write_data and read_data

LIGGGHTS에서 simuldation data를 저장하는 방법은 총 3가지가 있다.

write_data, write_restart, write_dump

write_data와 write_dump는 text 포맷으로 저장하며, write_restart는 binary 포맷을 지원한다.

 

문제는 저장 후 load시 simulation box 변경을 하는 경우이다. atom의 pluviation단계와 이후 단계에서 simulation영역이 달라지는 경우 LIGGGHTS에서는 load-balancing을 통한 processor grid를 재설정 하지 않기 때문에, simulation box의 사이즈를 조정하며 processor당 할당되는 simulation 영역을 최적화 해주어야 한다.

 

그런데, write_restart는 저장되는 정보는 가장 많으나 atom remap등과 같은 processor당 할당 atom등과 같은 정보들을 가지고 있기 때문에 read_restart단계에서 simulation box의 사이즈 조정이 불가능하다. (single processor의 경우 가능)

 

예를들어, time step의 경우 write_restart를 사용하는 경우 저장되지만 write_data로는 저장되지 않는다. 그리고, read_data, creat_box명령어는 time step을 0으로 초기화 한다.

따라서, time step의 조정은 다음의 명령어를 사용한다.

reset_timestep N

 

따라서, 가장 기본적인 정보 (atom ID, type, x, y, z, density, radius)만을 저장하여 read하는 경우 simulation box size의 크기 조정이 가능하므로 이 방법을 사용할 수 있다.

그런데, text포맷을 사용하므로 atom의 개수가 기하 급수적으로 늘어난다면? 이건 나중에 닥쳤을때 해결책을 찾아보도록 하자.

### This is test file for read_data

### 1. Initializaion Phase

# Preliminaries
atom_style                 granular
atom_modify                map array                                  # necessary?
boundary                   f f f                                      # default is p p p
newton                     off                                        # need more information and examples
communicate                single vel yes
units                      si                                         # This command cannot be used after the simulation box
hard_particles             yes
dimension                  3                                          # default value is 3

# Neighbor listing
neighbor                   0.003 bin
neigh_modify               delay 0

# Declare domain
region                     domain_1 block -0.1 0.1 -0.1 0.1 -0.1 0.1 units box   # xmin-max ymin-max zmin-max
create_box                 2 domain_1  # Declare number of atom types used in the simulation, This affect "fix property/global"

variable                   dt_ equal 0.00001

timestep                   ${dt_}
fix                        grav_acc all gravity 9.81 vector 0.0 0.0 -1.0

### 2. Setup properties
# Material and interaction properties required
fix                         m_1 all property/global youngsModulus peratomtype 2.e7 2.e7
fix                         m_2 all property/global poissonsRatio peratomtype 0.25 0.25
fix                         m_3 all property/global coefficientRestitution peratomtypepair 2 0.1 0.1 0.1 0.1
fix                         m_4 all property/global coefficientFriction peratomtypepair 2 0.01 0.01 0.01 0.01

pair_style                 gran model hertz tangential history #Hertzian without cohesion
pair_coeff                 * *

### 3. Create atoms
create_atoms               1  single 0.0 0.0   0.00   # atom #2

set                        atom 1  type 1 density 2000 diameter 0.005

### 4. Setup variables
variable                   step_now equal step
variable                   time_now equal step*v_dt_

### 4. Import Mesh from STL
fix                        box_base   all mesh/surface file base.stl        type 2 scale 1.0
fix                        box_side   all mesh/surface file side_wall.stl   type 2 scale 1.0
fix                        box_moving_L all mesh/surface file moving_wall_L.stl type 2 scale 1.0
fix                        box_moving_R all mesh/surface file moving_wall_R.stl type 2 scale 1.0

fix                        gran_walls all wall/gran model hertz tangential history mesh n_meshes 4 meshes box_base box_side box_moving_L box_moving_R

### 4. Set equation of motion
fix                        integral_eq_motion all nve/sphere
compute                    rke all erotate/sphere update_on_run_end yes


### 5. Create Imaging informations
run 1
dump                       dump_mesh_base     all mesh/vtk 100 post/base_mesh_*.vtk   id vel box_base
dump                       dump_mesh_side     all mesh/vtk 100 post/side_mesh_*.vtk   id vel box_side
dump                       dump_stl_moving_L  all mesh/stl 100 post/moving_L_stl_*.stl  box_moving_L
dump                       dump_stl_moving_R  all mesh/stl 100 post/moving_R_stl_*.stl  box_moving_R
dump                       dump_atoms all custom/vtk 100 post/atoms*.vtk id type x y z vx vy vz omegax omegay omegaz density diameter

### Setup print
fix                        print_time  all print 100 "current step, dt, time = ${step_now}, ${dt_}, ${time_now}" screen yes

### 7. Run
run                        10000 upto

print                      "     "
print                      "===="
print                      "simulation end"
print                      "===="

change_box                 all x final -0.05 0.05 y final -0.05 0.05 z final -0.05 0.05

write_data                 akt.txt

 

 

Simulation box는 앞선 파일의 change_box를 사용하기 보다는 아래의 write_data로 만들어지는 파일에서 수정하는 것이 사소한 오류를 줄일 수 있다.

LAMMPS data file via write_data, version Version LIGGGHTS-PUBLIC 3.8.0, compiled 2023-04-24-22:04:34 by jinsun, git commit 5207ed861b1351eb03ccd7bc4c4e612b00c8ff56, timestep = 10000

1 atoms
2 atom types

-5.0000000000000003e-02 5.0000000000000003e-02 xlo xhi
-5.0000000000000003e-02 5.0000000000000003e-02 ylo yhi
-5.0000000000000003e-02 5.0000000000000003e-02 zlo zhi

Atoms

1 1 5.0000000000000001e-03 2.0000000000000000e+03 0.0000000000000000e+00 0.0000000000000000e+00 -1.2501482905408676e-02 0 0 0

Velocities

1 0.0000000000000000e+00 0.0000000000000000e+00 -4.0535180816119558e-14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00

 

이건 이어지는 해석 파일

# Preliminaries
atom_style                 granular
atom_modify                map array                                  # necessary?
boundary                   f f f                                      # default is p p p
newton                     off                                        # need more information and examples
communicate                single vel yes
units                      si                                         # This command cannot be used after the simulation box
hard_particles             yes
dimension                  3                                          # default value is 3


# Neighbor listing
neighbor                   0.003 bin
neigh_modify               delay 0


read_data             akt.txt

variable                   dt_ equal 0.00001

timestep                   ${dt_}
fix                        grav_acc all gravity 9.81 vector 0.0 0.0 -1.0

### 2. Setup properties
# Material and interaction properties required
fix                         m_1 all property/global youngsModulus peratomtype 2.e7 2.e7
fix                         m_2 all property/global poissonsRatio peratomtype 0.25 0.25
fix                         m_3 all property/global coefficientRestitution peratomtypepair 2 0.1 0.1 0.1 0.1
fix                         m_4 all property/global coefficientFriction peratomtypepair 2 0.01 0.01 0.01 0.01

pair_style                 gran model hertz tangential history #Hertzian without cohesion
pair_coeff                 * *

## 4. Setup variables
variable                   step_now equal step
variable                   time_now equal step*v_dt_

### 4. Import Mesh from STL
fix                        box_base   all mesh/surface file base.stl        type 2 scale 1.0
fix                        box_side   all mesh/surface file side_wall.stl   type 2 scale 1.0
fix                        box_moving_L all mesh/surface file moving_wall_L.stl type 2 scale 1.0
fix                        box_moving_R all mesh/surface file moving_wall_R.stl type 2 scale 1.0

fix                        gran_walls all wall/gran model hertz tangential history mesh n_meshes 4 meshes box_base box_side box_moving_L box_moving_R

### 4. Set equation of motion
fix                        integral_eq_motion all nve/sphere
compute                    rke all erotate/sphere update_on_run_end yes


### 5. Create Imaging informations
run 1
dump                       dump_mesh_base     all mesh/vtk 100 post/base_mesh_*.vtk   id vel box_base
dump                       dump_mesh_side     all mesh/vtk 100 post/side_mesh_*.vtk   id vel box_side
dump                       dump_stl_moving_L  all mesh/stl 100 post/moving_L_stl_*.stl  box_moving_L
dump                       dump_stl_moving_R  all mesh/stl 100 post/moving_R_stl_*.stl  box_moving_R
dump                       dump_atoms all custom/vtk 100 post/atoms*.vtk id type x y z vx vy vz omegax omegay omegaz density diameter

### Setup print
fix                        print_time  all print 100 "current step, dt, time = ${step_now}, ${dt_}, ${time_now}" screen yes

### 7. Run
reset_timestep             10000
run                        20000 upto

print                      "     "
print                      "===="
print                      "simulation end"
print                      "===="