update docs to reflect the state of reserving space for topology info with molecule files

NOTE: The molecule command can be used to define molecules with bonds,

angles, dihedrals, imporopers, or special bond lists of neighbors

within a molecular topology, so that you can later add the molecules

to your simulation, via one or more of the commands listed above.  If

such molecules do not already exist when LAMMPS creates the simulation

box, via the "create_box"_create_box.html or

"read_data"_read_data.html command, when you later add them you may

overflow the pre-allocated data structures which store molecular

topology information with each atom, and an error will be generated.

Both the "create_box"_create_box.html command and the data files read

by the "read_data"_read_data.html command have "extra" options which

to your simulation, via one or more of the commands listed above.

Since this topology-related information requires that suitable storage

is reserved when LAMMPS creates the simulation box (e.g. when using

the "create_box"_create_box.html command or the

"read_data"_read_data.html command) suitable space has to be reserved

so you do not overflow those pre-allocated data structures when adding

molecules later.  Both the "create_box"_create_box.html command and

the "read_data"_read_data.html command have "extra" options which

insure space is allocated for storing topology info for molecules that

are added later.

The format of an individual molecule file is similar to the data file

read by the "read_data"_read_data.html commands, and is as follows.

The format of an individual molecule file is similar but

(not identical) to the data file read by the "read_data"_read_data.html

commands, and is as follows.

A molecule file has a header and a body.  The header appears first.

The first line of the header is always skipped; it typically contains