forked from lijiext/lammps
clean-up of example files
This commit is contained in:
Steve Plimpton
parent
ed52f9ea5e
commit
fe2fca4e9b
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# calculate the energy volume curve for InP zincblende
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# define volume range and filename
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variable ndelta equal 100
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variable volatom_min equal 20.0
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variable volatom_max equal 29.0
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variable evsvolfile string evsvol.dat
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# set up cell
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units metal
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boundary p p p
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# setup loop variables for box volume
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variable amin equal ${volatom_min}^(1/3)*2
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variable delta equal (${volatom_max}-${volatom_min})/${ndelta}
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variable scale equal (${delta}/v_volatom+1)^(1/3)
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# set up 8 atom InP zincblende unit cell
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lattice diamond ${amin}
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region box prism &
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0 1 &
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0 1 &
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0 1 &
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0 0 0
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create_box 2 box
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create_atoms 1 box &
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basis 5 2 &
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basis 6 2 &
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basis 7 2 &
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basis 8 2
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mass 1 114.76
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mass 2 30.98
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# choose potential
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pair_style vashishta
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pair_coeff * * InP.vashishta In P
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# setup neighbor style
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neighbor 1.0 nsq
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neigh_modify once no every 1 delay 0 check yes
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# setup output
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thermo_style custom step temp pe press vol
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thermo_modify norm no
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variable volatom equal vol/atoms
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variable eatom equal pe/atoms
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print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}
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# loop over range of volumes
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label loop
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variable i loop ${ndelta}
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change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap
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# calculate energy
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# no energy minimization needed for zincblende
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run 0
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print "${volatom} ${eatom}" append ${evsvolfile}
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next i
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jump SELF loop
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# calculate the energy volume curve for InP zincblende
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# define volume range and filename
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variable ndelta equal 100
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variable volatom_min equal 20.0
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variable volatom_max equal 29.0
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variable evsvolfile string evsvol.dat
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# set up cell
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units metal
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boundary p p p
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# setup loop variables for box volume
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variable amin equal ${volatom_min}^(1/3)*2
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variable delta equal (${volatom_max}-${volatom_min})/${ndelta}
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variable scale equal (${delta}/v_volatom+1)^(1/3)
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# set up 8 atom InP zincblende unit cell
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lattice diamond ${amin}
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region box prism &
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0 1 &
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0 1 &
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0 1 &
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0 0 0
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create_box 2 box
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create_atoms 1 box &
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basis 5 2 &
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basis 6 2 &
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basis 7 2 &
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basis 8 2
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mass 1 114.76
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mass 2 30.98
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# choose potential
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pair_style vashishta/table 100000 0.2
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pair_coeff * * InP.vashishta In P
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# setup neighbor style
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neighbor 1.0 nsq
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neigh_modify once no every 1 delay 0 check yes
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# setup output
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thermo_style custom step temp pe press vol
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thermo_modify norm no
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variable volatom equal vol/atoms
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variable eatom equal pe/atoms
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print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}
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# loop over range of volumes
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label loop
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variable i loop ${ndelta}
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change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap
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# calculate energy
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# no energy minimization needed for zincblende
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run 0
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print "${volatom} ${eatom}" append ${evsvolfile}
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next i
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jump SELF loop
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# test Vashishta potential for quartz
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units metal
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boundary p p p
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atom_style atomic
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read_data data.quartz
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replicate 4 4 4
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velocity all create 2000.0 277387 mom yes
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displace_atoms all move 0.05 0.9 0.4 units box
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pair_style vashishta
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pair_coeff * * SiO.1990.vashishta Si O
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neighbor 0.3 bin
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neigh_modify delay 10
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fix 1 all nve
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thermo 10
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timestep 0.001
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#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
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#dump_modify 1 element Si O
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run 100
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# test Vashishta potential for quartz
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units metal
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boundary p p p
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variable ntable index 100000
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atom_style atomic
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read_data data.quartz
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replicate 4 4 4
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velocity all create 2000.0 277387 mom yes
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displace_atoms all move 0.05 0.9 0.4 units box
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pair_style vashishta/table ${ntable} 0.2
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pair_coeff * * SiO.1990.vashishta Si O
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neighbor 0.3 bin
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neigh_modify delay 10
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fix 1 all nve
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thermo 10
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timestep 0.001
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#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
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#dump_modify 1 element Si O
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run 100
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File diff suppressed because it is too large
Load Diff
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@ -1,128 +0,0 @@
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LAMMPS (15 Feb 2016)
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# calculate the energy volume curve for InP zincblende
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# define volume range and filename
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variable ndelta equal 100
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variable volatom_min equal 20.0
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variable volatom_max equal 29.0
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variable evsvolfile string evsvol.dat
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# set up cell
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units metal
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boundary p p p
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# setup loop variables for box volume
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variable amin equal ${volatom_min}^(1/3)*2
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variable amin equal 20^(1/3)*2
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variable delta equal (${volatom_max}-${volatom_min})/${ndelta}
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variable delta equal (29-${volatom_min})/${ndelta}
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variable delta equal (29-20)/${ndelta}
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variable delta equal (29-20)/100
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variable scale equal (${delta}/v_volatom+1)^(1/3)
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variable scale equal (0.09/v_volatom+1)^(1/3)
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# set up 8 atom InP zincblende unit cell
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lattice diamond ${amin}
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lattice diamond 5.42883523318981
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Lattice spacing in x,y,z = 5.42884 5.42884 5.42884
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region box prism 0 1 0 1 0 1 0 0 0
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create_box 2 box
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Created triclinic box = (0 0 0) to (5.42884 5.42884 5.42884) with tilt (0 0 0)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
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Created 8 atoms
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mass 1 114.76
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mass 2 30.98
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# choose potential
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pair_style vashishta
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pair_coeff * * InP.vashishta In P
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Reading potential file InP.vashishta with DATE: 2015-10-14
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# setup neighbor style
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neighbor 1.0 nsq
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neigh_modify once no every 1 delay 0 check yes
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# setup output
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thermo_style custom step temp pe press vol
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thermo_modify norm no
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variable volatom equal vol/atoms
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variable eatom equal pe/atoms
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print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}
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print "# Volume [A^3/atom] Energy [eV/atom]" file evsvol.dat
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# Volume [A^3/atom] Energy [eV/atom]
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# loop over range of volumes
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label loop
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variable i loop ${ndelta}
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variable i loop 100
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change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap
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change_box all x scale 1.00149775560818 y scale ${scale} z scale ${scale} remap
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change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale ${scale} remap
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change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale 1.00149775560818 remap
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triclinic box = (-0.00406553 0 0) to (5.4329 5.42884 5.42884) with tilt (0 0 0)
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triclinic box = (-0.00406553 -0.00406553 0) to (5.4329 5.4329 5.42884) with tilt (0 0 0)
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triclinic box = (-0.00406553 -0.00406553 -0.00406553) to (5.4329 5.4329 5.4329) with tilt (0 0 0)
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# calculate energy
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# no energy minimization needed for zincblende
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run 0
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7
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ghost atom cutoff = 7
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Memory usage per processor = 2.33394 Mbytes
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Step Temp PotEng Press Volume
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0 0 -24.633958 315900.5 160.72
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Loop time of 3.09944e-06 on 4 procs for 0 steps with 8 atoms
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0.0% 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 | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 3.099e-06 | | |100.00
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Nlocal: 2 ave 2 max 2 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 320 ave 320 max 320 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 140 ave 140 max 140 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 560
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Ave neighs/atom = 70
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Neighbor list builds = 0
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Dangerous builds = 0
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print "${volatom} ${eatom}" append ${evsvolfile}
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print "${volatom} ${eatom}" append evsvol.dat
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20.09 -3.07924477327226
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next i
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jump SELF loop
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ERROR: Label wasn't found in input script (../input.cpp:207)
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@ -1,86 +0,0 @@
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LAMMPS (15 Feb 2016)
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# test Vashishta potential for quartz
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units metal
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boundary p p p
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atom_style atomic
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read_data data.quartz
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triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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9 atoms
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replicate 4 4 4
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triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)
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1 by 1 by 1 MPI processor grid
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576 atoms
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velocity all create 2000.0 277387 mom yes
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displace_atoms all move 0.05 0.9 0.4 units box
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pair_style vashishta
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pair_coeff * * SiO.1990.vashishta Si O
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Reading potential file SiO.1990.vashishta with DATE: 2015-10-14
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neighbor 0.3 bin
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neigh_modify delay 10
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fix 1 all nve
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thermo 10
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timestep 0.001
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#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
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#dump_modify 1 element Si O
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run 100
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.3
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ghost atom cutoff = 10.3
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binsize = 5.15 -> bins = 6 4 5
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Memory usage per processor = 2.05839 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 2000 -5280.875 0 -5132.2259 -20502.321
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10 895.65237 -5198.402 0 -5131.833 419.34676
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20 932.93463 -5201.1569 0 -5131.8169 -21407.961
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30 936.09591 -5201.3998 0 -5131.8248 -32531.168
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40 930.05159 -5201.0073 0 -5131.8816 -46445.212
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50 904.64676 -5199.062 0 -5131.8245 -31402.385
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60 1005.5353 -5206.5725 0 -5131.8365 -29790.442
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70 941.02343 -5201.7644 0 -5131.8232 -23046.796
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80 1020.1044 -5207.6763 0 -5131.8574 -13488.675
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90 912.75535 -5199.651 0 -5131.8108 2715.5897
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100 998.97588 -5206.1008 0 -5131.8523 6024.3651
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Loop time of 2.1758 on 1 procs for 100 steps with 576 atoms
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Performance: 3.971 ns/day, 6.044 hours/ns, 45.960 timesteps/s
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99.9% CPU use with 1 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 | 2.096 | 2.096 | 2.096 | 0.0 | 96.33
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Neigh | 0.074266 | 0.074266 | 0.074266 | 0.0 | 3.41
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Comm | 0.0039184 | 0.0039184 | 0.0039184 | 0.0 | 0.18
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Output | 0.00011158 | 0.00011158 | 0.00011158 | 0.0 | 0.01
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Modify | 0.00092316 | 0.00092316 | 0.00092316 | 0.0 | 0.04
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Other | | 0.0006278 | | | 0.03
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Nlocal: 576 ave 576 max 576 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4926 ave 4926 max 4926 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 210470 ave 210470 max 210470 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 210470
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Ave neighs/atom = 365.399
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Neighbor list builds = 10
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Dangerous builds = 10
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Total wall time: 0:00:02
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@ -1,86 +0,0 @@
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LAMMPS (15 Feb 2016)
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# test Vashishta potential for quartz
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units metal
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boundary p p p
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atom_style atomic
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read_data data.quartz
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triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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9 atoms
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replicate 4 4 4
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triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)
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2 by 1 by 2 MPI processor grid
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576 atoms
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velocity all create 2000.0 277387 mom yes
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displace_atoms all move 0.05 0.9 0.4 units box
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pair_style vashishta
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pair_coeff * * SiO.1990.vashishta Si O
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Reading potential file SiO.1990.vashishta with DATE: 2015-10-14
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neighbor 0.3 bin
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neigh_modify delay 10
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fix 1 all nve
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thermo 10
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timestep 0.001
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#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
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#dump_modify 1 element Si O
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run 100
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.3
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ghost atom cutoff = 10.3
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binsize = 5.15 -> bins = 6 4 5
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Memory usage per processor = 2.00703 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 2000 -5280.875 0 -5132.2259 -20502.321
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10 895.65237 -5198.402 0 -5131.833 419.34676
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20 932.93463 -5201.1569 0 -5131.8169 -21407.961
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30 936.09591 -5201.3998 0 -5131.8248 -32531.168
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40 930.05159 -5201.0073 0 -5131.8816 -46445.212
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50 904.64676 -5199.062 0 -5131.8245 -31402.385
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60 1005.5353 -5206.5725 0 -5131.8365 -29790.442
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70 941.02343 -5201.7644 0 -5131.8232 -23046.796
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80 1020.1044 -5207.6763 0 -5131.8574 -13488.675
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90 912.75535 -5199.651 0 -5131.8108 2715.5897
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100 998.97588 -5206.1008 0 -5131.8523 6024.3651
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Loop time of 0.580982 on 4 procs for 100 steps with 576 atoms
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|
||||
Performance: 14.871 ns/day, 1.614 hours/ns, 172.122 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.51474 | 0.51703 | 0.51923 | 0.2 | 88.99
|
||||
Neigh | 0.017053 | 0.01726 | 0.017457 | 0.1 | 2.97
|
||||
Comm | 0.04357 | 0.045723 | 0.048217 | 0.8 | 7.87
|
||||
Output | 0.00022483 | 0.00024056 | 0.0002687 | 0.1 | 0.04
|
||||
Modify | 0.00026703 | 0.00027239 | 0.00027704 | 0.0 | 0.05
|
||||
Other | | 0.0004541 | | | 0.08
|
||||
|
||||
Nlocal: 144 ave 146 max 143 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 3031 ave 3032 max 3030 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 52617.5 ave 53258 max 52208 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 210470
|
||||
Ave neighs/atom = 365.399
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
|
||||
Total wall time: 0:00:00
|
||||
Loading…
Reference in New Issue