#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import re
from functools import reduce
import numpy
import scipy.linalg
from pyscf import gto
from pyscf.lib import logger
from pyscf import lo
from pyscf import __config__

BASE = getattr(__config__, 'BASE', 0)
MAP_TOL = getattr(__config__, 'mo_mapping_mo_map_tol', 0.5)
ORTH_METHOD = getattr(__config__, 'mo_mapping_mo_comps_orth_method', 'meta_lowdin')


def mo_map(mol1, mo1, mol2, mo2, base=BASE, tol=.5):
    '''Given two orbitals, based on their overlap <i|j>, search all
    orbital-pairs which have significant overlap.

    Returns:
        Two lists.  First list is the orbital-pair indices, second is the
        overlap value.
    '''
    s = gto.intor_cross('int1e_ovlp', mol1, mol2)
    s = reduce(numpy.dot, (mo1.T, s, mo2))
    idx = numpy.argwhere(abs(s) > tol) + base
    for i,j in idx:
        logger.info(mol1, '<mo-1|mo-2>  %d  %d  %12.8f',
                    i, j, s[i,j])
    return idx, s

def mo_1to1map(s):
    '''Given <i|j>, search for the 1-to-1 mapping between i and j.

    Returns:
        a list [j-close-to-i for i in <bra|]
    '''
    s1 = abs(s)
    like_input = []
    for i in range(s1.shape[0]):
        k = numpy.argmax(s1[i])
        like_input.append(k)
        s1[:,k] = 0
    return like_input

def mo_comps(aolabels_or_baslst, mol, mo_coeff, cart=False,
             orth_method=ORTH_METHOD):
    '''Given AO(s), show how the AO(s) are distributed in MOs.

    Args:
        aolabels_or_baslst : filter function or AO labels or AO index
            If it's a function,  the AO indices are the items for which the
            function return value is true.

    Kwargs:
        cart : bool
            whether the orbital coefficients are based on cartesian basis.
        orth_method : str
            The localization method to generated orthogonal AO upon which the AO
            contribution are computed.  It can be one of 'meta_lowdin',
            'lowdin' or 'nao'.

    Returns:
        A list of float to indicate the total contributions (normalized to 1) of
        localized AOs

    Examples:

    >>> from pyscf import gto, scf
    >>> from pyscf.tools import mo_mapping
    >>> mol = gto.M(atom='H 0 0 0; F 0 0 1', basis='6-31g')
    >>> mf = scf.RHF(mol).run()
    >>> comp = mo_mapping.mo_comps('F 2s', mol, mf.mo_coeff)
    >>> print('MO-id    F-2s components')
    >>> for i,c in enumerate(comp):
    ...     print('%-3d      %.10f' % (i, c))
    MO-id    components
    0        0.0000066344
    1        0.8796915532
    2        0.0590259826
    3        0.0000000000
    4        0.0000000000
    5        0.0435028851
    6        0.0155889103
    7        0.0000000000
    8        0.0000000000
    9        0.0000822361
    10       0.0021017982
    '''
    import copy
    if cart and not mol.cart:
        assert(mo_coeff.shape[0] == mol.nao_nr(cart=True))
        mol = copy.copy(mol)
        mol.cart = True
    s = mol.intor_symmetric('int1e_ovlp')
    lao = lo.orth.orth_ao(mol, orth_method, s=s)

    idx = gto.mole._aolabels2baslst(mol, aolabels_or_baslst)
    if len(idx) == 0:
        logger.warn(mol, 'Required orbitals are not found')
    mo1 = reduce(numpy.dot, (lao[:,idx].T, s, mo_coeff))
    s1 = numpy.einsum('ki,ki->i', mo1, mo1)
    return s1

del(BASE, MAP_TOL, ORTH_METHOD)

@@ -699,16 +699,38 @@
 .linalg%0A
+from pyscf import lib%0A
 from pys
@@ -3386,48 +3386,46 @@
     
-import copy%0A    if cart and not mol.
+with lib.temporary_env(mol, 
 cart
+=cart)
 :%0A  
@@ -3469,77 +3469,14 @@
 .nao
-_nr(cart=True))%0A        mol = copy.copy(mol)%0A        mol.cart = True%0A
+)%0A    
     
@@ -3513,16 +3513,20 @@
 _ovlp')%0A
+    
     lao 
@@ -3567,16 +3567,20 @@
 , s=s)%0A%0A
+    
     idx 
@@ -3632,16 +3632,20 @@
 baslst)%0A
+    
     if l
@@ -3658,16 +3658,20 @@
 ) == 0:%0A
+    
         
@@ -3722,16 +3722,20 @@
 found')%0A
+    
     mo1 
@@ -3783,16 +3783,20 @@
 coeff))%0A
+    
     s1 =

Update mo_comps function