From cab3380b5546a356a74304adda953804dff1741d Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Sun, 20 Jan 2019 13:35:40 +0100 Subject: [PATCH 1/5] Updating the list of potentials in fix_adapt_fep.txt There are several potentials that contain the method extract() but they are not included in the "fix adapt" and "fix adapt/fep" A small update of the list is attempted here. The same potentials might be added to the documentation of fix_adapt if it is useful. --- doc/src/fix_adapt_fep.txt | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt index 7e30a1d29d..12b7a2791d 100644 --- a/doc/src/fix_adapt_fep.txt +++ b/doc/src/fix_adapt_fep.txt @@ -114,13 +114,23 @@ styles and their energy formulas for the meaning of these parameters: "born"_pair_born.html: a,b,c: type pairs: "buck"_pair_buck.html: a,c: type pairs: +"buck/mdf"_pair_mdf.html: a,c: type pairs: "coul/cut"_pair_coul.html: scale: type pairs: "coul/debye"_pair_coul.html: scale: type pairs: "coul/long"_pair_coul.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"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs: "lj/cut"_pair_lj.html: epsilon,sigma: type pairs: "lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: +"lj/mdf"_pair_mdf.html: epsilon,sigma: 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"_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: +"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 From e789715d92c16c34f2454f84fcdb1c9487c3e0fd Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Mon, 21 Jan 2019 23:12:34 +0100 Subject: [PATCH 2/5] Update fix_adapt_fep.txt --- doc/src/fix_adapt_fep.txt | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt index 12b7a2791d..e18a2e7771 100644 --- a/doc/src/fix_adapt_fep.txt +++ b/doc/src/fix_adapt_fep.txt @@ -116,15 +116,21 @@ styles and their energy formulas for the meaning of these parameters: "buck"_pair_buck.html: a,c: type pairs: "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 pairs: "coul/long"_pair_coul.html: scale: 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"_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,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"_pair_morse.html: D0,R0,alpha: type pairs: From 24bede9ffff882c67fd0045c4cd3360276ca6ba0 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Tue, 22 Jan 2019 19:37:58 +0100 Subject: [PATCH 3/5] Update fix_adapt_fep.txt --- doc/src/fix_adapt_fep.txt | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt index e18a2e7771..01634d0a85 100644 --- a/doc/src/fix_adapt_fep.txt +++ b/doc/src/fix_adapt_fep.txt @@ -113,29 +113,42 @@ 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/dsf"_pair_coul.html: coulombic_cutoff: 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"_pair_class2.html: epsilon,sigma,coulombic_cutoff: 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,coulombic_cutoff: 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"_pair_morse.html: D0,R0,alpha: 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=:) From ade023861dfdeda465e7cf6477448a942f59e842 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Tue, 22 Jan 2019 19:42:52 +0100 Subject: [PATCH 4/5] Update compute_fep.txt --- doc/src/compute_fep.txt | 51 +++++++++++++++++++++++++++++++---------- 1 file changed, 39 insertions(+), 12 deletions(-) diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt index 5b3a6915dd..45068121c5 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: -"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 From a5248090fac9656201b4ab6298d40982be981f07 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Tue, 22 Jan 2019 19:46:35 +0100 Subject: [PATCH 5/5] Update fix_adapt.txt --- doc/src/fix_adapt.txt | 33 ++++++++++++++++++++++++++++++--- 1 file changed, 30 insertions(+), 3 deletions(-) diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index 0ca28fb869..1ee1383ca6 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