Fix USER-YAFF documentation issues
Steven Vandenbrande
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@ -26,7 +26,7 @@ as defined in "(Allinger)"_#mm3-allinger1989
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where r0 is the equilibrium value of the bond, and K is a
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where r0 is the equilibrium value of the bond, and K is a
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prefactor. The anharmonic prefactors have units angstrom^(-n):
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prefactor. The anharmonic prefactors have units angstrom^(-n):
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-2.55 angstrom^(-1) and (7/12)2.55$2 angstrom^(-2). The code takes
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-2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes
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care of the necessary unit conversion for these factors internally.
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care of the necessary unit conversion for these factors internally.
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Note that the MM3 papers contains an error in Eq (1):
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Note that the MM3 papers contains an error in Eq (1):
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(7/12)2.55 should be replaced with (7/12)2.55^2
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(7/12)2.55 should be replaced with (7/12)2.55^2
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@ -54,5 +54,5 @@ page for more info.
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:line
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:line
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:link(mm3-allinger1989)
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:link(mm3-allinger1989)
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[(Allinger)] Allinger, Yuh, Lii, JACS, 111,94, 8551-8566
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[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
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(1990),
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(1989),
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@ -596,6 +596,7 @@ pair_lj_long.html
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pair_lj_smooth.html
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pair_lj_smooth.html
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pair_lj_smooth_linear.html
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pair_lj_smooth_linear.html
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pair_lj_soft.html
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pair_lj_soft.html
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pair_lj_switch3_coulgauss.html
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pair_lubricate.html
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pair_lubricate.html
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pair_lubricateU.html
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pair_lubricateU.html
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pair_mdf.html
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pair_mdf.html
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@ -605,6 +606,7 @@ pair_meam_sw_spline.html
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pair_meso.html
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pair_meso.html
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pair_mgpt.html
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pair_mgpt.html
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pair_mie.html
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pair_mie.html
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pair_mm3_switch3_coulgauss.html
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pair_momb.html
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pair_momb.html
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pair_morse.html
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pair_morse.html
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pair_multi_lucy.html
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pair_multi_lucy.html
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@ -668,6 +670,7 @@ bond_harmonic_shift.html
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bond_harmonic_shift_cut.html
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bond_harmonic_shift_cut.html
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bond_hybrid.html
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bond_hybrid.html
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bond_morse.html
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bond_morse.html
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bond_mm3.html
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bond_none.html
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bond_none.html
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bond_nonlinear.html
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bond_nonlinear.html
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bond_oxdna.html
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bond_oxdna.html
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@ -30,7 +30,7 @@ pair_coeff 1 0.2 2.5 1.2 :pre
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[Description:]
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[Description:]
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The {lj/switch3/coulgauss} style evaluates the LJ
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The {lj/switch3/coulgauss} style evaluates the LJ
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vdW potentia
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vdW potential
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:c,image(Eqs/pair_lj_switch3.jpg)
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:c,image(Eqs/pair_lj_switch3.jpg)
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@ -60,6 +60,7 @@ Alejandre
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alessandro
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alessandro
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Alessandro
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Alessandro
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aliceblue
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aliceblue
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Allinger
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allocaters
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allocaters
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allosws
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allosws
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AlO
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AlO
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@ -410,6 +411,7 @@ cossq
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costheta
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costheta
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Couette
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Couette
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coul
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coul
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coulgauss
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coulombic
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coulombic
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Coulombic
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Coulombic
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Coulombics
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Coulombics
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@ -566,6 +568,7 @@ discretized
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disp
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disp
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dissipative
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dissipative
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Dissipative
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Dissipative
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distharm
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dl
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dl
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dlambda
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dlambda
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DLAMMPS
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DLAMMPS
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@ -2493,6 +2496,7 @@ Springer
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springgreen
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springgreen
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spx
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spx
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spz
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spz
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sqdistharm
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sqrt
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sqrt
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src
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src
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srd
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srd
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@ -2801,6 +2805,8 @@ Valone
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valuev
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valuev
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Valuev
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Valuev
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Vanden
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Vanden
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Vandenbrande
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Vanduyfhuys
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varavg
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varavg
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Varshalovich
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Varshalovich
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Varshney
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Varshney
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@ -2958,6 +2964,8 @@ xy
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xyz
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xyz
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xz
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xz
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xzhou
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xzhou
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YAFF
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yaff
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Yamada
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Yamada
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Yazdani
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Yazdani
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Ybar
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Ybar
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@ -2976,6 +2984,7 @@ ys
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ysu
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ysu
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yu
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yu
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Yu
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Yu
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Yuh
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yukawa
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yukawa
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Yukawa
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Yukawa
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Yusof
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Yusof
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