# LAMMPS build recipe
## ENV prepare
apps/tmux/tmux
module load intel/2023_2
module load miniconda3
cd ~/src/lammps
wget https://github.com/lammps/lammps/archive/refs/tags/stable_2Aug2023_update2.tar.gz
tar -zxv -f stable_2Aug2023_update2.tar.gz
git clone https://github.com/lammps/lammps.git
cd lammps
git tag -l
git checkout <tag_name>
## Building QUIP
git clone --recursive https://github.com/libAtoms/QUIP.git
git pull
export QUIP_ROOT=/home/p00acy00/src/lammps/QUIP
export QUIP_ARCH=linux_x86_64_ifort_icc_openmp
cd ${QUIP_ROOT}
make config
make libquip
給LAMMPS用的QUIP不能編mpi版本，也不要編openmp版本的，因為lib/quip/Makefile.lammps裡偵測F95的程式沒寫好，會一直找不到fortran compiler。
QUIP_ARCH選linux_x86_64_ifort_icc_openmp的話，要新增F95=ifort，還要把每個FLAGS裡的-openmp改成-qopenmp。
## Building n2p2
git clone --recursive https://github.com/CompPhysVienna/n2p2.git
git pull
cd n2p2/src
make libnnpif MODE=static COMP=intel
ln -s /home/lammps/src/auxlib/n2p2/include includelink
ln -s /home/lammps/src/auxlib/n2p2/lib liblink
## Building LAMMPS
cd lammps-stable_2Aug2023_update3/src/MAKE
cp OPTIONS/Makefile.intel_cpu_intelmpi .
```
```
cd ..
make yes-most
make yes-intel
make yes-openmp
make yes-ml-quip
make pu
make clean-all
make intel_cpu_intelmpi
## Test LAMMPS with QUIP
cd lammps-stable_2Aug2023_update2/examples/PACKAGES/quip/
lmp_intel_cpu_intelmpi -in in.sw
lmp_intel_cpu_intelmpi -in in.molecular
lmp_intel_cpu_intelmpi -in in.GAP
module load intel/2024_01_46
cd src/lammps/gsl-2.7.1
./configure --prefix=$HOME/apps/gsl-2.7.1 CC=icx CXX=icpx
##
> Atom IDs are not required for atomic systems which do not store bond topology information, though IDs are enabled by default. The atom_modify id no command will turn them off. Atom IDs are required for molecular systems with bond topology (bonds, angles, dihedrals, etc). Similarly, some force or compute or fix styles require atom IDs. Thus, if you model a molecular system or use one of those styles with more than 2 billion atoms, you need the “bigbig” setting.
n2p2適用stable_29Oct2020.tar.gz
更新的版本使用要改
1. src/neigh_request.h
這檔案把一些變數改宣告成protected，所以要把nnp會用到的class宣告成friend class，
在第30行新增
friend class PairNNP;
2. src/Makefile.package
lammps新版不再使用USER-XXX方式擴充，
所以無法使用make yes-user-xxx方式，
要手動copy檔案，
並修改Makefile.package，
要確定有nnp的include(PKG_INC)和lib(PKG_PATH)路徑，
還要加上PKG_LIB = -lnnpif -lnnp
或是依據../../lib/nnp/lib/Makefile.lammps-extra所定義的名稱
修改
PKG_SYSINC = $(hdnnp_SYSINC)
PKG_SYSLIB = $(hdnnp_SYSLIB)
PKG_SYSPATH = $(hdnnp_SYSPATH)
PKG_SYSINC = $(plugin_SYSINC)
PKG_SYSLIB = $(plugin_SYSLIB)
PKG_SYSPATH = $(plugin_SYSPATH)
3.編譯n2p2 lammps的interface
In n2p2 folder
cd src
make libnnpif
4.到lammps資料夾建立nnp lib的連結
cd lib
ln -s <path-to-n2p2> nnp
cp phononlifetime-r108/src/compute_sed.*
cp phononlifetime-r108/src/memory.*
cp n2p2/src/interface/LAMMPS/src/USER-NNP/pair_nnp.*