mirror of https://github.com/lammps/lammps.git
small changes to examples scripts for regression purposes
This commit is contained in:
Steve Plimpton
parent
8e32f623f1
commit
1225f7d1e0
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@ -10,7 +10,7 @@ velocity all create 1.44 320984 loop geom
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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neigh_modify exclude molecule all
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neigh_modify exclude molecule/intra all
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pair_style line/lj 2.5
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pair_coeff * * 1.0 1.0 1.0 0.25 2.5
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@ -33,8 +33,10 @@ compute 2 all ke
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compute 3 all pe
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variable toteng equal (c_1+c_2+c_3)/atoms
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compute_modify thermo_temp extra/dof -350
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thermo 1000
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thermo_style custom step temp f_2 pe ke c_1 c_2 c_3 v_toteng
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thermo_style custom step f_2 pe ke c_1 c_2 c_3 v_toteng
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run 10000
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@ -36,7 +36,7 @@ velocity small create 1.44 87287 loop geom
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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neigh_modify exclude molecule big include big
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neigh_modify exclude molecule/intra big include big
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comm_modify mode multi group big vel yes
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neigh_modify include big
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@ -68,13 +68,15 @@ compute tbig big temp
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variable pebig equal pe*atoms/count(big)
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variable ebig equal etotal*atoms/count(big)
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compute_modify tbig extra/dof -350
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compute 1 big erotate/asphere
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compute 2 all ke
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compute 3 all pe
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variable toteng equal (c_1+c_2+c_3)/atoms
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thermo 1000
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thermo_style custom step temp c_tsmall f_2[9] c_1 etotal &
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thermo_style custom step c_tsmall f_2[9] c_1 etotal &
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v_pebig v_ebig press
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thermo_modify temp tbig
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@ -35,7 +35,7 @@ velocity small create 1.44 87287 loop geom
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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neigh_modify exclude molecule big include big
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neigh_modify exclude molecule/intra big include big
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comm_modify mode multi group big vel yes
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neigh_modify include big
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@ -66,6 +66,8 @@ compute tbig big temp
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variable pebig equal pe*atoms/count(big)
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variable ebig equal etotal*atoms/count(big)
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compute_modify tbig extra/dof -4500
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compute 1 big erotate/asphere
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compute 2 all ke
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compute 3 all pe
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@ -1,5 +1,5 @@
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# Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme
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log log.dpd-shardlow
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boundary p p p
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units metal
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@ -1,6 +1,5 @@
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# INPUT FILE FOR DPD_Fluid
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log log.dpd-vv
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boundary p p p
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units metal # ev, ps
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@ -1,5 +1,5 @@
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# Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme
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log log.dpde-shardlow
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boundary p p p
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units metal # ev, ps
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@ -1,6 +1,5 @@
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# INPUT FILE FOR DPD_Fluid
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log log.dpde-vv
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boundary p p p
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units metal # ev, ps
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@ -1,5 +1,5 @@
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# Input File for DPD fluid under isoenthalpic conditions using the VV-SSA integration scheme
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log log.dpdh-shardlow
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boundary p p p
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units metal # ev, ps
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@ -1,5 +1,5 @@
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# Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme
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log log.dpdp-shardlow
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boundary p p p
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units metal
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@ -1,6 +1,5 @@
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# Example for running DPD-RX
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log log.dpdrx-shardlow
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boundary p p p
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units metal # ev, ps
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atom_style dpd
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@ -1,5 +1,5 @@
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# RDX coarse-grain model
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log log.multi-lucy
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units metal # ev, ps
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atom_style dpd
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atom_modify map array
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@ -1,5 +1,4 @@
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variable sname index adamantane_ionized
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log ${sname}.nve.log
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units electron
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newton on
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@ -1,5 +1,4 @@
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variable sname index Be-solid
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log ${sname}.spe.log
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units electron
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newton on
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@ -1,5 +1,4 @@
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variable sname index ch4
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log ${sname}.nve.log
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units electron
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newton on
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@ -1,5 +1,4 @@
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variable sname index ch4
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log ${sname}.nve.log
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units electron
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newton on
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@ -1,5 +1,4 @@
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variable sname index ch4_ionized
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log ${sname}.nvt.log
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units electron
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newton on
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@ -15,6 +14,7 @@ pair_coeff * *
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comm_modify vel yes
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# minimize
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min_style cg
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min_modify line quadratic
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minimize 0 1.0e-6 10000 100000
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@ -1,5 +1,4 @@
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variable sname index h_atom.ang
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log ${sname}.spe.log
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units real
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newton on
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@ -1,5 +1,4 @@
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variable sname index h_atom.bohr
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log ${sname}.spe.log
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units electron
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newton on
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@ -1,5 +1,4 @@
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variable sname index h2
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log ${sname}.spe.log
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units electron
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newton on
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@ -47,4 +46,4 @@ unfix 3
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#fix 1 all nve/eff
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run 100000
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run 10000
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@ -1,5 +1,4 @@
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variable sname index h2bulk
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log ${sname}.npt.log
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units electron
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newton on
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@ -41,7 +40,8 @@ dump 2 all xyz 10000 ${sname}.npt.xyz
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compute 1 all property/atom spin eradius
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dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
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run 10000000
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thermo 1
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run 10
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unfix 1
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undump 2
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@ -1,5 +1,4 @@
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variable sname index h2bulk
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log ${sname}.nve.log
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units electron
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newton on
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@ -18,13 +17,13 @@ comm_modify vel yes
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compute effTemp all temp/eff
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thermo 1000
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thermo 10
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thermo_style custom step pe temp press
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thermo_modify temp effTemp
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# structure minimization
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min_style cg
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minimize 0 1.0e-4 1000 10000
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minimize 0 1.0e-4 10 10
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timestep 0.001
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@ -41,7 +40,7 @@ dump 2 all xyz 1000 ${sname}.nve.xyz
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compute 1 all property/atom spin eradius
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dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
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run 100000
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run 10
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unfix 1
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#unfix 2
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@ -1,5 +1,4 @@
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variable sname index h2bulk.ang
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log ${sname}.nve.log
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units real
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newton on
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@ -29,13 +28,13 @@ variable epauli equal c_energies[2]
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variable ecoul equal c_energies[3]
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variable erres equal c_energies[4]
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thermo 100
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thermo 10
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thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
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thermo_modify temp effTemp press effPress flush yes
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# structure minimization
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min_style cg
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minimize 0 1.0e-4 1000 10000
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minimize 0 1.0e-4 10 10
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timestep 0.001
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@ -52,7 +51,7 @@ dump 2 all xyz 1000 ${sname}.nve.xyz
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compute 1 all property/atom spin eradius
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dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
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run 100000
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run 10
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unfix 1
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#unfix 2
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@ -1,5 +1,4 @@
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variable sname index Li-dendritic
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log ${sname}.min.log
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units electron
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newton on
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@ -7,8 +6,8 @@ boundary p p p
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atom_style electron
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#read_data data.${sname}
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read_restart ${sname}.min.restart2
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read_data data.${sname}
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#read_restart ${sname}.min.restart2
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pair_style eff/cut 50.112
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pair_coeff * *
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@ -1,5 +1,4 @@
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variable sname index Li-dendritic
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log ${sname}.min.log
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units electron
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newton on
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@ -29,7 +28,7 @@ compute 1 all property/atom spin eradius
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#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q c_1[1] c_1[2]
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#dump 2 all xyz 100 ${sname}.min.xyz
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min_modify line quadratic dmax 0.05
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minimize 0 1.0e-7 1000 2000
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minimize 0 1.0e-7 100 100
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write_restart ${sname}.min.restart
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@ -46,7 +45,7 @@ dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1
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dump 2 all xyz 100 ${sname}.nvt.xyz
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restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
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run 10000
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run 100
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undump 1
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undump 2
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@ -1,5 +1,4 @@
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variable sname index Li.ang
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log ${sname}.spe.log
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units real
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newton on
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@ -46,13 +45,13 @@ fix 0 all temp/rescale/eff 1 10.0 3000.0 0.05 1.0
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#fix 0 all langevin/eff 3000.0 3000.0 10.0 699483
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fix 1 all nve/eff
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run 1000
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run 200
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unfix 0
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unfix 1
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fix 1 all nvt/eff temp 3000.0 3000.0 100.0
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compute 1 all property/atom spin eradius ervel
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dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
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dump 1 all custom 500 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
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run 100000
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run 500
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@ -1,5 +1,4 @@
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variable sname index Li.bohr
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log ${sname}.spe.log
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units electron
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newton off
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@ -35,15 +34,15 @@ thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain
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thermo_modify temp effTemp press effPress
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min_style cg
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minimize 0 1e-6 100 2000
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minimize 0 1e-6 100 200
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fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5
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fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
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compute 1 all property/atom spin eradius
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dump 1 all custom 1 ${sname}.spe.lammpstrj &
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dump 1 all custom 100 ${sname}.spe.lammpstrj &
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id type q c_1[1] c_1[2] x y z
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run 1000
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run 100
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@ -92,6 +92,8 @@ fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindl
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# 'Turn' drum by switching the direction of gravity
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unfix grav
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unfix ins1
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unfix ins2
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fix grav all gravity 10 vector 0 -1 0
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variable theta equal 2*PI*elapsed/20000.0
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@ -24,7 +24,7 @@ compute charge2 type2 property/atom q
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compute q2 type2 reduce ave c_charge2
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variable qtot equal count(type1)*c_q1+count(type2)*c_q2
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thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
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thermo_style custom step pe c_q1 c_q2 v_qtot
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thermo 10
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timestep 0.0001
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@ -39,7 +39,7 @@ neigh_modify every 10 delay 0 check yes
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timestep 0.0004
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thermo_style custom step temp etotal pe evdwl ecoul elong &
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c_q1 c_q2 v_qsum press spcpu
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c_q1 c_q2 v_qsum press
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thermo_modify norm yes
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thermo 10
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