#polymer chain test #units====================================================================== ============================ units real dimension 3 atom_style full boundary p p p timestep 1 #force field======================================================================= ============================ pair_style lj/class2/coul/cut 10 12 bond_style class2 angle_style class2 dihedral_style class2 improper_style class2 dielectric 1.0 pair_modify tail yes special_bonds lj 0 0 1 coul 0 0 1 dihedral yes #atom definitionh================================================================= =============== read_data densitytest.lammps05 #initialize velocity==================================================================== =============================== velocity all create 300 4654653 rot yes dist gaussian velocity all zero linear #modify================================================================= neighbor 0.3 bin neigh_modify every 2 delay 10 check yes #=========================================================================== ======================================thermo setting thermo 100 thermo_style custom step temp press pe ke etotal vol lx ly lz pxx pyy pzz pxy pxz pyz timestep 1 #=========================================================================== ========================================minimization #=========================================================================== ==========================================running variable myvolume equal vol variable mytemp equal temp variable mypress equal press variable mylx equal lx variable mypxx equal pxx variable myly equal ly variable mypyy equal pyy variable mylz equal lz variable mypzz equal pzz variable mypxy equal pxy variable mypyz equal pyz variable mypxz equal pxz variable mype equal pe variable myke equal ke variable myetotal equal etotal variable myepair equal epair variable myebond equal ebond variable myeangle equal eangle variable myedihed equal edihed variable myeimp equal eimp variable myecoul equal ecoul variable myevdwl equal evdwl variable myetail equal etail minimize 1e-12 1e-14 1000000000 10000000000000 #define output====================================================================== ====================================== fix myenergy all ave/time 1 10 100 v_mytemp v_myvolume v_mypress v_mylx v_myly v_mylz v_mypxx v_mypyy v_mypzz v_mypxy v_mypyz v_mypxz v_myetotal v_myke v_mype v_myepair v_myevdwl v_myecoul v_myetail v_myebond v_myeangle v_myedihed v_myeimp file volume500K.PE8 fix mystress all ave/time 1 1000 10000 v_mypress v_mylx v_myly v_mylz v_mypxx v_mypyy v_mypzz v_mypxy v_mypyz v_mypxz file mystress.data dump 1 all atom 100 smallbigepoxy.pos dump_modify 1 image yes dump 2 all atom 100 smallbigepoxy2.pos #=========================================================================== ================================= fix 1 all nvt 300 300 100 drag 2 fix beforemydensityx all ave/spatial 1 100 100 x lower 1 density/number density/mass file beforemydensityallx.file units box fix beforemydensityy all ave/spatial 1 100 100 y lower 1 density/number density/mass file beforemydensityally.file units box fix beforemydensityz all ave/spatial 1 100 100 z lower 1 density/number density/mass file beforemydensityallz.file units box run 1000 unfix 1