Hbond Counting and Outputting Python Code

The code can read in the LAMMPS dump frame and count the hbonds based on geometric criteria (customizable). Meantime generating POSCARs for VASP runs with both full water solvation and partial preserved solvation(non-hbonded removed).

06/21/18 Update: Fixed angle detection issue and loop optimization.

02/27/17 Update: Added support for TI4P water model support, also support CxHyOz system on Pt, xyz>0.

06/27/16 Update: Added the function to calculate the dipole moment for each hydrogen bond found.

04/05/16 Update: Now the code works fast enough so that you don't have to wait minutes for a single frame hbond searching. Default criteria, AD<3.5 ADH<30 AHD>120.

03/10/16 Update: Output improment, now tells the donar oxygen(s) and the acceptor oxgen(s).

12/12/15 Update: Improvement in calculation speed by cleaning out some legacy float-string conversions. Now can recenter the system to align the bottom Pt to the bottom of box. Formatting improvement.

12/02/15 Update: Reconfigured PBC, now works with all 8 neighboring cells. Known issue: computational time doubled.

11/12/15 Update: Now compatible with C3HxOx adsorbates.

10/22/15 Update: Reconfigured outputting algorithm, now can export with POSCARS partial fixed flags on for NEB-dimer/geometry optimization or, simply all fixed coordinates for single point energy calc.

IMPORTANT

Default settings:

For Atom types,

rC = [2,3,4,5] rHS = [10,11] rOS = [6,7] rHW = [9] rOW = [8]

For POSCAR ouput,

fixedposcar = 1, all atom are fixed. fixedposcar = 0, hbonded atoms are not held fixed.