From fd1e84f5bb294b5cb7e6eede716caf6ca006f0eb Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 20 Aug 2010 00:37:59 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4541 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_qeq_comb.html | 115 ++++++++++++++++++++++++++++++++++++++++++ doc/fix_qeq_comb.txt | 99 ++++++++++++++++++++++++++++++++++++ 2 files changed, 214 insertions(+) create mode 100644 doc/fix_qeq_comb.html create mode 100644 doc/fix_qeq_comb.txt diff --git a/doc/fix_qeq_comb.html b/doc/fix_qeq_comb.html new file mode 100644 index 0000000000..e9c854f163 --- /dev/null +++ b/doc/fix_qeq_comb.html @@ -0,0 +1,115 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

fix qeq/comb command +

+

Syntax: +

+
fix ID group-ID qeq/comb Nevery precision keyword value ... 
+
+ +

Examples: +

+
fix 1 surface qeq/comb 10 0.0001 
+
+

Description: +

+

This fix is designed for use with the pair_style comb command which +implements the COMB COMB (Charge-Optimized Many-Body) potential as +described in (COMB_1) and (COMB_2). It performs +the charge equilibration portion of the calculation using the +so-called QEq method, whereby the charge on each atom is adjusted to +minimize the energy of the system. +

+

Only charges on the atoms in the specified group are equilibrated. +The fix relies on the pair style (COMB in this case) to calculate the +per-atom electronegativity (effective force on the charges). An +electronegativity equalization calculation (or QEq) is performed in an +interative fashion, which in parallel requires communication at each +iteration for processors to exchange charge information about nearby +atoms with each other. See Rappe_and_Goddard and +Rick_and_Stuart for details. +

+

During a run, charge equilibration is peformed every Nevery time +steps. Charge equilibration is also always enforced on the first step +of each run. The precision argument controls the tolerance for the +difference in electronegativity for all atoms during charge +equilibration. Precision is a trade-off between the cost of +performing charge equilibration (more iterations) and accuracy. +

+

If the file keyword is used, then information about each +equilibration calculation is written to the specifed file. +

+

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. +

+

This fix produces a per-atom vector which can be accessed by various +output commands. The vector stores the +gradient of the charge on each atom. The per-atom values be accessed +on any timestep. +

+

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 command currently only supports pair style comb. +

+

Related commands: +

+

pair_style comb +

+

Default: +

+

No file output is performed. +

+
+ + + +

(COMB_1) J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007), +

+ + +

(COMB_2) T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R. +Phillpot, Phys Rev B, 81, 125328 (2010). +

+ + +

(Rappe_and_Goddard) A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358 +(1991). +

+ + +

(Rick_and_Stuart) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys +101, 16141 (1994). +

+ diff --git a/doc/fix_qeq_comb.txt b/doc/fix_qeq_comb.txt new file mode 100644 index 0000000000..ee787f0774 --- /dev/null +++ b/doc/fix_qeq_comb.txt @@ -0,0 +1,99 @@ +"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 qeq/comb command :h3 + +[Syntax:] + +fix ID group-ID qeq/comb Nevery precision keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +qeq/comb = style name of this fix command :l +Nevery = perform charge equilibration every this many steps :l +precision = convergence criterion for charge equilibration :l +zero or more keyword/value pairs may be appended :l +keyword = {file} :l + {file} value = filename + filename = name of file to write QEQ equilibration info to :pre +:ule + +[Examples:] + +fix 1 surface qeq/comb 10 0.0001 :pre + +[Description:] + +This fix is designed for use with the pair_style comb command which +implements the COMB COMB (Charge-Optimized Many-Body) potential as +described in "(COMB_1)"_#COMB_1 and "(COMB_2)"_#COMB_2. It performs +the charge equilibration portion of the calculation using the +so-called QEq method, whereby the charge on each atom is adjusted to +minimize the energy of the system. + +Only charges on the atoms in the specified group are equilibrated. +The fix relies on the pair style (COMB in this case) to calculate the +per-atom electronegativity (effective force on the charges). An +electronegativity equalization calculation (or QEq) is performed in an +interative fashion, which in parallel requires communication at each +iteration for processors to exchange charge information about nearby +atoms with each other. See "Rappe_and_Goddard"_#Rappe_and_Goddard and +"Rick_and_Stuart"_#Rick_and_Stuart for details. + +During a run, charge equilibration is peformed every {Nevery} time +steps. Charge equilibration is also always enforced on the first step +of each run. The {precision} argument controls the tolerance for the +difference in electronegativity for all atoms during charge +equilibration. {Precision} is a trade-off between the cost of +performing charge equilibration (more iterations) and accuracy. + +If the {file} keyword is used, then information about each +equilibration calculation is written to the specifed file. + +[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. + +This fix produces a per-atom vector which can be accessed by various +"output commands"_Section_howto.html#4_15. The vector stores the +gradient of the charge on each atom. The per-atom values be accessed +on any timestep. + +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 command currently only supports "pair style {comb}"_pair_comb.html. + +[Related commands:] + +"pair_style comb"_pair_comb.html + +[Default:] + +No file output is performed. + +:line + +:link(COMB_1) +[(COMB_1)] J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007), + +:link(COMB_2) +[(COMB_2)] T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R. +Phillpot, Phys Rev B, 81, 125328 (2010). + +:link(Rappe_and_Goddard) +[(Rappe_and_Goddard)] A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358 +(1991). + +:link(Rick_and_Stuart) +[(Rick_and_Stuart)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys +101, 16141 (1994).