diff --git a/doc/Eqs/pair_airebo.tex b/doc/Eqs/pair_airebo.tex new file mode 100644 index 0000000000..6c40b2ef58 --- /dev/null +++ b/doc/Eqs/pair_airebo.tex @@ -0,0 +1,11 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + E = \frac{1}{2} \sum_i \sum_{j \neq i} + \left[ E^{REBO}_{ij} + E^{LJ}_{ij} + + \sum_{k \neq i,j} \sum_{l \neq i,j,k} E^{TORSION}_{kijl} \right] +$$ + +\end{document} \ No newline at end of file diff --git a/doc/Section_history.html b/doc/Section_history.html index bced3bb538..2175446e68 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -31,12 +31,13 @@ GranFlow for granular materials. are being worked on; some haven't been implemented because of lack of time or interest; others are just a lot of work!

-

Creation of atoms: @@ -181,8 +182,10 @@ commands)

Pre- and post-processing: diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index 983036a817..e411358bd7 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -130,9 +130,11 @@ commands) improper potentials: harmonic, cvff, class 2 (COMPASS) hybrid potentials: multiple pair, bond, angle, dihedral, improper \ potentials can be used in one simlulation + overlayed potentials: multiple pair potentials can be superposed polymer potentials: all-atom, united-atom, bead-spring, breakable water potentials: TIP3P, TIP4P, SPC - long-range Coulombics: Ewald, PPPM (similar to particle-mesh Ewald) + long-range Coulombics and dispersion: Ewald, \ + PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones CHARMM, AMBER, OPLS force-field compatibility :ul Creation of atoms: :h4 @@ -178,8 +180,10 @@ Output: :h4 log file of thermodynanmic info text dump files of atom coords, velocities, other per-atom quantities binary restart files - per-atom energy, stress, centro-symmetry parameter + per-atom quantities (energy, stress, centro-symmetry parameter, etc) user-defined system-wide (log file) or per-atom (dump file) calculations + spatial and time averaging of per-atom quantities + time averaging of system-wide quantities atom snapshots in native, XYZ, XTC, DCD formats :ul Pre- and post-processing: :h4