Loading doc/src/Examples.rst +2 −0 Original line number Diff line number Diff line Loading @@ -133,6 +133,8 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | reax | RDX and TATB models using the ReaxFF | +-------------+------------------------------------------------------------------+ | rerun | use of rerun and read\_dump commands | +-------------+------------------------------------------------------------------+ | rigid | rigid bodies modeled as independent or coupled | +-------------+------------------------------------------------------------------+ | shear | sideways shear applied to 2d solid, with and without a void | Loading doc/txt/Examples.txt +1 −0 Original line number Diff line number Diff line Loading @@ -94,6 +94,7 @@ python: using embedded Python in a LAMMPS input script qeq: use of the QEQ package for charge equilibration rdf-adf: computing radial and angle distribution functions for water reax: RDX and TATB models using the ReaxFF rerun: use of rerun and read_dump commands rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void snap: NVE dynamics for BCC tantalum crystal using SNAP potential Loading examples/README +1 −0 Original line number Diff line number Diff line Loading @@ -101,6 +101,7 @@ prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script qeq: use of QEQ package for charge equilibration reax: RDX and TATB and several other models using ReaxFF rerun: use of rerun and read_dump commands rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void snap: examples for using several bundled SNAP potentials Loading examples/rerun/README 0 → 100644 +17 −0 Original line number Diff line number Diff line Examples of how to use the rerun and read_dump commands in.first - run on any number of procs for any size problem in.rerun - run on same or different proc count for same size problem in.read_dump - ditto to in.rerun The thermo output on the same timesteps should be identical to within round-off errors. in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma In both bases the time averaged RDF is computed 10x times, every 100 steps for 1000 total. In the rerun, the pair style cutoff is changed so the RDF can be computed to a longer distance without re-running the simulation. The RDF values in the 2 files should be the same (within round-off) for the first 50 bins. examples/rerun/in.first 0 → 100644 +33 −0 Original line number Diff line number Diff line # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z units lj atom_style atomic lattice fcc 0.8442 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve dump 1 all custom 100 lj.dump id type x y z vx vy vz thermo 100 run 1000 Loading
doc/src/Examples.rst +2 −0 Original line number Diff line number Diff line Loading @@ -133,6 +133,8 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | reax | RDX and TATB models using the ReaxFF | +-------------+------------------------------------------------------------------+ | rerun | use of rerun and read\_dump commands | +-------------+------------------------------------------------------------------+ | rigid | rigid bodies modeled as independent or coupled | +-------------+------------------------------------------------------------------+ | shear | sideways shear applied to 2d solid, with and without a void | Loading
doc/txt/Examples.txt +1 −0 Original line number Diff line number Diff line Loading @@ -94,6 +94,7 @@ python: using embedded Python in a LAMMPS input script qeq: use of the QEQ package for charge equilibration rdf-adf: computing radial and angle distribution functions for water reax: RDX and TATB models using the ReaxFF rerun: use of rerun and read_dump commands rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void snap: NVE dynamics for BCC tantalum crystal using SNAP potential Loading
examples/README +1 −0 Original line number Diff line number Diff line Loading @@ -101,6 +101,7 @@ prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script qeq: use of QEQ package for charge equilibration reax: RDX and TATB and several other models using ReaxFF rerun: use of rerun and read_dump commands rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void snap: examples for using several bundled SNAP potentials Loading
examples/rerun/README 0 → 100644 +17 −0 Original line number Diff line number Diff line Examples of how to use the rerun and read_dump commands in.first - run on any number of procs for any size problem in.rerun - run on same or different proc count for same size problem in.read_dump - ditto to in.rerun The thermo output on the same timesteps should be identical to within round-off errors. in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma In both bases the time averaged RDF is computed 10x times, every 100 steps for 1000 total. In the rerun, the pair style cutoff is changed so the RDF can be computed to a longer distance without re-running the simulation. The RDF values in the 2 files should be the same (within round-off) for the first 50 bins.
examples/rerun/in.first 0 → 100644 +33 −0 Original line number Diff line number Diff line # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z units lj atom_style atomic lattice fcc 0.8442 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve dump 1 all custom 100 lj.dump id type x y z vx vy vz thermo 100 run 1000
