Fix USER-YAFF documentation issues

ca31147d · Steven Vandenbrande · 60b137f2 · 60b137f2 · ca31147d · 60b137f2
Commit ca31147d authored 6 years ago by Steven Vandenbrande
--- a/doc/src/Eqs/angle_cross.jpg
+++ b/doc/src/Eqs/angle_cross.jpg
--- a/doc/src/Eqs/angle_mm3.jpg
+++ b/doc/src/Eqs/angle_mm3.jpg
--- a/doc/src/Eqs/bond_mm3.jpg
+++ b/doc/src/Eqs/bond_mm3.jpg
--- a/doc/src/Eqs/improper_distharm.jpg
+++ b/doc/src/Eqs/improper_distharm.jpg
--- a/doc/src/Eqs/improper_sqdistharm.jpg
+++ b/doc/src/Eqs/improper_sqdistharm.jpg
--- a/doc/src/Eqs/pair_coulgauss.jpg
+++ b/doc/src/Eqs/pair_coulgauss.jpg
--- a/doc/src/Eqs/pair_lj_switch3.jpg
+++ b/doc/src/Eqs/pair_lj_switch3.jpg
--- a/doc/src/Eqs/pair_mm3_switch3.jpg
+++ b/doc/src/Eqs/pair_mm3_switch3.jpg
--- a/doc/src/Eqs/pair_switch3.jpg
+++ b/doc/src/Eqs/pair_switch3.jpg
--- 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
+[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
-(1990),
+(1989),
--- 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

--- 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)

--- 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