# This is the control script for LAMMPS echo both log 2.1_Initialize.out #------------------------------------------------------------------------------- # Stage 2.1: Initialize LAMMPS run for 3-d periodic #------------------------------------------------------------------------------- units real boundary p p p atom_style full pair_style lj/class2/coul/cut 9.5 pair_modify mix sixthpower bond_style class2 angle_style class2 dihedral_style class2 improper_style class2 special_bonds lj/coul 0.0 0.0 1.0 box tilt large read_data structure.dat include parameters.dat neighbor 2.0 bin neigh_modify delay 0 every 1 check yes variable R equal 0.00198722 variable sysvol equal vol variable sysmass equal mass(all)/6.0221367e+23 variable sysdensity equal v_sysmass/v_sysvol/1.0e-24 variable coulomb equal ecoul+elong variable etotal equal etotal variable pe equal pe variable ke equal ke variable evdwl equal evdwl variable epair equal epair variable ebond equal ebond variable eangle equal eangle variable edihed equal edihed variable eimp equal eimp variable lx equal lx variable ly equal ly variable lz equal lz variable Nthermo equal 0 variable cella equal lx variable cellb equal sqrt(ly*ly+xy*xy) variable cellc equal sqrt(lz*lz+xz*xz+yz*yz) variable cellalpha equal acos((xy*xz+ly*yz)/(v_cellb*v_cellc)) variable cellbeta equal acos(xz/v_cellc) variable cellgamma equal acos(xy/v_cellb) variable p equal press variable pxx equal pxx variable pyy equal pyy variable pzz equal pzz variable pyz equal pyz variable pxz equal pxz variable pxy equal pxy variable sxx equal -pxx variable syy equal -pyy variable szz equal -pzz variable syz equal -pyz variable sxz equal -pxz variable sxy equal -pxy variable fmax equal fmax variable fnorm equal fnorm variable time equal step*dt+0.000001 variable surfacetension equal 0.5*v_lz*(0.5*(v_sxx+v_syy)-v_szz) thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul elong pe ke thermo_modify flush yes # # Set up the fixed and movable groups # group movable union all group fixed subtract all movable log 2_Minimization.out #------------------------------------------------------------------------------- # Stage 2.2: Minimization #------------------------------------------------------------------------------- min_style cg min_modify dmax 0.05 #line fast reset_timestep 0 thermo_style custom step fmax fnorm press vol v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy pe v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma dump sci all custom 1000 2.xyz id mol type q xs ys zs thermo 100 fix 2_2_2 fixed setforce 0.0 0.0 0.0 minimize 0.0 1.0 1000 10000 undump sci unfix 2_2_2 log 3_NVT.out #------------------------------------------------------------------------------- # Stage 3: NVT integration for 10 ps with a timestep of 1 fs # Temperature 400 K #------------------------------------------------------------------------------- reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul elong pe ke thermo 100 fix 1 movable nvt temp 400 400 100 drag 1.0 fix 2 movable ave/time 1 1000 1000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 3_ave.txt fix 3 movable ave/time 20 1 20 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 3_inst.txt restart 1000 3.restart dump trj all custom 50 VMD_3.lammpstrj id mol type xs ys zs ix iy iz q timestep 1 run 1000 undump trj restart 0 dump sci all custom 1000 3.xyz id mol type q xs ys zs run 0 undump sci unfix 1 unfix 2 unfix 3 log 4_NPT.out #------------------------------------------------------------------------------- # Stage 4: NPT integration for 1 ps with a timestep of 1 fs # Temperature 300 K # Pressure 1 atm #------------------------------------------------------------------------------- reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul elong pe ke thermo 100 fix 1 movable npt temp 300 300 100 iso 1 1 100 drag 0 mtk yes nreset 20 fix 2 movable ave/time 1 99 100 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 4_ave.txt off 1 fix 3 movable ave/time 20 1 20 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 4_inst.txt off 1 restart 1000 4.restart dump trj all custom 50 VMD_4.lammpstrj id mol type xs ys zs ix iy iz q timestep 1 run 1000 undump trj restart 0 dump sci all custom 1000 4.xyz id mol type q xs ys zs run 0 undump sci unfix 1 unfix 2 unfix 3