forked from lijiext/lammps
Merge branch 'core_soft' of https://github.com/agiliopadua/lammps into combined-user-fep-soft-updates
Resolved Conflicts: doc/src/compute_fep.txt doc/src/fix_adapt_fep.txt
This commit is contained in:
Axel Kohlmeyer
commit
a6ecd3d08c
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@ -128,52 +128,40 @@ commands to be changed, if the pair style supports it.
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The {pstyle} argument is the name of the pair style. For example,
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{pstyle} could be specified as "lj/cut". The {pparam} argument is the
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name of the parameter to change. This is a (non-exclusive) list of
|
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name of the parameter to change. This is a list of
|
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pair styles and parameters that can be used with this compute. See
|
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the doc pages for individual pair styles and their energy formulas for
|
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the meaning of these parameters:
|
||||
|
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"born"_pair_born.html: a,b,c: type pairs:
|
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"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global:
|
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"buck"_pair_buck.html: a,c: type pairs:
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"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global:
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"buck/mdf"_pair_mdf.html: a,c: type pairs:
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"buck/mdf"_pair_mdf.html: aparm,cparm: type pairs:
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"coul/cut"_pair_coul.html: scale: type pairs:
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"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:
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"coul/debye"_pair_coul.html: scale: type pairs:
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"coul/dsf"_pair_coul.html: coulombic_cutoff: type global:
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"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs:
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"coul/long/soft"_pair_lj_soft.html: scale, lambda, coulombic_cutoff: type pairs:
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"eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs:
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"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
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"coul/long/soft"_pair_lj_soft.html: scale, lambda: type pairs:
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"eam"_pair_eam.html: scale: type pairs:
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"gauss"_pair_gauss.html: a: type pairs:
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"lennard/mdf"_pair_mdf.html: A,B: type pairs:
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"lennard/mdf"_pair_mdf.html: aparm,bparm: type pairs:
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"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
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"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs:
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"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
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"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
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"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
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"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs:
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"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global:
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"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
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"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
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"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:
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"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
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"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:
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"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
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"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
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"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
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"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
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"lubricate"_pair_lubricate.html: mu: global:
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"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs:
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"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs:
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"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs:
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"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs:
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"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs:
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"reax/c"_pair_reaxc.html: chi, eta, gamma: type global:
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"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global:
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"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global:
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"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global:
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"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:
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"table"_pair_table.html: table_cutoff: type pairs:
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"ufm"_pair_ufm.html: epsilon,sigma: type pairs:
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"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:
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"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:
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"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:
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"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:
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"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:
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"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:
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"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
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Note that it is easy to add new potentials and their parameters to
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this list. All it typically takes is adding an extract() method to
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the pair_*.cpp file associated with the potential.
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@ -263,7 +251,7 @@ package"_Build_package.html doc page for more info.
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[Related commands:]
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"fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html,
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"pair_style lj/soft/coul/soft"_pair_lj_soft.html
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"pair_fep_soft"_pair_fep_soft.html
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[Default:]
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|
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@ -113,54 +113,38 @@ can be varied by this fix. See the doc pages for individual pair
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styles and their energy formulas for the meaning of these parameters:
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"born"_pair_born.html: a,b,c: type pairs:
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"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global:
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"buck"_pair_buck.html: a,c: type pairs:
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"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global:
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"buck/mdf"_pair_mdf.html: a,c: type pairs:
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"buck/mdf"_pair_mdf.html: aparm,cparm: type pairs:
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"coul/cut"_pair_coul.html: scale: type pairs:
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"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:
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"coul/debye"_pair_coul.html: scale: type pairs:
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"coul/dsf"_pair_coul.html: coulombic_cutoff: type global:
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"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs:
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"coul/long/soft"_pair_lj_soft.html: scale, lambda, coulombic_cutoff: type pairs:
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"eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs:
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"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
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"coul/long/soft"_pair_lj_soft.html: scale, lambda: type pairs:
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"eam"_pair_eam.html: scale: type pairs:
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"gauss"_pair_gauss.html: a: type pairs:
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"lennard/mdf"_pair_mdf.html: A,B: type pairs:
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"lennard/mdf"_pair_mdf.html: aparm,bparm: type pairs:
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"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
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"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs:
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"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
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"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
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"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
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"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs:
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"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global:
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"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
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"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
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"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:
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"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
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"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:
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"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
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"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
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"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
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"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
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"lubricate"_pair_lubricate.html: mu: global:
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"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs:
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"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs:
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"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs:
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"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs:
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"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs:
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"reax/c"_pair_reaxc.html: chi, eta, gamma: type global:
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"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global:
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"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global:
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"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global:
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"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:
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"table"_pair_table.html: table_cutoff: type pairs:
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"ufm"_pair_ufm.html: epsilon,sigma: type pairs:
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"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:
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"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:
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"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:
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"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:
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"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:
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"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:
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"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
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NOTE: It is easy to add new potentials and their parameters to this
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list. All it typically takes is adding an extract() method to the
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pair_*.cpp file associated with the potential.
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Some parameters are global settings for the pair style, e.g. the
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viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.
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Other parameters apply to atom type pairs within the pair style,
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e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.
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Note that for many of the potentials, the parameter that can be varied
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is effectively a prefactor on the entire energy expression for the
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potential, e.g. the lj/cut epsilon. The parameters listed as "scale"
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@ -282,7 +266,7 @@ minimization"_minimize.html.
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[Related commands:]
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"compute fep"_compute_fep.html, "fix adapt"_fix_adapt.html, "compute
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ti"_compute_ti.html
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ti"_compute_ti.html, "pair_fep_soft"_pair_fep_soft.html
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[Default:]
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|
|
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@ -99,6 +99,14 @@ cutoff distance.
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:line
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A version of these styles with a soft core, {lj/cut/soft}, suitable for use in
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free energy calculations, is part of the USER-FEP package and is documented with
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the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is
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only available if LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info.
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:line
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Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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@ -159,7 +167,7 @@ package"_Build_package.html doc page for more info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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"pair_coeff"_pair_coeff.html, "pair_fep_soft"_pair_fep_soft.html
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[Default:] none
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|
|
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@ -16,18 +16,21 @@ pair_style lj/cut/tip4p/long/soft command :h3
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pair_style lj/cut/tip4p/long/soft/omp command :h3
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pair_style lj/charmm/coul/long/soft command :h3
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pair_style lj/charmm/coul/long/soft/omp command :h3
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pair_style coul/cut/soft command :h3
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pair_style lj/class2/soft command :h3
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pair_style lj/class2/coul/cut/soft command :h3
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pair_style lj/class2/coul/long/soft command :h3
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pair_style coul/cut/soft command :h3
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pair_style coul/cut/soft/omp command :h3
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pair_style coul/long/soft command :h3
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pair_style coul/long/soft/omp command :h3
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pair_style tip4p/long/soft command :h3
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pair_style tip4p/long/soft/omp command :h3
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pair_style morse/soft command :h3
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[Syntax:]
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pair_style style args :pre
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style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft}
|
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style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {lj/class2/soft} or {lj/class2/coul/cut/soft} or {lj/class2/coul/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft} or {morse/soft}
|
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args = list of arguments for a particular style :ul
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{lj/cut/soft} args = n alpha_lj cutoff
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n, alpha_LJ = parameters of soft-core potential
|
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|
|
@ -51,6 +54,17 @@ args = list of arguments for a particular style :ul
|
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
|
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
|
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
|
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{lj/class2/soft} args = n alpha_lj cutoff
|
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n, alpha_LJ = parameters of soft-core potential
|
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cutoff = global cutoff for Lennard-Jones interactions (distance units)
|
||||
{lj/class2/coul/cut/soft} args = n alpha_LJ alpha_C cutoff (cutoff2)
|
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n, alpha_LJ, alpha_C = parameters of soft-core potential
|
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
{lj/class2/coul/long/soft} args = n alpha_LJ alpha_C cutoff (cutoff2)
|
||||
n, alpha_LJ, alpha_C = parameters of soft-core potential
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
{coul/cut/soft} args = n alpha_C cutoff
|
||||
n, alpha_C = parameters of the soft-core potential
|
||||
cutoff = global cutoff for Coulomb interactions (distance units)
|
||||
|
|
@ -63,6 +77,10 @@ args = list of arguments for a particular style :ul
|
|||
qdist = distance from O atom to massless charge (distance units)
|
||||
n, alpha_C = parameters of the soft-core potential
|
||||
cutoff = global cutoff for Coulomb interactions (distance units)
|
||||
{morse/soft} args = n lf cutoff
|
||||
n = soft-core parameter
|
||||
lf = transformation range is lf < lambda < 1
|
||||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
:pre
|
||||
|
||||
[Examples:]
|
||||
|
|
@ -93,6 +111,12 @@ pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
|
|||
pair_coeff * * 0.28 3.1 1.0
|
||||
pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 :pre
|
||||
|
||||
pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5
|
||||
pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 9.5
|
||||
pair_coeff * * 0.28 3.1 1.0
|
||||
pair_coeff 1 1 0.28 3.1 0.0 10.0
|
||||
pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 :pre
|
||||
|
||||
pair_style coul/long/soft 1.0 10.0 9.5
|
||||
pair_coeff * * 1.0
|
||||
pair_coeff 1 1 1.0 9.5 :pre
|
||||
|
|
@ -101,17 +125,31 @@ pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
|
|||
pair_coeff * * 1.0
|
||||
pair_coeff 1 1 1.0 9.5 :pre
|
||||
|
||||
pair_style morse/soft 4 0.9 10.0
|
||||
pair_coeff * * 100.0 2.0 1.5 1.0
|
||||
pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {lj/cut/soft} style and sub-styles compute the 12/6 Lennard-Jones
|
||||
and Coulomb potential modified by a soft core, in order to avoid
|
||||
singularities during free energy calculations when sites are created
|
||||
or annihilated "(Beutler)"_#Beutler,
|
||||
These pair styles have a soft repulsive core, tuneable by a parameter lambda,
|
||||
in order to avoid singularities during free energy calculations when sites are
|
||||
created or annihilated "(Beutler)"_#Beutler. When lambda tends to 0 the pair
|
||||
interaction vanishes with a soft repulsive core. When lambda tends to 1, the pair
|
||||
interaction approaches the normal, non-soft potential. These pair styles
|
||||
are suited for "alchemical" free energy calculations using the "fix
|
||||
adapt/fep"_fix_adapt_fep.html and "compute fep"_compute_fep.html commands.
|
||||
|
||||
The {lj/cut/soft} style and related sub-styles compute the 12-6 Lennard-Jones
|
||||
and Coulomb potentials modified by a soft core, with the functional form
|
||||
|
||||
:c,image(Eqs/pair_lj_soft.jpg)
|
||||
|
||||
Coulomb interactions are also damped with a soft core at short
|
||||
distance,
|
||||
The {lj/class2/soft} style is a 9-6 potential with the exponent of the
|
||||
denominator of the first term in brackets taking the value 1.5 instead of 2
|
||||
(other details differ, see the form of the potential in
|
||||
"pair_class2"_pair_class2.html).
|
||||
|
||||
Coulomb interactions can also be damped with a soft core at short distance,
|
||||
|
||||
:c,image(Eqs/pair_coul_soft.jpg)
|
||||
|
||||
|
|
@ -119,34 +157,32 @@ In the Coulomb part C is an energy-conversion constant, q_i and q_j
|
|||
are the charges on the 2 atoms, and epsilon is the dielectric constant
|
||||
which can be set by the "dielectric"_dielectric.html command.
|
||||
|
||||
The coefficient lambda is an activation parameter. When lambda = 1 the
|
||||
pair potential is identical to a Lennard-Jones term or a Coulomb term
|
||||
or a combination of both. When lambda = 0 the interactions are
|
||||
deactivated. The transition between these two extrema is smoothed by a
|
||||
soft repulsive core in order to avoid singularities in potential
|
||||
energy and forces when sites are created or annihilated and can overlap
|
||||
"(Beutler)"_#Beutler.
|
||||
The coefficient lambda is an activation parameter. When lambda = 1 the pair
|
||||
potential is identical to a Lennard-Jones term or a Coulomb term or a
|
||||
combination of both. When lambda = 0 the interactions are deactivated. The
|
||||
transition between these two extrema is smoothed by a soft repulsive core in
|
||||
order to avoid singularities in potential energy and forces when sites are
|
||||
created or annihilated and can overlap "(Beutler)"_#Beutler.
|
||||
|
||||
The parameters n, alpha_LJ and alpha_C are set in the
|
||||
"pair_style"_pair_style.html command, before the cutoffs. Usual
|
||||
choices for the exponent are n = 2 or n = 1. For the remaining
|
||||
coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
|
||||
appropriate choices. Plots of the LJ and Coulomb terms are shown
|
||||
below, for lambda ranging from 1 to 0 every 0.1.
|
||||
"pair_style"_pair_style.html command, before the cutoffs. Usual choices for the
|
||||
exponent are n = 2 or n = 1. For the remaining coefficients alpha_LJ = 0.5 and
|
||||
alpha_C = 10 Angstrom^2 are appropriate choices. Plots of the 12/6 LJ and
|
||||
Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1.
|
||||
|
||||
:image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg)
|
||||
:c
|
||||
|
||||
For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles,
|
||||
the following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands, or by mixing as described below:
|
||||
For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles, as well
|
||||
as for the equivalent {class2} versions, the following coefficients must be
|
||||
defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html
|
||||
command as in the examples above, or in the data file or restart files read by
|
||||
the "read_data"_read_data.html or "read_restart"_read_restart.html commands, or
|
||||
by mixing as described below:
|
||||
|
||||
epsilon (energy units)
|
||||
sigma (distance units)
|
||||
lambda (activation parameter between 0 and 1)
|
||||
lambda (activation parameter, between 0 and 1)
|
||||
cutoff1 (distance units)
|
||||
cutoff2 (distance units) :ul
|
||||
|
||||
|
|
@ -160,24 +196,29 @@ since it has no Coulombic terms. For the {coul/cut/soft} and
|
|||
{coul/long/soft} only lambda and the optional cutoff2 are to be
|
||||
specified.
|
||||
|
||||
Style {lj/cut/tip4p/long/soft} implements a soft-core version of the
|
||||
TIP4P water model. The usage of this pair style is documented in the
|
||||
"pair_lj"_pair_lj.html styles. The soft-core version introduces the
|
||||
lambda parameter to the list of arguments, after epsilon and sigma in
|
||||
the "pair_coeff"_pair_coeff.html command. The parameters n, alpha_LJ
|
||||
and alpha_C are set in the "pair_style"_pair_style.html command,
|
||||
before the cutoffs.
|
||||
Style {lj/cut/tip4p/long/soft} implements a soft-core version of the TIP4P water
|
||||
model. The usage of the TIP4P pair style is documented in the
|
||||
"pair_lj"_pair_lj.html styles. In the soft version the parameters n, alpha_LJ
|
||||
and alpha_C are set in the "pair_style"_pair_style.html command, after the
|
||||
specific parameters of the TIP4P water model and before the cutoffs. The
|
||||
activation parameter lambda is supplied as an argument of the the
|
||||
"pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the
|
||||
optional cutoffs.
|
||||
|
||||
Style {lj/charmm/coul/long/soft} implements a soft-core version of the
|
||||
CHARMM version of LJ interactions with an additional switching
|
||||
function S(r) that ramps the energy and force smoothly to zero between
|
||||
an inner and outer cutoff. The usage of this pair style is documented
|
||||
in the "pair_charmm"_pair_charmm.html styles. The soft-core version
|
||||
introduces the lambda parameter to the list of arguments, after
|
||||
epsilon and sigma in the "pair_coeff"_pair_coeff.html command (and
|
||||
before the optional eps14 and sigma14). The parameters n,
|
||||
alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html
|
||||
command, before the cutoffs.
|
||||
Style {lj/charmm/coul/long/soft} implements a soft-core version of the modified
|
||||
12-6 LJ potential used in CHARMM and documented in the
|
||||
"pair_lj_charmm"_pair_charmm.html style. In the soft version the parameters n,
|
||||
alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before
|
||||
the global cutoffs. The activation parameter lambda is introduced as an argument
|
||||
of the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and
|
||||
before the optional eps14 and sigma14.
|
||||
|
||||
Style {lj/class2/soft} implements a soft-core version of the 9-6 potential in
|
||||
"pair_class2"_pair_class2.html. In the soft version the parameters n, alpha_LJ
|
||||
and alpha_C are set in the "pair_style"_pair_style.html command, before the
|
||||
global cutoffs. The activation parameter lambda is introduced as an argument of
|
||||
the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and before
|
||||
the optional cutoffs.
|
||||
|
||||
The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} sub-styles
|
||||
are designed to be combined with other pair potentials via the
|
||||
|
|
@ -189,7 +230,7 @@ occur. These sub-styles are suitable to represent charges embedded in
|
|||
the Lennard-Jones radius of another site (for example hydrogen atoms
|
||||
in several water models).
|
||||
|
||||
NOTES: When using the soft-core Coulomb potentials with long-range
|
||||
NOTE: When using the soft-core Coulomb potentials with long-range
|
||||
solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free
|
||||
energy calculation in which sites holding electrostatic charges are
|
||||
being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html
|
||||
|
|
@ -202,6 +243,31 @@ Waals site is present during the free-energy route, thus avoiding
|
|||
overlap of the charges. Examples are provided in the LAMMPS source
|
||||
directory tree, under examples/USER/fep.
|
||||
|
||||
NOTE: To avoid division by zero do not set sigma = 0 in the {lj/cut/soft} and
|
||||
related styles; use the lambda parameter instead to activate/deactivate
|
||||
interactions, or use epsilon = 0 and sigma = 1. Alternatively, when sites do not
|
||||
interact though the Lennard-Jones term the {coul/long/soft} or similar sub-style
|
||||
can be used via the "pair_style hybrid/overlay"_pair_hybrid.html command.
|
||||
|
||||
:line
|
||||
|
||||
The {morse/soft} variant modifies the "pair_morse"_pair_morse.html style at
|
||||
short range to have a soft core. The functional form differs from that of the
|
||||
{lj/soft} styles, and is instead given by:
|
||||
|
||||
:c,image(Eqs/pair_morse_soft.jpg)
|
||||
|
||||
The {morse/soft} style requires the following pair coefficients:
|
||||
|
||||
D0 (energy units)
|
||||
alpha (1/distance units)
|
||||
r0 (distance units)
|
||||
lambda (unitless, between 0.0 and 1.0)
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The last coefficient is optional. If not specified, the global morse cutoff is
|
||||
used.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
|
|
@ -228,40 +294,56 @@ instructions on how to use the accelerated styles effectively.
|
|||
|
||||
[Mixing, shift, tail correction, restart info]:
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for this pair style can be mixed.
|
||||
The default mix value is {geometric}. See the "pair_modify" command
|
||||
for details.
|
||||
The different versions of the {lj/cut/soft} pair styles support mixing. For atom
|
||||
type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff
|
||||
distance for these pair style can be mixed. The default mix value is
|
||||
{geometric} for 12-6 styles.
|
||||
|
||||
These pair styles support the "pair_modify"_pair_modify.html shift
|
||||
option for the energy of the Lennard-Jones portion of the pair
|
||||
The mixing rule for epsilon and sigma for {lj/class2/soft} 9-6 potentials is to use the
|
||||
{sixthpower} formulas. The "pair_modify mix"_pair_modify.html setting is thus
|
||||
ignored for class2 potentials for epsilon and sigma. However it is still
|
||||
followed for mixing the cutoff distance. See the "pair_modify"_pair_modify.html
|
||||
command for details.
|
||||
|
||||
The {morse/soft} pair style does not support mixing. Thus, coefficients for all
|
||||
LJ pairs must be specified explicitly.
|
||||
|
||||
All of the pair styles with soft core support the "pair_modify"_pair_modify.html
|
||||
shift option for the energy of the Lennard-Jones portion of the pair
|
||||
interaction.
|
||||
|
||||
These pair styles support the "pair_modify"_pair_modify.html tail
|
||||
option for adding a long-range tail correction to the energy and
|
||||
pressure for the Lennard-Jones portion of the pair interaction.
|
||||
The different versions of the {lj/cut/soft} pair styles support the
|
||||
"pair_modify"_pair_modify.html tail option for adding a long-range tail
|
||||
correction to the energy and pressure for the Lennard-Jones portion of the pair
|
||||
interaction.
|
||||
|
||||
These pair styles write information to "binary restart
|
||||
files"_restart.html, so pair_style and pair_coeff commands do not need
|
||||
to be specified in an input script that reads a restart file.
|
||||
NOTE: The analytical form of the tail corrections for energy and pressure used
|
||||
in the {lj/cut/soft} potentials are approximate, being identical to that of the
|
||||
corresponding non-soft potentials scaled by a factor lambda^n. For real-space
|
||||
cutoffs greater than 2.5 sigma and alpha_LJ = 0.5, the error affecting the tail
|
||||
correction is below 0.2% when lambda = 0 (worse case). This error disappears as
|
||||
lambda approaches 1. Note that this is the error affecting the long-range tail
|
||||
(itself a correction to the interaction energy) which includes other
|
||||
approximations, namely that the system is homogenous (local density equal the
|
||||
average density) beyond the cutoff.
|
||||
|
||||
The {morse/soft} pair style does not support the "pair_modify"_pair_modify.html
|
||||
tail option for adding long-range tail corrections to energy and pressure.
|
||||
|
||||
All of these pair styles write information to "binary restart
|
||||
files"_restart.html, so pair_style and pair_coeff commands do not need to be
|
||||
specified in an input script that reads a restart file.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
To avoid division by zero do not set sigma = 0; use the lambda
|
||||
parameter instead to activate/deactivate interactions, or use
|
||||
epsilon = 0 and sigma = 1. Alternatively, when sites do not
|
||||
interact though the Lennard-Jones term the {coul/long/soft} or
|
||||
similar sub-style can be used via the
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html command.
|
||||
|
||||
:line
|
||||
|
||||
All of the plain {soft} pair styles are part of the USER-FEP package.
|
||||
The {long} styles also requires the KSPACE package to be installed.
|
||||
They are only enabled if LAMMPS was built with those packages. See
|
||||
the "Build package"_Build_package.html doc page for more info.
|
||||
The pair styles with soft core are only enabled if LAMMPS was built with the
|
||||
USER-FEP package. The {long} versions also require the KSPACE package to be
|
||||
installed. The soft {tip4p} versions also require the MOLECULE package to be
|
||||
installed. These styles are only enabled if LAMMPS was built with those
|
||||
packages. See the "Build package"_Build_package.html doc page for more
|
||||
info. Note that the KSPACE and MOLECULE packages are installed by default.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
@ -260,6 +260,14 @@ pair_style command.
|
|||
|
||||
:line
|
||||
|
||||
A version of these styles with a soft core, {lj/cut/soft}, suitable for use in
|
||||
free energy calculations, is part of the USER-FEP package and is documented with
|
||||
the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is
|
||||
only available if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
|
|
|
|||
|
|
@ -154,6 +154,14 @@ specified in the pair_style command.
|
|||
|
||||
:line
|
||||
|
||||
A version of these styles with a soft core, {lj/cut/soft}, suitable for use in
|
||||
free energy calculations, is part of the USER-FEP package and is documented with
|
||||
the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is
|
||||
only available if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
|
|
|
|||
|
|
@ -12,7 +12,6 @@ pair_style morse/omp command :h3
|
|||
pair_style morse/opt command :h3
|
||||
pair_style morse/smooth/linear command :h3
|
||||
pair_style morse/smooth/linear/omp command :h3
|
||||
pair_style morse/soft command :h3
|
||||
pair_style morse/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
|
@ -25,10 +24,6 @@ args = list of arguments for a particular style :ul
|
|||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
{morse/smooth/linear} args = cutoff
|
||||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
{morse/soft} args = n lf cutoff
|
||||
n = soft-core parameter
|
||||
lf = transformation range is lf < lambda < 1
|
||||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
:pre
|
||||
|
||||
[Examples:]
|
||||
|
|
@ -38,10 +33,6 @@ pair_style morse/smooth/linear 2.5
|
|||
pair_coeff * * 100.0 2.0 1.5
|
||||
pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre
|
||||
|
||||
pair_style morse/soft 4 0.9 10.0
|
||||
pair_coeff * * 100.0 2.0 1.5 1.0
|
||||
pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {morse} computes pairwise interactions with the formula
|
||||
|
|
@ -77,24 +68,11 @@ the {morse} and {morse/smooth/linear} styles.
|
|||
|
||||
:line
|
||||
|
||||
The {morse/soft} variant is similar to the {lj/cut/soft} pair style
|
||||
in that it modifies the potential at short range to have a soft core.
|
||||
This helps to avoid singularities during free energy calculation in
|
||||
which sites are created or annihilated. The formula differs from that
|
||||
of {lj/cut/soft}, and is instead given by:
|
||||
|
||||
:c,image(Eqs/pair_morse_soft.jpg)
|
||||
|
||||
The {morse/soft} style requires the following pair coefficients:
|
||||
|
||||
D0 (energy units)
|
||||
alpha (1/distance units)
|
||||
r0 (distance units)
|
||||
lamda (unitless, between 0.0 and 1.0)
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The last coefficient is optional. If not specified, the global morse
|
||||
cutoff is used.
|
||||
A version of the {morse} style with a soft core, {morse/soft}, suitable for use in
|
||||
free energy calculations, is part of the USER-FEP package and is documented with
|
||||
the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is only
|
||||
available if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -151,12 +129,8 @@ The {morse/smooth/linear} pair style is only enabled if LAMMPS was
|
|||
built with the USER-MISC package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
The {morse/soft} pair style is only enabled if LAMMPS was built with
|
||||
the USER-FEP package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
"pair_coeff"_pair_coeff.html, "pair_fep_soft"_pair_fep_soft.html
|
||||
|
||||
[Default:] none
|
||||
|
|
|
|||
Loading…
Reference in New Issue