View source for LAMMPS Input Deck for Atomistic Deformation of Amorphous Polyethylene

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Here is an example LAMMPS input script.  The 'fname' variable is the name of the LAMMPS data file which contains the atom positions along with all of the bond, angle, and dihedral angle lists.  An example LAMMPS datafile for PE is attached below after the input script.

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#####################################################
#                                                   #
# DEFORM DREIDING LAMMPS INPUT SCRIPT               #
#                                                   #
# Filename: in.deform_dreiding.txt                  #
# Author: Mark Tschopp, 2010                        #
#                                                   #
# The methodology outlined here follows that from   #
# Hossain, Tschopp, et al. 2010, Polymer.  Please   #
# cite accordingly. The following script requires   #
# a LAMMPS data file containing the coordinates and #
# appropriate bond/angle/dihedral lists for each    #
# united atom.                                      #
#                                                   #
# Execute the script through:                       #
# lmp_exe < in.deform_dreiding.txt                  #
#                                                   #
#####################################################

# VARIABLES
variable fname index PE_nc10_cl1000.dat
variable simname index PE_nc10_cl1000

# Initialization
units		real
boundary	p p p
atom_style	molecular
log 		log.${simname}.txt
read_data	${fname}

# Dreiding potential information
neighbor	0.4 bin
neigh_modify	every 10 one 10000
bond_style      harmonic
bond_coeff	1 350 1.53
angle_style     harmonic
angle_coeff	1 60 109.5
dihedral_style	multi/harmonic
dihedral_coeff	1 1.73 -4.49 0.776 6.99 0.0
pair_style	lj/cut 10.5
pair_coeff	1 1 0.112 4.01 10.5

#####################################################
# Equilibration Stage 1 (Langevin dynamics at 500 K)
velocity 	all create 500.0 1231
fix		1 all nve/limit 0.05
fix		2 all langevin 500.0 500.0 10.0 904297
thermo_style	custom step temp press
thermo          100
timestep	1
run		10000
unfix 1
unfix 2
write_restart 	restart.${simname}.dreiding1

#####################################################
# Equilibration Stage 2 (NPT dynamics at 500 K)
fix		1 all npt temp 500.0 500.0 50 iso 0 0 1000 drag 2
fix  		2 all momentum 1 linear 1 1 1
thermo_style	custom step temp press
thermo          100
timestep	0.5
reset_timestep	0
run		50000
unfix 1
unfix 2
write_restart 	restart.${simname}.dreiding2

#####################################################
# Equilibration Stage 3 (NPT dynamics from 500 K --> 100 K)
fix		1 all npt temp 500 100 50 iso 0 0 1000 drag 2
fix		2 all momentum 1 linear 1 1 1
thermo_style	custom step temp press
thermo          10
timestep	0.5
reset_timestep 	0
run		50000
unfix 1
unfix 2
write_restart 	restart.${simname}.dreiding3

#####################################################
# Equilibration Stage 4 (NPT dynamics at 100 K)
fix		1 all npt temp 100 100 50 iso 0 0 1000 drag 2
fix		2 all momentum 1 linear 1 1 1
thermo_style	custom step temp press epair ebond eangle edihed pxx pyy pzz lx ly lz
thermo          10
timestep	0.5
reset_timestep 	0
run		50000
unfix 1
unfix 2
write_restart 	restart.${simname}.dreiding4

#####################################################
# Uniaxial Tensile Deformation
run 0
variable tmp equal "lx"
variable L0 equal ${tmp}
variable strain equal "(lx - v_L0)/v_L0"
variable p1 equal "v_strain"
variable p2 equal "-pxx/10000*1.01325"
variable p3 equal "-pyy/10000*1.01325"
variable p4 equal "-pzz/10000*1.01325"
variable p5 equal "lx"
variable p6 equal "ly"
variable p7 equal "lz"
variable p8 equal "temp"
variable t2 equal "epair"
variable t3 equal "ebond"
variable t4 equal "eangle"
variable t5 equal "edihed"
fix		1 all npt temp 100 100 50 y 0 0 1000 z 0 0 1000 drag 2
fix		2 all deform 1 x erate 1e-5 units box remap x
fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6} ${p7} ${p8}" file ${simname}.def1.txt screen no
fix def2 all print 100 "${p1} ${t2} ${t3} ${t4} ${t5}" file ${simname}.def2.txt screen no
thermo_style	custom step temp pxx pyy pzz lx ly lz epair ebond eangle edihed
thermo          100
timestep	1
reset_timestep	0
run		171800
unfix 1
unfix 2
unfix def1
unfix def2

print "All done"

</pre>

[[Category: LAMMPS]]
[[Category: Input Deck]]
[[Category: Script]]