Summary
为了方便取拿，总结了一下LAMMPS的input文件，主要包括以下部分及内容：
Initialization
#####################
# 1. Initialization #
#####################
# Box and units (use LJ units and periodic boundaries)
units lj # use lennard-jones (i.e. dimensionless) units
atom_style full # angle:atoms with bonds and angles; full:
boundary p p p # p p p : all boundaries are periodic; p p f: x/y are periodic
# Neighbours list
neighbor 0.5 bin
neigh_modify every 1 delay 3 check yes one 10000
# Medium
dielectric 0.333
Atom Data
######################
# 2. Atom definition #
######################
# READ "start" data file
read_data initial_configuration.txt
Setting
####################################
# 3 Setting: Bond - Nonbond - Pair #
####################################
# Bonds
bond_style fene
special_bonds fene #<=== I M P O R T A N T prevents LJ from being counted twice
# For style FENE, specify: bond type / K (energy/distance^2) / R0 (distance) / epsilon / sigma
bond_coeff 1 30.0 1.5 1.0 1.0
# Angles
angle_style cosine/delta
angle_ceoff 1 1.0 180.0
# Non-bonded
pair_style lj/cut/coul/long 2.5 2.5
pair_modify shift yes mix arithmetic # option to ensure energy is calculated corectly
# pair_coeff for LJ, specify 4: atom type interacting with / atom type / energy / mean diameter of the two atom types / cutoff
pair_coeff 1 1 1.0 1.0 1.12246152962189
#################
# 4 Additional #
#################
# Define groups
group substrates type 1
group bot_substr id <= 81
group top_substr subtract substrates bot_substr
group polymers type 2
group ctr_ions type 3
group salt substract all polymers ctr_ions
group dump_group subtract all top_substr
# Generate regular RESTART files to store state of simulation
#restart 50000 polymer.restart
# Reset timestep / set timestep of integrator
reset_timestep 0
timestep 0.005
RUN
#########
# 5.1 Output #
#########
## Output thermodynamic info (temperature, energy, pressure, etc.)
thermo 1000
compute real_temp not_substr temp
thermo_style custom step temp dt c_real_temp press vol etotal ke pe ebond eangle evdwl ecoul elong
## Output thermodynamic info to file
variable t equal step
variable mytemp equal temp
variable myepair equal epair
fix mythermofile all print 1000 "$t ${mytemp} ${myepair}" file thermo_output.dat screen no
## Set up a compute for R_g and write it to a file
compute myRG2compute all gyration
variable RG2 equal c_myRG2compute
fix myRG2file all print 1000 "$t ${RG2}" file radius_of_gyration_squared.dat screen no
###################
# 5.2 Fix and Run #
###################
# Set up fixes
variable seed equal 54654651 # a seed for the thermostat
fix 1 all nve # NVE integrator
fix 2 all langevin 1.0 1.0 100.0 ${seed} # langevin thermostat
# now do a longer run and write a final restart file
run_style verlet
run 50000
write_restart final.restart
Case
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