Read lammps dump trajectory.
Project description
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()
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ReadLammpsTraj-1.1.8.tar.gz
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