From a21d4e4817af443e8a376bcc46804abedbff02c2 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 5 Sep 2007 16:05:47 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@830 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 8 ++--- doc/Section_commands.txt | 1 + doc/fix.html | 1 + doc/fix.txt | 1 + doc/fix_nve_limit.html | 72 +++++++++++++++++++++++++++++++++++++++ doc/fix_nve_limit.txt | 67 ++++++++++++++++++++++++++++++++++++ doc/pair_soft.html | 5 +-- doc/pair_soft.txt | 5 +-- 8 files changed, 152 insertions(+), 8 deletions(-) create mode 100644 doc/fix_nve_limit.html create mode 100644 doc/fix_nve_limit.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 18a771c79b..a0c45a432e 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -321,10 +321,10 @@ description: addforceaveforceave/spatialave/timecomdeformdepositdrag efieldenforce2dfreezegran/diaggravitygyrationheatindent langevinlineforcemsdmomentumnphnptnpt/aspherenve -nve/aspherenve/dipolenve/grannve/noforcenvtnvt/aspherenvt/sllodorient/fcc -planeforcepoemspourprintrdfrecenterrigidsetforce -shakespringspring/rgspring/selftemp/rescaletmdviscouswall/gran -wall/lj126wall/lj93wall/reflectwiggle +nve/aspherenve/dipolenve/grannve/limitnve/noforcenvtnvt/aspherenvt/sllod +orient/fccplaneforcepoemspourprintrdfrecenterrigid +setforceshakespringspring/rgspring/selftemp/rescaletmdviscous +wall/granwall/lj126wall/lj93wall/reflectwiggle
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 2f61764647..36251751c4 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -403,6 +403,7 @@ description: "nve/asphere"_fix_nve_asphere.html, "nve/dipole"_fix_nve_dipole.html, "nve/gran"_fix_nve_gran.html, +"nve/limit"_fix_nve_limit.html, "nve/noforce"_fix_nve_noforce.html, "nvt"_fix_nvt.html, "nvt/asphere"_fix_nvt_asphere.html, diff --git a/doc/fix.html b/doc/fix.html index 4e4bb699c0..ab40ccc149 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -99,6 +99,7 @@ for individual fixes for info on which ones can be restarted.
  • fix nve/asphere - NVT for aspherical particles
  • fix nve/dipole - NVE for point dipolar particles
  • fix nve/gran - NVE for granular particles +
  • fix nve/limit - NVE with limited step length
  • fix nve/noforce - NVE without forces (v only)
  • fix nvt - constant NVT time integration via Nose/Hoover
  • fix nvt/asphere - NVT for aspherical particles diff --git a/doc/fix.txt b/doc/fix.txt index 05ad174ece..b6eafa05d4 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -98,6 +98,7 @@ Here is an alphabetic list of fix styles available in LAMMPS: "fix nve/asphere"_fix_nve_asphere.html - NVT for aspherical particles "fix nve/dipole"_fix_nve_dipole.html - NVE for point dipolar particles "fix nve/gran"_fix_nve_gran.html - NVE for granular particles +"fix nve/limit"_fix_nve_limit.html - NVE with limited step length "fix nve/noforce"_fix_nve_noforce.html - NVE without forces (v only) "fix nvt"_fix_nvt.html - constant NVT time integration via Nose/Hoover "fix nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles diff --git a/doc/fix_nve_limit.html b/doc/fix_nve_limit.html new file mode 100644 index 0000000000..945bc8ac82 --- /dev/null +++ b/doc/fix_nve_limit.html @@ -0,0 +1,72 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    fix nve/limit command +

    +

    Syntax: +

    +
    fix ID group-ID nve/limit xmax 
+
    + +

    Examples: +

    +
    fix 1 all nve/limit 0.1 
+
    +

    Description: +

    +

    Perform constant NVE updates of position and velocity for atoms in the +group each timestep. A limit is imposed on the maximum distance an +atom can move in one timestep. This is useful when starting a +simulation with a configuration containing highly overlapped atoms. +Normally this would generate huge forces which would blow atoms out of +the simulation box, causing LAMMPS to stop with an error. +

    +

    Using this fix can overcome that problem. Forces on atoms must still +be computable (which typically means 2 atoms must have a separation +distance > 0.0). But large velocities generated by large forces are +reset to a value that corresponds to a displacement of length xmax +in a single timestep. Xmax is specified in distance units; see the +units command for details. The value of xmax should be +consistent with the neighbor skin distance and the frequency of +neighbor list re-building, so that pairwise interactions are not +missed on successive timesteps as atoms move. See the +neighbor and neigh_modify commands +for details. +

    +

    Note that if a velocity reset occurs the integrator will not conserve +energy. On steps where no velocity resets occur, this integrator is +exactly like the fix nve command. Since forces are +unaltered, pressures computed by thermodynamic output will still be +very large for overlapped configurations. +

    +

    Restart, fix_modify, thermo 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 quantities calculated by this fix can be +output by the thermo_style custom command. 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: none +

    +

    Related commands: +

    +

    fix nve, fix nve/noforce, +pair_style soft +

    +

    Default: none +

    + diff --git a/doc/fix_nve_limit.txt b/doc/fix_nve_limit.txt new file mode 100644 index 0000000000..2555580f4e --- /dev/null +++ b/doc/fix_nve_limit.txt @@ -0,0 +1,67 @@ +"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/limit command :h3 + +[Syntax:] + +fix ID group-ID nve/limit xmax :pre + +ID, group-ID are documented in "fix"_fix.html command +nve = style name of this fix command +xmax = maximum distance an atom can move in one timestep (distance units) :ul + +[Examples:] + +fix 1 all nve/limit 0.1 :pre + +[Description:] + +Perform constant NVE updates of position and velocity for atoms in the +group each timestep. A limit is imposed on the maximum distance an +atom can move in one timestep. This is useful when starting a +simulation with a configuration containing highly overlapped atoms. +Normally this would generate huge forces which would blow atoms out of +the simulation box, causing LAMMPS to stop with an error. + +Using this fix can overcome that problem. Forces on atoms must still +be computable (which typically means 2 atoms must have a separation +distance > 0.0). But large velocities generated by large forces are +reset to a value that corresponds to a displacement of length {xmax} +in a single timestep. {Xmax} is specified in distance units; see the +"units"_units.html command for details. The value of {xmax} should be +consistent with the neighbor skin distance and the frequency of +neighbor list re-building, so that pairwise interactions are not +missed on successive timesteps as atoms move. See the +"neighbor"_neighbor.html and "neigh_modify"_neigh_modify.html commands +for details. + +Note that if a velocity reset occurs the integrator will not conserve +energy. On steps where no velocity resets occur, this integrator is +exactly like the "fix nve"_fix_nve.html command. Since forces are +unaltered, pressures computed by thermodynamic output will still be +very large for overlapped configurations. + +[Restart, fix_modify, thermo 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 quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. 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:] none + +[Related commands:] + +"fix nve"_fix_nve.html, "fix nve/noforce"_fix_nve_noforce.html, +"pair_style soft"_pair_soft.html + +[Default:] none diff --git a/doc/pair_soft.html b/doc/pair_soft.html index 098d2de85b..caeaaea2f2 100644 --- a/doc/pair_soft.html +++ b/doc/pair_soft.html @@ -33,7 +33,8 @@ pair_coeff 1 1 0.0 60.0 3.0 blow up as r goes to 0. A is a pre-factor that varies in time from the start to the end of the run. The run command documents how to make the ramping take place across multiple runs. Rc is the -cutoff. +cutoff. See the fix nve/limit command for +another way to push apart overlapping atoms.

    The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples @@ -86,7 +87,7 @@ to be specified in an input script that reads a restart file.

    Related commands:

    -

    pair_coeff +

    pair_coeff, fix nve/limit

    Default: none

    diff --git a/doc/pair_soft.txt b/doc/pair_soft.txt index 6894ced294..36a04a2c00 100644 --- a/doc/pair_soft.txt +++ b/doc/pair_soft.txt @@ -30,7 +30,8 @@ It is useful for pushing apart overlapping atoms, since it does not blow up as r goes to 0. A is a pre-factor that varies in time from the start to the end of the run. The "run"_run.html command documents how to make the ramping take place across multiple runs. Rc is the -cutoff. +cutoff. See the "fix nve/limit"_fix_nve_limit.html command for +another way to push apart overlapping atoms. The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples @@ -83,6 +84,6 @@ to be specified in an input script that reads a restart file. [Related commands:] -"pair_coeff"_pair_coeff.html +"pair_coeff"_pair_coeff.html, "fix nve/limit"_fix_nve_limit.html [Default:] none