Packmol
packmolの入手・コンパイル
wget https://github.com/m3g/packmol/archive/refs/tags/v20.14.4+docs1.tar.gz
tar -xzvf v20.14.4+docs1.tar.gz
cd packmol-20.14.4-docs1/
ls -CFAUTHORS CMakeLists.txt LICENSE Makefile README.md app/ compile_cmake.sh configure* fpm.toml header release.sh* solvate.tcl* src/ testing/
./configureSetting compiler to /usr/bin/gfortran
makeCompiling packmol with /usr/bin/gfortran
Flags: -O3 –fast-math -march=native -funroll-loops
Packmol succesfully built.
ls -CFAUTHORS LICENSE README.md compile_cmake.sh fpm.toml packmol* solvate.tcl* testing/
CMakeLists.txt Makefile app/ configure* header release.sh* src/
morii-k@SurfaceLaptop-4:~/packmol-20.14.4-docs1$
packmolのインプットの作成
mkdir argon_melt_ini_coords_240620_1350
cd argon_melt_ini_coords_240620_1350/
touch packmol.in
touch Ar.xyzcat packmol.intolerance 2.0
filetype xyz
output out.xyz
structure Ar.xyz
number 60
inside box 0 0 0 10 10 10
end structure
cat Ar.xyz1
#Ar
Ar 0 0 0
$HOME/packmol-20.14.4-docs1/packmol < packmol.in検証
- VMD
- VESTA
.xyz形式からLAMMPSの入力ファイル形式に変換
.xyzファイルに単位セルの情報を追記
アルゴン分子結晶の単位セルの情報（https://www.webelements.com/argon/crystal_structure.html）を、out.xyzファイルの2行目に追記する．：
- a: 525.6 pm=5.256 Å
- b: 525.6 pm=5.256 Å
- c: 525.6 pm=5.256 Å
- α: 90.000°
- β: 90.000°
- γ: 90.000°
pwd
/home/morii-k/packmol-20.14.4-docs1/argon_melt_ini_coords_240620_1350
ls -CF
Ar.xyz out.xyz packmol.inhead -5 out.xyz
100
Built with Packmol
Ar 9.631477 -0.001898 17.061972
Ar 0.007148 1.663943 2.039236
Ar 10.244424 10.287318 3.820063sed --in-place "2c 5.256 5.256 5.256 90 90 90" out.xyzhead -5 out.xyz
100
5.256 5.256 5.256 90 90 90
Ar 9.631477 -0.001898 17.061972
Ar 0.007148 1.663943 2.039236
Ar 10.244424 10.287318 3.820063LAMMPSの入力ファイル形式に変換
phase0をインストール
wget https://azuma.nims.go.jp/ugdb/servlet/dl?f=phase0_2024.01.tar.gz–2024-06-24 15:40:31– https://azuma.nims.go.jp/ugdb/servlet/dl?f=phase0_2024.01.tar.gz
Resolving azuma.nims.go.jp (azuma.nims.go.jp)… 144.213.7.64
Connecting to azuma.nims.go.jp (azuma.nims.go.jp)|144.213.7.64|:443… connected.
HTTP request sent, awaiting response… 302 302
Location: /cms1/downloads/software/phase0_2024.01.tar.gz [following]
–2024-06-24 15:40:31– https://azuma.nims.go.jp/cms1/downloads/software/phase0_2024.01.tar.gz
Reusing existing connection to azuma.nims.go.jp:443.
HTTP request sent, awaiting response… 200 OK
Length: 93830860 (89M) [application/x-tar]
Saving to: ‘dl?f=phase0_2024.01.tar.gz’
dl?f=phase0_2024.01.tar.gz 100%[=================================================>] 89.48M 2.63MB/s in 34s
2024-06-24 15:41:06 (2.61 MB/s) – ‘dl?f=phase0_2024.01.tar.gz’ saved [93830860/93830860]
tar -zxvf dl?f=phase0_2024.01.tar.gzcd phase0_2024.01/
ls -CF
README doc/ phase-system_COPYRIGHT.txt samples/ src_phase_3d/ src_wan_interp/ tools/
band_symm/ install.sh* phase-system_eula-en.pdf src_bm/ src_spectrum/ src_workfunc/ util/
bin/ install_3d.sh* phase-system_eula-ja.pdf src_phase/ src_stm/ test/ls -CF ~/phase0_2024.01/bin
animate.pl* dos.py* piou/
band.pl* dynm2tr2.pl* plot_multiple_defect_formation_energy.py*
band_kpoint.pl* extract_slice.py* prep_piezo.pl*
band_local_decomp.py* freq.pl* prep_strfrc.pl*
band_orbital_proj.pl* geninp.py* prep_zeff.pl*
band_unfold.pl* inpcheck.py* surface_projected_bulk_band.py*
berry.pl* phonon_band.pl* wfsq.py*
calc_defect_formation_energy.py* phonon_band_atom_proj.py* workfunc.pl*
conv.py* phonon_dos.pl*
dos.pl* phonon_energy.pl*conv.pyのインストールが完了した．
conv.pyを用いてLAMMPSの入力ファイル形式に変換
$HOME/phase0_2024.01/bin/conv.py --batch --input_type=xyz --output_type=LAMMPS_input --input_file=out.xyz --output_file=config.atoms
atomic configuration converter utility.
Copyright (C) PHASE System Consortium
INFO: the number of frames defined in this XYZ file : 1
INFO: converting input file 'out.xyz' (xyz file) to output file 'config.atoms' (LAMMPS_input file)
INFO: the number of frames to output : 1
INFO: ... done
INFO:ls -CF
Ar.xyz config.atoms out.xyz packmol.in
head -20 config.atoms
LAMMPS input file generated by the PHASE I/O utility
# created on : 06/24/24 16:00:47
100 atoms
1 atom types
0 5.256 xlo xhi
0 5.256 ylo yhi
0 5.256 zlo zhi
0 0 0 xy xz yz
Atoms
1 1 9.631477 -0.001898 17.061972
2 1 0.007148 1.663943 2.039236
3 1 10.244424 10.287318 3.820063
4 1 9.795622 13.242042 19.431851
5 1 4.052893 0.004867 5.66693
6 1 17.261808 3.34644 3.416667
7 1 7.052095 1.871045 20.066611
8 1 10.879357 6.768397 1.147721
(snip)LAMMPSで分子動力学計算を実行
LAMMPSのインプットスクリプトの作成
touch lj.input
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 300.0 10
# 4) Force fields
pair_style lj/cut 10.215
pair_coeff 1 1 0.01032 3.405
# 5) Settings
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.01
# 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_modify 1 sort id element Ar
# 8) Actions
run 10000# Ar crystallization
# 1) Initialization
# units real
units lj
atom_style atomic
# 2) Setup simulation box
boundary p p p
region mybox1 block 0 3 0 3 0 3
create_box 1 mybox1
# 1') Initialization
read_data config.atoms
# 3) Setup atoms
mass 1 39.95
velocity all create 300.0 10
# 4) Force fields
pair_style lj/cut 10.215
pair_coeff 1 1 0.01032 3.405
# 5) Settings
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.01
# 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_modify 1 sort id element Ar
# 8) Actions
run 10000LAMMPSの実行
mpirun -np 4 /lammps-2Aug2023/src/lmp_mpi -in lj.input
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