ReadLammpsTraj 1.1.6

Read lammps dump trajectory.

ReadLammpsTraj

• Read lammps dump trajectory

Installation

• github:

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

• pip

  pip install ReadLammpsTraj
  

Usage

• A example to calculate density in demo folder:

  # calculating the density from lammps traj
  import numpy as np
  import matplotlib.pyplot as plt
  import ReadLammpsTraj as RLT
  from pathlib import Path
  import periodictable as pt
  
  def cal_density():
  	path = "./"
  	f = "1000.lammpstrj"
  	# lammpsdata = "1_npt_dissociation.data"
  	Path(path+"imgs/").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
  	id_range = [1,10000]
  	# # element mass
  	# O_mass = pt.elements.symbol('O').mass
  	# H_mass = pt.elements.symbol('H').mass
  	# C_mass = pt.elements.symbol('C').mass
  	# mass_dict = {1:O_mass,2:H_mass,3:C_mass+4*H_mass,4:C_mass+4*H_mass}
  	mass_dict = {}
  	# mass_dict = RLT.read_mass(path+lammpsdata)
  
  	direction = "z"
  
  	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,mass_dict,density_type="mass",direction=direction)
  			z, rho = md.oneframe_moldensity(position,Nz,id_range,mass_dict,id_type="atom",density_type="mass",direction=direction)
  
  			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+"imgs/density.png",dpi=300)
  	plt.show()
  
  
  if __name__ == '__main__':
  	cal_density()