Flat polymer surface using shrink-wrapped boundary

Dear lammps users

I am preparing an epoxy to implement an indentation( following by scratch) test on it. My problem is that, I need to use shrink-wrapped boundary condition in one dimension. However, despite equilibrium state using periodic boundaries, I cannot reach to a flat( semi-flat) surface to preform the test. Do you have any idea how I can reach to a flat surface to use it for indentation test and get the reliable results ?

Thank you very much in advance
Bests

Saeed Doagou-R
saeed.doagu.r@…24…

An example of my code can bee seen below

3D Pure Epoxy Simulation

boundary p p s
units metal

#neighbor 1 bin
neigh_modify delay 5

atom_style full

read_data d.40.txt

special_bonds amber

defenition of forcefield

pair_style lj/charmm/coul/charmm 6 8

pair_coeff 1 1 0.0047042 3.399669508
pair_coeff 1 2 0.004170867 3.399669508
pair_coeff 1 3 0.005864103 3.324834016
pair_coeff 1 4 0.005864103 3.199840926
pair_coeff 1 5 0.00652379 3.233071448
pair_coeff 1 6 0.001782079 2.234373985
pair_coeff 1 7 0.0000 1.699834754
pair_coeff 1 8 0.001741898 2.999655984
pair_coeff 1 9 0.001782079 3.024601148
pair_coeff 2 2 0.003698 3.399669508
pair_coeff 2 3 0.005199267 3.324834016
pair_coeff 2 4 0.005199267 3.199840926
pair_coeff 2 5 0.005784163 3.233071448
pair_coeff 2 6 0.001580038 2.234373985
pair_coeff 2 7 0 1.699834754
pair_coeff 2 8 0.001544413 2.999655984
pair_coeff 2 9 0.001580038 3.024601148
pair_coeff 3 3 0.00731 3.249998524
pair_coeff 3 4 0.00731 3.125005434
pair_coeff 3 5 0.008132345 3.158235956
pair_coeff 3 6 0.002221482 2.159538493
pair_coeff 3 7 0 1.624999262
pair_coeff 3 8 0.002171394 2.924820492
pair_coeff 3 9 0.002221482 2.949765656
pair_coeff 4 4 0.00731 3.000012343
pair_coeff 4 5 0.008132345 3.033242866
pair_coeff 4 6 0.002221482 2.034545403
pair_coeff 4 7 0 1.500006172
pair_coeff 4 8 0.002171394 2.799827401
pair_coeff 4 9 0.002221482 2.824772566
pair_coeff 5 5 0.0090472 3.066473388
pair_coeff 5 6 0.002471389 2.067775925
pair_coeff 5 7 0 1.533236694
pair_coeff 5 8 0.002415666 2.833057924
pair_coeff 5 9 0.002471389 2.858003088
pair_coeff 6 6 0.0006751 1.069078462
pair_coeff 6 7 0 0.534539231
pair_coeff 6 8 0.000659878 1.834360461
pair_coeff 6 9 0.0006751 1.859305625
pair_coeff 7 7 0 0
pair_coeff 7 8 0 1.29982123
pair_coeff 7 9 0 1.324766394
pair_coeff 8 8 0.000645 2.59964246
pair_coeff 8 9 0.000659878 2.624587624
pair_coeff 9 9 0.0006751 2.649532788

bond_style harmonic

bond_coeff 1 13.33 1.526
bond_coeff 2 13.76 1.41
bond_coeff 3 12.9 1.4
bond_coeff 4 20.167 1.4
bond_coeff 5 13.631 1.51
bond_coeff 6 14.491 1.449
bond_coeff 7 18.662 1.01
bond_coeff 8 13.76 1.41
bond_coeff 9 14.62 1.09
bond_coeff 10 15.781 1.08
bond_coeff 11 23.779 0.96

angle_style charmm

angle_coeff 1 1.505 109.5 0 0
angle_coeff 2 2.15 109.5 0 0
angle_coeff 3 1.72 109.5 0 0
angle_coeff 4 2.15 109.5 0 0
angle_coeff 5 2.15 109.5 0 0
angle_coeff 6 2.365 108.5 0 0
angle_coeff 7 2.58 109.5 0 0
angle_coeff 8 2.15 118.4 0 0
angle_coeff 9 1.505 120 0 0
angle_coeff 10 3.01 120 0 0
angle_coeff 11 2.709 120 0 0
angle_coeff 12 3.01 120 0 0
angle_coeff 13 2.709 114 0 0
angle_coeff 14 3.01 109.5 0 0
angle_coeff 15 3.44 109.7 0 0
angle_coeff 16 2.15 118 0 0
angle_coeff 17 2.66 113 0 0
angle_coeff 18 2.1887 108.7 0 0
angle_coeff 19 2.15 109.5 0 0
angle_coeff 20 1.505 109.5 0 0

dihedral_style charmm

dihedral_coeff 1 0.049 3 0 0
dihedral_coeff 2 0.0602 3 0 0
dihedral_coeff 3 0.0602 3 0 0
dihedral_coeff 4 0.049 3 0 0
dihedral_coeff 5 0.0602 3 0 0
dihedral_coeff 6 0.0602 3 0 0
dihedral_coeff 7 0.0602 3 0 0
dihedral_coeff 8 0.049 3 0 0
dihedral_coeff 9 0.049 3 0 0
dihedral_coeff 10 0.15 2 180 0
dihedral_coeff 11 0.6235 2 180 0
dihedral_coeff 12 0.6235 2 180 0
dihedral_coeff 13 0.6235 2 180 0
dihedral_coeff 14 0.6235 2 180 0
dihedral_coeff 15 0.6235 2 180 0
dihedral_coeff 16 0 2 0 0
dihedral_coeff 17 0.6235 2 180 0
dihedral_coeff 18 0.0602 3 0 0
dihedral_coeff 19 0 2 0 0
dihedral_coeff 20 0.6235 2 180 0
dihedral_coeff 21 0.0215 3 0 0
dihedral_coeff 22 0.0215 3 0 0
dihedral_coeff 23 0.0602 3 0 0
dihedral_coeff 24 0.0602 3 0 0
dihedral_coeff 25 0 2 0 0
dihedral_coeff 26 0.0602 3 0 0
dihedral_coeff 27 0.0602 3 0 0
dihedral_coeff 28 0.0602 3 0 0
dihedral_coeff 29 0 2 0 0
dihedral_coeff 30 0 2 0 0
dihedral_coeff 31 0 2 0 0
dihedral_coeff 32 0.0602 3 0 0

velocity all create 1000 2349852
fix 1 all nve/limit 0.05
fix 2 all langevin 1000 1000 100 909900
timestep 0.001

thermo 5000

dump 1 all xyz 10000 dump1-*.xyz
run 150000

write_restart equ.restart

unfix 1
unfix 2
undump 1

Dear lammps users

  I am preparing an epoxy to implement an indentation( following by
scratch) test on it. My problem is that, I need to use shrink-wrapped
boundary condition in one dimension. However, despite equilibrium state
using periodic boundaries, I cannot reach to a flat( semi-flat) surface to
preform the test. Do you have any idea how I can reach to a flat surface to
use it for indentation test and get the reliable results ?

Thank you very much in advance
Bests

Saeed Doagou-R
[email protected]...

An example of my code can bee seen below
# 3D Pure Epoxy Simulation
boundary p p s
units metal
#neighbor 1 bin
neigh_modify delay 5
atom_style full
read_data d.40.txt
special_bonds amber
# defenition of forcefield
pair_style lj/charmm/coul/charmm 6 8
pair_coeff 1 1 0.0047042 3.399669508
pair_coeff 1 2 0.004170867 3.399669508
pair_coeff 1 3 0.005864103 3.324834016
pair_coeff 1 4 0.005864103 3.199840926
pair_coeff 1 5 0.00652379 3.233071448
pair_coeff 1 6 0.001782079 2.234373985
pair_coeff 1 7 0.0000 1.699834754
pair_coeff 1 8 0.001741898 2.999655984
pair_coeff 1 9 0.001782079 3.024601148
pair_coeff 2 2 0.003698 3.399669508
pair_coeff 2 3 0.005199267 3.324834016
pair_coeff 2 4 0.005199267 3.199840926
pair_coeff 2 5 0.005784163 3.233071448
pair_coeff 2 6 0.001580038 2.234373985
pair_coeff 2 7 0 1.699834754
pair_coeff 2 8 0.001544413 2.999655984
pair_coeff 2 9 0.001580038 3.024601148
pair_coeff 3 3 0.00731 3.249998524
pair_coeff 3 4 0.00731 3.125005434
pair_coeff 3 5 0.008132345 3.158235956
pair_coeff 3 6 0.002221482 2.159538493
pair_coeff 3 7 0 1.624999262
pair_coeff 3 8 0.002171394 2.924820492
pair_coeff 3 9 0.002221482 2.949765656
pair_coeff 4 4 0.00731 3.000012343
pair_coeff 4 5 0.008132345 3.033242866
pair_coeff 4 6 0.002221482 2.034545403
pair_coeff 4 7 0 1.500006172
pair_coeff 4 8 0.002171394 2.799827401
pair_coeff 4 9 0.002221482 2.824772566
pair_coeff 5 5 0.0090472 3.066473388
pair_coeff 5 6 0.002471389 2.067775925
pair_coeff 5 7 0 1.533236694
pair_coeff 5 8 0.002415666 2.833057924
pair_coeff 5 9 0.002471389 2.858003088
pair_coeff 6 6 0.0006751 1.069078462
pair_coeff 6 7 0 0.534539231
pair_coeff 6 8 0.000659878 1.834360461
pair_coeff 6 9 0.0006751 1.859305625
pair_coeff 7 7 0 0
pair_coeff 7 8 0 1.29982123
pair_coeff 7 9 0 1.324766394
pair_coeff 8 8 0.000645 2.59964246
pair_coeff 8 9 0.000659878 2.624587624
pair_coeff 9 9 0.0006751 2.649532788
bond_style harmonic
bond_coeff 1 13.33 1.526
bond_coeff 2 13.76 1.41
bond_coeff 3 12.9 1.4
bond_coeff 4 20.167 1.4
bond_coeff 5 13.631 1.51
bond_coeff 6 14.491 1.449
bond_coeff 7 18.662 1.01
bond_coeff 8 13.76 1.41
bond_coeff 9 14.62 1.09
bond_coeff 10 15.781 1.08
bond_coeff 11 23.779 0.96
angle_style charmm
angle_coeff 1 1.505 109.5 0 0
angle_coeff 2 2.15 109.5 0 0
angle_coeff 3 1.72 109.5 0 0
angle_coeff 4 2.15 109.5 0 0
angle_coeff 5 2.15 109.5 0 0
angle_coeff 6 2.365 108.5 0 0
angle_coeff 7 2.58 109.5 0 0
angle_coeff 8 2.15 118.4 0 0
angle_coeff 9 1.505 120 0 0
angle_coeff 10 3.01 120 0 0
angle_coeff 11 2.709 120 0 0
angle_coeff 12 3.01 120 0 0
angle_coeff 13 2.709 114 0 0
angle_coeff 14 3.01 109.5 0 0
angle_coeff 15 3.44 109.7 0 0
angle_coeff 16 2.15 118 0 0
angle_coeff 17 2.66 113 0 0
angle_coeff 18 2.1887 108.7 0 0
angle_coeff 19 2.15 109.5 0 0
angle_coeff 20 1.505 109.5 0 0
dihedral_style charmm
dihedral_coeff 1 0.049 3 0 0
dihedral_coeff 2 0.0602 3 0 0
dihedral_coeff 3 0.0602 3 0 0
dihedral_coeff 4 0.049 3 0 0
dihedral_coeff 5 0.0602 3 0 0
dihedral_coeff 6 0.0602 3 0 0
dihedral_coeff 7 0.0602 3 0 0
dihedral_coeff 8 0.049 3 0 0
dihedral_coeff 9 0.049 3 0 0
dihedral_coeff 10 0.15 2 180 0
dihedral_coeff 11 0.6235 2 180 0
dihedral_coeff 12 0.6235 2 180 0
dihedral_coeff 13 0.6235 2 180 0
dihedral_coeff 14 0.6235 2 180 0
dihedral_coeff 15 0.6235 2 180 0
dihedral_coeff 16 0 2 0 0
dihedral_coeff 17 0.6235 2 180 0
dihedral_coeff 18 0.0602 3 0 0
dihedral_coeff 19 0 2 0 0
dihedral_coeff 20 0.6235 2 180 0
dihedral_coeff 21 0.0215 3 0 0
dihedral_coeff 22 0.0215 3 0 0
dihedral_coeff 23 0.0602 3 0 0
dihedral_coeff 24 0.0602 3 0 0
dihedral_coeff 25 0 2 0 0
dihedral_coeff 26 0.0602 3 0 0
dihedral_coeff 27 0.0602 3 0 0
dihedral_coeff 28 0.0602 3 0 0
dihedral_coeff 29 0 2 0 0
dihedral_coeff 30 0 2 0 0
dihedral_coeff 31 0 2 0 0
dihedral_coeff 32 0.0602 3 0 0
velocity all create 1000 2349852
fix 1 all nve/limit 0.05
fix 2 all langevin 1000 1000 100 909900
timestep 0.001

You might want to try heating it up gradually, instead of 1000K right
away. Also the tdamp is too big; try 0.1.

Ray