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[lammps-users] regarding the temperature
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[lammps-users] regarding the temperature


From: bahman daneshian <bahmanpbamp@...24...>
Date: Fri, 18 May 2018 16:02:55 +0200

Dear Lammps experts,

I am simulating impact of a particle on a similar type substrate with LAMMPS . my problem is about calculating the particle temperature as a moving object actually.

First  the initial structure of the particle  and its energy minimize at the room temperature(300K) with fix nve and fix temp/rescale and then the particle is thrown toward the substrate. I applied the compute temp/com in order to calculate the particle temperature  as a moving object as per the Lammps document. 

These are the problems:

1- Exactly upon  throwing the particle ( after unfix temp/rescale) the particle temperature decreases about 150K which is not expected. I have no idea why temperature decreases TOO MUCH upon unfixing. How about minimizing the particle at the room temperature longer???

2- and then the temperature increases until the end of the simulation. However, it is expected that the temp. only increases at the impact moment and then decreases to a steady or constant temp at the end of the simulation.

So, any comment could be highly appreciated. 

below you can find my input file:

#Phase 1 ------------------------------------------Simulation main setup----------------------------------
dimension        3
units    real
atom_style     charge
boundary       p p p


variable radius equal 50 # makes 100 Ang or 10nm particle
variable n equal 50 # makes 81*3.786 length=306

variable a1 equal 3.786
variable a2 equal 3.786
variable a3 equal 9.514

variable boxx equal "v_n*v_a1"
variable boxy equal "v_n*v_a2"


variable diameter equal "2*v_radius"
variable x0 equal "0.5*v_boxx"
variable y0 equal "0.5*v_boxy"
variable subs_thick equal "3*v_a3"               #v_a3 equal 9.514
variable subslow_thick equal "1*v_a3"
variable z_gap equal "0.5*v_radius"
variable distance equal "v_subs_thick+v_subslow_thick+v_z_gap+v_radius"
variable boxz equal "v_distance+v_diameter+v_radius"

#simulation box
region box block 0 ${boxx} 0 ${boxy} 0 ${boxz} units box
create_box      2 box    #2 is number of atoms

# it was very difficult to finally find these positions
lattice custom 1 a1 3.786  0.00000  0.00000   a2  0.0000   3.786  0.00000  a3 0 0 9.514  &
basis 0.0000 0.2500 0.3750 &
basis 0.0000 0.7500 0.6250 &
basis 0.5000 0.7500 0.8750 &
basis 0.5000 0.2500 0.1250 &
basis 0.0000 0.0000 0.1700 &
basis 0.0000 0.7500 0.4200 &
basis 0.5000 0.2500 0.3300 &
basis 0.5000 0.7500 0.0800 &
basis 0.500 0.5000 0.6700 &
basis 0.500 0.2500 0.9200 &
basis 0.000 0.7500 0.8300 &
basis 0.000 0.2500 0.5800
mass 1 47.86000
mass 2 15.99940


#particle
region         particle sphere  ${x0} ${y0} ${distance} ${radius} units box
create_atoms 2 region particle &
basis 1 1 &
basis 2 1 &
basis 3 1 &
basis 4 1 &
basis 5 2 &
basis 6 2 &
basis 7 2 &
basis 8 2 &
basis 9 2 &
basis 10 2 &
basis 11 2 &
basis 12 2
group particle region particle
set type 1 charge 2.196 
set type 2  charge -1.098



#substrate 
region          substrate block 0 ${boxx} 0 ${boxy} ${subslow_thick} ${subs_thick} units box
create_atoms 2 region substrate &
basis 1 1 &
basis 2 1 &
basis 3 1 &
basis 4 1 &
basis 5 2 &
basis 6 2 &
basis 7 2 &
basis 8 2 &
basis 9 2 &
basis 10 2 &
basis 11 2 &
basis 12 2
group substrate region substrate
set type 1 charge 2.196 
set type 2  charge -1.098
#group        model union particle substrate


#lower_substrate 
region          lower_substrate block 0  ${boxx} 0  ${boxy}  0 ${subslow_thick} units box
create_atoms 2 region lower_substrate &
basis 1 1 &
basis 2 1 &
basis 3 1 &
basis 4 1 &
basis 5 2 &
basis 6 2 &
basis 7 2 &
basis 8 2 &
basis 9 2 &
basis 10 2 &
basis 11 2 &
basis 12 2
group lower_substrate region lower_substrate
set type 1 charge 2.196 
set type 2  charge -1.098
group        model union particle substrate

#--Phase 2----------------------------------------Buckingham Potential-----------------------------------------------

pair_style buck/coul/long 15
pair_coeff   1 1   717647.40 0.154 121.067
pair_coeff   1 2   391049.10 0.194 290.331
pair_coeff   2 2   271716.30 0.234 696.888

neighbor 2.0 bin # skin distance for real units  is by default 2.0
neigh_modify every 1 delay 0 check yes

kspace_style pppm 0.0001
neigh_modify delay 5

#---Phase 3----------------------------------------Compute---how can I monitor Vparticle??!! ------------------------
compute temp_substrate  all temp/region substrate
compute temp_particle_com particle temp/com
compute  temp_particle  all temp/region particle

#----Phase 4-------------------------------------Initial Equilibration at 300K ----------------------------------------
reset_timestep 0
timestep 1.0 # or 2
velocity all create 300 12345 mom yes rot no


fix 1 lower_substrate setforce 0.0 0.0 0.0
fix 2 particle nve
fix 3 substrate nve
fix 4 substrate temp/rescale 100 300.0 300.0 10.0 1.0
fix 5 particle temp/rescale 100 300.0 300.0 10.0 1.0


thermo 100
thermo_modify lost ignore flush yes
thermo_style custom   step   c_temp_particle   c_temp_particle_com  c_temp_substrate  
dump 1 all xyz 100 dump1000.txt 

run 7000
unfix 5



#----Phase 5---------------------------------------Particle Impact at the room temperature -------------------

velocity particle set 0 0 -0.010 units box 

thermo 100
thermo_style custom   step   c_temp_particle   c_temp_particle_com  
                                                                                                                                                               
run 50000





Best regards
Bahman Daneshian