From 55af408961c4bf8a5dad399902591a63fa391c50 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 14 Jan 2009 14:29:55 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2473 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_intro.html | 20 ++++++++++---------- doc/Section_intro.txt | 18 +++++++++--------- doc/bond_fene.html | 6 +++--- doc/bond_fene.txt | 6 +++--- doc/bond_fene_expand.html | 6 +++--- doc/bond_fene_expand.txt | 6 +++--- doc/pair_eam.html | 4 +++- doc/pair_eam.txt | 4 +++- 8 files changed, 37 insertions(+), 33 deletions(-) diff --git a/doc/Section_intro.html b/doc/Section_intro.html index f56ebd4ba7..f560c86ff9 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -98,8 +98,8 @@ favorite interatomic potential, boundary condition, or atom type, see this section, which describes how you can add it to LAMMPS.

-

General features: h4 -

+

General features +

-

Kinds of systems LAMMPS can simulate: +

Kinds of systems LAMMPS can simulate

(atom style command)

@@ -128,7 +128,7 @@ LAMMPS.
  • point dipolar particles
  • hybrid combinations of these -

    Force fields: +

    Force fields

    (pair style, bond style, angle style, dihedral style, @@ -150,9 +150,9 @@ commands)

  • water potentials: TIP3P, TIP4P, SPC
  • implicit solvent potentials: hydrodynamic lubrication, Debye
  • long-range Coulombics and dispersion: Ewald, PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones -
  • CHARMM, AMBER, OPLS, GROMACS, force-field compatibility +
  • force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options -

    Creation of atoms: +

    Creation of atoms

    (read_data, lattice, create_atoms, delete_atoms, @@ -163,7 +163,7 @@ commands)

  • delete geometric or logical groups of atoms (e.g. voids)
  • displace atoms -

    Ensembles, constraints, and boundary conditions: +

    Ensembles, constraints, and boundary conditions

    (fix command)

    @@ -182,7 +182,7 @@ commands)
  • non-equilibrium molecular dynamics (NEMD)
  • variety of additional boundary conditions and constraints -

    Integrators: +

    Integrators

    (run, run_style, temper commands)

    @@ -192,7 +192,7 @@ commands)
  • rRESPA hierarchical timestepping
  • parallel tempering (replica exchange) -

    Output: +

    Output

    (dump, restart commands)

    @@ -205,7 +205,7 @@ commands)
  • time averaging of system-wide quantities
  • atom snapshots in native, XYZ, XTC, DCD formats -

    Pre- and post-processing: +

    Pre- and post-processing

    Our group has also written and released a separate toolkit called Pizza.py which provides tools for doing setup, analysis, diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index 982399b30c..bb9afb0e58 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -95,7 +95,7 @@ favorite interatomic potential, boundary condition, or atom type, see "this section"_Section_modify.html, which describes how you can add it to LAMMPS. -General features: h4 +General features :h4 runs on a single processor or in parallel distributed-memory message-passing parallelism (MPI) @@ -110,7 +110,7 @@ General features: h4 syntax for looping over runs and breaking out of loops run a series of simluations from one script :ul -Kinds of systems LAMMPS can simulate: :h4 +Kinds of systems LAMMPS can simulate :h4 ("atom style"_atom_style.html command) atomic (e.g. box of Lennard-Jonesium) @@ -124,7 +124,7 @@ Kinds of systems LAMMPS can simulate: :h4 point dipolar particles hybrid combinations of these :ul -Force fields: :h4 +Force fields :h4 ("pair style"_pair_style.html, "bond style"_bond_style.html, "angle style"_angle_style.html, "dihedral style"_dihedral_style.html, "improper style"_improper_style.html, "kspace style"_kspace_style.html @@ -152,9 +152,9 @@ commands) implicit solvent potentials: hydrodynamic lubrication, Debye long-range Coulombics and dispersion: Ewald, \ PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones - CHARMM, AMBER, OPLS, GROMACS, force-field compatibility :ul + force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options :ul -Creation of atoms: :h4 +Creation of atoms :h4 ("read_data"_read_data.html, "lattice"_lattice.html, "create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html, "displace_atoms"_displace_atoms.html commands) @@ -164,7 +164,7 @@ Creation of atoms: :h4 delete geometric or logical groups of atoms (e.g. voids) displace atoms :ul -Ensembles, constraints, and boundary conditions: :h4 +Ensembles, constraints, and boundary conditions :h4 ("fix"_fix.html command) 2d or 3d systems @@ -182,7 +182,7 @@ Ensembles, constraints, and boundary conditions: :h4 non-equilibrium molecular dynamics (NEMD) variety of additional boundary conditions and constraints :ul -Integrators: :h4 +Integrators :h4 ("run"_run.html, "run_style"_run_style.html, "temper"_temper.html commands) velocity-Verlet integrator @@ -191,7 +191,7 @@ Integrators: :h4 rRESPA hierarchical timestepping parallel tempering (replica exchange) :ul -Output: :h4 +Output :h4 ("dump"_dump.html, "restart"_restart.html commands) log file of thermodynamic info @@ -203,7 +203,7 @@ Output: :h4 time averaging of system-wide quantities atom snapshots in native, XYZ, XTC, DCD formats :ul -Pre- and post-processing: :h4 +Pre- and post-processing :h4 Our group has also written and released a separate toolkit called "Pizza.py"_pizza which provides tools for doing setup, analysis, diff --git a/doc/bond_fene.html b/doc/bond_fene.html index 49fe2823c6..4dcc2447f8 100644 --- a/doc/bond_fene.html +++ b/doc/bond_fene.html @@ -48,9 +48,9 @@ or read_restart commands: "molecular" package (which it is by default). See the Making LAMMPS section for more info on packages.

    -

    You typically should specify special_bonds 0 1 1 -to use this bond style. LAMMPS will issue a warning it that's not the -case. +

    You typically should specify special_bonds fene +or special_bonds lj/coul 0 1 1 to use this bond +style. LAMMPS will issue a warning it that's not the case.

    Related commands:

    diff --git a/doc/bond_fene.txt b/doc/bond_fene.txt index 78f399e8fd..8d0ab6c254 100644 --- a/doc/bond_fene.txt +++ b/doc/bond_fene.txt @@ -45,9 +45,9 @@ This bond style can only be used if LAMMPS was built with the "molecular" package (which it is by default). See the "Making LAMMPS"_Section_start.html#2_3 section for more info on packages. -You typically should specify "special_bonds 0 1 1"_special_bonds.html -to use this bond style. LAMMPS will issue a warning it that's not the -case. +You typically should specify "special_bonds fene"_special_bonds.html" +or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond +style. LAMMPS will issue a warning it that's not the case. [Related commands:] diff --git a/doc/bond_fene_expand.html b/doc/bond_fene_expand.html index 586f9b91e5..190e14ca31 100644 --- a/doc/bond_fene_expand.html +++ b/doc/bond_fene_expand.html @@ -53,9 +53,9 @@ or read_restart commands: "molecular" package (which it is by default). See the Making LAMMPS section for more info on packages.

    -

    You typically should specify special_bonds 0 1 1 -to use this bond style. LAMMPS will issue a warning it that's not the -case. +

    You typically should specify special_bonds fene +or special_bonds lj/coul 0 1 1 to use this bond +style. LAMMPS will issue a warning it that's not the case.

    Related commands:

    diff --git a/doc/bond_fene_expand.txt b/doc/bond_fene_expand.txt index 142766ff86..b12bb6de07 100644 --- a/doc/bond_fene_expand.txt +++ b/doc/bond_fene_expand.txt @@ -50,9 +50,9 @@ This bond style can only be used if LAMMPS was built with the "molecular" package (which it is by default). See the "Making LAMMPS"_Section_start.html#2_3 section for more info on packages. -You typically should specify "special_bonds 0 1 1"_special_bonds.html -to use this bond style. LAMMPS will issue a warning it that's not the -case. +You typically should specify "special_bonds fene"_special_bonds.html" +or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond +style. LAMMPS will issue a warning it that's not the case. [Related commands:] diff --git a/doc/pair_eam.html b/doc/pair_eam.html index 1fb8315ca9..c079ae01e2 100644 --- a/doc/pair_eam.html +++ b/doc/pair_eam.html @@ -90,7 +90,9 @@ http://enpub.fulton.asu.edu/cms/potentials/main/main.htm

    These potentials should be usable with LAMMPS, though the alternate formats would need to be converted to the DYNAMO format used by LAMMPS -and described on this page. +and described on this page. The NIST site is maintained by Chandler +Becker (cbecker at nist.gov) who is good resource for info on +interatomic potentials and file formats.

    diff --git a/doc/pair_eam.txt b/doc/pair_eam.txt index d7d3553fdb..46f0ce150e 100644 --- a/doc/pair_eam.txt +++ b/doc/pair_eam.txt @@ -82,7 +82,9 @@ http://enpub.fulton.asu.edu/cms/potentials/main/main.htm :pre These potentials should be usable with LAMMPS, though the alternate formats would need to be converted to the DYNAMO format used by LAMMPS -and described on this page. +and described on this page. The NIST site is maintained by Chandler +Becker (cbecker at nist.gov) who is good resource for info on +interatomic potentials and file formats. :line