我正在尝试LAMMPS在环境中运行脚本Colab。但是，每当我尝试将fix命令与RIGID包中的参数一起使用时，控制台都会给我同样的错误。
我测试了不同的安装和构建方法，例如通过apt存储库和CMAKE：
Method 1
!add-apt-repository -y ppa:gladky-anton/lammps
!add-apt-repository -y ppa:openkim/latest
!apt update
!apt install -y lammps-stable
Method 2
!apt install -y cmake build-essential git ccache
!rm -rf lammps
!git clone -b release https://github.com/lammps/lammps.git mylammps
!rm -rf build
!mkdir build
!apt install -y fftw3
!cd build; cmake ../mylammps/cmake/presets/most.cmake -D CMAKE_INSTALL_PREFIX=/usr \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache -D BUILD_SHARED_LIBS=on\
-D PKG_GPU=on -D GPU_API=cuda -D LAMMPS_EXCEPTIONS=on -D PKG_BODY=on\
-D PKG_KSPACE=on -D PKG_MOLECULE=on -D PKG_MANYBODY=on -D PKG_ASPHERE=on\
-D PKG_EXTRA-MOLECULE=on -D PKG_KSPACE=on -D PKG_CG-DNA=on -D PKG_ATC=on\
-D PKG_ EXTRA-FIX=on -D PKG_FIX=on\
-D PKG_RIGID=on -D PKG_POEMS=on -D PKG_MACHDYN=on -D PKG_DPD-SMOOTH=on\
-D PKG_PYTHON=on ../mylammps/cmake
!cd build; make -j 2
!cd build; make install; make install-python
我还通过调用external scriptusing 该file()方法并编写命令来LAMMPS使用该command()方法对其进行了测试。
我code在python脚本中返回错误的部分是::
!pip install --user mpi4py
#!pip install lammps-cython
from mpi4py import MPI
from lammps import lammps
#from lammps import PyLammps
#from lammps import Lammps
import glob
from google.colab import files
from google.colab import drive
L = lammps()
...
L.command("fix freeze teflon setforce 0.0 0.0 0.0")
L.command("fix fSHAKE water shake 0.0001 10 0 b 1 a 1")
L.command("fix fRIGID RIG rigid molecule")
或者 LAMMPS 脚本中的相同行称为：
#Using an external script
!pip install --user mpi4py
#!pip install lammps-cython
from mpi4py import MPI
from lammps import lammps
#from lammps import PyLammps
#from lammps import Lammps
import glob
from google.colab import files
from google.colab import drive
L = lammps()
...
L.file(input[0])
me = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
print("Proc %d out of %d procs has" % (me,nprocs),L)
MPI.Finalize()
输出错误是：
---------------------------------------------------------------------------
Exception Traceback (most recent call last)
<ipython-input-60-a968719e9bc6> in <module>()
1 L = lammps()
----> 2 L.file(input[0])
3 me = MPI.COMM_WORLD.Get_rank()
4 nprocs = MPI.COMM_WORLD.Get_size()
5 print("Proc %d out of %d procs has" % (me,nprocs),L)
1 frames
/usr/local/lib/python3.7/site-packages/lammps/core.py in file(self, path)
559
560 with ExceptionCheck(self):
--> 561 self.lib.lammps_file(self.lmp, path)
562
563 # -------------------------------------------------------------------------
/usr/local/lib/python3.7/site-packages/lammps/core.py in __exit__(self, exc_type, exc_value, traceback)
47 def __exit__(self, exc_type, exc_value, traceback):
48 if self.lmp.has_exceptions and self.lmp.lib.lammps_has_error(self.lmp.lmp):
---> 49 raise self.lmp._lammps_exception
50
51 # -------------------------------------------------------------------------
Exception: ERROR: Unrecognized fix style 'shake' is part of the RIGID package which is not enabled in this LAM
有什么建议我能做什么？