diff --git a/doc/src/Eqs/angle_cross.jpg b/doc/src/Eqs/angle_cross.jpg index 3a5522382b82e6ff1c5869f4404a1be6e93940c7..b0f3fcf83ac2621807c7ae58772bfbddd1d94824 100644 Binary files a/doc/src/Eqs/angle_cross.jpg and b/doc/src/Eqs/angle_cross.jpg differ diff --git a/doc/src/Eqs/angle_mm3.jpg b/doc/src/Eqs/angle_mm3.jpg index ef234c3ed0df54f5b357b9b29250b055b5a9a631..5b9f3e34f091f5a2d439294e9c5a1802a2885fb4 100644 Binary files a/doc/src/Eqs/angle_mm3.jpg and b/doc/src/Eqs/angle_mm3.jpg differ diff --git a/doc/src/Eqs/bond_mm3.jpg b/doc/src/Eqs/bond_mm3.jpg index b8bbbbf7b0a7f31e33ecec2809a62feab7455492..2c17739db57e8d147166ab0a4cc768cf80f534af 100644 Binary files a/doc/src/Eqs/bond_mm3.jpg and b/doc/src/Eqs/bond_mm3.jpg differ diff --git a/doc/src/Eqs/improper_distharm.jpg b/doc/src/Eqs/improper_distharm.jpg index cef334351def212812752f494d0790d176857f53..e55036b5bf092c1b35b8ba42427b78f562238947 100644 Binary files a/doc/src/Eqs/improper_distharm.jpg and b/doc/src/Eqs/improper_distharm.jpg differ diff --git a/doc/src/Eqs/improper_sqdistharm.jpg b/doc/src/Eqs/improper_sqdistharm.jpg index 6f5cc97f4331492b921c1c67bbcb9ce127586148..b1a84e995e655ca32d6529122fa971bc1ef1e574 100644 Binary files a/doc/src/Eqs/improper_sqdistharm.jpg and b/doc/src/Eqs/improper_sqdistharm.jpg differ diff --git a/doc/src/Eqs/pair_coulgauss.jpg b/doc/src/Eqs/pair_coulgauss.jpg index c4eb34604365e3268e87d4a22e4067af12952752..bf84d90c4a1b4a7774e3933bfef6e949c9603cf7 100644 Binary files a/doc/src/Eqs/pair_coulgauss.jpg and b/doc/src/Eqs/pair_coulgauss.jpg differ diff --git a/doc/src/Eqs/pair_lj_switch3.jpg b/doc/src/Eqs/pair_lj_switch3.jpg index 1cc04de6a813c084dbec30453b9f89fc114625b6..a1f98ea2c24bcac86871e1476901791edc83dc62 100644 Binary files a/doc/src/Eqs/pair_lj_switch3.jpg and b/doc/src/Eqs/pair_lj_switch3.jpg differ diff --git a/doc/src/Eqs/pair_mm3_switch3.jpg b/doc/src/Eqs/pair_mm3_switch3.jpg index caad9bbe99ee9e3a1d7f85280fd5d26fbd4511fb..5d662584a7d1fec8d273c87ce3bf0b16a904f6d4 100644 Binary files a/doc/src/Eqs/pair_mm3_switch3.jpg and b/doc/src/Eqs/pair_mm3_switch3.jpg differ diff --git a/doc/src/Eqs/pair_switch3.jpg b/doc/src/Eqs/pair_switch3.jpg index 1b0528c080f4265ed6220a2eaa66d74b925a2465..e6327ee5ff1d2b6e586e4d0fdfc879a4b9977a56 100644 Binary files a/doc/src/Eqs/pair_switch3.jpg and b/doc/src/Eqs/pair_switch3.jpg differ diff --git a/doc/src/bond_mm3.txt b/doc/src/bond_mm3.txt index bfc802036e8f387d4496632330bc3c4b8bf80dc8..c3d0e39f52cf4885a7bd271cc00b8f60413b6163 100644 --- a/doc/src/bond_mm3.txt +++ b/doc/src/bond_mm3.txt @@ -26,7 +26,7 @@ as defined in "(Allinger)"_#mm3-allinger1989 where r0 is the equilibrium value of the bond, and K is a prefactor. The anharmonic prefactors have units angstrom^(-n): --2.55 angstrom^(-1) and (7/12)2.55$2 angstrom^(-2). The code takes +-2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes care of the necessary unit conversion for these factors internally. Note that the MM3 papers contains an error in Eq (1): (7/12)2.55 should be replaced with (7/12)2.55^2 @@ -54,5 +54,5 @@ page for more info. :line :link(mm3-allinger1989) -[(Allinger)] Allinger, Yuh, Lii, JACS, 111,94, 8551-8566 -(1990), +[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566 +(1989), diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 73b2723dc3ee033639b8b1392cdaee2a087cff91..5ae3456ad4be214edce5fc66e0d55b4e6418db26 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -596,6 +596,7 @@ pair_lj_long.html pair_lj_smooth.html pair_lj_smooth_linear.html pair_lj_soft.html +pair_lj_switch3_coulgauss.html pair_lubricate.html pair_lubricateU.html pair_mdf.html @@ -605,6 +606,7 @@ pair_meam_sw_spline.html pair_meso.html pair_mgpt.html pair_mie.html +pair_mm3_switch3_coulgauss.html pair_momb.html pair_morse.html pair_multi_lucy.html @@ -668,6 +670,7 @@ bond_harmonic_shift.html bond_harmonic_shift_cut.html bond_hybrid.html bond_morse.html +bond_mm3.html bond_none.html bond_nonlinear.html bond_oxdna.html diff --git a/doc/src/pair_lj_switch3_coulgauss.txt b/doc/src/pair_lj_switch3_coulgauss.txt index b13b78a7440c550b7840cda45aae763f2e398cee..1277cff9aa995ed3663050dd966729ac42db6a17 100644 --- a/doc/src/pair_lj_switch3_coulgauss.txt +++ b/doc/src/pair_lj_switch3_coulgauss.txt @@ -30,7 +30,7 @@ pair_coeff 1 0.2 2.5 1.2 :pre [Description:] The {lj/switch3/coulgauss} style evaluates the LJ -vdW potentia +vdW potential :c,image(Eqs/pair_lj_switch3.jpg) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 5c44bf8afacabf5f89be643111740ec4f2a7279f..8807b2d680766839db90849a37662f5f53d02b6d 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -60,6 +60,7 @@ Alejandre alessandro Alessandro aliceblue +Allinger allocaters allosws AlO @@ -410,6 +411,7 @@ cossq costheta Couette coul +coulgauss coulombic Coulombic Coulombics @@ -566,6 +568,7 @@ discretized disp dissipative Dissipative +distharm dl dlambda DLAMMPS @@ -2493,6 +2496,7 @@ Springer springgreen spx spz +sqdistharm sqrt src srd @@ -2801,6 +2805,8 @@ Valone valuev Valuev Vanden +Vandenbrande +Vanduyfhuys varavg Varshalovich Varshney @@ -2958,6 +2964,8 @@ xy xyz xz xzhou +YAFF +yaff Yamada Yazdani Ybar @@ -2976,6 +2984,7 @@ ys ysu yu Yu +Yuh yukawa Yukawa Yusof