speed improvement when using wildcards or DREIDING

The changes in this commit can significantly increase the speed of moltemplate.sh when the user's LT files contain wildcard characters ('*' characters) in any of the LAMMPS coeffs or coeff commands. In particular, simulations using the DREIDING force field ("dreiding.lt", which uses wildcard characters frequently) should be faster to prepare. Some coarse-grained force fields also make frequent use of wildcard characters.

fixed serious bug in "bond type" count in data files

Fixed a serious bug (the number of bond types in the generated data files are incorrect). LAMMPS would crash when run using data files generated by moltemplate. This bug was caused by a typo introduced in version v2.20.0 on 2022-1-11.

fixed a bug parsing blank lines with whitespace

Fixed a bug introduced in the previous version (v2.20.0) causing moltemplate to misinterpret blank lines containing nothing but white space (spaces or tabs). Thanks to github user conandolley103 (Tue Le) for reporting this bug!

improved ltemplify.py (whitespace) compatibility and improved dump2data.py and raw2data.py

1. Improved compatibility with ltemplify.py. This required adding better support in moltemplate.sh for atom types and names containing whitespace (which ltemplify.py frequently generates).
2. Improved performance and behavior of dump2data.py and raw2data.py.

This update might break some people's LT files.

fixed bugs in genpoly_lt.py and genpoly_modify_lt.py

1. Now you can omit the bond type in genpoly_lt.py.
2. The "-inherits" argument finally works in genpoly_modify_lt.py.

corrections to ellipsoid orientation code (read dump)

1. Bugfix: read dump now handles ellipsoid orientation correctly.
2. Corrected the MOLC citation.

Thanks to Otello Roscioni for discovering both problems and correcting them.

fixed an issue importing XYZ coordinates

Depending on the version of awk installed, not all users were effected.
Hopefully the new awk code (at line 572 of moltemplate.sh) should be more robust and work with all flavors of awk.
Thanks to Daoud El Kadiri for reporting and locating the error (and helping with debugging)!

a few small bug fixes

This is a minor update.

A bug was fixed that prevented moltemplate (ttree.py) from crashing when applied to nonsensical input. Another bug was fixed in genpoly_lt.py. Thanks to Sean Steadley (NC State University) and Reginaldo Gonçalves Leão Jr for reporting these bugs!

bug fixed (mixtures of ellipsoidal and ordinary particles)

Previously, moltemplate users could prepare simulations containing particles that were either all-ellipsoidal, or all point-like partlcles. But there was a bug which prevented simulations containing some ellipsoidal particles mixed with ordinary (non-ellipsoidal) particles. Hopefully this has been fixed now.

several bugs fixed (ltemplify.py, dump2data.py, lttree_postprocess.py)

Several bugs were fixed in ltemplify.py, dump2data.py, and lttree_postprocess.py. The ice and other water examples have been fixed (replacing "fix shake" with "fix rattle" everywhere). Thanks to Nathan Odendahl (UC Berkeley), and github user "davidfir3" for feedback, bug reporting, and bug fixing!