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Finally updated the github tutorial

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oywg11 2018-03-13 17:43:25 +02:00
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commit bbb2a6d641
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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
group adsorbate type 3 4
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ILP/graphene/hBN 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
pair_coeff * * ILP/graphene/hBN BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ILP/graphene/hBN
variable Tersoff equal c_0
variable Ecoul equal c_1
variable EILP equal c_2
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
thermo_modify line one format float %.15f
thermo_modify flush yes norm no lost warn #ignore
dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 100000

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# Interlayer Potential for graphitic and boron nitride systems
#
# Cite J. Chem.Theory Comput. 2016, 12, 2896-905 and J. Phys. Chem. C 2017, 121, 22826-22835.
# beta alpha delta epsilon C d sR reff C6 S rcut
C C 3.22 9.200 1.20 0.010 0.800 15.0 0.704 3.586 522.915 43.363442016573508 2.0
B B 3.10 8.000 1.60 0.460 0.450 15.0 0.800 3.786 1037.322 43.363442016573508 2.0
N N 3.34 8.000 1.20 0.210 0.680 15.0 0.800 3.365 310.433 43.363442016573508 2.0
H H 2.70 9.000 20.0 0.310 0.130 15.0 0.784 2.798 37.870 43.363442016573508 1.2
C B 3.02 10.00 1.20 0.370 0.180 15.0 0.784 3.691 657.408 43.363442016573508 2.0
B C 3.02 10.00 1.20 0.370 0.180 15.0 0.784 3.691 657.408 43.363442016573508 2.0
C N 3.40 10.00 1.20 0.210 0.360 15.0 0.784 3.481 366.955 43.363442016573508 2.0
N C 3.40 10.00 1.20 0.210 0.360 15.0 0.784 3.481 366.955 43.363442016573508 2.0
B N 3.17 7.500 1.80 0.200 0.130 15.0 0.800 3.576 516.681 43.363442016573508 2.0
N B 3.17 7.500 1.80 0.200 0.130 15.0 0.800 3.576 516.681 43.363442016573508 2.0
C H 2.80 9.000 20.0 0.310 0.130 15.0 0.784 3.197 131.989 43.363442016573508 1.5
H C 2.80 9.000 20.0 0.310 0.130 15.0 0.784 3.197 131.989 43.363442016573508 2.2
B H 2.80 9.000 20.0 0.310 0.130 15.0 0.784 3.292 185.686 43.363442016573508 1.5
H B 2.80 9.000 20.0 0.310 0.130 15.0 0.784 3.292 185.686 43.363442016573508 2.2
N H 2.70 9.000 20.0 0.250 0.130 15.0 0.784 3.082 90.589 43.363442016573508 1.5
H N 2.70 9.000 20.0 0.250 0.130 15.0 0.784 3.082 90.589 43.363442016573508 2.2