forked from lijiext/lammps
Merge pull request #1829 from lammps/rerun-example
added rerun example dir
This commit is contained in:
Axel Kohlmeyer
GitHub
commit
7ebddb6088
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@ -133,6 +133,8 @@ Lowercase directories
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+-------------+------------------------------------------------------------------+
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| reax | RDX and TATB models using the ReaxFF |
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+-------------+------------------------------------------------------------------+
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| rerun | use of rerun and read\_dump commands |
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+-------------+------------------------------------------------------------------+
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| rigid | rigid bodies modeled as independent or coupled |
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+-------------+------------------------------------------------------------------+
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| shear | sideways shear applied to 2d solid, with and without a void |
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@ -94,6 +94,7 @@ python: using embedded Python in a LAMMPS input script
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qeq: use of the QEQ package for charge equilibration
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rdf-adf: computing radial and angle distribution functions for water
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reax: RDX and TATB models using the ReaxFF
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rerun: use of rerun and read_dump commands
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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
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snap: NVE dynamics for BCC tantalum crystal using SNAP potential
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@ -101,6 +101,7 @@ prd: parallel replica dynamics of vacancy diffusion in bulk Si
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python: use of PYTHON package to invoke Python code from input script
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qeq: use of QEQ package for charge equilibration
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reax: RDX and TATB and several other models using ReaxFF
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rerun: use of rerun and read_dump commands
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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
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snap: examples for using several bundled SNAP potentials
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@ -0,0 +1,17 @@
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Examples of how to use the rerun and read_dump commands
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in.first - run on any number of procs for any size problem
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in.rerun - run on same or different proc count for same size problem
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in.read_dump - ditto to in.rerun
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The thermo output on the same timesteps should be identical
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to within round-off errors.
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in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma
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in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma
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In both bases the time averaged RDF is computed 10x times, every 100
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steps for 1000 total. In the rerun, the pair style cutoff is changed
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so the RDF can be computed to a longer distance without re-running the
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simulation. The RDF values in the 2 files should be the same (within
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round-off) for the first 50 bins.
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@ -0,0 +1,33 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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dump 1 all custom 100 lj.dump id type x y z vx vy vz
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thermo 100
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run 1000
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@ -0,0 +1,36 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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dump 1 all custom 100 lj.dump id type x y z
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compute myRDF all rdf 50 cutoff 2.5
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fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
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thermo 100
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run 1000
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@ -0,0 +1,31 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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pair_style lj/cut 5.0
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pair_coeff 1 1 1.0 1.0
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neighbor 0.3 bin
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compute myRDF all rdf 100 cutoff 5.0
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fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
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thermo 100
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rerun lj.dump dump x y z
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@ -0,0 +1,37 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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thermo 100
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read_dump lj.dump 200 x y z vx vy vz
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run 0 post no
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read_dump lj.dump 800 x y z vx vy vz
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run 0 post no
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read_dump lj.dump 600 x y z vx vy vz
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run 0 post no
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read_dump lj.dump 400 x y z vx vy vz
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run 0 post no
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@ -0,0 +1,29 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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thermo 100
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rerun lj.dump first 200 last 800 every 200 &
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dump x y z vx vy vz
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@ -0,0 +1,97 @@
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LAMMPS (09 Jan 2020)
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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create_atoms CPU = 0.00173283 secs
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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dump 1 all custom 100 lj.dump id type x y z vx vy vz
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thermo 100
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run 1000
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 24 24 24
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 7.869 | 7.869 | 7.869 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
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200 0.75953175 -5.7618892 0 -4.6226272 0.20910575
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300 0.74624286 -5.741962 0 -4.6226327 0.32016436
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400 0.74155675 -5.7343359 0 -4.6220356 0.3777989
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500 0.73249345 -5.7206946 0 -4.6219887 0.44253023
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600 0.72087255 -5.7029314 0 -4.6216563 0.55730354
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700 0.71489947 -5.693532 0 -4.6212164 0.61322381
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800 0.70876958 -5.6840594 0 -4.6209382 0.66822293
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900 0.70799522 -5.6828388 0 -4.6208791 0.66961272
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1000 0.70325878 -5.6750833 0 -4.6202281 0.7112575
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Loop time of 6.3349 on 4 procs for 1000 steps with 32000 atoms
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Performance: 68193.673 tau/day, 157.856 timesteps/s
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99.8% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 4.3538 | 4.6712 | 5.0021 | 12.8 | 73.74
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Neigh | 0.59378 | 0.65229 | 0.75202 | 8.0 | 10.30
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Comm | 0.28101 | 0.69839 | 1.0586 | 38.5 | 11.02
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Output | 0.21601 | 0.21682 | 0.21718 | 0.1 | 3.42
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Modify | 0.074002 | 0.074803 | 0.075779 | 0.2 | 1.18
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Other | | 0.0214 | | | 0.34
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Nlocal: 8000 ave 8049 max 7942 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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Nghost: 8632.5 ave 8685 max 8591 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Neighs: 299934 ave 303105 max 295137 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Total # of neighbors = 1199738
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Ave neighs/atom = 37.4918
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:00:06
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@ -0,0 +1,105 @@
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LAMMPS (09 Jan 2020)
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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create_atoms CPU = 0.00100017 secs
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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dump 1 all custom 100 lj.dump id type x y z
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compute myRDF all rdf 50 cutoff 2.5
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fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
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thermo 100
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run 1000
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 24 24 24
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) compute rdf, occasional
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attributes: half, newton on, cut 2.8
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 8.487 | 8.487 | 8.487 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
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200 0.75953175 -5.7618892 0 -4.6226272 0.20910575
|
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300 0.74624286 -5.741962 0 -4.6226327 0.32016436
|
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400 0.74155675 -5.7343359 0 -4.6220356 0.3777989
|
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500 0.73249345 -5.7206946 0 -4.6219887 0.44253023
|
||||
600 0.72087255 -5.7029314 0 -4.6216563 0.55730354
|
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700 0.71489947 -5.693532 0 -4.6212164 0.61322381
|
||||
800 0.70876958 -5.6840594 0 -4.6209382 0.66822293
|
||||
900 0.70799522 -5.6828388 0 -4.6208791 0.66961272
|
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1000 0.70325878 -5.6750833 0 -4.6202281 0.7112575
|
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Loop time of 7.44016 on 4 procs for 1000 steps with 32000 atoms
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|
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Performance: 58063.267 tau/day, 134.406 timesteps/s
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99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
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MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
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---------------------------------------------------------------
|
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Pair | 5.3881 | 5.5809 | 5.7111 | 5.4 | 75.01
|
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Neigh | 0.80101 | 0.82776 | 0.85702 | 2.2 | 11.13
|
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Comm | 0.31801 | 0.48426 | 0.72201 | 22.5 | 6.51
|
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Output | 0.17801 | 0.17801 | 0.17801 | 0.0 | 2.39
|
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Modify | 0.31201 | 0.33076 | 0.33701 | 1.9 | 4.45
|
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Other | | 0.0385 | | | 0.52
|
||||
|
||||
Nlocal: 8000 ave 8049 max 7942 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Nghost: 8632.5 ave 8685 max 8591 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 299934 ave 303105 max 295137 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 1199738
|
||||
Ave neighs/atom = 37.4918
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:07
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.00183487 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 5.0
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
||||
compute myRDF all rdf 100 cutoff 5.0
|
||||
fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
|
||||
|
||||
thermo 100
|
||||
|
||||
rerun lj.dump dump x y z
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65, bins = 13 13 13
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute rdf, occasional
|
||||
attributes: half, newton on, cut 5.3
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.19 | 15.19 | 15.19 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -7.1616928 0 -7.1616928 -6.8899898
|
||||
100 0 -6.1442754 0 -6.1442754 -1.0825318
|
||||
200 0 -6.1472483 0 -6.1472483 -1.0817213
|
||||
300 0 -6.1274033 0 -6.1274033 -0.95961014
|
||||
400 0 -6.1202956 0 -6.1202956 -0.8988851
|
||||
500 0 -6.1067136 0 -6.1067136 -0.82660368
|
||||
600 0 -6.0893179 0 -6.0893179 -0.70264528
|
||||
700 0 -6.0803044 0 -6.0803044 -0.64232743
|
||||
800 0 -6.0710303 0 -6.0710303 -0.5824798
|
||||
900 0 -6.0698963 0 -6.0698963 -0.58057929
|
||||
1000 0 -6.0627642 0 -6.0627642 -0.53599799
|
||||
Loop time of 3.07661 on 4 procs for 11 steps with 32000 atoms
|
||||
|
||||
Performance: 1544.558 tau/day, 3.575 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.077 | | |100.00
|
||||
|
||||
Nlocal: 8000 ave 8049 max 7942 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Nghost: 20028 ave 20060 max 19988 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 2.10417e+06 ave 2.12604e+06 max 2.07878e+06 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 8416685
|
||||
Ave neighs/atom = 263.021
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.001724 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
read_dump lj.dump 200 x y z vx vy vz
|
||||
orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
32000 atoms before read
|
||||
32000 atoms in snapshot
|
||||
0 atoms purged
|
||||
32000 atoms replaced
|
||||
0 atoms trimmed
|
||||
0 atoms added
|
||||
32000 atoms after read
|
||||
run 0 post no
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 24 24 24
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.75953173 -5.7618854 0 -4.6226234 0.20912952
|
||||
Loop time of 2.26498e-06 on 4 procs for 0 steps with 32000 atoms
|
||||
|
||||
|
||||
read_dump lj.dump 800 x y z vx vy vz
|
||||
orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
32000 atoms before read
|
||||
32000 atoms in snapshot
|
||||
0 atoms purged
|
||||
32000 atoms replaced
|
||||
0 atoms trimmed
|
||||
0 atoms added
|
||||
32000 atoms after read
|
||||
run 0 post no
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
800 0.70876957 -5.6840545 0 -4.6209334 0.66823926
|
||||
Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
|
||||
|
||||
|
||||
read_dump lj.dump 600 x y z vx vy vz
|
||||
orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
32000 atoms before read
|
||||
32000 atoms in snapshot
|
||||
0 atoms purged
|
||||
32000 atoms replaced
|
||||
0 atoms trimmed
|
||||
0 atoms added
|
||||
32000 atoms after read
|
||||
run 0 post no
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
600 0.72087256 -5.7029306 0 -4.6216556 0.55729873
|
||||
Loop time of 7.7486e-07 on 4 procs for 0 steps with 32000 atoms
|
||||
|
||||
|
||||
read_dump lj.dump 400 x y z vx vy vz
|
||||
orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
32000 atoms before read
|
||||
32000 atoms in snapshot
|
||||
0 atoms purged
|
||||
32000 atoms replaced
|
||||
0 atoms trimmed
|
||||
0 atoms added
|
||||
32000 atoms after read
|
||||
run 0 post no
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.74155677 -5.7343336 0 -4.6220332 0.37780193
|
||||
Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,86 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.00100017 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
rerun lj.dump first 200 last 800 every 200 dump x y z vx vy vz
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 24 24 24
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.716 | 6.718 | 6.721 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.75953173 -5.7618854 0 -4.6226234 0.20912952
|
||||
400 0.74155677 -5.7343336 0 -4.6220332 0.37780193
|
||||
600 0.72087256 -5.7029306 0 -4.6216556 0.55729873
|
||||
800 0.70876957 -5.6840545 0 -4.6209334 0.66823926
|
||||
Loop time of 0.375898 on 4 procs for 4 steps with 32000 atoms
|
||||
|
||||
Performance: 4596.990 tau/day, 10.641 timesteps/s
|
||||
98.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.3759 | | |100.00
|
||||
|
||||
Nlocal: 8000 ave 8073 max 7933 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 8693.25 ave 8731 max 8658 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 299786 ave 302947 max 293888 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 1199142
|
||||
Ave neighs/atom = 37.4732
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
# Time-averaged data for fix 2
|
||||
# TimeStep Number-of-rows
|
||||
# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
|
||||
1000 50
|
||||
1 0.025 0 0
|
||||
2 0.075 0 0
|
||||
3 0.125 0 0
|
||||
4 0.175 0 0
|
||||
5 0.225 0 0
|
||||
6 0.275 0 0
|
||||
7 0.325 0 0
|
||||
8 0.375 0 0
|
||||
9 0.425 0 0
|
||||
10 0.475 0 0
|
||||
11 0.525 0 0
|
||||
12 0.575 0 0
|
||||
13 0.625 0 0
|
||||
14 0.675 0 0
|
||||
15 0.725 0 0
|
||||
16 0.775 0 0
|
||||
17 0.825 0 0
|
||||
18 0.875 1.53863e-05 6.25e-06
|
||||
19 0.925 0.0217263 0.00986875
|
||||
20 0.975 0.506735 0.265431
|
||||
21 1.025 1.92083 1.33605
|
||||
22 1.075 2.8749 3.09855
|
||||
23 1.125 2.7805 4.96541
|
||||
24 1.175 2.21879 6.59047
|
||||
25 1.225 1.67622 7.92484
|
||||
26 1.275 1.25407 9.00629
|
||||
27 1.325 0.963413 9.90353
|
||||
28 1.375 0.774441 10.6802
|
||||
29 1.425 0.656196 11.3871
|
||||
30 1.475 0.589364 12.0672
|
||||
31 1.525 0.560681 12.7589
|
||||
32 1.575 0.560195 13.4961
|
||||
33 1.625 0.587995 14.3197
|
||||
34 1.675 0.632155 15.2605
|
||||
35 1.725 0.706585 16.3758
|
||||
36 1.775 0.805303 17.7216
|
||||
37 1.825 0.925415 19.3565
|
||||
38 1.875 1.05672 21.3271
|
||||
39 1.925 1.17634 23.6394
|
||||
40 1.975 1.2557 26.2375
|
||||
41 2.025 1.30009 29.0653
|
||||
42 2.075 1.30889 32.0546
|
||||
43 2.125 1.27704 35.1135
|
||||
44 2.175 1.21808 38.17
|
||||
45 2.225 1.13622 41.1536
|
||||
46 2.275 1.05072 44.0382
|
||||
47 2.325 0.973786 46.8303
|
||||
48 2.375 0.910095 49.5533
|
||||
49 2.425 0.866474 52.256
|
||||
50 2.475 0.841724 54.991
|
||||
|
|
@ -0,0 +1,104 @@
|
|||
# Time-averaged data for fix 2
|
||||
# TimeStep Number-of-rows
|
||||
# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
|
||||
1000 100
|
||||
1 0.025 0 0
|
||||
2 0.075 0 0
|
||||
3 0.125 0 0
|
||||
4 0.175 0 0
|
||||
5 0.225 0 0
|
||||
6 0.275 0 0
|
||||
7 0.325 0 0
|
||||
8 0.375 0 0
|
||||
9 0.425 0 0
|
||||
10 0.475 0 0
|
||||
11 0.525 0 0
|
||||
12 0.575 0 0
|
||||
13 0.625 0 0
|
||||
14 0.675 0 0
|
||||
15 0.725 0 0
|
||||
16 0.775 0 0
|
||||
17 0.825 0 0
|
||||
18 0.875 1.53863e-05 6.25e-06
|
||||
19 0.925 0.021685 0.00985
|
||||
20 0.975 0.506834 0.265463
|
||||
21 1.025 1.92047 1.33588
|
||||
22 1.075 2.87514 3.09853
|
||||
23 1.125 2.78062 4.96547
|
||||
24 1.175 2.21869 6.59046
|
||||
25 1.225 1.67626 7.92486
|
||||
26 1.275 1.25409 9.00633
|
||||
27 1.325 0.963245 9.90341
|
||||
28 1.375 0.774535 10.6802
|
||||
29 1.425 0.65626 11.3871
|
||||
30 1.475 0.58925 12.0672
|
||||
31 1.525 0.560782 12.759
|
||||
32 1.575 0.560133 13.496
|
||||
33 1.625 0.588008 14.3197
|
||||
34 1.675 0.632185 15.2605
|
||||
35 1.725 0.706541 16.3757
|
||||
36 1.775 0.805341 17.7216
|
||||
37 1.825 0.925351 19.3565
|
||||
38 1.875 1.05677 21.3271
|
||||
39 1.925 1.17639 23.6395
|
||||
40 1.975 1.25571 26.2376
|
||||
41 2.025 1.30011 29.0655
|
||||
42 2.075 1.30883 32.0547
|
||||
43 2.125 1.27702 35.1134
|
||||
44 2.175 1.21813 38.17
|
||||
45 2.225 1.13617 41.1536
|
||||
46 2.275 1.05073 44.0382
|
||||
47 2.325 0.97376 46.8302
|
||||
48 2.375 0.91012 49.5533
|
||||
49 2.425 0.866556 52.2563
|
||||
50 2.475 0.841651 54.991
|
||||
51 2.525 0.839516 57.8301
|
||||
52 2.575 0.848795 60.8153
|
||||
53 2.625 0.868861 63.991
|
||||
54 2.675 0.896335 67.393
|
||||
55 2.725 0.925794 71.0395
|
||||
56 2.775 0.961909 74.9685
|
||||
57 2.825 0.999727 79.2005
|
||||
58 2.875 1.03745 83.749
|
||||
59 2.925 1.07355 88.6208
|
||||
60 2.975 1.10406 93.8039
|
||||
61 3.025 1.11993 99.2397
|
||||
62 3.075 1.12062 104.86
|
||||
63 3.125 1.10531 110.586
|
||||
64 3.175 1.07711 116.345
|
||||
65 3.225 1.04268 122.097
|
||||
66 3.275 1.00838 127.834
|
||||
67 3.325 0.974855 133.55
|
||||
68 3.375 0.949817 139.289
|
||||
69 3.425 0.936519 145.116
|
||||
70 3.475 0.92942 151.069
|
||||
71 3.525 0.930926 157.205
|
||||
72 3.575 0.940561 163.581
|
||||
73 3.625 0.94956 170.199
|
||||
74 3.675 0.964202 177.107
|
||||
75 3.725 0.97905 184.312
|
||||
76 3.775 0.991906 191.81
|
||||
77 3.825 1.00093 199.577
|
||||
78 3.875 1.01248 207.641
|
||||
79 3.925 1.02301 216.001
|
||||
80 3.975 1.03474 224.673
|
||||
81 4.025 1.04171 233.624
|
||||
82 4.075 1.04725 242.849
|
||||
83 4.125 1.04997 252.325
|
||||
84 4.175 1.04758 262.01
|
||||
85 4.225 1.03985 271.856
|
||||
86 4.275 1.02755 281.817
|
||||
87 4.325 1.00883 291.826
|
||||
88 4.375 0.99045 301.882
|
||||
89 4.425 0.97287 311.986
|
||||
90 4.475 0.958469 322.166
|
||||
91 4.525 0.952552 332.512
|
||||
92 4.575 0.948064 343.037
|
||||
93 4.625 0.952592 353.845
|
||||
94 4.675 0.958837 364.96
|
||||
95 4.725 0.970831 376.457
|
||||
96 4.775 0.985248 388.372
|
||||
97 4.825 0.998873 400.707
|
||||
98 4.875 1.0119 413.462
|
||||
99 4.925 1.02446 426.643
|
||||
100 4.975 1.03613 440.245
|
||||
Loading…
Reference in New Issue