GROMACS

Fixing handling of perturbation mass changes.

Fixes redmine #1232

in force.c, sum_dhdl

• moved F_DKDL to match the order in efpt_names. Not required, but
  harmonizes the code (lack of clarity probably helped cause the
  problems before), has no code effect.

• no longer treating the F_DKDL term separately from the other
  derivative components. Will be added to F_DVDL if the mass-lambda
  term is not separately specified. Results in a bit of a misnomer
  (F_DVDL becomes the derivative of the entire hamiltonian), but
  makes it much easier to collapse all molecular perturbation terms
  into a single component for output, where it is no longer really
  F_DVDL. I think that's better than always printing out a F_DVDL
  and a F_DKDL for everything where F_DKDL will probably usually
  be zero.

in md_support.c, compute_globals

• Synchronize the behaviors of the dhdls by writing first to the linear component
  corresponding to the mass, and then later transferring it to F_DKDL

in group.h, struct gmx_ekindata_t * add pointer to per-thread accumulation variable for dekindl

in tgroup.c, sum_ekin

• For velocity verlet integrators, computes the dekindl correctly as
  the derivatives of the current ekin. Shouldn't really affect the results
  in any significant way, since the average contribution will be the same
  regardless, but this is more consistent.

in tgroup.c, init_ekindata

• reduce use of numeric constants in allocating memory

• initialize new ekindata_t member

in update.c, calc_ke_part_normal

• zero the accumulator for dekindl before using it,
  fixing bug introduced in 7b6508e8

in update.c, in calc_ke_part_normal and calc_ke_part_visc

• sign error in mass change; if mass B is greater than mass A, then the
  change in free energy is positive, not negative.

Change-Id: I9deaf546bca66d400e0eb2c4015abeeda302dd1d

Fixing handling of perturbation mass changes.

Fixes redmine #1232

in force.c, sum_dhdl

• moved F_DKDL to match the order in efpt_names. Not required, but
  harmonizes the code (lack of clarity probably helped cause the
  problems before), has no code effect.

• no longer treating the F_DKDL term separately from the other
  derivative components. Will be added to F_DVDL if the mass-lambda
  term is not separately specified. Results in a bit of a misnomer
  (F_DVDL becomes the derivative of the entire hamiltonian), but
  makes it much easier to collapse all molecular perturbation terms
  into a single component for output, where it is no longer really
  F_DVDL. I think that's better than always printing out a F_DVDL
  and a F_DKDL for everything where F_DKDL will probably usually
  be zero.

in md_support.c, compute_globals

• Synchronize the behaviors of the dhdls by writing first to the linear component
  corresponding to the mass, and then later transferring it to F_DKDL

in group.h, struct gmx_ekindata_t * add pointer to per-thread accumulation variable for dekindl

in tgroup.c, sum_ekin

• For velocity verlet integrators, computes the dekindl correctly as
  the derivatives of the current ekin. Shouldn't really affect the results
  in any significant way, since the average contribution will be the same
  regardless, but this is more consistent.

in tgroup.c, init_ekindata

• reduce use of numeric constants in allocating memory

• initialize new ekindata_t member

in update.c, calc_ke_part_normal

• zero the accumulator for dekindl before using it,
  fixing bug introduced in 7b6508e8

in update.c, in calc_ke_part_normal and calc_ke_part_visc

• sign error in mass change; if mass B is greater than mass A, then the
  change in free energy is positive, not negative.

Change-Id: I9deaf546bca66d400e0eb2c4015abeeda302dd1d