Controling the temperature but unstable

LAMMPS LAMMPS General Discussion
1 
#------ initialization ------
units         metal
dimension     3
boundary      s s s
atom_style    atomic
neighbor      2.0 bin 
#-----geometric variable-----
variable   scale	equal 1.0
variable   tdamp	equal 10
variable	file string 0_twin
variable   theta	equal 20*3.1415926/180
#-----------------------------
variable  z_scale equal 375*${scale}
variable  z_1 equal ${scale}*124.5
variable  z_2 equal ${scale}*145.5
variable  z_3 equal ${scale}*175.5
variable  z_4 equal ${scale}*217.5
variable  z_5 equal ${scale}*240
variable  z_6 equal ${scale}*310
variable     low_1  equal 105*${scale}
variable     low_2  equal 87.9*${scale}
variable     low_3  equal 168.54*${scale}
variable     low_4  equal 250.02*${scale}
variable     low_5  equal 332.34*${scale}
variable     low_6  equal 415.5*${scale}
variable     high_1  equal 45*${scale}
variable     high_2  equal 45.9*${scale}
variable     high_3  equal 42.54*${scale}
variable     high_4  equal 40.02*${scale}
variable     high_5  equal 38.34*${scale}
variable     high_6  equal 37.5*${scale}
variable     cone_hi equal 300*${scale}

#------ generation ------
lattice fcc 3.6150 orient x 1 1 1 orient y 1 1 -2 orient z -1 1 0
region       sc prism -15 360 -140 140 -210 210 0.0 0.0 0.0 units box
create_box   3 sc
region model_1 prism  -${z_scale} ${z_1}  -140 140 -375 375 0.0 0.0 0.0 units box
region model_2 prism    ${z_1} ${z_2}     -140 140 -375 375 0.0 0.0 0.0 units box
region model_3 prism    ${z_2} ${z_3}     -140 140 -375 375 0.0 0.0 0.0 units box
region model_4 prism    ${z_3} ${z_4}     -140 140 -375 375 0.0 0.0 0.0 units box
region model_5 prism    ${z_4} ${z_5}     -140 140 -375 375 0.0 0.0 0.0 units box
region model_6 prism    ${z_5} ${z_6}     -140 140 -375 375 0.0 0.0 0.0 units box
create_atoms 1 region model_1
create_atoms 1 region model_3
create_atoms 1 region model_5

#-- twin --
lattice fcc 3.6150 orient x -1 -1 1 orient y 1 1 2 orient z -1 1 0
create_atoms 2 region model_2
create_atoms 2 region model_4
create_atoms 2 region model_6
#--------rotation----------------
group        wtf_1 region model_1
group        wtf_2 region model_2
group        wtf_3 region model_3
group        wtf_4 region model_4
group        wtf_5 region model_5
group        wtf_6 region model_6
group        nvtpart union wtf_1 wtf_2 wtf_3 wtf_4 wtf_5 wtf_6
displace_atoms  nvtpart rotate 0 0 0 0 1 0 -90

#-----shape------
region     fuck_1 cone z 0 0  ${low_1} ${high_1}  0 ${cone_hi}  side out  units box
region     fuck_2 cone z 0 0  ${low_2} ${high_2}  0 ${cone_hi}  side out  units box
region     fuck_3 cone z 0 0  ${low_3} ${high_3}  0 ${cone_hi}  side out  units box
region     fuck_4 cone z 0 0  ${low_4} ${high_4}  0 ${cone_hi}  side out  units box
region     fuck_5 cone z 0 0  ${low_5} ${high_5}  0 ${cone_hi}  side out  units box
region     fuck_6 cone z 0 0  ${low_6} ${high_6}  0 ${cone_hi}  side out  units box
delete_atoms region fuck_1
delete_atoms region fuck_2
delete_atoms region fuck_3
delete_atoms region fuck_4
delete_atoms region fuck_5
delete_atoms region fuck_6

lattice diamond 3.57
region     top prism -185 45 -105 105 302 312 0.0 0.0 0.0 units box
create_atoms 3 region top
lattice fcc 3.6150 orient x -1 -1 1 orient y 1 1 2 orient z -1 1 0
region     down prism -140 140 -140 140 -15 0 0.0 0.0 0.0 units box
create_atoms 1 region down
#------ mass ------
mass         1 63.550
mass         2 63.550
mass         3 12.0096
#------ force field ------
pair_style hybrid eam/alloy tersoff lj/cut 3.615
pair_coeff * * eam/alloy Cu_zhou.eam.alloy Cu Cu NULL 
pair_coeff * * tersoff SiC.tersoff NULL NULL C 
pair_coeff 1*2 3 lj/cut 0.001034 2 3.615
#------ computation ------
compute        peratom all pe/atom
#------ minimize ------
variable        t equal "time"
variable        temp equal "temp"
variable        pe equal "pe"
group top1 type 3
group down1 region down
displace_atoms top1 rotate 0 0 0 0 1 0 20
fix xwalls all wall/reflect xlo EDGE xhi EDGE
fix ywalls all wall/reflect ylo EDGE yhi EDGE
fix zwalls all wall/reflect zlo EDGE zhi EDGE
delete_atoms overlap 0.1 all all
fix top top1 setforce 0.0 0.0 0.0
dump           1 all custom 1000 ${file}_mini_*.dump id type xu yu zu c_peratom
#dump_modify  1 sort id scale no
thermo       500
thermo_style custom step temp pe
min_style cg
minimize 1.0e-12 1.0e-5 1000000 100000
undump 1
#-----------------------
#------ stage 4 ------   DEFORMATION
fix freeze down1 setforce 0.0 0.0 0.0
fix 1 all nve
fix 2 all temp/berendsen 100.0 100.0 ${tdamp}
dump           8 all custom 500 ${file}_*.dump id type xu yu zu c_peratom  
dump_modify    8 sort id  
thermo         500
thermo_style   custom step temp pe
run           100000
undump 8

dump           1 all custom 1000 ${file}_mini_*.dump id type xu yu zu c_peratom
#dump_modify  1 sort id scale no
thermo       500
thermo_style custom step temp pe
min_style cg
minimize 1.0e-12 1.0e-5 1000000 100000
undump 1
#------ stage 4 ------   DEFORMATION
velocity all create 200.0 4928459
fix 2 all temp/berendsen 200.0 200.0 ${tdamp}
dump           8 all custom 500 ${file}_*.dump id type xu yu zu c_peratom 
dump_modify    8 sort id  
thermo         500
thermo_style   custom step  temp pe
run           100000
unfix 2
undump 8

dump           1 all custom 1000 ${file}_mini_*.dump id type xu yu zu c_peratom
#dump_modify  1 sort id scale no
thermo       500
thermo_style custom step temp pe
min_style cg
minimize 1.0e-12 1.0e-5 1000000 100000
undump 1
#------ stage 4 ------   DEFORMATION
velocity all create 300.0 4928459
fix 2 all temp/berendsen 300.0 300.0 ${tdamp}
dump           8 all custom 500 ${file}_*.dump id type xu yu zu c_peratom  
dump_modify    8 sort id  
thermo         500
thermo_style   custom step  temp pe
run           100000
unfix 2
undump 8
write_restart	${file}_thermo.restart

dump           1 all custom 1000 ${file}_mini_*.dump id type xu yu zu c_peratom
#dump_modify  1 sort id scale no
thermo       50
thermo_style custom step temp pe
min_style cg
minimize 1.0e-12 1.0e-8 1000000 100000
undump 1
#------ stage 4 ------   DEFORMATION
velocity all create 300.0 4928459 
fix 2 all temp/berendsen 300.0 300.0 ${tdamp}
restart        1000 restart_nt-Cu_sametemp_*.restart
dump           8 all custom 500 ${file}_*.dump id type xu yu zu c_peratom  
thermo         500
thermo_style   custom step  temp pe etotal pxx pyy pzz fmax
run           100000
unfix 2
undump 8
write_restart	${file}_final.restart

Here is the video I made from the output
https://drive.google.com/file/d/1aSCqPMBHx_kpS4cieeMsXxhVhjnaPcWJ/view?usp=sharing
As you can see, it’s unstable.
How do I fix it by modifying the input

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2

Please, a bit of a background on what you are trying to achieve.

3

Hi @yoyoy,

Your input is extremely complex and convoluted. You make a very complex shape with several lattices orientations and combined region commands, and use a combination of several pair interaction (EAM, Tersoff and lennard-jones). This is clearly a non trivial choice. Also looking at the 6mn video it is nearly impossible to tell what you mean by “not stable”. There are some tiny structure changes but nothing dramatic. So no, I “cannot see”.

It is nearly impossible to help you in any significant way here. Your question is generic and you do not take time to explain what you’re doing and point to specific aspect on which you expect help from other members. :confused:

Also looking at your previous posts, it appears that you try to solve your own misuse of the code through forum posting. You are gaining zero insight on your own errors with this behaviour and this is building a bad habit. In this case, what you need would be more general discussions on your results and expectations, and also a need for serious reading of molecular dynamics/statistical physics textbooks. Explaining what you’re trying to achieve to another colleague or advisor might be better to solve your issue, if any, and give you proper insight on the science behind it.

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4

Thanks for your earnest response. I’ll think about it and read the molecular dynamics/statistical physics textbooks.

5

What would be equally important is to change your approach to building a simulation.
You should start with a minimal system and resolve the basic procedure first. At that point it is much easier to give advice and review your inputs, since they are much less convoluted.
Then you can make your input more complex and approach the final goal in steps and then you can look at potential issues one step step at a time and - again - it would be much easier to review and give advice. Also, you could much easier create a special test input that only evaluates the one feature added to the simulation with a simpler base simulation.

1 Like