Column browsing 《LAMMPS Example tutorial —In File, 》

One 、 Preface

Take homogeneous nucleation as an example , Realize the curing process of water .

Two 、Lammps Realization

1、 Core commands and force field settings

# Define SW potentials parameters.
  pair_style	sw 
  pair_coeff	* * mW.sw H2O
 
 fix		1 all npt temp ${
    T_fi} ${
    T_fi} ${
    damp_T} iso 1.0 1.0 ${
    damp_P}

2、 All the code

######################################     General Variables     #######################################

# Initalizes random number generator.
  #variable rnd equal round(random(0,999999,${
      RANDOM}))

# Initial definitions.
  variable          T			equal   350            			# Simulation temperature (K).
  variable          T_fi		equal   200            			# Supercooling temperature temperature (K).
  variable          kB      	equal   8.617343e-05   	# Boltzmann constant (eV/K).

# Time variables.
  variable          t_eq		equal   20000          	# Equilibration steps.
  variable          t_c			equal   100000         	# Temperature change steps.
  variable          dt			equal   0.005          		# Timestep (ps).
  variable          damp_T	equal   100*${
    dt}      	# Damp parameter for the thermostat (ps).
  variable          damp_P	equal   1000*${
    dt}
#------------------------------------------------------------------------------------------------------#


########################################     Atomic setup     ##########################################
# Defines the style of atoms, units and boundary conditions.
  dimension	3  
  atom_style	atomic 
  units		metal
  boundary	p p p

# Read atoms positions, velocities and box parameters.
  read_data			ini_system.data
  neigh_modify	delay	0
  #mass 1 18.01528
  group            	water	type	1
  velocity all create 200 97287 dist gaussian
# Define SW potentials parameters.
  pair_style	sw 
  pair_coeff	* * mW.sw H2O
  timestep          ${
    dt}
  minimize 1.0e-6 1.0e-8 1000 1000
  minimize 1.0e-5 1.0e-7 1000 10000
  minimize 1.0e-5 1.0e-7 1000 10000
  reset_timestep	0
#------------------------------------------------------------------------------------------------------#


################################     Fixes, computes and constraints     ###############################
# Integrator & thermostat.
  #fix f1 all nve
  #fix f2 all langevin $T $T ${
      damp_T} ${
      rnd}
  #variable rnd equal round(random(0,999999,0)) # Generates new rnd #.

# Compute****.
  compute          KE all    ke/atom 
  compute          PE all    pe/atom
  #compute c2 all pair ufm
#------------------------------------------------------------------------------------------------------#


##########################################     Output setup     ########################################
# Output variables.
  #variable step equal step
  #variable dU equal (c_c1-c_c2)/atoms # Driving-force during NEHI procedure.

# Thermo output.
  thermo_style	custom	step  temp  press pe ke etotal enthalpy epair vol density
  thermo				1000
#------------------------------------------------------------------------------------------------------#


##########################################     Run simulation     ######################################
  fix		1 all npt temp ${
    T_fi} ${
    T_fi} ${
    damp_T} iso 1.0 1.0 ${
    damp_P}
  dump	1    all custom 1000 equilibrate.dump	id	type x y z vx vy vz fx fy fz c_KE c_PE 
  run 		${
    t_c}    								# 20ps
  undump		1
  unfix 1
  write_data 200K.data

# Ice procress. 
  fix		2 all nvt temp ${
    T_fi} ${
    T_fi} ${
    damp_T} 
  dump   	2 all custom 10000 ice.dump	id	type x y z vx vy vz fx fy fz c_KE c_PE 
  run 		5000000    	
  write_data fianl.data

3、 ... and 、 Ice structure analysis

1. $\mathrm{Q}6\mathrm{M}\mathrm{a}\mathrm{t}\mathrm{l}\mathrm{a}\mathrm{b}$ Calculation

Please refer to the blog ：《 Key sequence parameter MATLAB—— Ice nucleation recognition 、 Melt identification （Steinhardt bond orientational order parameters）》

2. Ovito Calculation