結晶構造から融液の初期構造作成ログ | 融液 | Argon

pt1

参照元

分子動力学計算の実践講習 −溶融塩とイオン液体−

amorphous.tf.chiba-u.jp

参考文献

https://norman.jiht.ru/student/morozov/Rahman_PR64.pdf

pt2

アルゴン分子結晶の初期構造作成

pwd
$HOME/argon_melt_ini_coords_240625_1245

ls -CF
generate_config.py  lj.input

python3 generate_config.py
256 atoms
Generated config.atoms

cat config.atoms
Position Data

500 atoms
1 atom types

-26.28 26.28 xlo xhi
-26.28 26.28 ylo yhi
-26.28 26.28 zlo zhi

Atoms

1 1 -10.512 -10.512 -10.512
2 1 -10.512 -7.884 -7.884
3 1 -7.884 -10.512 -7.884
4 1 -7.884 -7.884 -10.512
(snip)
496 1 13.14 13.14 5.256
497 1 10.512 10.512 10.512
498 1 10.512 13.14 13.14
499 1 13.14 10.512 13.14
500 1 13.14 13.14 10.512

LAMMPSの入力ファイル作成

cat lj.input
# Ar crystallization

# 1) Initialization
# units         real
units         lj
atom_style    atomic

# 2) Setup simulation box
boundary      p p p

# 1') Initialization
read_data     config.atoms

# 3) Setup atoms
mass          1 39.95
velocity all  create 88.0 10

# 4) Force fields
pair_style    lj/cut 10.215
#pair_coeff    1 1 0.01032 3.405
pair_coeff    1 1 1.0 1.0

# 5) Settings
neighbor      0.5 bin
neigh_modify  every 1 delay 0 check yes
timestep      0.00001

# 6) Operations within timestepping
fix           1 all nve
#compute       myRDF all rdf 100
#fix           2 all ave/time 100 50 5000 c_myRDF[*] file lj.rdf mode vector

# 7) Output
thermo        100
thermo_style  custom time ke pe etotal temp
dump          1 all xyz 100 lj.xyz
dump          id all atom 100 lj.lammpstrj
dump_modify   1 sort id element Ar

# 8) Actions
run           10000

LAMMPSで分子動力学計算を実行

mpirun -np 4 $HOME/lammps-2Aug2023/src/lmp_mpi -in lj.input

ls -CF
config.atoms  generate_config.py  lj.input  lj.lammpstrj  lj.rdf  lj.xyz  log.lammps

2次解析