diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt index 5b3a6915dd4a6c3c442be5034caa03b7fb709602..45068121c572e1bb3549ace39e4c2373394e96c5 100644 --- a/doc/src/compute_fep.txt +++ b/doc/src/compute_fep.txt @@ -133,19 +133,46 @@ pair styles and parameters that can be used with this compute. See the doc pages for individual pair styles and their energy formulas for the meaning of these parameters: +"born"_pair_born.html: a,b,c: type pairs: +"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global: +"buck"_pair_buck.html: a,c: type pairs: +"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global: +"buck/mdf"_pair_mdf.html: a,c: type pairs: +"coul/cut"_pair_coul.html: scale: type pairs: +"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs: +"coul/debye"_pair_coul.html: scale: type pairs: +"coul/dsf"_pair_coul.html: coulombic_cutoff: type global: +"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs: +"coul/long/soft"_pair_lj_soft.html: scale, lambda, coulombic_cutoff: type pairs: +"eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs: +"gauss"_pair_gauss.html: a: type pairs: +"lennard/mdf"_pair_mdf.html: A,B: type pairs: +"lj/class2"_pair_class2.html: epsilon,sigma: type pairs: +"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs: "lj/cut"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/coul/cut"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/coul/long"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: +"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs: +"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global: +"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: "lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: -"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs: -"coul/long/soft"_pair_lj_soft.html: lambda: type pairs: -"lj/cut/coul/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: -"lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: -"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: -"tip4p/long/soft"_pair_lj_soft.html: lambda: type pairs: -"lj/charmm/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: -"born"_pair_born.html: a,b,c: type pairs: -"buck"_pair_buck.html: a,c : type pairs :tb(c=3,s=:) +"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: +"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs: +"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs: +"lubricate"_pair_lubricate.html: mu: global: +"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs: +"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs: +"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs: +"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs: +"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs: +"reax/c"_pair_reaxc.html: chi, eta, gamma: type global: +"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global: +"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global: +"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global: +"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global: +"table"_pair_table.html: table_cutoff: type pairs: +"ufm"_pair_ufm.html: epsilon,sigma: type pairs: +"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:) + Note that it is easy to add new potentials and their parameters to this list. All it typically takes is adding an extract() method to diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index 0ca28fb8694c6c5c4d4c2d39ab649dc79a9152a3..1ee1383ca640cbf0cf71067f9ed3c7d8e8ca3e67 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -112,17 +112,43 @@ pages for individual pair styles and their energy formulas for the meaning of these parameters: "born"_pair_born.html: a,b,c: type pairs: +"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global: "buck"_pair_buck.html: a,c: type pairs: +"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global: +"buck/mdf"_pair_mdf.html: a,c: type pairs: "coul/cut"_pair_coul.html: scale: type pairs: +"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs: "coul/debye"_pair_coul.html: scale: type pairs: -"coul/long"_pair_coul.html: scale: type pairs: +"coul/dsf"_pair_coul.html: coulombic_cutoff: type global: +"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs: +"coul/long/soft"_pair_lj_soft.html: scale, lambda, coulombic_cutoff: type pairs: "eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs: +"gauss"_pair_gauss.html: a: type pairs: +"lennard/mdf"_pair_mdf.html: A,B: type pairs: +"lj/class2"_pair_class2.html: epsilon,sigma: type pairs: +"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs: "lj/cut"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: +"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs: +"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global: +"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: +"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: "lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: +"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs: "lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs: "lubricate"_pair_lubricate.html: mu: global: -"gauss"_pair_gauss.html: a: type pairs: -"morse"_pair_morse.html: d0,r0,alpha: type pairs: +"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs: +"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs: +"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs: +"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs: +"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs: +"reax/c"_pair_reaxc.html: chi, eta, gamma: type global: +"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global: +"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global: +"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global: +"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global: +"table"_pair_table.html: table_cutoff: type pairs: +"ufm"_pair_ufm.html: epsilon,sigma: type pairs: "soft"_pair_soft.html: a: type pairs: "kim"_pair_kim.html: PARAM_FREE_*:i,j,...: global :tb(c=3,s=:) @@ -217,6 +243,7 @@ Currently {bond} does not support bond_style hybrid nor bond_style hybrid/overlay as bond styles. The only bonds that currently are working with fix_adapt are +"gromos"_bond_gromos.html: k, r0: type bonds: "harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:) :line diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt index 7e30a1d29d5b4354b7fae0761f50fc7d8d6e8dd3..01634d0a854ac7cb15a7d972fdd31a2df0ac3969 100644 --- a/doc/src/fix_adapt_fep.txt +++ b/doc/src/fix_adapt_fep.txt @@ -113,14 +113,43 @@ can be varied by this fix. See the doc pages for individual pair styles and their energy formulas for the meaning of these parameters: "born"_pair_born.html: a,b,c: type pairs: +"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global: "buck"_pair_buck.html: a,c: type pairs: +"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global: +"buck/mdf"_pair_mdf.html: a,c: type pairs: "coul/cut"_pair_coul.html: scale: type pairs: +"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs: "coul/debye"_pair_coul.html: scale: type pairs: -"coul/long"_pair_coul.html: scale: type pairs: +"coul/dsf"_pair_coul.html: coulombic_cutoff: type global: +"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs: +"coul/long/soft"_pair_lj_soft.html: scale, lambda, coulombic_cutoff: type pairs: +"eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs: +"gauss"_pair_gauss.html: a: type pairs: +"lennard/mdf"_pair_mdf.html: A,B: type pairs: +"lj/class2"_pair_class2.html: epsilon,sigma: type pairs: +"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs: "lj/cut"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: +"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs: +"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global: +"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: +"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: "lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: +"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs: +"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs: "lubricate"_pair_lubricate.html: mu: global: -"gauss"_pair_gauss.html: a: type pairs: +"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs: +"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs: +"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs: +"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs: +"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs: +"reax/c"_pair_reaxc.html: chi, eta, gamma: type global: +"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global: +"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global: +"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global: +"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global: +"table"_pair_table.html: table_cutoff: type pairs: +"ufm"_pair_ufm.html: epsilon,sigma: type pairs: "soft"_pair_soft.html: a: type pairs :tb(c=3,s=:) NOTE: It is easy to add new potentials and their parameters to this