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Merge branch 'patch-2' of https://github.com/evoyiatzis/lammps into combined-user-fep-soft-updates

This commit is contained in:
Axel Kohlmeyer 2019-01-24 15:35:52 +01:00
parent 536e34974a a5248090fa
commit 1be589fb33
3 changed files with 102 additions and 19 deletions
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51
doc/src/compute_fep.txt
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@ -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:
"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/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=:)
"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, 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:
"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

33
doc/src/fix_adapt.txt
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@ -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_*&#58i,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

37
doc/src/fix_adapt_fep.txt
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@ -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:
"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
"lubricate"_pair_lubricate.html: mu: global:
"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:
"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