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Add the dipole and spectrum post-processing script. #1928
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| from re import split | ||
| import numpy as np | ||
| import matplotlib.pyplot as plt | ||
| from ase.units import Bohr | ||
| from math import pi | ||
| from scipy.constants import c | ||
| from os import listdir | ||
| from os import mkdir | ||
| from shutil import move | ||
| from shutil import copyfile | ||
| from os import path | ||
| def Sp_plot(t_name,out,file,move=0,N_t=-1,dt=0.0034,direction=-1): | ||
| Dipole=dipole_read(t_name,out,file,direction=direction) | ||
| if(N_t==-1): | ||
| N_t=Dipole.shape[1] | ||
| N_t-=move | ||
| shift_omega_step=1 | ||
| lambda_x=(c/np.linspace(shift_omega_step,N_t-1,N_t-shift_omega_step)*dt*N_t*1e-6) | ||
| fig,ax=plt.subplots() | ||
| if(direction==1 or direction==-1): | ||
| alpha_x=np.fft.fft(Dipole[0][move:N_t]) | ||
| S_x=np.abs(alpha_x.imag) | ||
| ax.plot(lambda_x,S_x[shift_omega_step:],label='X') | ||
| if(direction==2 or direction==-1): | ||
| alpha_y=np.fft.fft(Dipole[1][move:N_t]) | ||
| S_y=np.abs(alpha_y.imag) | ||
| ax.plot(lambda_x,S_y[shift_omega_step:],label='Y') | ||
| if(direction==3 or direction==-1): | ||
| alpha_z=np.fft.fft(Dipole[2][move:N_t]) | ||
| S_z=np.abs(alpha_z.imag) | ||
| ax.plot(lambda_x,S_x[shift_omega_step:],label='Z') | ||
| ax.set_ylabel('Strength') | ||
| ax.set_xlabel('frequency(eV)') | ||
| ax.set_title("Spectra") | ||
| ax.set_xlim(80,200) | ||
| plt.legend() | ||
| plt.savefig('./'+out+'/'+file+'spec.png') | ||
|
|
||
| def Sp_field_plot(): | ||
| pass | ||
| def dipole_read(total_name,out,file,dt=0.0034,direction=-1): | ||
| #Initial | ||
| list_d=[[] for i in range(3)] | ||
| #N_t=nstep-move_step #step used in fft | ||
| #Read in cycle | ||
| m=0 #Dimension label | ||
| line=1 | ||
| with open(total_name,mode='r')as f1: | ||
| while(line!=''): | ||
| while(m<3): | ||
| line=f1.readline() | ||
| if(line==''):break | ||
| tmp=line.split() | ||
| if (m==0): | ||
| list_d[0].append(float(tmp[1])) | ||
| elif (m==1): | ||
| list_d[1].append(float(tmp[1])) | ||
| elif (m==2): | ||
| list_d[2].append(float(tmp[1])) | ||
| m+=1 | ||
| m=0 | ||
| #Plot part | ||
| Dipole=np.array(list_d) | ||
| N_t=Dipole.shape[1] | ||
| Ti=np.linspace(0,(N_t-1)*dt,N_t) | ||
| fig,ax=plt.subplots() | ||
| if(direction==1 or direction==-1): | ||
| ax.plot(Ti,Dipole[0],label='X') | ||
| if(direction==2 or direction==-1): | ||
| ax.plot(Ti,Dipole[1],label='Y') | ||
| if(direction==3 or direction==-1): | ||
| ax.plot(Ti,Dipole[2],label='Z') | ||
| ax.set_ylabel('Strength') | ||
| ax.set_xlabel('time(fs)') | ||
| ax.set_title('Dipole') | ||
| plt.legend() | ||
| plt.savefig('./'+out+'/'+file+'dipole.png') | ||
| return Dipole | ||
| #reading para | ||
| def autoanlysis(filename,dir,out): | ||
| list_dir=listdir("./"+dir+"/") | ||
| count=0 | ||
| print("total file: "+str(len(list_dir))) | ||
| #main cycle | ||
| for file in list_dir: | ||
| if(filename in file): | ||
| count+=1 | ||
| t_name="./"+dir+"/"+file | ||
| Sp_plot(t_name,out,file) | ||
|
|
||
| #main part | ||
| filename='dipole.dat' | ||
| dir='dipole_nomove' | ||
| out='PIC' | ||
| file='C2H2_nomove_X_dipole.dat' | ||
| if(not path.exists('./'+out)): | ||
| mkdir(out) | ||
| #direction='X' | ||
| #autoanlysis(filename,dir,out) | ||
| #single plot | ||
| t_name="./"+dir+"/"+file | ||
| Sp_plot(t_name,out,file,direction=1) | ||
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Please add annotation for how to use this script, I have two question:
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I think this script can be integrated into tools/plot-tools.