Delete tool.py

codes/tool.py

-import numpy as np
-from ase.constraints import FixScaled,FixAtoms
-from ase.io import Trajectory
-from dscribe.descriptors import SOAP
-import os
-import ase
-
-def sign(x):
-    if x<0:
-        return -1
-    else:
-        return 1
-
-def get_train_data(traj,data_folder,train_pos_indices):  
-        sys=Trajectory(traj)
-        ind_slab=sys[0].constraints[1].index
-        ind_free=np.delete(np.arange(len(sys[0])),ind_slab)
-        species=[]
-        elem=sys[0].get_chemical_symbols() 
-        #identification des espèces
-        for el in range(len(elem)): 
-            if elem[el] not in species:
-                species.append(elem[el])   
-        y_ini=np.load(data_folder+'/E.npy')
-        index_pos=np.load(data_folder+'/ind_pos.npy')
-        ind_train=[]
-        #select only 3 config per position
-        for i in range(len(index_pos)):
-            if i in train_pos_indices:
-                ind_train.append(index_pos[i,0])
-                ind_train.append((index_pos[i,1]-index_pos[i,0]+1)//2)
-                ind_train.append(index_pos[i,1])
-
-        y_train=np.array([y_ini[i] for i in ind_train])
-        return [sys[i] for i in ind_train],y_train,species
-
-def pos_to_relax(poscar_file,n=20):    
-        poscar=ase.io.read(poscar_file)
-        #position à relaxer
-        a=poscar.get_cell()[0,0]
-        b=poscar.get_cell()[1,1]
-        c=poscar.get_cell()[2,2]
-        #maillage
-        n=20
-        Xpos=[i*a/n for i in range(n)]
-        Ypos=[i*b/n for i in range(n)]
-        xx,yy=np.meshgrid(Xpos,Ypos)
-        xx,yy=np.ravel(xx),np.ravel(yy)
-        zz=np.empty(len(xx))
-        #zpos
-        atom_top=poscar.get_positions()
-        for i in range(len(xx)):        
-            dx = atom_top[:,0] - xx[i] 
-            dy = atom_top[:,1] - yy[i] 
-            dz = atom_top[:,2] - 18 
-            dxy=np.linalg.norm([dx,dy,dz],axis=0)
-            indice=np.where(dxy==np.min(dxy))[0][0]    
-            zz[i]=atom_top[indice,2]+1.6
-        return xx,yy,zz
-
-