NVT_inputfile.inp

units		real	                             #Angstroms, g/mol, etc.
atom_style	full                                 #Molecule + charge

timestep	2.0				     #Set the integrator time step (default = 1.0fs for real units)

boundary        p p p				     #Periodic Boundaries
read_data       Rb1Xe15_a96.cfg #Rb1_Xe16.cfg.lammps

replicate	1 1 1				     #cell replication (none = 1 1 1)

variable        dt equal 2.0
variable        ext_temp equal 420
variable        Tdamp equal 100.0*${dt}		     #units are time units, LAMMPS suggestion is 100 time steps
		      	    			     #(e.g. 50fs if time step is 0.5fs)
########
pair_style	 table linear 11600 #lj/cut 10.0  #LJ with 15.0ang cutoff, Coulomb with 15.0ang cutoff
#pair_modify     tail yes			     #Analytic Long-range Tail corrections, for the LJ interactions
pair_coeff	1 1  POT_XeXe2.pot  POT_XeXe 10.0
pair_coeff  1 2  POT_XeRb2.pot  POT_XeRb 10.0
pair_coeff  2 2  POT_XeRb2.pot  POT_XeRb 10.0 # usng fake potential for  RbRb
pair_write  1 1 16000 r 2.7 13.9  table_xexe.txt xexe
pair_write  1 2 16000 r 2.7 13.9  table_xerb.txt xerb
#########

bond_style	none nocoeff #harmonic   			     #Sets the bond type as harmonic
angle_style	none nocoeff #harmonic			     #Sets the triplet bond type as harmonic
dihedral_style	none				     #TraPPE N2 has no dihedrals (quadruplets)
improper_style	none				     #TraPPE N2 has no improper quadruplets


group xenon   type 1
group rubiduim type 2

#Neighbor List Parameters
#neighbor        2.0 bin			     #Skin (default = 2.0 bin for real units)
#neigh_modify    delay 1 every 1 check no
                                                     #  delay N =  never delay until at least N steps after previous build
                                                     #  every N =  build list every N steps
                                                     #  check no = build whenever delay/every criteria are met
                                                     #  check yes = build whenever delay/every criteria are met and atom moved > skin/2

#Create initial velocity distribution
velocity all create ${ext_temp} 4561 dist uniform

#Reset the time step counter
reset_timestep  0                                    #Reset the time step counter to 0

#Ensemble set-up: NVT ensemble, thermostatted by Nose-Hoover a chained thermostat, set at temperature $ext_temp
#fix             2 all rigid/nvt molecule temp ${ext_temp} ${ext_temp} ${Tdamp}
fix 2 all nvt temp ${ext_temp} ${ext_temp} ${Tdamp}
		      	       		   	     #start temperature = ext_temp
		      	       		   	     #end temperature = ext_temp
		      	    	      	      	     #Tdamp (in time units, fs)

#Output Style
dump          dump_1 all  custom 100 dump.min id type x y z vx vy vz

variable        Nevery equal 20                      #Specify the distance (in timesteps) between samples for computing ensemble aver$
                                                     #  (Interval between samples in a block)
variable        Nrepeat equal 50                     #Specify the number of samples per output  of thermodynamic averages
                                                     #  (Samples per block output)
variable        Nfreq equal ${Nevery}*${Nrepeat}     #Specify the dump interval (in timesteps)
                                                     #  (Some people call these blocks)
variable        KineticEnergy equal ke              # Kinetic energy
variable        TotalEnergy equal etotal
variable        PotentialEnergy equal epair          #Call the intermolecular potential energy $PotentialEnergy
variable        Pressure equal press                 #Call the pressure $Pressure
variable        Temperature equal temp               #Call the instantaneous temperature $Temperature
variable        Density equal density                #Call the instantaneous density $Density (will not change for NVT)

#fix             3 all ave/time ${Nevery} ${Nrepeat} ${Nfreq} v_Temperature v_Density v_PotentialEnergy v_Pressure file ave.dens_22.0molL.out format " %g"
fix             3 all ave/time ${Nevery} ${Nrepeat} ${Nfreq}  v_Temperature v_Density v_PotentialEnergy v_KineticEnergy v_TotalEnergy v_Pressure   file ave.mydata.out format " %g"

thermo          1000                                 #Specify the interval between screen output of thermodynamic averages
thermo_style    custom step temp density epair press #Format for screen output of thermodynamics
                                                     #  (MD step, temperature, internal energy, pressure)
#Run it!
write_restart ./restart_file
run           5000000
write_restart ./restart_file
undump        dump_1