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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4697 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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25
doc/Section_example.html
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@ -32,8 +32,10 @@ Site</A>.
</P> </P>
<DIV ALIGN=center><TABLE BORDER=1 > <DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR> <TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR> <TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR> <TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
<TR><TD >elastic</TD><TD > zero temperature elastic constant tensor of silicon</TD></TR> <TR><TD >elastic</TD><TD > zero temperature elastic constant tensor of silicon</TD></TR>
<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR> <TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR> <TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
@ -43,13 +45,14 @@ Site</A>.
<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR> <TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR> <TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR> <TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR> <TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR> <TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR> <TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
<TR><TD >peri</TD><TD > Peridynamics example of cylinder hit by projectile</TD></TR> <TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR> <TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
<TR><TD >prd</TD><TD > parallel replica dynamics of a vacancy diffusion in bulk Si</TD></TR> <TR><TD >prd</TD><TD > parallel replica dynamics of a vacancy diffusion in bulk Si</TD></TR>
<TR><TD >reax</TD><TD > simple example for ReaxFF force field</TD></TR> <TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR> <TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void <TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void
</TD></TR></TABLE></DIV> </TD></TR></TABLE></DIV>
@ -65,17 +68,13 @@ lmp_linux < in.indent # run the problem
</P> </P>
<PRE>../../tools/xmovie/xmovie -scale dump.indent <PRE>../../tools/xmovie/xmovie -scale dump.indent
</PRE> </PRE>
<P>There is also a directory "couple" in the examples sub-directory, <P>There is also a COUPLE directory which has examples of how to link to
which contains a stand-alone code umbrella.cpp that links LAMMPS as a LAMMPS as a library and drive it from a wrapper program. See the
library. The README describes how to build the code. The code itself README file for more info.
runs LAMMPS on a subset of processors, sets up a LAMMPS problem
by invoking LAMMPS input script commands one at a time, does
a run, grabs atom coordinates, changes one atom position, puts
them back into LAMMPS, and does another run.
</P> </P>
<P>This illustrates how an umbrella code could include new models and <P>There is also a USER directory which contains subdirectories of
physics while using LAMMPS to perform MD, or how the umbrella code user-provided examples for user packages. See the README files in
could call both LAMMPS and some other code to perform a coupled those directories for more info. See the doc/Section_start.html for
calculation. more info about user packages.
</P> </P>
</HTML> </HTML>

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doc/Section_example.txt
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@ -28,8 +28,10 @@ Site"_lws.
These are the sample problems in the examples sub-directories: These are the sample problems in the examples sub-directories:
colloid: big colloid particles in a small particle solvent, 2d system colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential
crack: crack propagation in a 2d solid crack: crack propagation in a 2d solid
dipole: point dipolar particles, 2d system dipole: point dipolar particles, 2d system
eim: NaCl using the EIM potential
elastic: zero temperature elastic constant tensor of silicon elastic: zero temperature elastic constant tensor of silicon
ellipse: ellipsoidal particles in spherical solvent, 2d system ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poiseuille flow in a 2d channel flow: Couette and Poiseuille flow in a 2d channel
@ -39,13 +41,14 @@ meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system melt: rapid melt of 3d LJ system
micelle: self-assembly of small lipid-like molecules into 2d bilayers micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt min: energy minimization of 2d LJ melt
msst: MSST shock dynamics
nemd: non-equilibrium MD of 2d sheared system nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer) peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamics example of cylinder hit by projectile peri: Peridynamic model of cylinder impacted by indenter
pour: pouring of granular particles into a 3d box, then chute flow pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of a vacancy diffusion in bulk Si prd: parallel replica dynamics of a vacancy diffusion in bulk Si
reax: simple example for ReaxFF force field reax: RDX and TATB models using the ReaxFF
rigid: rigid bodies modeled as independent or coupled rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void :tb(s=:) shear: sideways shear applied to 2d solid, with and without a void :tb(s=:)
@ -60,15 +63,11 @@ Running the simulation produces the files {dump.indent} and
../../tools/xmovie/xmovie -scale dump.indent :pre ../../tools/xmovie/xmovie -scale dump.indent :pre
There is also a directory "couple" in the examples sub-directory, There is also a COUPLE directory which has examples of how to link to
which contains a stand-alone code umbrella.cpp that links LAMMPS as a LAMMPS as a library and drive it from a wrapper program. See the
library. The README describes how to build the code. The code itself README file for more info.
runs LAMMPS on a subset of processors, sets up a LAMMPS problem
by invoking LAMMPS input script commands one at a time, does
a run, grabs atom coordinates, changes one atom position, puts
them back into LAMMPS, and does another run.
This illustrates how an umbrella code could include new models and There is also a USER directory which contains subdirectories of
physics while using LAMMPS to perform MD, or how the umbrella code user-provided examples for user packages. See the README files in
could call both LAMMPS and some other code to perform a coupled those directories for more info. See the doc/Section_start.html for
calculation. more info about user packages.

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@ -41,7 +41,6 @@ page</A> on the LAMMPS WWW site for more details.
<LI>Triangulated particles <LI>Triangulated particles
<LI>Stochastic rotation dynamics <LI>Stochastic rotation dynamics
<LI>Stokesian dynamics via fast lubrication dynamics <LI>Stokesian dynamics via fast lubrication dynamics
<LI>NPT with changing box shape (Parinello-Rahman)
<LI>Long-range point-dipole solver <LI>Long-range point-dipole solver
<LI>Per-atom energy and stress for long-range Coulombics <LI>Per-atom energy and stress for long-range Coulombics
<LI>Long-range Coulombics via Ewald and PPPM for triclinic boxes <LI>Long-range Coulombics via Ewald and PPPM for triclinic boxes

1
doc/Section_history.txt
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@ -38,7 +38,6 @@ Temperature accelerated dynamics
Triangulated particles Triangulated particles
Stochastic rotation dynamics Stochastic rotation dynamics
Stokesian dynamics via fast lubrication dynamics Stokesian dynamics via fast lubrication dynamics
NPT with changing box shape (Parinello-Rahman)
Long-range point-dipole solver Long-range point-dipole solver
Per-atom energy and stress for long-range Coulombics Per-atom energy and stress for long-range Coulombics
Long-range Coulombics via Ewald and PPPM for triclinic boxes Long-range Coulombics via Ewald and PPPM for triclinic boxes

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@ -173,7 +173,7 @@ commands)
</P> </P>
<UL><LI> 2d or 3d systems <UL><LI> 2d or 3d systems
<LI> orthogonal or non-orthogonal (triclinic symmetry) simulation domains <LI> orthogonal or non-orthogonal (triclinic symmetry) simulation domains
<LI> constant NVE, NVT, NPT, NPH integrators <LI> constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
<LI> thermostatting options for groups and geometric regions of atoms <LI> thermostatting options for groups and geometric regions of atoms
<LI> pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions <LI> pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
<LI> simulation box deformation (tensile and shear) <LI> simulation box deformation (tensile and shear)
@ -496,6 +496,19 @@ the list.
<DIV ALIGN=center><TABLE BORDER=1 > <DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >ipp Perl script tool </TD><TD > Reese Jones (Sandia)</TD></TR>
<TR><TD >eam_database and createatoms tools </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >electron force field (eFF) </TD><TD > Andres Jaramillo-Botero and Julius Su (Caltech)</TD></TR>
<TR><TD >embedded ion method (EIM) potential </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >COMB potential with charge equilibration </TD><TD > Tzu-Ray Shan (U Florida)</TD></TR>
<TR><TD >fix ave/correlate </TD><TD > Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)</TD></TR>
<TR><TD >pair_style peri/lps </TD><TD > Mike Parks (Sandia)</TD></TR>
<TR><TD >fix msst </TD><TD > Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)</TD></TR>
<TR><TD >thermo_style custom tpcpu & spcpu keywords </TD><TD > Axel Kohlmeyer (Temple U) </TD></TR>
<TR><TD >fix rigid/nve, fix rigid/nvt </TD><TD > Tony Sheh and Trung Dac Nguyen (U Michigan)</TD></TR>
<TR><TD >public SVN & Git repositories for LAMMPS </TD><TD > Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)</TD></TR>
<TR><TD >fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax </TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >compute heat/flux </TD><TD > German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)</TD></TR>
<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR> <TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>
<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR> <TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>
<TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR> <TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR>

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@ -172,7 +172,7 @@ Ensembles, constraints, and boundary conditions :h4
2d or 3d systems 2d or 3d systems
orthogonal or non-orthogonal (triclinic symmetry) simulation domains orthogonal or non-orthogonal (triclinic symmetry) simulation domains
constant NVE, NVT, NPT, NPH integrators constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
thermostatting options for groups and geometric regions of atoms thermostatting options for groups and geometric regions of atoms
pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
simulation box deformation (tensile and shear) simulation box deformation (tensile and shear)
@ -481,6 +481,19 @@ the list.
:link(sjp,http://www.sandia.gov/~sjplimp) :link(sjp,http://www.sandia.gov/~sjplimp)
ipp Perl script tool : Reese Jones (Sandia)
eam_database and createatoms tools : Xiaowang Zhou (Sandia)
electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
fix ave/correlate : Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)
pair_style peri/lps : Mike Parks (Sandia)
fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
public SVN & Git repositories for LAMMPS : Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax : Aidan Thompson (Sandia)
compute heat/flux : German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)
pair yukawa/colloid : Randy Schunk (Sandia) pair yukawa/colloid : Randy Schunk (Sandia)
fix wall/colloid : Jeremy Lechman (Sandia) fix wall/colloid : Jeremy Lechman (Sandia)
pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling : Paul Crozier (Sandia) pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling : Paul Crozier (Sandia)