# dataset slice boundaries istart = args.istart - 1 iend = args.iend import basis sys.path.insert(0, './') import inp # system definition spelist = inp.species xyzfile = read(inp.filename, ":") ndata = len(xyzfile) # basis definition [lmax, nmax] = basis.basiset(inp.dfbasis) llist = [] nlist = [] for spe in spelist: llist.append(lmax[spe]) for l in xrange(lmax[spe] + 1): nlist.append(nmax[(spe, l)]) llmax = max(llist) nnmax = max(nlist) # sparse-GPR parameters M = inp.Menv eigcut = inp.eigcut # paths to data
from ase import io from ase.io import read import basis sys.path.insert(0, './') import inp # read species spelist = inp.species spe_dict = {} for i in xrange(len(spelist)): spe_dict[i] = spelist[i] # read basis [llmax,lmax,nnmax,nmax] = basis.basiset(inp.basis) # read system xyzfile = read(inp.filename,":") ndata = len(xyzfile) #======================= system parameters atomic_symbols = [] atomic_valence = [] natoms = np.zeros(ndata,int) for i in xrange(len(xyzfile)): atomic_symbols.append(xyzfile[i].get_chemical_symbols()) atomic_valence.append(xyzfile[i].get_atomic_numbers()) natoms[i] = int(len(atomic_symbols[i])) natmax = max(natoms)