connectivity matrix calculated using the input structure does not correspond to the connectivity matrix that you wanted (for example, due to bond-lengths being too long in the input structure), then you might end up with some odd results. In short, TAKE CARE with your input structures!