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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2473 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-01-14 14:29:55 +00:00
parent ba4f46785b
commit 55af408961
8 changed files with 37 additions and 33 deletions
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20
doc/Section_intro.html
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@ -98,8 +98,8 @@ favorite interatomic potential, boundary condition, or atom type, see
<A HREF = "Section_modify.html">this section</A>, which describes how you can add it to
LAMMPS.
</P>
<P>General features: h4
</P>
<H4>General features
</H4>
<UL><LI> runs on a single processor or in parallel
<LI> distributed-memory message-passing parallelism (MPI)
<LI> spatial-decomposition of simulation domain for parallelism
@ -113,7 +113,7 @@ LAMMPS.
<LI> syntax for looping over runs and breaking out of loops
<LI> run a series of simluations from one script
</UL>
<H4>Kinds of systems LAMMPS can simulate:
<H4>Kinds of systems LAMMPS can simulate
</H4>
<P>(<A HREF = "atom_style.html">atom style</A> command)
</P>
@ -128,7 +128,7 @@ LAMMPS.
<LI> point dipolar particles
<LI> hybrid combinations of these
</UL>
<H4>Force fields:
<H4>Force fields
</H4>
<P>(<A HREF = "pair_style.html">pair style</A>, <A HREF = "bond_style.html">bond style</A>,
<A HREF = "angle_style.html">angle style</A>, <A HREF = "dihedral_style.html">dihedral style</A>,
@ -150,9 +150,9 @@ commands)
<LI> water potentials: TIP3P, TIP4P, SPC
<LI> implicit solvent potentials: hydrodynamic lubrication, Debye
<LI> long-range Coulombics and dispersion: Ewald, PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
<LI> CHARMM, AMBER, OPLS, GROMACS, force-field compatibility
<LI> force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options
</UL>
<H4>Creation of atoms:
<H4>Creation of atoms
</H4>
<P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,
<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,
@ -163,7 +163,7 @@ commands)
<LI> delete geometric or logical groups of atoms (e.g. voids)
<LI> displace atoms
</UL>
<H4>Ensembles, constraints, and boundary conditions:
<H4>Ensembles, constraints, and boundary conditions
</H4>
<P>(<A HREF = "fix.html">fix</A> command)
</P>
@ -182,7 +182,7 @@ commands)
<LI> non-equilibrium molecular dynamics (NEMD)
<LI> variety of additional boundary conditions and constraints
</UL>
<H4>Integrators:
<H4>Integrators
</H4>
<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "temper.html">temper</A> commands)
</P>
@ -192,7 +192,7 @@ commands)
<LI> rRESPA hierarchical timestepping
<LI> parallel tempering (replica exchange)
</UL>
<H4>Output:
<H4>Output
</H4>
<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
</P>
@ -205,7 +205,7 @@ commands)
<LI> time averaging of system-wide quantities
<LI> atom snapshots in native, XYZ, XTC, DCD formats
</UL>
<H4>Pre- and post-processing:
<H4>Pre- and post-processing
</H4>
<P>Our group has also written and released a separate toolkit called
<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,

18
doc/Section_intro.txt
View File

@ -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,

6
doc/bond_fene.html
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@ -48,9 +48,9 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>You typically should specify <A HREF = "special_bonds.html">special_bonds 0 1 1</A>
to use this bond style. LAMMPS will issue a warning it that's not the
case.
<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
style. LAMMPS will issue a warning it that's not the case.
</P>
<P><B>Related commands:</B>
</P>

6
doc/bond_fene.txt
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@ -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:]

6
doc/bond_fene_expand.html
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@ -53,9 +53,9 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>You typically should specify <A HREF = "special_bonds.html">special_bonds 0 1 1</A>
to use this bond style. LAMMPS will issue a warning it that's not the
case.
<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
style. LAMMPS will issue a warning it that's not the case.
</P>
<P><B>Related commands:</B>
</P>

6
doc/bond_fene_expand.txt
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@ -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:]

4
doc/pair_eam.html
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@ -90,7 +90,9 @@ http://enpub.fulton.asu.edu/cms/potentials/main/main.htm
</PRE>
<P>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.
</P>
<HR>

4
doc/pair_eam.txt
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@ -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