git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13615 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -101,8 +101,8 @@ favorite interatomic potential, boundary condition, or atom type, see
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<A HREF = "Section_modify.html">Section_modify</A>, which describes how you can add
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it to LAMMPS.
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</P>
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<H4>General features
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</H4>
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<H5>General features
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</H5>
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<UL><LI> runs on a single processor or in parallel
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<LI> distributed-memory message-passing parallelism (MPI)
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<LI> spatial-decomposition of simulation domain for parallelism
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@ -118,8 +118,8 @@ it to LAMMPS.
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<LI> build as library, invoke LAMMPS thru library interface or provided Python wrapper
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<LI> couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both
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</UL>
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<H4>Particle and model types
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</H4>
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<H5>Particle and model types
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</H5>
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<P>(<A HREF = "atom_style.html">atom style</A> command)
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</P>
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<UL><LI> atoms
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@ -135,8 +135,8 @@ it to LAMMPS.
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<LI> rigid collections of particles
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<LI> hybrid combinations of these
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</UL>
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<H4>Force fields
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</H4>
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<H5>Force fields
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</H5>
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<P>(<A HREF = "pair_style.html">pair style</A>, <A HREF = "bond_style.html">bond style</A>,
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<A HREF = "angle_style.html">angle style</A>, <A HREF = "dihedral_style.html">dihedral style</A>,
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<A HREF = "improper_style.html">improper style</A>, <A HREF = "kspace_style.html">kspace style</A>
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@ -163,8 +163,8 @@ commands)
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<LI> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
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<LI> overlaid potentials: superposition of multiple pair potentials
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</UL>
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<H4>Atom creation
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</H4>
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<H5>Atom creation
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</H5>
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<P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,
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<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,
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<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "replicate.html">replicate</A> commands)
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@ -175,8 +175,8 @@ commands)
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<LI> replicate existing atoms multiple times
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<LI> displace atoms
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</UL>
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<H4>Ensembles, constraints, and boundary conditions
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</H4>
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<H5>Ensembles, constraints, and boundary conditions
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</H5>
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<P>(<A HREF = "fix.html">fix</A> command)
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</P>
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<UL><LI> 2d or 3d systems
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@ -194,8 +194,8 @@ commands)
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<LI> non-equilibrium molecular dynamics (NEMD)
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<LI> variety of additional boundary conditions and constraints
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</UL>
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<H4>Integrators
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</H4>
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<H5>Integrators
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</H5>
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<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A> commands)
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</P>
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<UL><LI> velocity-Verlet integrator
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@ -205,12 +205,12 @@ commands)
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<LI> rRESPA hierarchical timestepping
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<LI> rerun command for post-processing of dump files
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</UL>
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<H4>Diagnostics
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</H4>
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<H5>Diagnostics
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</H5>
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<UL><LI> see the various flavors of the <A HREF = "fix.html">fix</A> and <A HREF = "compute.html">compute</A> commands
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</UL>
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<H4>Output
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</H4>
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<H5>Output
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</H5>
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<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
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</P>
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<UL><LI> log file of thermodynamic info
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@ -223,15 +223,15 @@ commands)
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<LI> time averaging of system-wide quantities
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<LI> atom snapshots in native, XYZ, XTC, DCD, CFG formats
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</UL>
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<H4>Multi-replica models
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</H4>
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<H5>Multi-replica models
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</H5>
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<P><A HREF = "neb.html">nudged elastic band</A>
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<A HREF = "prd.html">parallel replica dynamics</A>
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<A HREF = "tad.html">temperature accelerated dynamics</A>
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<A HREF = "temper.html">parallel tempering</A>
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</P>
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<H4>Pre- and post-processing
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</H4>
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<H5>Pre- and post-processing
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</H5>
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<UL><LI>Various pre- and post-processing serial tools are packaged
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with LAMMPS; see these <A HREF = "Section_tools.html">doc pages</A>.
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@ -245,8 +245,8 @@ Pizza.py WWW site</A>.
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<H4>Specialized features
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</H4>
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<H5>Specialized features
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</H5>
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<P>These are LAMMPS capabilities which you may not think of as typical
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molecular dynamics options:
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</P>
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