Dear All,
I just checked in a new implementation of PIMD which is based on
multi-sander framework.
Meanwhile, the following executables has been remove from Makefile:
sander.PIMD, sander.CMD
sander.PIMD.A1ST, sander.CMD.A1ST. In the new implementation, all PIMD
simulations are
run through "sander.MPI". A new control parameter "ipimd" has been
introduced to indicate
simulation type, "ipimd=0" means normal PIMD simulation, "ipimd=1" means
primitive PIMD,
"ipimd=2" means normal-mode PIMD or CMD (depend on "adiab_param"). Test
case for this
new implementation can be found under directory "amber10/test/full_pimd".
The new implementation has the following advantages. Firstly, it is more
efficient because the
linear memory layout. Secondly, it is much easier to make it work with
other new features of
sander, for example: we can run PIMD with AMOEBA force field now.
Moreover, allthough AMOEBA
itself has not been parallelized yet, we can run AMEOBA-PIMD in parallel
as long as number of CPUs
is less than number of beads.
The shortcoming of the new implementation is also obvious, we will not
be able to run partial-PIMD
anymore. To overcome this, the old implementation will not be deleted
but will be merged into
sander.LES and we will be able to run partial-PIMD through sander.LES.
It will also be fast if the
quantum portion is reasonably small.
As you know, this is a major change, although I have tested the
code(with ifort and g95), there are still
some chances that some of your staff have been broken. Thus, if you
experienced some
unusual behavior of sander after cvs update, please contact me, and we
can figure it out together.
Thank you very much !
Sincerely,
Wei
Received on Wed Oct 18 2006 - 06:07:29 PDT
