output.py 文件源码

def parse_basis_set(self):
        """
        Parses the primitive exponents, coefficients and shell if BSSHOW specified in SEWARD.
        """
        found = self.find(_re_bas_0, _re_bas_1, _re_bas_2, keys_only=True)
        bmaps = [i + 1 for i in found[_re_bas_0]]
        atoms = [i + 2 for i in found[_re_bas_1]]
        alphs = [i + 1 for i in found[_re_bas_2]]
        widths = [11, 7, 8, 11, 10, 12]
        names = _re_bas_0.split()
        setmap, basmap = {}, []
        for seht, (start, atst) in enumerate(zip(bmaps, atoms)):
            stop = start
            while self[stop].strip(): stop += 1
            while self[atst].strip():
                setmap[self[atst].split()[0]] = seht
                atst += 1
            basmap.append(pd.read_fwf(StringIO('\n'.join(self[start:stop])),
                                      widths=widths, header=None, names=names))
            basmap[-1]['set'] = seht
        self.atom['set'] = self.atom['tag'].map(setmap)
        basmap = pd.concat(basmap).reset_index(drop=True)
        basmap['Shell'] = basmap['Shell'].map(lmap)
        prims, pset, shell = [], 0, 0
        for start, seht, L, nprim, nbas in zip(alphs, basmap['set'], basmap['Shell'],
                                               basmap['nPrim'], basmap['nBasis']):
            if pset != seht: shell = 0
            # In case contraction coefficients overflow to next line
            neat = len(self[start].split()) == len(self[start + 1].split())
            if neat: block = self.pandas_dataframe(start, start + nprim, nbas + 2)
            else:
                stop = start + 2 * nprim
                most = self[start:stop:2]
                extr = self[start + 1:stop:2]
                ncols = len(most[0].split()) + len(extr[0].split())
                block = pd.read_csv(StringIO('\n'.join([i + j for i, j in zip(most, extr)])),
                                    delim_whitespace=True, names=range(ncols))
            alps = (pd.concat([block[1]] * nbas).reset_index(drop=True)
                    .str.replace('D', 'E').astype(np.float64))
            ds = block[list(range(2, nbas + 2))].unstack().reset_index(drop=True)
            pdf = pd.concat([alps, ds], axis=1)
            pdf.columns = ['alpha', 'd']
            pdf['L'] = L
            pdf['shell'] = np.repeat(range(shell, shell + nbas), nprim)
            pdf['set'] = seht
            prims.append(pdf)
            shell += nbas
            pset = seht
        prims = pd.concat(prims).reset_index(drop=True)
        prims['frame'] = 0
        self.basis_set = prims