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@ -32,8 +32,10 @@ Site</A>.
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
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<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
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<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
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<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
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<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
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<TR><TD >elastic</TD><TD > zero temperature elastic constant tensor of silicon</TD></TR>
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<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
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<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
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@ -43,13 +45,14 @@ Site</A>.
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<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
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<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
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<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
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<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
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<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
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<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
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<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
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<TR><TD >peri</TD><TD > Peridynamics example of cylinder hit by projectile</TD></TR>
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<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
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<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
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<TR><TD >prd</TD><TD > parallel replica dynamics of a vacancy diffusion in bulk Si</TD></TR>
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<TR><TD >reax</TD><TD > simple example for ReaxFF force field</TD></TR>
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<TR><TD >prd</TD><TD > parallel replica dynamics of a vacancy diffusion in bulk Si</TD></TR>
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<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
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<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
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<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void
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</TD></TR></TABLE></DIV>
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@ -65,17 +68,13 @@ lmp_linux < in.indent # run the problem
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</P>
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<PRE>../../tools/xmovie/xmovie -scale dump.indent
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</PRE>
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<P>There is also a directory "couple" in the examples sub-directory,
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which contains a stand-alone code umbrella.cpp that links LAMMPS as a
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library. The README describes how to build the code. The code itself
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runs LAMMPS on a subset of processors, sets up a LAMMPS problem
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by invoking LAMMPS input script commands one at a time, does
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a run, grabs atom coordinates, changes one atom position, puts
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them back into LAMMPS, and does another run.
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<P>There is also a COUPLE directory which has examples of how to link to
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LAMMPS as a library and drive it from a wrapper program. See the
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README file for more info.
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</P>
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<P>This illustrates how an umbrella code could include new models and
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physics while using LAMMPS to perform MD, or how the umbrella code
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could call both LAMMPS and some other code to perform a coupled
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calculation.
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<P>There is also a USER directory which contains subdirectories of
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user-provided examples for user packages. See the README files in
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those directories for more info. See the doc/Section_start.html for
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more info about user packages.
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</P>
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</HTML>
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@ -28,8 +28,10 @@ Site"_lws.
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These are the sample problems in the examples sub-directories:
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colloid: big colloid particles in a small particle solvent, 2d system
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comb: models using the COMB potential
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crack: crack propagation in a 2d solid
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dipole: point dipolar particles, 2d system
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eim: NaCl using the EIM potential
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elastic: zero temperature elastic constant tensor of silicon
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ellipse: ellipsoidal particles in spherical solvent, 2d system
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flow: Couette and Poiseuille flow in a 2d channel
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@ -39,13 +41,14 @@ meam: MEAM test for SiC and shear (same as shear examples)
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melt: rapid melt of 3d LJ system
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micelle: self-assembly of small lipid-like molecules into 2d bilayers
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min: energy minimization of 2d LJ melt
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msst: MSST shock dynamics
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nemd: non-equilibrium MD of 2d sheared system
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obstacle: flow around two voids in a 2d channel
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peptide: dynamics of a small solvated peptide chain (5-mer)
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peri: Peridynamics example of cylinder hit by projectile
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peri: Peridynamic model of cylinder impacted by indenter
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pour: pouring of granular particles into a 3d box, then chute flow
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prd: parallel replica dynamics of a vacancy diffusion in bulk Si
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reax: simple example for ReaxFF force field
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prd: parallel replica dynamics of a vacancy diffusion in bulk Si
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reax: RDX and TATB models using the ReaxFF
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rigid: rigid bodies modeled as independent or coupled
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shear: sideways shear applied to 2d solid, with and without a void :tb(s=:)
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@ -60,15 +63,11 @@ Running the simulation produces the files {dump.indent} and
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../../tools/xmovie/xmovie -scale dump.indent :pre
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There is also a directory "couple" in the examples sub-directory,
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which contains a stand-alone code umbrella.cpp that links LAMMPS as a
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library. The README describes how to build the code. The code itself
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runs LAMMPS on a subset of processors, sets up a LAMMPS problem
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by invoking LAMMPS input script commands one at a time, does
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a run, grabs atom coordinates, changes one atom position, puts
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them back into LAMMPS, and does another run.
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There is also a COUPLE directory which has examples of how to link to
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LAMMPS as a library and drive it from a wrapper program. See the
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README file for more info.
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This illustrates how an umbrella code could include new models and
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physics while using LAMMPS to perform MD, or how the umbrella code
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could call both LAMMPS and some other code to perform a coupled
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calculation.
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There is also a USER directory which contains subdirectories of
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user-provided examples for user packages. See the README files in
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those directories for more info. See the doc/Section_start.html for
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more info about user packages.
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@ -41,7 +41,6 @@ page</A> on the LAMMPS WWW site for more details.
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<LI>Triangulated particles
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<LI>Stochastic rotation dynamics
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<LI>Stokesian dynamics via fast lubrication dynamics
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<LI>NPT with changing box shape (Parinello-Rahman)
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<LI>Long-range point-dipole solver
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<LI>Per-atom energy and stress for long-range Coulombics
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<LI>Long-range Coulombics via Ewald and PPPM for triclinic boxes
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@ -38,7 +38,6 @@ Temperature accelerated dynamics
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Triangulated particles
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Stochastic rotation dynamics
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Stokesian dynamics via fast lubrication dynamics
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NPT with changing box shape (Parinello-Rahman)
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Long-range point-dipole solver
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Per-atom energy and stress for long-range Coulombics
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Long-range Coulombics via Ewald and PPPM for triclinic boxes
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@ -173,7 +173,7 @@ commands)
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</P>
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<UL><LI> 2d or 3d systems
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<LI> orthogonal or non-orthogonal (triclinic symmetry) simulation domains
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<LI> constant NVE, NVT, NPT, NPH integrators
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<LI> constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
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<LI> thermostatting options for groups and geometric regions of atoms
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<LI> pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
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<LI> simulation box deformation (tensile and shear)
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@ -496,6 +496,19 @@ the list.
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >ipp Perl script tool </TD><TD > Reese Jones (Sandia)</TD></TR>
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<TR><TD >eam_database and createatoms tools </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
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<TR><TD >electron force field (eFF) </TD><TD > Andres Jaramillo-Botero and Julius Su (Caltech)</TD></TR>
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<TR><TD >embedded ion method (EIM) potential </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
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<TR><TD >COMB potential with charge equilibration </TD><TD > Tzu-Ray Shan (U Florida)</TD></TR>
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<TR><TD >fix ave/correlate </TD><TD > Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)</TD></TR>
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<TR><TD >pair_style peri/lps </TD><TD > Mike Parks (Sandia)</TD></TR>
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<TR><TD >fix msst </TD><TD > Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)</TD></TR>
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<TR><TD >thermo_style custom tpcpu & spcpu keywords </TD><TD > Axel Kohlmeyer (Temple U) </TD></TR>
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<TR><TD >fix rigid/nve, fix rigid/nvt </TD><TD > Tony Sheh and Trung Dac Nguyen (U Michigan)</TD></TR>
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<TR><TD >public SVN & Git repositories for LAMMPS </TD><TD > Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)</TD></TR>
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<TR><TD >fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax </TD><TD > Aidan Thompson (Sandia)</TD></TR>
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<TR><TD >compute heat/flux </TD><TD > German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)</TD></TR>
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<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>
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<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>
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<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
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2d or 3d systems
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orthogonal or non-orthogonal (triclinic symmetry) simulation domains
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constant NVE, NVT, NPT, NPH integrators
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constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
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thermostatting options for groups and geometric regions of atoms
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pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
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simulation box deformation (tensile and shear)
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@ -481,6 +481,19 @@ the list.
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:link(sjp,http://www.sandia.gov/~sjplimp)
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ipp Perl script tool : Reese Jones (Sandia)
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eam_database and createatoms tools : Xiaowang Zhou (Sandia)
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electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
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embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
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COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
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fix ave/correlate : Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)
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pair_style peri/lps : Mike Parks (Sandia)
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fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
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thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
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fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
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public SVN & Git repositories for LAMMPS : Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
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fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax : Aidan Thompson (Sandia)
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compute heat/flux : German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)
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pair yukawa/colloid : Randy Schunk (Sandia)
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fix wall/colloid : Jeremy Lechman (Sandia)
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pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling : Paul Crozier (Sandia)
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