Performance of scripted biases

If concurrent computation over multiple threads is available (this is indicated by the message ``SMP parallelism is available.'' printed at initialization time), it is useful to take advantage of the scripting interface to combine many components, all computed in parallel, into a single variable.

The default SMP schedule is the following:

1. distribute the computation of all components across available threads;
2. on a single thread, collect the results of multi-component variables using polynomial combinations (see ), or scripted functions (see );
3. distribute the computation of all biases across available threads;
4. compute on a single thread any scripted biases implemented via the keyword scriptedColvarForces.
5. communicate on a single thread forces to VMD.

The following options allow to fine-tune this schedule:

• scriptingAfterBiases $\langle\,$ Scripted colvar forces need updated biases?$\,\rangle$
  Context: global
  Acceptable values: boolean
  Default value: on
  Description: This flag specifies that the calc_colvar_forces procedure (last step in the list above) is executed only after all biases have been updated (next-to-last step) For example, this allows using the energy of a restraint bias, or the force applied on a colvar, to calculate additional scripted forces, such as boundary constraints. When this flag is set to off, it is assumed that only the values of the variables (but not the energy of the biases or applied forces) will be used by calc_colvar_forces: this can be used to schedule the calculation of scripted forces and biases concurrently to increase performance.