diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index 70c7ef68f71cfe7bf675730caa5819890510bfe2..adf11dcfcfa9822f4c736f1cb7203ca0e02c446c 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -67,7 +67,7 @@ parameters. This is followed by that number of integers giving the degree of each order parameter. Because {Q}2 and all odd-degree order parameters are zero for atoms in cubic crystals (see "Steinhardt"_#Steinhardt), the default order parameters are {Q}4, -{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn}=12, {Q}4 +{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn} =12, {Q}4 = sqrt(7/3)/8 = 0.19094.... The numerical values of all order parameters up to {Q}12 for a range of commonly encountered high-symmetry structures are given in Table I of "Mickel et diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index defd98d520d06489d8e93e93369cb33bdfb4b2d5..1c3787e696638191373d0b563f461c37d42dddad 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -224,7 +224,7 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz}, notation. Each of these sub-blocks contains one column for each bispectrum component, the same as for compute {sna/atom} -For example, if {K}=30 and ntypes=1, the number of columns in the per-atom +For example, if {K} =30 and ntypes=1, the number of columns in the per-atom arrays generated by {sna/atom}, {snad/atom}, and {snav/atom} are 30, 90, and 180, respectively. With {quadratic} value=1, the numbers of columns are 930, 2790, and 5580, respectively. diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index cd4d6adfdf03dc2e8332ffb3eec9e338de1b2240..cfb26138fdaa468c3074b1ef6fa1f1dfe6c6eb8c 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -83,7 +83,7 @@ the following dynamic equation: :c,image(Eqs/fix_controller1.jpg) where {c} is the continuous time analog of the control variable, -{e}={pvar}-{setpoint} is the error in the process variable, and +{e} ={pvar}-{setpoint} is the error in the process variable, and {alpha}, {Kp}, {Ki}, and {Kd} are constants set by the corresponding keywords described above. The discretized version of this equation is: @@ -106,10 +106,10 @@ the value of {alpha} to reflect this, while leaving {Kp}, {Ki}, and When choosing the values of the four constants, it is best to first pick a value and sign for {alpha} that is consistent with the magnitudes and signs of {pvar} and {cvar}. The magnitude of {Kp} -should then be tested over a large positive range keeping {Ki}={Kd}=0. +should then be tested over a large positive range keeping {Ki} = {Kd} =0. A good value for {Kp} will produce a fast response in {pvar}, without overshooting the {setpoint}. For many applications, proportional -feedback is sufficient, and so {Ki}={Kd}=0 can be used. In cases where +feedback is sufficient, and so {Ki} = {Kd} =0 can be used. In cases where there is a substantial lag time in the response of {pvar} to a change in {cvar}, this can be counteracted by increasing {Kd}. In situations where {pvar} plateaus without reaching {setpoint}, this can be diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 9f82fc0fb66f5755f08c22c07c8418b148ec5141..46452a1f7e932eaf2531525f7ee6d557fceffb37 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -58,7 +58,7 @@ required in order to eliminate velocity components along the bonds In order to formulate individual constraints for SHAKE and RATTLE, focus on a single molecule whose bonds are constrained. Let Ri and Vi be the position and velocity of atom {i} at time {n}, for -{i}=1,...,{N}, where {N} is the number of sites of our reference +{i} =1,...,{N}, where {N} is the number of sites of our reference molecule. The distance vector between sites {i} and {j} is given by :c,image(Eqs/fix_rattle_rij.jpg) diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt index 24d319bdb9a3db4a33467cbbb785492a5a25b72e..17c9c0f400f4cdf5dfc67966d5b1f51d4d0f4672 100644 --- a/doc/src/fix_smd_integrate_tlsph.txt +++ b/doc/src/fix_smd_integrate_tlsph.txt @@ -14,15 +14,12 @@ fix ID group-ID smd/integrate_tlsph keyword values :pre ID, group-ID are documented in "fix"_fix.html command smd/integrate_tlsph = style name of this fix command -zero or more keyword/value pairs may be appended :ul - -keyword = {limit_velocity} :l +zero or more keyword/value pairs may be appended +keyword = {limit_velocity} :ul {limit_velocity} value = max_vel max_vel = maximum allowed velocity :pre -:ule - [Examples:] fix 1 all smd/integrate_tlsph diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt index 0dfb9451de3efb4a72cc7f6af5ce59bccef5b91e..28e38c7f970a9d99a07294bd77f4fb66a54ced00 100644 --- a/doc/src/fix_smd_integrate_ulsph.txt +++ b/doc/src/fix_smd_integrate_ulsph.txt @@ -14,9 +14,8 @@ fix ID group-ID smd/integrate_ulsph keyword :pre ID, group-ID are documented in "fix"_fix.html command smd/integrate_ulsph = style name of this fix command -zero or more keyword/value pairs may be appended :ul - -keyword = adjust_radius or limit_velocity +zero or more keyword/value pairs may be appended +keyword = adjust_radius or limit_velocity :ul adjust_radius values = adjust_radius_factor min_nn max_nn adjust_radius_factor = factor which scale the smooth/kernel radius @@ -28,7 +27,7 @@ limit_velocity values = max_velocity [Examples:] -fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 :pre +fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre [Description:] @@ -38,7 +37,7 @@ See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are -{adjust_radius_factor}=1.02, {min_nn}=15, and {max_nn}=20. +{adjust_radius_factor} =1.02, {min_nn} =15, and {max_nn} =20. The {limit_velocity} keyword will control the velocity, scaling the norm of the velocity vector to max_vel in case it exceeds this velocity limit. diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt index 2a70c598cef7a0a5d41ab82aac6d706562e53a1e..eeaa3387a44a834cfe4361a75e40d2610d29bdb6 100644 --- a/doc/src/pair_smd_hertz.txt +++ b/doc/src/pair_smd_hertz.txt @@ -28,7 +28,7 @@ The parameter <contact_stiffness> has units of pressure and should equal roughly of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles. The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close -particles can approach each other. Usually, {scale_factor}=1.0. +particles can approach each other. Usually, {scale_factor} =1.0. :line diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt index 76d3891a3c995d2778920b0ad55406e90eb63f1d..c32bf3a22ea89c35efd3231b0ffbfdd72590a810 100644 --- a/doc/src/pair_smd_triangulated_surface.txt +++ b/doc/src/pair_smd_triangulated_surface.txt @@ -29,7 +29,7 @@ The parameter <contact_stiffness> has units of pressure and should equal roughly of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close -particles can approach the triangulated surface. Usually, {scale_factor}=1.0. +particles can approach the triangulated surface. Usually, {scale_factor} =1.0. :line diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt index 393bbc066525c90db749a8d80acdfedca93ad4a9..268fe78d02294eca17134ff7fcffb276512db2be 100644 --- a/doc/src/pair_smd_ulsph.txt +++ b/doc/src/pair_smd_ulsph.txt @@ -12,8 +12,8 @@ pair_style smd/ulsph command :h3 pair_style smd/ulsph args :pre -these keywords must be given :l -keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT} or {*NO_VELOCITY_GRADIENT} and {*GRADIENT_CORRECTION} or {*NO_GRADIENT_CORRECTION} +these keywords must be given :ul +keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT} or {*NO_VELOCITY_GRADIENT} and {*GRADIENT_CORRECTION} or {*NO_GRADIENT_CORRECTION} :pre [Examples:]