diff --git a/doc/Section_commands.html b/doc/Section_commands.html index bebb8da72c..c69566e177 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -341,12 +341,12 @@ of each style or click on the style itself for a full description: efieldenforce2devaporateexternalfreezegcmcgravityheat indentlangevinlineforcemomentummovemsstnebnph nphugnph/aspherenph/spherenptnpt/aspherenpt/spherenvenve/asphere -nve/limitnve/linenve/noforcenve/spherenve/trinvtnvt/aspherenvt/sllod -nvt/sphereorient/fccplaneforcepoemspourpress/berendsenprintqeq/comb -reax/bondsrecenterrestrainrigidrigid/nverigid/nvtsetforceshake -springspring/rgspring/selfsrdstore/forcestore/statetemp/berendsentemp/rescale -thermal/conductivitytmdttmviscosityviscouswall/colloidwall/granwall/harmonic -wall/lj126wall/lj93wall/reflectwall/regionwall/srd +nve/asphere/noforcenve/limitnve/linenve/noforcenve/spherenve/trinvtnvt/asphere +nvt/sllodnvt/sphereorient/fccplaneforcepoemspourpress/berendsenprint +qeq/combreax/bondsrecenterrestrainrigidrigid/nverigid/nvtsetforce +shakespringspring/rgspring/selfsrdstore/forcestore/statetemp/berendsen +temp/rescalethermal/conductivitytmdttmviscosityviscouswall/colloidwall/gran +wall/harmonicwall/lj126wall/lj93wall/reflectwall/regionwall/srd

These are fix styles contributed by users, which can be used if @@ -413,21 +413,22 @@ potentials. Click on the style itself for a full description:

- - - - - - - - - - - - - - - + + + + + + + + + + + + + + +
nonehybridhybrid/overlayadp
airebobornborn/coul/longbuck
buck/coul/cutbuck/coul/longcolloidcomb
coul/cutcoul/debyecoul/longdipole/cut
dpddpd/tstatdsmceam
eam/alloyeam/fseimgauss
gaybernegran/hertz/historygran/hookegran/hooke/history
hbond/dreiding/ljhbond/dreiding/morseline/ljlj/charmm/coul/charmm
lj/charmm/coul/charmm/implicitlj/charmm/coul/longlj/class2lj/class2/coul/cut
lj/class2/coul/longlj/cutlj/cut/coul/cutlj/cut/coul/debye
lj/cut/coul/longlj/cut/coul/long/tip4plj/expandlj/gromacs
lj/gromacs/coul/gromacslj/smoothlj96/cutlubricate
meammorseperi/lpsperi/pmb
reaxreboresquaredsoft
swtabletersofftersoff/zbl
tri/ljyukawayukawa/colloid +
airebobornborn/coul/longbrownian
brownian/polybuckbuck/coul/cutbuck/coul/long
colloidcombcoul/cutcoul/debye
coul/longdipole/cutdpddpd/tstat
dsmceameam/alloyeam/fs
eimgaussgaybernegran/hertz/history
gran/hookegran/hooke/historyhbond/dreiding/ljhbond/dreiding/morse
line/ljlj/charmm/coul/charmmlj/charmm/coul/charmm/implicitlj/charmm/coul/long
lj/class2lj/class2/coul/cutlj/class2/coul/longlj/cut
lj/cut/coul/cutlj/cut/coul/debyelj/cut/coul/longlj/cut/coul/long/tip4p
lj/expandlj/gromacslj/gromacs/coul/gromacslj/smooth
lj96/cutlubricatelubricate/polylubricateU
lubricateU/polymeammorseperi/lps
peri/pmbreaxreboresquared
softswtabletersoff
tersoff/zbltri/ljyukawayukawa/colloid

These are pair styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 713d0cfe4c..e8ca9cf708 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -437,6 +437,7 @@ of each style or click on the style itself for a full description: "npt/sphere"_fix_npt_sphere.html, "nve"_fix_nve.html, "nve/asphere"_fix_nve_asphere.html, +"nve/asphere/noforce"_fix_nve_asphere_noforce.html, "nve/limit"_fix_nve_limit.html, "nve/line"_fix_nve_line.html, "nve/noforce"_fix_nve_noforce.html, @@ -617,6 +618,8 @@ potentials. Click on the style itself for a full description: "airebo"_pair_airebo.html, "born"_pair_born.html, "born/coul/long"_pair_born.html, +"brownian"_pair_brownian.html, +"brownian/poly"_pair_brownian.html, "buck"_pair_buck.html, "buck/coul/cut"_pair_buck.html, "buck/coul/long"_pair_buck.html, @@ -658,6 +661,9 @@ potentials. Click on the style itself for a full description: "lj/smooth"_pair_lj_smooth.html, "lj96/cut"_pair_lj96.html, "lubricate"_pair_lubricate.html, +"lubricate/poly"_pair_lubricate.html, +"lubricateU"_pair_lubricateU.html, +"lubricateU/poly"_pair_lubricateU.html, "meam"_pair_meam.html, "morse"_pair_morse.html, "peri/lps"_pair_peri.html, diff --git a/doc/fix.html b/doc/fix.html index 6d84638722..b2cac319d7 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -198,11 +198,12 @@ list of fix styles available in LAMMPS:

  • npt/asphere - NPT for aspherical particles
  • npt/sphere - NPT for spherical particles
  • nve - constant NVE time integration -
  • nve/asphere - NVT for aspherical particles -
  • nve/limit - NVE with limited step length +
  • nve/asphere - NVE for aspherical particles +
  • nve/asphere/noforce - NVE for aspherical particles without forces +
  • nve/limit - NVE with limited step length
  • nve/line - NVE for line segments
  • nve/noforce - NVE without forces (v only) -
  • nve/sphere - NVT for spherical particles +
  • nve/sphere - NVE for spherical particles
  • nve/tri - NVE for triangles
  • nvt - constant NVT time integration via Nose/Hoover
  • nvt/asphere - NVT for aspherical particles diff --git a/doc/fix.txt b/doc/fix.txt index 6b824cf10c..4c0df45d11 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -193,11 +193,12 @@ list of fix styles available in LAMMPS: "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles "nve"_fix_nve.html - constant NVE time integration -"nve/asphere"_fix_nve_asphere.html - NVT for aspherical particles -"nve/limit"_fix_nve_limit.html - NVE with limited step length +"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles +"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces" +nve/limit"_fix_nve_limit.html - NVE with limited step length "nve/line"_fix_nve_line.html - NVE for line segments "nve/noforce"_fix_nve_noforce.html - NVE without forces (v only) -"nve/sphere"_fix_nve_sphere.html - NVT for spherical particles +"nve/sphere"_fix_nve_sphere.html - NVE for spherical particles "nve/tri"_fix_nve_tri.html - NVE for triangles "nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles diff --git a/doc/fix_nve_asphere_noforce.html b/doc/fix_nve_asphere_noforce.html new file mode 100644 index 0000000000..4dd6f31ad6 --- /dev/null +++ b/doc/fix_nve_asphere_noforce.html @@ -0,0 +1,70 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    fix nve/asphere/noforce command +

    +

    Syntax: +

    +
    fix ID group-ID nve/asphere/noforce 
+
    + +

    Examples: +

    +

    fix 1 all nve/asphere/noforce +

    +

    Description: +

    +

    Perform updates of position and orientation, but not velocity or +angular momentum for atoms in the group each timestep. In other +words, the force and torque on the atoms is ignored and their velocity +and angular momentum are not updated. The atom velocities and +angularm momenta are used to update their positions and orientation. +

    +

    This is useful as an implicit time integrator for Fast Lubrication +Dynamics, since the velocity and angular momentum are updated by the +pair_style lubricuteU command. +

    +
    + +

    Restart, fix_modify, output, run start/stop, minimize info: +

    +

    No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various output +commands. No parameter of this fix can +be used with the start/stop keywords of the run command. +This fix is not invoked during energy minimization. +

    +

    Restrictions: +

    +

    This fix is part of the ASPHERE package. It is only enabled if LAMMPS +was built with that package. See the Making +LAMMPS section for more info. +

    +

    This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the atom_style ellipsoid +command. +

    +

    All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical as defined by their +shape attribute. +

    +

    Related commands: +

    +

    fix nve/noforce, fix +nve/asphere +

    +

    Default: none +

    + diff --git a/doc/fix_nve_asphere_noforce.txt b/doc/fix_nve_asphere_noforce.txt new file mode 100755 index 0000000000..bc7bc698d2 --- /dev/null +++ b/doc/fix_nve_asphere_noforce.txt @@ -0,0 +1,65 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix nve/asphere/noforce command :h3 + +[Syntax:] + +fix ID group-ID nve/asphere/noforce :pre + +ID, group-ID are documented in "fix"_fix.html command +nve/asphere/noforce = style name of this fix command :ul + +[Examples:] + +fix 1 all nve/asphere/noforce + +[Description:] + +Perform updates of position and orientation, but not velocity or +angular momentum for atoms in the group each timestep. In other +words, the force and torque on the atoms is ignored and their velocity +and angular momentum are not updated. The atom velocities and +angularm momenta are used to update their positions and orientation. + +This is useful as an implicit time integrator for Fast Lubrication +Dynamics, since the velocity and angular momentum are updated by the +"pair_style lubricuteU"_pair_lubricateU.txt command. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various "output +commands"_Section_howto.html#howto_15. No parameter of this fix can +be used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the ASPHERE package. It is only enabled if LAMMPS +was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the "atom_style ellipsoid"_atom_style.html +command. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical as defined by their +shape attribute. + +[Related commands:] + +"fix nve/noforce"_fix_nve_noforce.html, "fix +nve/asphere"_fix_nve_asphere.html + +[Default:] none diff --git a/doc/fix_wall.html b/doc/fix_wall.html index 8bc4f23aa2..b4612a7f31 100644 --- a/doc/fix_wall.html +++ b/doc/fix_wall.html @@ -40,11 +40,14 @@
  • zero or more keyword/value pairs may be appended -
  • keyword = units +
  • keyword = units or fld 
      units value = lattice or box
     lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units 
+    box = the wall position is defined in simulation box units
+  fld value = yes or no
+    yes = invoke the wall constraint to be compatible with implicit FLD
+    yes = invoke the wall constraint in the normal way
    @@ -162,6 +165,13 @@ A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacings.

    +

    The fld keyword can be used with a yes setting to invoke the wall +constraint before pairwise interactions are computed. This allows an +implicit FLD model using pair_style lubricateU +to include the wall force in its calculations. If the setting is +no, wall forces are imposed after pairwise interactions, in the +usual manner. +

    Here are examples of variable definitions that move the wall position diff --git a/doc/fix_wall.txt b/doc/fix_wall.txt index a3614c2433..14bab6db03 100644 --- a/doc/fix_wall.txt +++ b/doc/fix_wall.txt @@ -28,10 +28,13 @@ face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l sigma = size factor for wall-particle interaction (distance units) cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre zero or more keyword/value pairs may be appended :l -keyword = {units} :l +keyword = {units} or {fld} :l {units} value = {lattice} or {box} {lattice} = the wall position is defined in lattice units - {box} = the wall position is defined in simulation box units :pre + {box} = the wall position is defined in simulation box units + {fld} value = {yes} or {no} + {yes} = invoke the wall constraint to be compatible with implicit FLD + {yes} = invoke the wall constraint in the normal way :pre :ule [Examples:] @@ -148,6 +151,13 @@ A {lattice} value means the distance units are in lattice spacings. The "lattice"_lattice.html command must have been previously used to define the lattice spacings. +The {fld} keyword can be used with a {yes} setting to invoke the wall +constraint before pairwise interactions are computed. This allows an +implicit FLD model using "pair_style lubricateU"_pair_lubricateU.html +to include the wall force in its calculations. If the setting is +{no}, wall forces are imposed after pairwise interactions, in the +usual manner. + :line Here are examples of variable definitions that move the wall position diff --git a/doc/fix_wall_reflect.txt b/doc/fix_wall_reflect.txt index 6e7a07f573..197f84bc25 100644 --- a/doc/fix_wall_reflect.txt +++ b/doc/fix_wall_reflect.txt @@ -94,16 +94,16 @@ in a time-dependent fashion using equal-style "variables"_variable.html. variable ramp equal ramp(0,10) -fix 1 all wall xlo v_ramp 1.0 1.0 2.5 :pre +fix 1 all wall xlo v_ramp :pre variable linear equal vlinear(0,20) -fix 1 all wall xlo v_linear 1.0 1.0 2.5 :pre +fix 1 all wall xlo v_linear :pre variable wiggle equal swiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 :pre +fix 1 all wall xlo v_wiggle :pre variable wiggle equal cwiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 :pre +fix 1 all wall xlo v_wiggle :pre The ramp(lo,hi) function adjusts the wall position linearly from lo to hi over the course of a run. The linear(c0,velocity) function does diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html index 750a34767b..ffec9ec605 100644 --- a/doc/pair_coeff.html +++ b/doc/pair_coeff.html @@ -91,6 +91,8 @@ the pair_style command, and coefficients specified by the associated

  • pair_style airebo - AIREBO potential of Stuart
  • pair_style born - Born-Mayer-Huggins potential
  • pair_style born/coul/long - Born-Mayer-Huggins with long-range Coulomb +
  • pair_style brownian - Brownian potential for Fast Lubrication Dynamics +
  • pair_style brownian/poly - Brownian potential for Fast Lubrication Dynamics with polydispersity
  • pair_style buck - Buckingham potential
  • pair_style buck/coul/cut - Buckingham with cutoff Coulomb
  • pair_style buck/coul/long - Buckingham with long-range Coulomb @@ -131,6 +133,9 @@ the pair_style command, and coefficients specified by the associated
  • pair_style lj/smooth - smoothed Lennard-Jones potential
  • pair_style lj96/cut - Lennard-Jones 9/6 potential
  • pair_style lubricate - hydrodynamic lubrication forces +
  • pair_style lubricate/poly - hydrodynamic lubrication forces with polydispersity +
  • pair_style lubricateU - hydrodynamic lubrication forces for Fast Lubrication Dynamics +
  • pair_style lubricateU/poly - hydrodynamic lubrication forces for Fast Lubrication Dynamics with polydispersity
  • pair_style meam - modified embedded atom method (MEAM)
  • pair_style morse - Morse potential
  • pair_style peri/lps - peridynamic LPS potential diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt index 02aebc35f6..c9b9881946 100644 --- a/doc/pair_coeff.txt +++ b/doc/pair_coeff.txt @@ -88,6 +88,8 @@ the pair_style command, and coefficients specified by the associated "pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart "pair_style born"_pair_born.html - Born-Mayer-Huggins potential "pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulomb +"pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics +"pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity "pair_style buck"_pair_buck.html - Buckingham potential "pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb "pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb @@ -128,6 +130,9 @@ the pair_style command, and coefficients specified by the associated "pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential "pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential "pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces +"pair_style lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity +"pair_style lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics +"pair_style lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics with polydispersity "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) "pair_style morse"_pair_morse.html - Morse potential "pair_style peri/lps"_pair_peri.html - peridynamic LPS potential diff --git a/doc/pair_lubricate.html b/doc/pair_lubricate.html deleted file mode 100644 index 0605657b2c..0000000000 --- a/doc/pair_lubricate.html +++ /dev/null @@ -1,178 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lubricate command -

    -

    pair_style lubricate/omp command -

    -

    Syntax: -

    -
    pair_style lubricate mu squeeze shear pump twist cutinner cutoff T_target seed 
-
    - -

    Examples: -

    -
    pair_style lubricate 1.5 1 1 1 0 2.3 2.4 1.3 5878598
-pair_coeff 1 1 1.8 2.0
-pair_coeff * * 
-
    -
    pair_style lubricate 1.0 1 1 1 0 2.3 2.4 1.3 5878598
-pair_coeff * *
-variable mu equal ramp(1,2)
-fix 1 all adapt 1 pair lubricate mu * * v_mu 
-
    -

    Description: -

    -

    Style lubricate computes pairwise interactions between mono-disperse -spherical particles via this formula from (Ball and Melrose) -

    -
    -
    -

    which represents the dissipation W between two nearby particles due to -their relative velocities in the presence of a background solvent with -viscosity mu. Note that this is dynamic viscosity which has units of -mass/distance/time, not kinematic viscosity. -

    -

    The viscosity mu can be varied in a time-dependent manner over the -course of a simluation, in which case in which case the pair_style -setting for mu will be overridden. See the fix adapt -command for details. -

    -

    Rc is the outer cutoff specified in the pair_style command, the -translational velocities of the 2 particles are v1 and v2, the angular -velocities are w1 and w2, and n is the unit vector in the direction -from particle 1 to 2. The 4 terms represent four modes of pairwise -interaction: squeezing, shearing, pumping, and twisting. The 4 flags -in the pair_style command turn on or off each of these modes by -including or excluding each term. The 4 coefficients on each term are -functions of the separation distance of the particles and the -viscosity. Details are given in (Ball and Melrose), including -the forces and torques that result from taking derivatives of this -equation with respect to velocity (see Appendix A). -

    -

    Unlike most pair potentials, the two specified cutoffs (cutinner and -cutoff) refer to the surface-to-surface separation between two -particles, not center-to-center distance. Currently, this pair style -can only be used for mono-disperse extended spheres (same radii), so -that separation is r_ij - 2*radius, where r_ij is the center-to-center -distance between the particles. Within the inner cutoff cutinner, -the forces and torques are evaluated at a separation of cutinner. The -outer cutoff is the separation distance beyond which the pair-wise -forces are zero. -

    -

    A Langevin thermostatting term is also added to the pairwise force, -similar to that provided by the fix langevin or -pair_style dpd commands. The target temperature for -the thermostat is the specified T_target. The seed is used for -the random numbers generated for the thermostat. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    - -

    The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair_style command are used. Otherwise both -must be specified. -

    -
    - -

    Styles with a cuda, gpu, 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 hardware, -as discussed in this section of the manual. -The accelerated styles take the same arguments and should produce the -same results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT -packages, respectively. They are only enabled if LAMMPS was built with -those packages. See the Making LAMMPS -section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See this section of the manual for more -instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the two cutoff distances for this -pair style can be mixed. The default mix value is geometric. See -the "pair_modify" command for details. -

    -

    This pair style does not support the pair_modify -shift option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    This pair style requires that atoms be finite-size spheres with a -diameter, as defined by the atom_style sphere -command. -

    -

    Per-particle or per-type polydispersity is not yet supported by this -pair style; all particles must have the same diameter. -

    -

    This pair style requires you to use the communicate vel -yes option so that velocites are stored by ghost -atoms. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Ball) Ball and Melrose, Physica A, 247, 444-472 (1997). -

    - diff --git a/doc/pair_lubricate.txt b/doc/pair_lubricate.txt deleted file mode 100644 index c244dae435..0000000000 --- a/doc/pair_lubricate.txt +++ /dev/null @@ -1,171 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -pair_style lubricate command :h3 -pair_style lubricate/omp command :h3 - -[Syntax:] - -pair_style lubricate mu squeeze shear pump twist cutinner cutoff T_target seed :pre - -mu = dynamic viscosity (dynamic viscosity units) -squeeze = 0/1 for squeeze force off/on -shear = 0/1 for shear force off/on -pump = 0/1 for pump force off/on -twist = 0/1 for twist force off/on -cutinner = (distance units) -cutoff = outer cutoff for interactions (distance units) -T_target = desired temperature (temperature units) -seed = random number seed (positive integer) :ul - -[Examples:] - -pair_style lubricate 1.5 1 1 1 0 2.3 2.4 1.3 5878598 -pair_coeff 1 1 1.8 2.0 -pair_coeff * * :pre - -pair_style lubricate 1.0 1 1 1 0 2.3 2.4 1.3 5878598 -pair_coeff * * -variable mu equal ramp(1,2) -fix 1 all adapt 1 pair lubricate mu * * v_mu :pre - -[Description:] - -Style {lubricate} computes pairwise interactions between mono-disperse -spherical particles via this formula from "(Ball and Melrose)"_#Ball - -:c,image(Eqs/pair_lubricate.jpg) - -which represents the dissipation W between two nearby particles due to -their relative velocities in the presence of a background solvent with -viscosity mu. Note that this is dynamic viscosity which has units of -mass/distance/time, not kinematic viscosity. - -The viscosity mu can be varied in a time-dependent manner over the -course of a simluation, in which case in which case the pair_style -setting for mu will be overridden. See the "fix adapt"_fix_adapt.html -command for details. - -Rc is the outer cutoff specified in the pair_style command, the -translational velocities of the 2 particles are v1 and v2, the angular -velocities are w1 and w2, and n is the unit vector in the direction -from particle 1 to 2. The 4 terms represent four modes of pairwise -interaction: squeezing, shearing, pumping, and twisting. The 4 flags -in the pair_style command turn on or off each of these modes by -including or excluding each term. The 4 coefficients on each term are -functions of the separation distance of the particles and the -viscosity. Details are given in "(Ball and Melrose)"_#Ball, including -the forces and torques that result from taking derivatives of this -equation with respect to velocity (see Appendix A). - -Unlike most pair potentials, the two specified cutoffs (cutinner and -cutoff) refer to the surface-to-surface separation between two -particles, not center-to-center distance. Currently, this pair style -can only be used for mono-disperse extended spheres (same radii), so -that separation is r_ij - 2*radius, where r_ij is the center-to-center -distance between the particles. Within the inner cutoff {cutinner}, -the forces and torques are evaluated at a separation of cutinner. The -outer {cutoff} is the separation distance beyond which the pair-wise -forces are zero. - -A Langevin thermostatting term is also added to the pairwise force, -similar to that provided by the "fix langevin"_fix_langevin.html or -"pair_style dpd"_pair_dpd.html commands. The target temperature for -the thermostat is the specified {T_target}. The {seed} is used for -the random numbers generated for the thermostat. - -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: - -cutinner (distance units) -cutoff (distance units) :ul - -The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair_style command are used. Otherwise both -must be specified. - -:line - -Styles with a {cuda}, {gpu}, {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 hardware, -as discussed in "this section"_Section_accelerate.html of the manual. -The accelerated styles take the same arguments and should produce the -same results, except for round-off and precision issues. - -These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT -packages, respectively. They are only enabled if LAMMPS was built with -those packages. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. - -See "this section"_Section_accelerate.html of the manual for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the two cutoff distances for this -pair style can be mixed. The default mix value is {geometric}. See -the "pair_modify" command for details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its 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. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. - -This pair style requires that atoms be finite-size spheres with a -diameter, as defined by the "atom_style sphere"_atom_style.html -command. - -Per-particle or per-type polydispersity is not yet supported by this -pair style; all particles must have the same diameter. - -This pair style requires you to use the "communicate vel -yes"_communicate.html option so that velocites are stored by ghost -atoms. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Ball) -[(Ball)] Ball and Melrose, Physica A, 247, 444-472 (1997). diff --git a/doc/pair_style.html b/doc/pair_style.html index b00d2360e5..82720df044 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -93,6 +93,8 @@ the pair_style command, and coefficients specified by the associated
  • pair_style airebo - AIREBO potential of Stuart
  • pair_style born - Born-Mayer-Huggins potential
  • pair_style born/coul/long - Born-Mayer-Huggins with long-range Coulomb +
  • pair_style brownian - Brownian potential for Fast Lubrication Dynamics +
  • pair_style brownian/poly - Brownian potential for Fast Lubrication Dynamics with polydispersity
  • pair_style buck - Buckingham potential
  • pair_style buck/coul/cut - Buckingham with cutoff Coulomb
  • pair_style buck/coul/long - Buckingham with long-range Coulomb @@ -133,6 +135,9 @@ the pair_style command, and coefficients specified by the associated
  • pair_style lj/smooth - smoothed Lennard-Jones potential
  • pair_style lj96/cut - Lennard-Jones 9/6 potential
  • pair_style lubricate - hydrodynamic lubrication forces +
  • pair_style lubricate/poly - hydrodynamic lubrication forces with polydispersity +
  • pair_style lubricateU - hydrodynamic lubrication forces for Fast Lubrication Dynamics +
  • pair_style lubricateU/poly - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
  • pair_style meam - modified embedded atom method (MEAM)
  • pair_style morse - Morse potential
  • pair_style peri/lps - peridynamic LPS potential diff --git a/doc/pair_style.txt b/doc/pair_style.txt index c450e3272a..4b23d62068 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -90,6 +90,8 @@ the pair_style command, and coefficients specified by the associated "pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart "pair_style born"_pair_born.html - Born-Mayer-Huggins potential "pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulomb +"pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics +"pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity "pair_style buck"_pair_buck.html - Buckingham potential "pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb "pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb @@ -130,6 +132,9 @@ the pair_style command, and coefficients specified by the associated "pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential "pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential "pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces +"pair_style lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity +"pair_style lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics +"pair_style lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) "pair_style morse"_pair_morse.html - Morse potential "pair_style peri/lps"_pair_peri.html - peridynamic LPS potential