Loading doc/src/Commands_pair.txt +12 −9 Original line number Diff line number Diff line Loading @@ -63,13 +63,13 @@ OPT. "comb (o)"_pair_comb.html, "comb3"_pair_comb.html, "coul/cut (gko)"_pair_coul.html, "coul/cut/soft (o)"_pair_lj_soft.html, "coul/cut/soft (o)"_pair_fep_soft.html, "coul/debye (gko)"_pair_coul.html, "coul/diel (o)"_pair_coul_diel.html, "coul/dsf (gko)"_pair_coul.html, "coul/long (gko)"_pair_coul.html, "coul/long/cs (g)"_pair_cs.html, "coul/long/soft (o)"_pair_lj_soft.html, "coul/long/soft (o)"_pair_fep_soft.html, "coul/msm (o)"_pair_coul.html, "coul/shield"_pair_coul_shield.html, "coul/streitz"_pair_coul.html, Loading Loading @@ -114,32 +114,35 @@ OPT. "lj/charmm/coul/charmm (iko)"_pair_charmm.html, "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, "lj/charmm/coul/long (gikot)"_pair_charmm.html, "lj/charmm/coul/long/soft (o)"_pair_lj_soft.html, "lj/charmm/coul/long/soft (o)"_pair_fep_soft.html, "lj/charmm/coul/msm (o)"_pair_charmm.html, "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, "lj/charmmfsw/coul/long"_pair_charmm.html, "lj/class2 (gko)"_pair_class2.html, "lj/class2/coul/cut (ko)"_pair_class2.html, "lj/class2/coul/cut/soft"_pair_fep_soft.html, "lj/class2/coul/long (gko)"_pair_class2.html, "lj/class2/coul/long/soft"_pair_fep_soft.html, "lj/class2/soft"_pair_fep_soft.html, "lj/cubic (go)"_pair_lj_cubic.html, "lj/cut (gikot)"_pair_lj.html, "lj/cut/coul/cut (gko)"_pair_lj.html, "lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, "lj/cut/coul/cut/soft (o)"_pair_fep_soft.html, "lj/cut/coul/debye (gko)"_pair_lj.html, "lj/cut/coul/dsf (gko)"_pair_lj.html, "lj/cut/coul/long (gikot)"_pair_lj.html, "lj/cut/coul/long/cs"_pair_cs.html, "lj/cut/coul/long/soft (o)"_pair_lj_soft.html, "lj/cut/coul/long/soft (o)"_pair_fep_soft.html, "lj/cut/coul/msm (go)"_pair_lj.html, "lj/cut/coul/wolf (o)"_pair_lj.html, "lj/cut/dipole/cut (go)"_pair_dipole.html, "lj/cut/dipole/long (g)"_pair_dipole.html, "lj/cut/dipole/sf (go)"_pair_dipole.html, "lj/cut/soft (o)"_pair_lj_soft.html, "lj/cut/soft (o)"_pair_fep_soft.html, "lj/cut/thole/long (o)"_pair_thole.html, "lj/cut/tip4p/cut (o)"_pair_lj.html, "lj/cut/tip4p/long (ot)"_pair_lj.html, "lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, "lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html, "lj/expand (gko)"_pair_lj_expand.html, "lj/expand/coul/long (g)"_pair_lj_expand.html, "lj/gromacs (gko)"_pair_gromacs.html, Loading Loading @@ -170,7 +173,7 @@ OPT. "momb"_pair_momb.html, "morse (gkot)"_pair_morse.html, "morse/smooth/linear (o)"_pair_morse.html, "morse/soft"_pair_morse.html, "morse/soft"_pair_fep_soft.html, "multi/lucy"_pair_multi_lucy.html, "multi/lucy/rx (k)"_pair_multi_lucy_rx.html, "nb3b/harmonic"_pair_nb3b_harmonic.html, Loading Loading @@ -230,7 +233,7 @@ OPT. "thole"_pair_thole.html, "tip4p/cut (o)"_pair_coul.html, "tip4p/long (o)"_pair_coul.html, "tip4p/long/soft (o)"_pair_lj_soft.html, "tip4p/long/soft (o)"_pair_fep_soft.html, "tri/lj"_pair_tri_lj.html, "ufm (got)"_pair_ufm.html, "vashishta (gko)"_pair_vashishta.html, Loading doc/src/Install_git.txt +2 −9 Original line number Diff line number Diff line Loading @@ -48,15 +48,8 @@ your machine and "unstable" is one of the 3 branches listed above. between them at any time using "git checkout <branch name>".) Once the command completes, your directory will contain the same files as if you unpacked a current LAMMPS tarball, with two exceptions: 1) No LAMMPS packages are initially installed in the src dir (a few packages are installed by default in the tarball src dir). You can install whichever packages you wish before building LAMMPS; type "make package" from the src dir to see the options, and the "Packages"_Packages.html doc page for a discussion of packages. 2) The HTML documentation files are not included. They can be fetched as if you unpacked a current LAMMPS tarball, with the exception, that the HTML documentation files are not included. They can be fetched from the LAMMPS website by typing "make fetch" in the doc directory. Or they can be generated from the content provided in doc/src by typing "make html" from the the doc directory. Loading doc/src/Install_svn.txt +2 −9 Original line number Diff line number Diff line Loading @@ -36,15 +36,8 @@ where "mylammps" is the name of the directory you wish to create on your machine. Once the command completes, your directory will contain the same files as if you unpacked a current LAMMPS tarball, with two exceptions: 1) No LAMMPS packages are initially installed in the src dir (a few packages are installed by default in the tarball src dir). You can install whichever packages you wish before building LAMMPS; type "make package" from the src dir to see the options, and the "Packages"_Packages.html doc page for a discussion of packages. 2) The HTML documentation files are not included. They can be fetched as if you unpacked a current LAMMPS tarball, with the exception, that the HTML documentation files are not included. They can be fetched from the LAMMPS website by typing "make fetch" in the doc directory. Or they can be generated from the content provided in doc/src by typing "make html" from the the doc directory. Loading doc/src/Packages_details.txt +1 −1 Original line number Diff line number Diff line Loading @@ -1306,7 +1306,7 @@ src/USER-FEP: filenames -> commands src/USER-FEP/README "fix adapt/fep"_fix_adapt_fep.html "compute fep"_compute_fep.html "pair_style */soft"_pair_lj_soft.html "pair_style */soft"_pair_fep_soft.html examples/USER/fep tools/fep/README tools/fep :ul Loading doc/src/compute_fep.txt +29 −14 Original line number Diff line number Diff line Loading @@ -128,24 +128,39 @@ commands to be changed, if the pair style supports it. The {pstyle} argument is the name of the pair style. For example, {pstyle} could be specified as "lj/cut". The {pparam} argument is the name of the parameter to change. This is a (non-exclusive) list of name of the parameter to change. This is a list of 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=:) "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_fep_soft.html: lambda: type pairs: "coul/long, coul/msm"_pair_coul.html: scale: type pairs: "coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs: "eam"_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: type pairs: "lj/cut"_pair_lj.html: epsilon,sigma: type pairs: "lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: "lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs: "lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: "lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs: "lj/cut/tip4p/long/soft"_pair_fep_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: "mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: 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,nn,mm: type pairs: "nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs: "ufm"_pair_ufm.html: epsilon,sigma,scale: 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 Loading Loading @@ -236,7 +251,7 @@ package"_Build_package.html doc page for more info. [Related commands:] "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html, "pair_style lj/soft/coul/soft"_pair_lj_soft.html "pair_fep_soft"_pair_fep_soft.html [Default:] Loading Loading
doc/src/Commands_pair.txt +12 −9 Original line number Diff line number Diff line Loading @@ -63,13 +63,13 @@ OPT. "comb (o)"_pair_comb.html, "comb3"_pair_comb.html, "coul/cut (gko)"_pair_coul.html, "coul/cut/soft (o)"_pair_lj_soft.html, "coul/cut/soft (o)"_pair_fep_soft.html, "coul/debye (gko)"_pair_coul.html, "coul/diel (o)"_pair_coul_diel.html, "coul/dsf (gko)"_pair_coul.html, "coul/long (gko)"_pair_coul.html, "coul/long/cs (g)"_pair_cs.html, "coul/long/soft (o)"_pair_lj_soft.html, "coul/long/soft (o)"_pair_fep_soft.html, "coul/msm (o)"_pair_coul.html, "coul/shield"_pair_coul_shield.html, "coul/streitz"_pair_coul.html, Loading Loading @@ -114,32 +114,35 @@ OPT. "lj/charmm/coul/charmm (iko)"_pair_charmm.html, "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, "lj/charmm/coul/long (gikot)"_pair_charmm.html, "lj/charmm/coul/long/soft (o)"_pair_lj_soft.html, "lj/charmm/coul/long/soft (o)"_pair_fep_soft.html, "lj/charmm/coul/msm (o)"_pair_charmm.html, "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, "lj/charmmfsw/coul/long"_pair_charmm.html, "lj/class2 (gko)"_pair_class2.html, "lj/class2/coul/cut (ko)"_pair_class2.html, "lj/class2/coul/cut/soft"_pair_fep_soft.html, "lj/class2/coul/long (gko)"_pair_class2.html, "lj/class2/coul/long/soft"_pair_fep_soft.html, "lj/class2/soft"_pair_fep_soft.html, "lj/cubic (go)"_pair_lj_cubic.html, "lj/cut (gikot)"_pair_lj.html, "lj/cut/coul/cut (gko)"_pair_lj.html, "lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, "lj/cut/coul/cut/soft (o)"_pair_fep_soft.html, "lj/cut/coul/debye (gko)"_pair_lj.html, "lj/cut/coul/dsf (gko)"_pair_lj.html, "lj/cut/coul/long (gikot)"_pair_lj.html, "lj/cut/coul/long/cs"_pair_cs.html, "lj/cut/coul/long/soft (o)"_pair_lj_soft.html, "lj/cut/coul/long/soft (o)"_pair_fep_soft.html, "lj/cut/coul/msm (go)"_pair_lj.html, "lj/cut/coul/wolf (o)"_pair_lj.html, "lj/cut/dipole/cut (go)"_pair_dipole.html, "lj/cut/dipole/long (g)"_pair_dipole.html, "lj/cut/dipole/sf (go)"_pair_dipole.html, "lj/cut/soft (o)"_pair_lj_soft.html, "lj/cut/soft (o)"_pair_fep_soft.html, "lj/cut/thole/long (o)"_pair_thole.html, "lj/cut/tip4p/cut (o)"_pair_lj.html, "lj/cut/tip4p/long (ot)"_pair_lj.html, "lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, "lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html, "lj/expand (gko)"_pair_lj_expand.html, "lj/expand/coul/long (g)"_pair_lj_expand.html, "lj/gromacs (gko)"_pair_gromacs.html, Loading Loading @@ -170,7 +173,7 @@ OPT. "momb"_pair_momb.html, "morse (gkot)"_pair_morse.html, "morse/smooth/linear (o)"_pair_morse.html, "morse/soft"_pair_morse.html, "morse/soft"_pair_fep_soft.html, "multi/lucy"_pair_multi_lucy.html, "multi/lucy/rx (k)"_pair_multi_lucy_rx.html, "nb3b/harmonic"_pair_nb3b_harmonic.html, Loading Loading @@ -230,7 +233,7 @@ OPT. "thole"_pair_thole.html, "tip4p/cut (o)"_pair_coul.html, "tip4p/long (o)"_pair_coul.html, "tip4p/long/soft (o)"_pair_lj_soft.html, "tip4p/long/soft (o)"_pair_fep_soft.html, "tri/lj"_pair_tri_lj.html, "ufm (got)"_pair_ufm.html, "vashishta (gko)"_pair_vashishta.html, Loading
doc/src/Install_git.txt +2 −9 Original line number Diff line number Diff line Loading @@ -48,15 +48,8 @@ your machine and "unstable" is one of the 3 branches listed above. between them at any time using "git checkout <branch name>".) Once the command completes, your directory will contain the same files as if you unpacked a current LAMMPS tarball, with two exceptions: 1) No LAMMPS packages are initially installed in the src dir (a few packages are installed by default in the tarball src dir). You can install whichever packages you wish before building LAMMPS; type "make package" from the src dir to see the options, and the "Packages"_Packages.html doc page for a discussion of packages. 2) The HTML documentation files are not included. They can be fetched as if you unpacked a current LAMMPS tarball, with the exception, that the HTML documentation files are not included. They can be fetched from the LAMMPS website by typing "make fetch" in the doc directory. Or they can be generated from the content provided in doc/src by typing "make html" from the the doc directory. Loading
doc/src/Install_svn.txt +2 −9 Original line number Diff line number Diff line Loading @@ -36,15 +36,8 @@ where "mylammps" is the name of the directory you wish to create on your machine. Once the command completes, your directory will contain the same files as if you unpacked a current LAMMPS tarball, with two exceptions: 1) No LAMMPS packages are initially installed in the src dir (a few packages are installed by default in the tarball src dir). You can install whichever packages you wish before building LAMMPS; type "make package" from the src dir to see the options, and the "Packages"_Packages.html doc page for a discussion of packages. 2) The HTML documentation files are not included. They can be fetched as if you unpacked a current LAMMPS tarball, with the exception, that the HTML documentation files are not included. They can be fetched from the LAMMPS website by typing "make fetch" in the doc directory. Or they can be generated from the content provided in doc/src by typing "make html" from the the doc directory. Loading
doc/src/Packages_details.txt +1 −1 Original line number Diff line number Diff line Loading @@ -1306,7 +1306,7 @@ src/USER-FEP: filenames -> commands src/USER-FEP/README "fix adapt/fep"_fix_adapt_fep.html "compute fep"_compute_fep.html "pair_style */soft"_pair_lj_soft.html "pair_style */soft"_pair_fep_soft.html examples/USER/fep tools/fep/README tools/fep :ul Loading
doc/src/compute_fep.txt +29 −14 Original line number Diff line number Diff line Loading @@ -128,24 +128,39 @@ commands to be changed, if the pair style supports it. The {pstyle} argument is the name of the pair style. For example, {pstyle} could be specified as "lj/cut". The {pparam} argument is the name of the parameter to change. This is a (non-exclusive) list of name of the parameter to change. This is a list of 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=:) "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_fep_soft.html: lambda: type pairs: "coul/long, coul/msm"_pair_coul.html: scale: type pairs: "coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs: "eam"_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: type pairs: "lj/cut"_pair_lj.html: epsilon,sigma: type pairs: "lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: "lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs: "lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: "lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs: "lj/cut/tip4p/long/soft"_pair_fep_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: "mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: 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,nn,mm: type pairs: "nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs: "ufm"_pair_ufm.html: epsilon,sigma,scale: 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 Loading Loading @@ -236,7 +251,7 @@ package"_Build_package.html doc page for more info. [Related commands:] "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html, "pair_style lj/soft/coul/soft"_pair_lj_soft.html "pair_fep_soft"_pair_fep_soft.html [Default:] Loading
