The schedule used to determine the 4-d coordinate offset for nonbonded decoupling in single topology calculations is currently suboptimal in a way that is easy to fix.
Brief background:
Before #893, decoupling of dummy atoms was controlled by a single alchemical schedule w(lam). The 4-d coordinates for dummy atoms were then determined by w_a(lam) = w(lam) for dummy atoms in A, or w_b(lam) = cutoff - w(lam) for dummy atoms in B. The latter functional form was hardcoded.
Hence, the single alchemical schedule was constrained to be symmetric (e.g. needed to "slow" near $\lambda=0$, where dummy atoms in A decouple, and also "slow" near $\lambda=1$, where dummy atoms in B couple).
Since #893, we no longer have this functional form imposed on us. In #900 we opted to just maintain the status quo, using the existing symmetric pre-optimized schedule and reproducing the same functional form for w_a and w_b (even though there was no requirement for w_a and w_b to each be symmetric).
This PR modifies the existing 4-d decoupling schedule to be more gradual, taking advantage of the fact that w_a and w_b no longer need to be individually symmetric. The modification was done by taking the relevant half of the existing pre-optimized schedule depending on whether the atom in question is being coupled or decoupled.
The schedule used to determine the 4-d coordinate offset for nonbonded decoupling in single topology calculations is currently suboptimal in a way that is easy to fix.
Brief background:
w(lam). The 4-d coordinates for dummy atoms were then determined byw_a(lam) = w(lam)for dummy atoms in A, orw_b(lam) = cutoff - w(lam)for dummy atoms in B. The latter functional form was hardcoded.w_aandw_b(even though there was no requirement forw_aandw_bto each be symmetric).This PR modifies the existing 4-d decoupling schedule to be more gradual, taking advantage of the fact that
w_aandw_bno longer need to be individually symmetric. The modification was done by taking the relevant half of the existing pre-optimized schedule depending on whether the atom in question is being coupled or decoupled.