# My initial run: Energy minimization & Production run of the system CO2-EPM2 units real atom_style full boundary p p p bond_style harmonic angle_style harmonic read_data data1.data #write_data data.* #neighbor 2.0 bin #neigh_modify delay 0 every 1 check yes lattice fcc 1 timestep 1.0 thermo 100 pair_style lj/cut/coul/long 12.0 pair_modify tail yes pair_coeff 1 1 0.055890 2.7570 pair_coeff 1 2 0.094560 2.8920 pair_coeff 2 2 0.159980 3.0330 kspace_style pppm 1e-4 #region tbox block 0.0 40.1 0.0 40.1 0 120.2 #region gpbox1 block 0.0 40.1 0.0 40.1 0 40.0 #region gpbox2 block 0.0 40.1 0.0 40.1 80.1 120.2 #region mbox1 block 0.0 40.1 0.0 40.1 0 10.0 #region mbox2 block 0.0 40.1 0.0 40.1 10.0 20.0 #region mbox3 block 0.0 40.1 0.0 40.1 20.0 30.0 #region mbox4 block 0.0 40.1 0.0 40.1 30.0 40.0 #region mbox5 block 0.0 40.1 0.0 40.1 40.0 50.1 #region mbox6 block 0.0 40.1 0.0 40.1 50.1 60.1 #region mbox7 block 0.0 40.1 0.0 40.1 60.1 70.1 #region mbox8 block 0.0 40.1 0.0 40.1 70.1 80.1 #region mbox9 block 0.0 40.1 0.0 40.1 80.1 90.1 #region mbox10 block 0.0 40.1 0.0 40.1 90.1 100.1 #region mbox11 block 0.0 40.1 0.0 40.1 100.1 110.1 #region mbox12 block 0.0 40.1 0.0 40.1 110.1 120.2 #group nc type 1 #group no type 2 #group Rgp1 region gpbox1 #group Rgp2 region gpbox2 #group R1 region mbox1 #group R2 region mbox2 #group R3 region mbox3 #group R4 region mbox4 #group R5 region mbox5 #group R6 region mbox6 #group R7 region mbox7 #group R8 region mbox8 #group R9 region mbox9 #group R10 region mbox10 #group R11 region mbox11 #group R12 region mbox12 #variable nCO21 equal count(nc,gpbox1) #variable nCO22 equal count(nc,gpbox2) #variable m equal mass(all)/6.02214e23 #variable v equal vol*1.0e-24 #variable d equal v_m/v_v #variable mgp1 equal mass(Rgp1,gpbox1)/6.02214e23 #variable vgp1 equal (vol/3)*1.0e-24 #variable dgp1 equal v_mgp1/v_vgp1 #variable mgp2 equal mass(Rgp2,gpbox2)/6.02214e23 #variable vgp2 equal (vol/3)*1.0e-24 #variable dgp2 equal v_mgp2/v_vgp2 #variable d1 equal mass(R1)/(vol*1.0e-24*6.02214e23) #variable d2 equal mass(R2)/(vol*1.0e-24*6.02214e23) #variable d3 equal mass(R3)/(vol*1.0e-24*6.02214e23) #variable d4 equal mass(R4)/(vol*1.0e-24*6.02214e23) #variable d5 equal mass(R5)/(vol*1.0e-24*6.02214e23) #variable d6 equal mass(R6)/(vol*1.0e-24*6.02214e23) #variable d7 equal mass(R7)/(vol*1.0e-24*6.02214e23) #variable d8 equal mass(R8)/(vol*1.0e-24*6.02214e23) #variable d9 equal mass(R9)/(vol*1.0e-24*6.02214e23) #variable d10 equal mass(R10)/(vol*1.0e-24*6.02214e23) #variable d11 equal mass(R11)/(vol*1.0e-24*6.02214e23) #variable d12 equal mass(R12)/(vol*1.0e-24*6.02214e23) velocity all create 230 432567 dist uniform minimize 0.0 1.0 100000 800000 #compute 1 all entropy/atom 0.25 5 #compute peratom all stress/atom NULL #compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] #variable pressure equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) #compute MSDo no msd #compute MSDc nc msd #compute MSDt all msd #compute MSD1 R1 msd #compute MSD2 R2 msd #compute MSD3 R3 msd #ompute MSD4 R4 msd #compute MSD5 R5 msd #compute MSD6 R6 msd #compute MSD7 R7 msd #compute MSD8 R8 msd #ompute MSD9 R9 msd #compute MSD10 R10 msd #compute MSD11 R11 msd #compute MSD12 R12 msd thermo 1000 thermo_style custom lx ly lz vol step temp press pxx pyy pzz pxy pxz pyz pe etotal density dump 1 all xyz 100000 dumpCO2pure.xyz dump_modify 1 element C1 O2 fix 1 all shake 0.0001 10 1000 b 1 fix 2 all nvt temp 230.0 230.0 100.0 #run 100000 #unfix 1 #unfix 2 #fix 3 all shake 0.0001 10 1000 b 1 #fix 4 all nvt temp 235.0 235.0 100.0 #run 100000 #unfix 3 #unfix 4 #change_box all x final 0.0 40.1 y final 0.0 40.1 z final 0.0 120.1 boundary p p p remap units box #displace_atoms all move 0.0 0.0 0.0 units box #fix 5 all shake 0.0001 10 1000 b 1 #fix 6 all nvt temp 240.0 240.0 100.0 #run 100000 #unfix 5 #unfix 6 #fix 7 all shake 0.0001 10 1000 b 1 #fix 8 all nvt temp 245.0 245.0 100.0 #run 100000 #unfix 7 #unfix 8 #fix 9 all shake 0.0001 10 1000 b 1 #fix 10 all nvt temp 250.0 250.0 100.0 restart 5000000 PureCO2VLE.restart run 10000000