ReadLammpsTraj 1.1.0

Read lammps dump trajectory.

ReadLammpsTraj

• Read lammps dump trajectory

Installation

git clone https://github.com/eastsheng/ReadLammpsTraj
cd ReadLammpsTraj
pip install .

Usage

• A example to calculate density in demo folder:

  # calculating the density from lammps traj
  # id mol type mass x y z vx vy vz fx fy fz q
  import numpy as np
  import matplotlib.pyplot as plt
  import ReadLammpsTraj as RLT
  from pathlib import Path
  
  def cal_density():
  	path = "./"
  	f = "1000.lammpstrj"
  
  	Path(path+"density/").mkdir(parents=True,exist_ok=True)
  
  	md = RLT.ReadLammpsTraj(path+f)
  	md.read_info()
  	# # number of frames
  	mframe,nframe = 1, 1
  	# # chunk number in z
  	Nz = 100
  	mol_n = [1,1000]
  	# 鍒嗗瓙搴忓彿
  
  	Calculate = True #True#False
  
  	if Calculate==True:
  		rho_nframe = np.zeros(Nz).reshape(Nz,1)
  		for i in range(mframe,nframe+1):
  			position = md.read_mxyz(i)
  			z, rho = md.oneframe_alldensity(position,Nz,density_type="mass")
  			# z, rho = md.oneframe_moldensity(position,Nz,mol_n=mol_n,id_type="mol",density_type="mass")
  
  			rho_nframe = rho_nframe+rho
  
  			print(i,"---",nframe)
  		nf = (nframe-mframe+1)
  		rho=rho_nframe/nf #all
  		print("Average density =",rho.mean(),"g/mL")
  	#---- end ----------------------------------------------
  	plt.rc('font', family='Times New Roman', size=26)
  	fig = plt.figure(figsize=(12,8))
  	fig.subplots_adjust(bottom=0.2,left=0.2)
  	ax=fig.add_subplot(111)
  	ax.plot(z,rho,'r--',label='All',linewidth=2)
  
  	# ax.legend(loc="center")
  	ax.legend(loc="best")
  
  	ax.set_ylabel('Density(g/mL)',fontweight='bold',size=32)
  	ax.set_xlabel('z(脜)',fontweight='bold',size=32)	
  	# ax.set_ylim(-0.05,1.5)
  
  	plt.savefig(path+"density/density.png",dpi=300)
  	plt.show()
  
  
  if __name__ == '__main__':
  	cal_density()