read_restart	restart.PA6_3M16cc.eq2

# VARIAES
variable fname index data.PA6_3M16cc
variable simname index PA6_3M16cc


# Dreiding potential information

neighbor	0.4 bin			
neigh_modify	every 10 one 10000	

bond_style      harmonic
bond_coeff	1 1834.44 1.483 	# 1  C-C
bond_coeff	2 1515.82 1.535		# 2  C-C2
bond_coeff	3 1453.42 1.074 	# 3  C-H
bond_coeff	4 1881.86 1.441 	# 4  C-N
bond_coeff	5 1370.18 1.357 	# 5  C2-N
bond_coeff	6 2442.40 1.210 	# 6  C2-O
bond_coeff	7 1950.02 1.008 	# 7  H-N

angle_style     cosine/squared
angle_coeff	1 165.64 121.68 	# 1  C-C-C
angle_coeff	2 165.64 121.68 	# 2  C-C-C2
angle_coeff	3 127.96 118.21 	# 3  C-C-H
angle_coeff	4 165.64 121.68 	# 4  C-C-N
angle_coeff	5 95.20 119.24 		# 5  C-C2-N
angle_coeff	6 329.58 122.18 	# 6  C-C2-O
angle_coeff	7 518.10 112.11		# 7  C-N-C2
angle_coeff	8 152.04 98.43		# 8  C-N-H
angle_coeff	9 200.96 106.48		# 9  C2-C-H
angle_coeff	10 226.50 109.48	# 10  C2-N-H
angle_coeff	11 108.24 119.64	# 11  H-C-H
angle_coeff	12 244.30 104.12	# 12  H-C-N
angle_coeff	13 108.24 119.64	# 13  H-N-H
angle_coeff	14 409.06 120.09	# 14  N-C2-O

dihedral_style	harmonic
dihedral_coeff	1 5.70 1 0	# 1  C-C-C-C
dihedral_coeff	1 5.70 1 3
dihedral_coeff	2 5.70 1 0	# 2  C-C-C-C2
dihedral_coeff	2 5.70 1 3
dihedral_coeff	3 6.16 1 0	# 3  C-C-C-H
dihedral_coeff	3 6.16 1 3
dihedral_coeff	4 5.70 1 0	# 4  C-C-C-N
dihedral_coeff	4 5.70 1 3
dihedral_coeff	5 -1.34 1 0	# 5  C-C-C2-N
dihedral_coeff	5 24.62 1 1
dihedral_coeff	5 -1.94 1 2
dihedral_coeff	5 -4.68 1 3
dihedral_coeff	5 1.26 1 4
dihedral_coeff	5 -0.20 1 5
dihedral_coeff	5 0.14 1 6
dihedral_coeff	6 0 1 0		# 6  C-C-C2-O
dihedral_coeff	7 -5.32 1 0	# 7  C-C-N-C2
dihedral_coeff	7 1.56 1 1
dihedral_coeff	7 7.34 1 2
dihedral_coeff	7 -0.52 1 3
dihedral_coeff	7 1.28 1 4
dihedral_coeff	7 -0.28 1 5
dihedral_coeff	7 0.18 1 6
dihedral_coeff	8 0 1 0		# 8  C-C-N-H
dihedral_coeff	9 24.76 1 0	# 9  C-C2-N-C
dihedral_coeff	9 -25.76 1 2
dihedral_coeff	10 24.76 1 0	# 10  C-C2-N-H
dihedral_coeff	10 -15.76 1 2
dihedral_coeff	11 1.10 1 0	# 11  C2-C-C-H
dihedral_coeff	11 1.10 1 3
dihedral_coeff	12 5.70 1 0	# 12  H-C-C-H
dihedral_coeff	12 5.70 1 3
dihedral_coeff	13 6.16 1 0	# 13  H-C-C-N
dihedral_coeff	13 6.16 1 3
dihedral_coeff	14 0 1 0	# 14  H-C-C2-N
dihedral_coeff	15 0 1 0	# 15  H-C-C2-O
dihedral_coeff	16 0 1 0	# 16  H-C-N-C2
dihedral_coeff	17 0 1 0	# 17  H-C-N-H
dihedral_coeff	18 24.76 1 0	# 18  O-C2-N-C
dihedral_coeff	18 -20.50 1 2
dihedral_coeff	19 24.76 1 0	# 19  O-C2-N-H
dihedral_coeff	19 -17.80 1 2

improper_style harmonic
improper_coeff * 50 0.0

pair_style	lj/cut/coul/cut 9
pair_coeff	1 1 0.0792 3.423 9	# C-C
pair_coeff	1 2 0.0792 3.423 9	# C-C2
pair_coeff	1 3 0.0398 3.123 9	# C-H
pair_coeff	1 4 0.0783 3.344 9	# C-N
pair_coeff	1 5 0.0871 3.229 9	# C-O
pair_coeff	2 2 0.0792 3.423 9	# C2-C2
pair_coeff	2 3 0.0398 3.123 9	# C2-H
pair_coeff	2 4 0.0783 3.344 9	# C2-N
pair_coeff	2 5 0.0871 3.229 9	# C2-O
pair_coeff	3 3 0.2821 2.972 9	# H-H
pair_coeff	3 4 0.0396 3.083 9	# H-N
pair_coeff	3 5 0.0280 2.689 9	# H-O
pair_coeff	4 4 0.0553 3.173 9	# N-N
pair_coeff	4 5 0.0466 2.976 9	# N-O
pair_coeff	5 5 0.0667 3.005 9	# O-O


#####################################################
# 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"			


dump 		1 all cfg 1000 dump.deform_*.cfg mass type xs ys zs
dump_modify	1 element C C H N O


fix		1 all npt temp 293 293 50 y 0 0 1000 z 0 0 1000 drag 2.0
fix		2 all deform 1 x erate 5e-6 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		200000

unfix 1
unfix 2
unfix def1
unfix def2

undump 1
print "All done"