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!

updated DREIDING to fix hydrogen bonds

The order of the @atom types listed in the "dreiding.lt" file has been modified to (hopefully) make sure that LAMMPS does not get confused regarding which atoms are hydrogen-bond donors and acceptors. This is an attempt to address issue #46.

I think this is working now. However, if you use hydrogen bonds with DREIDING, then please double-check the "system.in.settings" files created by moltemplate.sh, and check each "pair_coeff" command containing the text "hbond/dreiding/lj". Make sure that the atom types are listed in the correct order, with donor atom types listed before acceptor atoms. Before doing this, I suggest running cleanup_moltemplate.sh first. (Otherwise the number of pair_coeff commands in the "system.in.settings" file might be too large to check by hand. The "cleanup_moltemplate.sh" program should work without issue with DREIDING simulation files as long as your main LT file is named "system.lt". Just type "cleanup_moltemplate.sh" into the terminal after running moltemplate.sh. In the future, when "dreiding.lt" is debugged, this extra effort won't be necessary.)

Many thanks to Aileen Huang ([email protected]) for reporting this issue!

updated MARTINI and OPLSAA and added DRYMARTINI

-The MARTINI force field implementation has been incorrect for years, apparently. (It might still be, but at least MARTINI simulations now show no visually obvious signs of failure.) We obtained the MARTINI force field parameters from the EMC program instead of the original source (the cgmartini.nl web site). I am still not positive that the MARTINI force field parameters provided by EMC are compatible with the most recent MARTINI files. (If not, please let me know.) Consequently, it might be necessary to reimplement MARTINI using the original source files in the future.
-The "drymartini.lt" force field file was also added (although it has not yet been tested.)
-I fixed a (hopefully) minor problem in the OPLSAA implementation. I was using a non-bonded distance cutoff that may have been too short (10 Angstroms instead of 11). (The 1996 OPLSAA paper used an 11 Angstrom cutoff for most interactions.) Hopefully this change not significantly effect most simulation results. (Note to users: We do make mistakes, so it's never a bad idea to double-check the global settings in the force-field files we provide.)
-Finally, I added some messages that tell users what papers to cite when they run moltemplate. (Hopefully this is not too annoying.)

use "python3" by default instead of "python"

moltemplate.sh only switches to python" or "python2" if "python3" is not available.

Also: The installation instructions in the README.md file have also been elaborated to help users with python installation difficulty.