def read_CHGCAR(fname='CHGCAR', specorder=None): """ Read CHGCAR file and get information of cell, atoms, and volumetric data. Parameters ---------- fname : str File name to be read. """ nsys = NAPSystem() with open(fname, 'r') as f: # 1st line: comment f.readline() # 2nd: lattice constant nsys.alc = float(f.readline().split()[0]) # 3rd-5th: cell vectors nsys.a1 = np.array([float(x) for x in f.readline().split()]) nsys.a2 = np.array([float(x) for x in f.readline().split()]) nsys.a3 = np.array([float(x) for x in f.readline().split()]) # 6th: species names or number of each species buff = f.readline().split() if not buff[0].isdigit(): spcs = copy.deepcopy(buff) buff = f.readline().split() if specorder is None: nsys.specorder = spcs else: nsys.specorder = specorder for s in spcs: if s not in nsys.specorder: nsys.specorder.append(s) num_species = np.array([int(n) for n in buff]) try: spcs except NameError: spcs = nsys.specorder #...Check number of species in POSCAR file and in specorder if len(num_species) > len(nsys.specorder): msg = ''' ers of species in POSCAR is greater than the one in specorder, which should be the same or less. er of species in POSCAR = {0:d} need to specify the species order correctly with --specorder option. '''.format(len(num_species)) raise ValueError(msg) natm = np.sum(num_species) sids = [0 for i in range(natm)] poss = np.zeros((natm, 3)) vels = np.zeros((natm, 3)) frcs = np.zeros((natm, 3)) #print("Number of atoms = {0:5d}".format(natm)) # 7th or 8th line: comment c7 = f.readline() if c7[0] in ('s', 'S'): c7 = f.readline() if c7[0] in ('c', 'C'): # positions are in Cartesian coordinate hi = nsys.get_hmat_inv() coord = 'cartesian' else: # such as "Direct" coord = 'scaled' #...Atom positions for i in range(natm): buff = f.readline().split() sid = 1 m = 0 sindex = 0 for n in num_species: m += n if i < m: if spcs and nsys.specorder: sid = nsys.specorder.index(spcs[sindex]) + 1 break sid += 1 sindex += 1 sids[i] = sid pos = [float(buff[0]), float(buff[1]), float(buff[2])] if coord == 'cartesian': x1, x2, x3 = cartesian_to_scaled(hi, pos[0], pos[1], pos[2]) elif coord == 'scaled': x1, x2, x3 = pos[0], pos[1], pos[2] poss[i][:] = [x1, x2, x3] #...Up to here, code should be the same as read_POSCAR, in case of CHGCAR lines follow nsys.atoms[['x', 'y', 'z']] = poss nsys.atoms[['vx', 'vy', 'vz']] = vels nsys.atoms[['fx', 'fy', 'fz']] = frcs nsys.atoms['sid'] = sids #...Read volumetric data f.readline() # should be one blank line ndiv = [int(x) for x in f.readline().split()] ndata = ndiv[0] * ndiv[1] * ndiv[2] voldata = np.zeros(ndata) inc = 0 while True: line = [float(d) for d in f.readline().split()] for d in line: voldata[inc] = d inc += 1 if inc >= ndata: break #...Stop reading CHGCAR file here, ignoring the rest of file nsys.ndiv = copy.copy(ndiv) nsys.voldata = np.reshape(voldata, ndiv, order='F') return nsys
def read_xsf(fname="xsf", specorder=None): from nappy.elements import get_symbol_from_number nsys = NAPSystem() if specorder is None: nsys.specorder = [] else: nsys.specorder = specorder f = open(fname, 'r') mode = 'None' ixyz = 0 iatm = 0 natm = -1 for line in f.readlines(): if 'CRYSTAL' in line: mode = 'CRYSTAL' continue elif 'PRIMVEC' in line: mode = 'PRIMVEC' continue elif 'PRIMCOORD' in line: mode = 'PRIMCOORD' # Before going further, create inversed h-matrix hi = nsys.get_hmat_inv() # print 'Inversed h-matrix:' # print hi continue if mode == 'CRYSTAL': pass elif mode == 'PRIMVEC': if ixyz == 0: arr = [float(x) for x in line.split()] nsys.a1[0] = arr[0] nsys.a1[1] = arr[1] nsys.a1[2] = arr[2] elif ixyz == 1: arr = [float(x) for x in line.split()] nsys.a2[0] = arr[0] nsys.a2[1] = arr[1] nsys.a2[2] = arr[2] elif ixyz == 2: arr = [float(x) for x in line.split()] nsys.a3[0] = arr[0] nsys.a3[1] = arr[1] nsys.a3[2] = arr[2] ixyz += 1 elif mode == 'PRIMCOORD': data = line.split() if len(data) == 1: natm = int(data[0]) sids = [0 for i in range(natm)] poss = np.zeros((natm, 3)) vels = np.zeros((natm, 3)) frcs = np.zeros((natm, 3)) continue elif len(data) == 2: natm = int(data[0]) nspcs = int(data[1]) sids = [0 for i in range(natm)] poss = np.zeros((natm, 3)) vels = np.zeros((natm, 3)) frcs = np.zeros((natm, 3)) continue elif len(data) == 4 or len(data) == 7: if iatm >= natm: continue symbol = get_symbol_from_number(int(data[0])) if symbol not in nsys.specorder: nsys.specorder.append(symbol) sid = nsys.specorder.index(symbol) + 1 sids[iatm] = sid # ai.set_sid(sid) xc = float(data[1]) yc = float(data[2]) zc = float(data[3]) xi, yi, zi = cartesian_to_scaled(hi, xc, yc, zc) poss[iatm, :] = [xi, yi, zi] # print 'iatm,symbol,sid,xc,yc,zc = ',iatm,symbol,sid,xc,yc,zc else: continue iatm += 1 nsys.alc = 1.0 nsys.atoms[['x', 'y', 'z']] = poss nsys.atoms[['vx', 'vy', 'vz']] = vels nsys.atoms[['fx', 'fy', 'fz']] = frcs nsys.atoms['sid'] = sids f.close() return nsys
def read_POSCAR(fname='POSCAR', specorder=None): nsys = NAPSystem() with open(fname, 'r') as f: # 1st line: comment f.readline() # 2nd: lattice constant nsys.alc = float(f.readline().split()[0]) # 3rd-5th: cell vectors nsys.a1 = np.array([float(x) for x in f.readline().split()]) nsys.a2 = np.array([float(x) for x in f.readline().split()]) nsys.a3 = np.array([float(x) for x in f.readline().split()]) # 6th: species names or number of each species buff = f.readline().split() if not buff[0].isdigit(): spcs = copy.deepcopy(buff) buff = f.readline().split() if specorder is None: nsys.specorder = spcs else: nsys.specorder = specorder for s in spcs: if s not in nsys.specorder: nsys.specorder.append(s) num_species = np.array([int(n) for n in buff]) try: spcs except NameError: spcs = nsys.specorder #...Check number of species in POSCAR file and in specorder if len(num_species) > len(nsys.specorder): msg = ''' ers of species in POSCAR is greater than the one in specorder, which should be the same or less. er of species in POSCAR = {0:d} need to specify the species order correctly with --specorder option. '''.format(len(num_species)) raise ValueError(msg) natm = np.sum(num_species) sids = [0 for i in range(natm)] # poss = [ np.zeros(3) for i in range(natm) ] # vels = [ np.zeros(3) for i in range(natm) ] # frcs = [ np.zeros(3) for i in range(natm) ] poss = np.zeros((natm, 3)) vels = np.zeros((natm, 3)) frcs = np.zeros((natm, 3)) #print("Number of atoms = {0:5d}".format(natm)) # 7th or 8th line: comment c7 = f.readline() if c7[0] in ('s', 'S'): c7 = f.readline() if c7[0] in ('c', 'C'): # positions are in Cartesian coordinate hi = nsys.get_hmat_inv() coord = 'cartesian' else: # such as "Direct" coord = 'scaled' #...Atom positions for i in range(natm): buff = f.readline().split() sid = 1 m = 0 sindex = 0 for n in num_species: m += n if i < m: if spcs and nsys.specorder: sid = nsys.specorder.index(spcs[sindex]) + 1 break sid += 1 sindex += 1 sids[i] = sid pos = [float(buff[0]), float(buff[1]), float(buff[2])] if coord == 'cartesian': x1, x2, x3 = cartesian_to_scaled(hi, pos[0], pos[1], pos[2]) elif coord == 'scaled': x1, x2, x3 = pos[0], pos[1], pos[2] poss[i, :] = [x1, x2, x3] nsys.atoms[['x', 'y', 'z']] = poss nsys.atoms[['vx', 'vy', 'vz']] = vels nsys.atoms[['fx', 'fy', 'fz']] = frcs nsys.atoms['sid'] = sids return nsys
def read_dump(fname="dump", specorder=None): nsys = NAPSystem() f = open(fname, 'r') mode = 'None' ixyz = 0 iatm = 0 natm = -1 symbol = None if specorder is None: nsys.specorder = [] else: nsys.specorder = specorder nsys.alc = 1.0 xy = 0.0 xz = 0.0 yz = 0.0 aux_exists = { 'x': -1, 'y': -1, 'z': -1, 'xu': -1, 'yu': -1, 'zu': -1, 'fx': -1, 'fy': -1, 'fz': -1, 'ekin': -1, 'epot': -1, 'sxx': -1, 'syy': -1, 'szz': -1, 'syz': -1, 'sxz': -1, 'sxy': -1, 'chg': -1, 'chi': -1 } ivx = -1 ivy = -1 ivz = -1 ifx = -1 ify = -1 ifz = -1 for line in f.readlines(): data = line.split() if 'ITEM' in line: if 'NUMBER OF ATOMS' in line: mode = 'NUMBER OF ATOMS' continue elif 'BOX BOUNDS' in line: mode = 'BOX BOUNDS' continue elif 'ATOMS' in line: mode = 'ATOMS' aux_names = [name for i, name in enumerate(data) if i > 1] aux_names.remove('id') aux_names.remove('type') if ('x' not in aux_names and 'xu' not in aux_names) or \ ('y' not in aux_names and 'zu' not in aux_names) or \ ('z' not in aux_names and 'zu' not in aux_names): raise ValueError( 'Not enough coordinate info.\nCheck the dump file format.' ) try: ix = aux_names.index('x') + 2 except Exception: ix = aux_names.index('xu') + 2 try: iy = aux_names.index('y') + 2 except Exception: iy = aux_names.index('yu') + 2 try: iz = aux_names.index('z') + 2 # iauxstart = 5 except Exception: iz = aux_names.index('zu') + 2 # iauxstart = 5 try: ivx = aux_names.index('vx') + 2 ivy = aux_names.index('vy') + 2 ivz = aux_names.index('vz') + 2 # iauxstart = 8 except Exception: pass try: ifx = aux_names.index('fx') + 2 ify = aux_names.index('fy') + 2 ifz = aux_names.index('fz') + 2 except Exception: pass # for s in ('x','xu','y','yu','z','zu','vx','vy','vz'): # if s in aux_names: # aux_names.remove(s) if len(aux_names) > 0: auxs = np.zeros((natm, len(aux_names))) continue elif 'TIMESTEP' in line: mode = 'TIMESTEP' continue if mode == 'TIMESTEP': timestep = int(data[0]) elif mode == 'NUMBER OF ATOMS': natm = int(data[0]) sids = [0 for i in range(natm)] # poss = [ np.zeros(3) for i in range(natm) ] # vels = [ np.zeros(3) for i in range(natm) ] # frcs = [ np.zeros(3) for i in range(natm) ] poss = np.zeros((natm, 3)) vels = np.zeros((natm, 3)) frcs = np.zeros((natm, 3)) elif mode == 'BOX BOUNDS': if ixyz == 0: xlo_bound = float(data[0]) xhi_bound = float(data[1]) if len(data) > 2: xy = float(data[2]) elif ixyz == 1: ylo_bound = float(data[0]) yhi_bound = float(data[1]) if len(data) > 2: xz = float(data[2]) elif ixyz == 2: zlo_bound = float(data[0]) zhi_bound = float(data[1]) if len(data) > 2: yz = float(data[2]) ixyz += 1 if ixyz > 2: xlo = xlo_bound - min(0.0, xy, xz, xy + xz) xhi = xhi_bound - max(0.0, xy, xz, xy + xz) ylo = ylo_bound - min(0.0, yz) yhi = yhi_bound - max(0.0, yz) zlo = zlo_bound zhi = zhi_bound #...Original definition of lattice vectors could be different # from this, because the definition in dump format # requires y,z-components of vector a1 to be zero. nsys.a1 = np.array([xhi - xlo, 0., 0.], dtype=float) nsys.a2 = np.array([xy, yhi - ylo, 0.], dtype=float) nsys.a3 = np.array([xz, yz, zhi - zlo], dtype=float) hmat = nsys.get_hmat() hmati = nsys.get_hmat_inv() elif mode == 'ATOMS': if iatm < natm: symbol = None if data[1].isdigit(): sid = int(data[1]) sids[iatm] = sid symbol = nsys.specorder[sid - 1] else: symbol = data[1] if symbol not in nsys.specorder: nsys.specorder.append(symbol) sid = nsys.specorder.index(symbol) + 1 sids[iatm] = sid r0 = [float(data[ix]), float(data[iy]), float(data[iz])] if ivx > 0 and ivy > 0 and ivz > 0: v0 = [float(data[ivx]), float(data[ivy]), float(data[ivz])] else: v0 = [0., 0., 0.] if ifx > 0 and ify > 0 and ifz > 0: f0 = [float(data[ifx]), float(data[ify]), float(data[ifz])] else: f0 = [0., 0., 0.] sr = np.dot(hmati, r0) sv = np.dot(hmati, v0) sr[0] = pbc(sr[0]) sr[1] = pbc(sr[1]) sr[2] = pbc(sr[2]) # poss[iatm][:] = sr[:] # vels[iatm][:] = sv[:] poss[iatm, :] = sr[:] vels[iatm, :] = sv[:] frcs[iatm, :] = f0[:] if len(aux_names) > 0: # auxs[iatm,:] = [ float(x) for x in data[iauxstart:] ] auxs[iatm, :] = [float(x) for x in data[2:]] iatm += 1 nsys.atoms[['x', 'y', 'z']] = poss nsys.atoms[['vx', 'vy', 'vz']] = vels nsys.atoms[['fx', 'fy', 'fz']] = frcs nsys.atoms['sid'] = sids for ia in range(len(aux_names)): name = aux_names[ia] if name in ('x', 'xu', 'y', 'yu', 'z', 'zu', 'vx', 'vy', 'vz', 'fx', 'fy', 'fz'): continue aux = auxs[:, ia] nsys.atoms[name] = aux.tolist() f.close() return nsys
def make_polycrystal(grns,uc,n1,n2,n3,two_dim=False): """ THIS ROUTINE IS NOT THAT UNIVERSAL. Each grain has to have neighboring grains within a supercell, otherwise there will be some unexpecting grain boundries. In order to do so, the system should be large enough and the number of grains should be large enough. """ #...Calc the minimum bond distance in unit cell and use it as penetration depth dmin = 1.0e+30 for i in range(uc.num_atoms()-1): for j in range(i+1,uc.num_atoms()): dij = uc.get_distance(i,j) dmin = min(dij,dmin) print(' Minimum bond distance in the unitcell: ',dmin) dmin = dmin *DMIN_RATE penetration_depth = dmin*2 print(' Minimum bond distance allowed in the new system: ',dmin) sv,nsv= shift_vector(two_dim) # print(' nsv =',nsv) # for i in range(nsv): # print(' i,sv[i]=',i,sv[i]) nsys= NAPSystem(specorder=uc.specorder) nsys.set_lattice(uc.alc,uc.a1*n1,uc.a2*n2,uc.a3*n3) hmat = nsys.get_hmat() hmati = nsys.get_hmat_inv() nmax = n1*n2*n3 *uc.num_atoms() sidsl = np.zeros(nmax,dtype=int) symsl = [] possl = np.zeros((nmax,3)) velsl = np.zeros((nmax,3)) frcsl = np.zeros((nmax,3)) ix0 = -n1/2-1 ix1 = n1/2+2 iy0 = -n2/2-1 iy1 = n2/2+2 iz0 = -n3/2-1 iz1 = n3/2+2 if two_dim: if n3 != 1: raise ValueError('n3 should be 1 in case two_dim is ON.') iz0 = 0 iz1 = 1 print(' x range = ',ix0,ix1) print(' y range = ',iy0,iy1) print(' z range = ',iz0,iz1) inc = 0 for ig in range(len(grns)): grain= grns[ig] rmat= grain.rmat # Rotation matrix of the grain pi= grain.point # Grain center in reduced coordinate api= np.dot(hmat,pi) # Grain center in Cartessian coordinate print(' grain-ID = ',ig+1) for ix in range(ix0,ix1): # print('ix=',ix) for iy in range(iy0,iy1): for iz in range(iz0,iz1): for m in range(uc.num_atoms()): sidt = uc.get_atom_attr(m,'sid') rt= np.zeros((3,)) pm = uc.get_atom_attr(m,'pos') rt[0]= (pm[0]+ix)/n1 rt[1]= (pm[1]+iy)/n2 rt[2]= (pm[2]+iz)/n3 #...rt to absolute position art= np.dot(hmat,rt) #...Rotate ari= np.dot(rmat,art) #...Shift origin to the grain center ari[0]= ari[0]+api[0] ari[1]= ari[1]+api[1] ari[2]= ari[2]+api[2] #...check distance from all the grain points di= distance(ari,api,two_dim) isOutside= False for jg in range(len(grns)): gj= grns[jg] for isv in range(nsv): pj= gj.point if jg == ig: if not two_dim and isv == 13: continue elif two_dim and isv == 4: continue svi= sv[isv] pj= pj +svi apj = np.dot(hmat,pj) dj= distance(ari,apj,two_dim) if dj +penetration_depth < di: # Allow some penetration here isOutside= True break if isOutside: break if isOutside: break #...here ri is inside this grain, register it #...Cartessian coord to reduced coord ri = np.dot(hmati,ari) ri[0]= pbc(ri[0]) ri[1]= pbc(ri[1]) ri[2]= pbc(ri[2]) sidsl[inc] = sidt possl[inc] = ri velsl[inc,:] = 0.0 frcsl[inc,:] = 0.0 symsl.append(nsys.specorder[sidt-1]) inc += 1 if inc > nmax: raise ValueError('inc > nmax') #...Create filled arrays from non-filled ones poss = np.array(possl[:inc]) vels = np.array(velsl[:inc]) frcs = np.array(frcsl[:inc]) nsys.add_atoms(symsl,poss,vels,frcs) #...remove too-close atoms at the grain boundaries print(' Making pair list in order to remove close atoms...') print(' Number of atoms: ',nsys.num_atoms()) nsys.make_pair_list(RCUT) nsys.write('POSCAR_orig') short_pairs = [] # dmin2= dmin**2 # xij= np.zeros((3,)) print(' Making the list of SHORT pairs...') for ia in range(nsys.num_atoms()): lst= nsys.get_atom_attr(ia,'lspr') for j in range(len(lst)): ja= lst[j] if ja > ia: continue dij = nsys.get_distance(ia,ja) if dij < dmin: short_pairs.append((ia,ja,dij)) print(' Number of short pairs: ',len(short_pairs)) #...Remove only relevant atoms, not all the atoms in the short_pairs. ls_remove = [] ls_not_remove = [] for pair in short_pairs: ia = pair[0] ja = pair[1] if ia not in ls_not_remove and ja not in ls_not_remove: ls_remove.append(ia) ls_not_remove.append(ja) elif ia not in ls_not_remove: ls_remove.append(ia) elif ja not in ls_not_remove: ls_remove.append(ja) else: # Both atoms are already in not_remove list, which should be avoided. ls_not_remove.remove(ia) ls_remove.append(ia) ls_not_remove.append(ja) #...Remove double registered IDs ls_remove = uniq(ls_remove) print(' Number of to be removed atoms: ',len(ls_remove)) nsys.remove_atoms(*ls_remove) return nsys