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Re: [lammps-users] regarding the temperature


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 18 May 2018 10:15:58 -0400



On Fri, May 18, 2018 at 10:02 AM, bahman daneshian <bahmanpbamp@...24...> wrote:
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???

​it is not the removal of the thermostat, that is the cause, but this command:

velocity particle set 0 0 -0.010 units box 
 

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.

​difficult to say. temp/rescale is a very bad choice as a ​thermostat for equilibration. there is no mention if you check, whether your total system is properly equilibrated and can properly conserve energy (and maintain the expected temperature). your problematic use of "velocity set" may have some bad impact as well.

axel.

 

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

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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.