Add readConfAndTopology
readConfAndTopology will replace read_tps_conf, reading to gmx_mtop_t
instead of to the deprecated t_topology struct.
With requireMasses=TRUE, read_tps_conf will generate a fatal error when
an atom is not found in the mass database, as it was originally
intended, since we don't want to calculate with incorrect masses.
The availability of masses is signaled by the haveMass bool in t_atoms.
The trajectory analysis framework now works with optional masses.
This is done by not requiring masses and attempting to look up masses
from the database when they were not present in the structure file.
Refs #1862.
Change-Id: I045649fa458a08415fd319c568d15ad514a30a9f
15 files changed: