def distance_distribution(V,W,L,n_frames=15,n_start=1): #finds end to end distances and plots a histogram with that data def hist(M1,M2,save_name,label): distance=particle_distance(M1,M2,L) hist_s,xs,max_hist=histogram(distance,bins=50) return xs,hist_s ######################################## #Plot Data for AA,AB,BB distances save_name='_time_'+'%i'%(n_start) start=n_start finish=n_start+n_frames max_hist=0 AB=hist(V[start:finish],W[start:finish],save_name,'A-B') AA=hist(W[start:finish],W[start:finish],save_name,'A-A') BB=hist(V[start:finish],V[start:finish],save_name,'B-B') pyplot.plot3(AA[0],AA[1],AB[0],AB[1],BB[0],BB[1],'s','g(s)', 'A-A','A-B','B-B',save='nnplot_'+save_name,showleg=True)
def find_defects_mod(CV,CW,VW,V,W,L,n_finish=1,n_start=0,delta=20,filters=0.2): from MD.analysis.nearest_neighbor import ws_neighbors_point from MD.analysis.nearest_neighbor import close_neighbors_point ####### debug = False x = np.arange(n_start,n_finish,delta) lattice = [] for i in range(CV.shape[0]): lattice.append(int(points.dist(CV[0],CV[i],L)[0])) for i in range(CW.shape[0]): lattice.append(int(points.dist(CV[0],CW[i],L)[0])) points.unique(lattice) lattice.sort() print lattice rmin = lattice[1] / 2.0 rmax = lattice[2] / 2.0 +1 #for interstitial s = min(W.shape[1],V.shape[1]) #for vacancy #s = max(W.shape[1],V.shape[1]) DW = np.zeros((len(x),CW.shape[0])) DV = np.zeros((len(x),CV.shape[0])) vac_count = np.zeros((len(x),1)) int_count = np.zeros((len(x),1)) fid = open('defects.txt','w') master = [[],[]] particle_frame = [] for index,k in enumerate(x): print 'frame',k # Identify the points on the bcc Lattice which belong to A and B type #lets look at one point first # Assign each point to its place on the lattice #find the closest point ##################### N = [] N_V = [] N_W = [] Vn = [] Wn = [] for i in V[k]: if abs(i[0]) < L[0]: Vn.append(i) for i in W[k]: if abs(i[0]) < L[0]: Wn.append(i) print 'Wn',len(Wn) print 'Vn',len(Vn) particle_frame.append(len(Wn)+len(Vn)) Wn = np.array(Wn) Vn = np.array(Vn) for i in range(CV.shape[0]): N = ws_neighbors_point(Vn,CV[i],L,i,rmin=rmin,rmax=rmax)[0] N_V.extend(N) num = len(N) if num == 0: N2 = ws_neighbors_point(Wn,CV[i],L,i,rmin=rmin,rmax=rmax)[0] N_W.extend(N2) num = -len(N2) DV[index][i] = num ########################### for i in range(CW.shape[0]): N = ws_neighbors_point(Wn,CW[i],L,i+W.shape[1],rmin=rmin,rmax=rmax)[0] N_W.extend(N) num = len(N) if num == 0: N2 = ws_neighbors_point(Vn,CW[i],L,i+V.shape[1],rmin=rmin,rmax=rmax)[0] N_V.extend(N2) num = -len(N2) DW[index][i] = num #find the atoms that haven't been placed on the lattice yet IV = points.difference(range(Vn.shape[0]),N_V) IW = points.difference(range(Wn.shape[0]),N_W) ## if debug: print 'atoms not added listed after first sorting' print IV, IW print DW[index] print DV[index] for i in IV: #find closest lattice point nw, dw = close_neighbors_point(CW,Vn[i],L) nv, dv = close_neighbors_point(CV,Vn[i],L) if dw <= dv: #check to see if there is already an atom at that point if DW[index][nw] == 1 or DW[index][nw] == -1: if DV[index][nv] == 0: DV[index][nv] = 1 N_V.extend([i]) else: DW[index][nw] = -2 N_V.extend([i]) if DW[index][nw] == 0: DW[index][nw] = -1 N_V.extend([i]) #check to see if there is already an atom at that point else: if DV[index][nv] == 1 or DV[index][nv] == -1: #if there isn't one at the other point add it if DW[index][nw] == 0: DW[index][nw] = -1 N_V.extend([i]) else: if DV[index][nv] == 1: DV[index][nv] = 2 if DV[index][nv] == -1: DV[index][nv] = -2 N_V.extend([i]) if DV[index][nv] == 0: DV[index][nv] = 1 N_V.extend([i]) for i in IW: nw, dw = close_neighbors_point(CW,Wn[i],L) nv, dv = close_neighbors_point(CV,Wn[i],L) if dv <= dw: if DV[index][nv] == 1 or DV[index][nv] == -1: if DW[index][nw] == 0: DW[index][nw] = 1 N_W.extend([i]) else: DV[index][nv] = -2 N_W.extend([i]) if DV[index][nv] == 0: DV[index][nv] = -1 N_W.extend([i]) else: if DW[index][nw] == 1 or DW[index][nw] == -1: if DV[index][nv] == 0: DV[index][nv] = -1 N_W.extend([i]) else: DW[index][nw] = 2 N_W.extend([i]) if DW[index][nw] == 0: DW[index][nw] = 1 N_W.extend([i]) #find the atoms that haven't been placed on the lattice yet IV = points.difference(range(Vn.shape[0]),N_V) IW = points.difference(range(Wn.shape[0]),N_W) ## if debug: print 'atoms not added list for debugging' print IV, IW print DW[index] print DV[index] print 'Defect list for lattice' #print out the vacency, substitutions def out_defect(A, index, fid, def_list, C=0): for i in range(A.shape[1]): if A[index][i] == 0: pr = 'vacecy at '+ str(i+C)+ '\n' try: def_list[0].extend(i+C) except: def_list[0].append(i+C) if debug: print pr fid.write(pr) if A[index][i] == -1: pr = 'substitution ' + str(i+C)+ '\n' if debug: print pr fid.write(pr) if A[index][i] == -2: pr = 'interstitial ' + str(i + C)+ '\n' try: def_list[1].extend(i+C) except: def_list[1].append(i+C) if debug: print pr fid.write(pr) if A[index][i] == 2: pr = 'interstitial ' + str(i + C)+ '\n' try: def_list[1].extend(i+C) except: def_list[1].append(i+C) if debug: print pr fid.write(pr) frame = 'Frame ' + str(k) + '\n' fid.write(frame) def_list = [[],[]] out_defect(DV, index, fid, def_list) out_defect(DW, index, fid, def_list, C = DV.shape[1]) if len(points.difference(def_list[0], master[0])) != 0: vac_count[index] += len(points.difference(def_list[1],master[1])) master[0] = def_list[0] if len(points.difference(def_list[1],master[1])) != 0: int_count[index] += len(points.difference(def_list[1],master[1])) master[1] = def_list[1] #find the atoms that haven't been placed on the lattice yet IV = points.difference(range(V.shape[1]),N_V) IW = points.difference(range(W.shape[1]),N_W) # Identify the defects surrounding each point #The total number of frames we are going to look at # Find the number of defects in each frame count = 0 substitutions = [] vacancies = [] intersticial = [] def count_def(A,check): count = 0 for i in A: if i == check: count +=1 return count def count_ldef(A,check): count = 0 for i in A: if i < check: count +=1 return count def count_adef(A,check): count = 0 for i in A: if abs(i) == check: count +=1 return count for k in range(DW.shape[0]): #find the points that are nearest neighbor that are different substitutions.append(count_ldef(DW[k],0)+count_ldef(DV[k],0)) vacancies.append(count_def(DW[k],0)+count_def(DV[k],0)) intersticial.append(count_adef(DW[k],2.0)+count_adef(DV[k],2.0)) print 'substitions' print substitutions print 'vacancies' print vacancies print 'interstitials' print intersticial util.pickle_dump(DV,'DV_s.pkl') util.pickle_dump(DW,'DW_s.pkl') util.pickle_dump([substitutions, vacancies, intersticial, x],'plot_def_s.pkl') pyplot.plot3(x, substitutions, x, particle_frame, x, intersticial, label1='substitutions',label2='number of particles',label3='intersticial', save='defects_per_frame_surface',showleg=True) #pyplot.plot(x, vac_count, save='defect_vac_diffusion_count') #pyplot.plot(x, int_count, save='defect_int_diffusion_count') return DV, DW, [substitutions, vacancies, intersticial, x]
MD.V = M.cord_auto(['V']) MD.W = M.cord_auto(['W']) MD.VW = M.cord_auto(['V','W']) util.pickle_dump(MD.V,'Vs.pkl') util.pickle_dump(MD.W,'Ws.pkl') util.pickle_dump(MD.VW,'VWs.pkl') CV = util.pickle_load('CV.pkl') CW = util.pickle_load('CW.pkl') try: print 'attempting to load DW, DV' DV = util.pickle_load('DV_s.pkl') DW = util.pickle_load('DW_s.pkl') plot_def = util.pickle_load('plot_def_s.pkl') except: print 'finding the defects' DV, DW, plot_def = find_defects_mod(CW,CV,MD.VW,MD.V,MD.W,MD.L,n_finish=MD.last-1,n_start=0,delta=1) plots = util.pickle_load('plot_def.pkl') for index,k in enumerate(x): Vn = [] Wn = [] for i in V[k]: if abs(i[0]) < L[0]: Vn.append(i) for i in W[k]: if abs(i[0]) < L[0]: Wn.append(i) particle_frame.append(len(Vn)+len(Wn)) pyplot.plot3(plots[3], plots[0], plots[3], particle_frame, plots[3], plots[2], label1='substitutions',label2='number of particles',label3='intersticial', save='defects_per_frame',showleg=True)