pyscf 2.6.2__py3-none-macosx_11_0_arm64.whl → 2.7.0__py3-none-macosx_11_0_arm64.whl

pyscf/dft/libxc.py

@@ -76,635 +76,32 @@ __version__ = libxc_version()
 __reference__ = libxc_reference()
 __reference_doi__ = libxc_reference_doi()
 
-# Runtime detection of available functionals
-dynamic_func = getattr(__config__, 'dft_libxc_dynamic', False)
-
-if dynamic_func:
-    def available_libxc_functionals():
-        # Number of functionals is
-        nfunc = _itrf.LIBXC_number_of_functionals()
-        # Get functional numbers
-        numbers = numpy.zeros(nfunc, dtype=numpy.intc)
-        _itrf.LIBXC_functional_numbers(numbers)
-        # Returned array
-        return {_itrf.LIBXC_functional_name(x).decode("UTF-8").upper() : x for x in numbers}
-
-    XC = XC_CODES = available_libxc_functionals()
-    PROBLEMATIC_XC = {}
-
-else:
-    # XC dict is generated by
-    #import pylibxc
-    #for xcname in pylibxc.util.xc_available_functional_names():
-    #    f = pylibxc.LibXCFunctional(xcname, 1)
-    #    f_id = f.get_number()
-    #    ref = f.get_references()
-    #    key = f"'{xcname.upper()}'"
-    #    print(f"{key:<31s}: {f_id:<3d}, # {ref[0]}")
-    XC = XC_CODES = {
-        'LDA_C_1D_CSC'                 : 18 , # M. Casula, S. Sorella, and G. Senatore, Phys. Rev. B 74, 245427 (2006)
-        'LDA_C_1D_LOOS'                : 26 , # P.-F. Loos, J. Chem. Phys. 138, 064108 (2013)
-        'LDA_C_2D_AMGB'                : 15 , # C. Attaccalite, S. Moroni, P. Gori-Giorgi, and G. B. Bachelet, Phys. Rev. Lett. 88, 256601 (2002)
-        'LDA_C_2D_PRM'                 : 16 , # S. Pittalis, E. Rasanen, and M. A. L. Marques, Phys. Rev. B 78, 195322 (2008)
-        'LDA_C_BR78'                   : 552, # G. B. Jr. and S. M. Rothstein, J. Chem. Phys. 69, 1177 (1978)
-        'LDA_C_CHACHIYO'               : 287, # T. Chachiyo, J. Chem. Phys. 145, 021101 (2016)
-        'LDA_C_CHACHIYO_MOD'           : 307, # T. Chachiyo and H. Chachiyo, Comput. Theor. Chem. 1172, 112669 (2020)
-        'LDA_C_GK72'                   : 578, # R. G. Gordon and Y. S. Kim, J. Chem. Phys. 56, 3122 (1972)
-        'LDA_C_GL'                     : 5  , # O. Gunnarsson and B. I. Lundqvist, Phys. Rev. B 13, 4274 (1976)
-        'LDA_C_GOMBAS'                 : 24 , # P. Gombas, Fortschr. Phys. 13, 137 (1965)
-        'LDA_C_HL'                     : 4  , # L. Hedin and B. I. Lundqvist, J. Phys. C: Solid State Phys. 4, 2064 (1971)
-        'LDA_C_KARASIEV'               : 579, # V. V. Karasiev, J. Chem. Phys. 145, 157101 (2016)
-        'LDA_C_KARASIEV_MOD'           : 308, # T. Chachiyo and H. Chachiyo, Comput. Theor. Chem. 1172, 112669 (2020)
-        'LDA_C_LP96'                   : 289, # S. Liu and R. G. Parr, Phys. Rev. A 53, 2211 (1996)
-        'LDA_C_MCWEENY'                : 551, # R. McWeeny, in The New World of Quantum Chemistry, edited by B. Pullman and R. Parr (Reidel, Boston, 1976) pp. 3--31
-        'LDA_C_ML1'                    : 22 , # E. I. Proynov and D. R. Salahub, Phys. Rev. B 49, 7874 (1994)
-        'LDA_C_ML2'                    : 23 , # E. I. Proynov and D. R. Salahub, Phys. Rev. B 49, 7874 (1994)
-        'LDA_C_OB_PW'                  : 14 , # G. Ortiz and P. Ballone, Phys. Rev. B 50, 1391 (1994)
-        'LDA_C_OB_PZ'                  : 11 , # G. Ortiz and P. Ballone, Phys. Rev. B 50, 1391 (1994)
-        'LDA_C_OW'                     : 574, # P. A. Stewart and P. M. W. Gill, J. Chem. Soc., Faraday Trans. 91, 4337 (1995)
-        'LDA_C_OW_LYP'                 : 573, # P. A. Stewart and P. M. W. Gill, J. Chem. Soc., Faraday Trans. 91, 4337 (1995)
-        'LDA_C_PK09'                   : 554, # E. Proynov and J. Kong, Phys. Rev. A 79, 014103 (2009)
-        'LDA_C_PMGB06'                 : 590, # S. Paziani, S. Moroni, P. Gori-Giorgi, and G. B. Bachelet, Phys. Rev. B 73, 155111 (2006)
-        'LDA_C_PW'                     : 12 , # J. P. Perdew and Y. Wang, Phys. Rev. B 45, 13244 (1992)
-        'LDA_C_PW_MOD'                 : 13 , # J. P. Perdew and Y. Wang, Phys. Rev. B 45, 13244 (1992), added extra digits to some constants as in the PBE routine (http://dft.rutgers.edu/pubs/PBE.asc)
-        'LDA_C_PW_RPA'                 : 25 , # J. P. Perdew and Y. Wang, Phys. Rev. B 45, 13244 (1992)
-        'LDA_C_PZ'                     : 9  , # J. P. Perdew and A. Zunger, Phys. Rev. B 23, 5048 (1981)
-        'LDA_C_PZ_MOD'                 : 10 , # J. P. Perdew and A. Zunger, Phys. Rev. B 23, 5048 (1981), modified to improve the matching between the low- and high-rs parts
-        'LDA_C_RC04'                   : 27 , # S. Ragot and P. Cortona, J. Chem. Phys. 121, 7671 (2004)
-        'LDA_C_RPA'                    : 3  , # M. Gell-Mann and K. A. Brueckner, Phys. Rev. 106, 364 (1957)
-        'LDA_C_RPW92'                  : 684, # M. Ruggeri, P. L. Rios, and A. Alavi, Phys. Rev. B 98, 161105 (2018)
-        'LDA_C_UPW92'                  : 683, # M. Ruggeri, P. L. Rios, and A. Alavi, Phys. Rev. B 98, 161105 (2018)
-        'LDA_C_VBH'                    : 17 , # U. von Barth and L. Hedin, J. Phys. C: Solid State Phys. 5, 1629 (1972)
-        'LDA_C_VWN'                    : 7  , # S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58, 1200 (1980)
-        'LDA_C_VWN_1'                  : 28 , # S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58, 1200 (1980)
-        'LDA_C_VWN_2'                  : 29 , # S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58, 1200 (1980)
-        'LDA_C_VWN_3'                  : 30 , # S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58, 1200 (1980)
-        'LDA_C_VWN_4'                  : 31 , # S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58, 1200 (1980)
-        'LDA_C_VWN_RPA'                : 8  , # S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58, 1200 (1980)
-        'LDA_C_WIGNER'                 : 2  , # E. Wigner, Trans. Faraday Soc. 34, 678 (1938)
-        'LDA_C_XALPHA'                 : 6  , # J. C. Slater, Phys. Rev. 81, 385 (1951)
-        'LDA_K_GDS08_WORKER'           : 100001, # L. M. Ghiringhelli and L. Delle Site, Phys. Rev. B 77, 073104 (2008)
-        'LDA_K_LP'                     : 51 , # C. Lee and R. G. Parr, Phys. Rev. A 35, 2377 (1987)
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-        'LDA_X_1D_SOFT'                : 21 , # N. Helbig, J. I. Fuks, M. Casula, M. J. Verstraete, M. A. L. Marques, I. V. Tokatly, and A. Rubio, Phys. Rev. A 83, 032503 (2011)
-        'LDA_X_2D'                     : 19 , # P. A. M. Dirac, Math. Proc. Cambridge Philos. Soc. 26, 376 (1930)
-        'LDA_X_ERF'                    : 546, # P. M. W. Gill, R. D. Adamson, and J. A. Pople, Mol. Phys. 88, 1005 (1996)
-        'LDA_X_RAE'                    : 549, # A. Rae, Chem. Phys. Lett. 18, 574 (1973)
-        'LDA_X_REL'                    : 532, # A. K. Rajagopal, J. Phys. C: Solid State Phys. 11, L943 (1978)
-        'LDA_X_SLOC'                   : 692, # K. Finzel and A. I. Baranov, Int. J. Quantum Chem. 117, 40 (2017)
-        'LDA_XC_1D_EHWLRG_1'           : 536, # M. T. Entwistle, M. J. P. Hodgson, J. Wetherell, B. Longstaff, J. D. Ramsden, and R. W. Godby, Phys. Rev. B 94, 205134 (2016)
-        'LDA_XC_1D_EHWLRG_2'           : 537, # M. T. Entwistle, M. J. P. Hodgson, J. Wetherell, B. Longstaff, J. D. Ramsden, and R. W. Godby, Phys. Rev. B 94, 205134 (2016)
-        'LDA_XC_1D_EHWLRG_3'           : 538, # M. T. Entwistle, M. J. P. Hodgson, J. Wetherell, B. Longstaff, J. D. Ramsden, and R. W. Godby, Phys. Rev. B 94, 205134 (2016)
-        'LDA_XC_BN05'                  : 588, # R. Baer and D. Neuhauser, Phys. Rev. Lett. 94, 043002 (2005)
-        'LDA_XC_GDSMFB'                : 577, # S. Groth, T. Dornheim, T. Sjostrom, F. D. Malone, W. M. C. Foulkes, and M. Bonitz, Phys. Rev. Lett. 119, 135001 (2017)
-        'LDA_XC_KSDT'                  : 259, # V. V. Karasiev, T. Sjostrom, J. Dufty, and S. B. Trickey, Phys. Rev. Lett. 112, 076403 (2014)
-        'LDA_XC_LP_A'                  : 547, # C. Lee and R. G. Parr, Phys. Rev. A 42, 193 (1990)
-        'LDA_XC_LP_B'                  : 548, # C. Lee and R. G. Parr, Phys. Rev. A 42, 193 (1990)
-        'LDA_XC_TETER93'               : 20 , # S. Goedecker, M. Teter, and J. Hutter, Phys. Rev. B 54, 1703 (1996)
-        'LDA_XC_TIH'                   : 599, # D. J. Tozer, V. E. Ingamells, and N. C. Handy, J. Chem. Phys. 105, 9200 (1996)
-        'LDA_XC_ZLP'                   : 43 , # Q. Zhao, M. Levy, and R. G. Parr, Phys. Rev. A 47, 918 (1993)
-        'HYB_LDA_XC_CAM_LDA0'          : 178, # M. A. Mosquera, C. H. Borca, M. A. Ratner, and G. C. Schatz, J. Phys. Chem. A 120, 1605 (2016)
-        'HYB_LDA_XC_LDA0'              : 177, # P. Rinke, A. Schleife, E. Kioupakis, A. Janotti, C. Rodl, F. Bechstedt, M. Scheffler, and C. G. Van de Walle, Phys. Rev. Lett. 108, 126404 (2012)
-        'GGA_C_ACGGA'                  : 39 , # A. Cancio, G. P. Chen, B. T. Krull, and K. Burke, J. Chem. Phys. 149, 084116 (2018)
-        'GGA_C_ACGGAP'                 : 176, # A. Cancio, G. P. Chen, B. T. Krull, and K. Burke, J. Chem. Phys. 149, 084116 (2018)
-        'GGA_C_AM05'                   : 135, # R. Armiento and A. E. Mattsson, Phys. Rev. B 72, 085108 (2005)
-        'GGA_C_APBE'                   : 186, # L. A. Constantin, E. Fabiano, S. Laricchia, and F. Della Sala, Phys. Rev. Lett. 106, 186406 (2011)
-        'GGA_C_BMK'                    : 280, # A. D. Boese and J. M. L. Martin, J. Chem. Phys. 121, 3405 (2004)
-        'GGA_C_CCDF'                   : 313, # J. T. Margraf, C. Kunkel, and K. Reuter, J. Chem. Phys. 150, 244116 (2019)
-        'GGA_C_CHACHIYO'               : 309, # T. Chachiyo and H. Chachiyo, Comput. Theor. Chem. 1172, 112669 (2020)
-        'GGA_C_CS1'                    : 565, # N. C. Handy and A. J. Cohen, J. Chem. Phys. 116, 5411 (2002)
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-        'GGA_C_GAPLOC'                 : 556, # E. Fabiano, P. E. Trevisanutto, A. Terentjevs, and L. A. Constantin, J. Chem. Theory Comput. 10, 2016 (2014)
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-        'GGA_C_HYB_TAU_HCTH'           : 283, # A. D. Boese and N. C. Handy, J. Chem. Phys. 116, 9559 (2002)
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-        'GGA_C_LYP'                    : 131, # C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988)
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-        'GGA_C_OP_G96'                 : 85 , # T. Tsuneda, T. Suzumura, and K. Hirao, J. Chem. Phys. 110, 10664 (1999)
-        'GGA_C_OP_PBE'                 : 86 , # T. Tsuneda, T. Suzumura, and K. Hirao, J. Chem. Phys. 110, 10664 (1999)
-        'GGA_C_OP_PW91'                : 262, # T. Tsuneda, T. Suzumura, and K. Hirao, J. Chem. Phys. 110, 10664 (1999)
-        'GGA_C_OP_XALPHA'              : 84 , # T. Tsuneda, T. Suzumura, and K. Hirao, J. Chem. Phys. 110, 10664 (1999)
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-        'GGA_C_PBE_SOL'                : 133, # J. P. Perdew, A. Ruzsinszky, G. I. Csonka, O. A. Vydrov, G. E. Scuseria, L. A. Constantin, X. Zhou, and K. Burke, Phys. Rev. Lett. 100, 136406 (2008)
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-        'HYB_MGGA_XC_TPSSH'            : 457, # V. N. Staroverov, G. E. Scuseria, J. Tao, and J. P. Perdew, J. Chem. Phys. 119, 12129 (2003)
-        'HYB_MGGA_XC_WB97M_V'          : 531, # N. Mardirossian and M. Head-Gordon, J. Chem. Phys. 144, 214110 (2016)
-        'HYB_MGGA_XC_X1B95'            : 447, # Y. Zhao and D. G. Truhlar, J. Phys. Chem. A 108, 6908 (2004)
-        'HYB_MGGA_XC_XB1K'             : 448, # Y. Zhao and D. G. Truhlar, J. Phys. Chem. A 108, 6908 (2004)
-    }
-
-    #PROBLEMATIC_XC = dict([(XC_CODES[x], x) for x in
-    #                       ('GGA_C_SPBE', 'MGGA_X_REVTPSS')])
-    PROBLEMATIC_XC = {}
+def available_libxc_functionals():
+    # Number of functionals is
+    nfunc = _itrf.LIBXC_number_of_functionals()
+    # Get functional numbers
+    func_ids = numpy.zeros(nfunc, dtype=numpy.intc)
+    _itrf.LIBXC_functional_numbers(func_ids)
+    # Returned array
+    return {_itrf.LIBXC_functional_name(x).decode("UTF-8").upper() : x for x in func_ids}
+
+XC = XC_CODES = available_libxc_functionals()
+PROBLEMATIC_XC = {}
+
+def print_XC_CODES():
+    '''
+    Dump the built-in libxc XC_CODES along with their references in a readable format.
+    '''
+    xc_codes = available_libxc_functionals()
+    print('XC = XC_CODES = {')
+    for name, func_id in xc_codes.items():
+        refs = xc_reference(func_id)
+        key = f"'{name}'"
+        print(key, func_id)
+        print(f'{key:<31s}: {func_id:<3d}, # {refs[0]}')
+        for r in refs[1:]:
+            print(f"                                      # {r}")
+    print('}')
 
 def _xc_key_without_underscore(xc_keys):
     new_xc = []
@@ -1136,7 +533,7 @@ def parse_xc(description):
                 fac, key = token.split('*')
                 if fac[0].isalpha():
                     fac, key = key, fac
-                fac = sign * float(fac)
+                fac = sign * float(fac.replace('E_', 'E-'))
             else:
                 fac, key = sign, token
 
@@ -1277,7 +674,8 @@ _NAME_WITH_DASH = {'SR-HF'    : 'SR_HF',
                    'LRC-WPBE' : 'LRC_WPBE',
                    'LRC-WPBEH': 'LRC_WPBEH',
                    'LC-VV10'  : 'LC_VV10',
-                   'CAM-B3LYP': 'CAM_B3LYP'}
+                   'CAM-B3LYP': 'CAM_B3LYP',
+                   'E-'       : 'E_'} # For scientific notation
 
 
 def eval_xc(xc_code, rho, spin=0, relativity=0, deriv=1, omega=None, verbose=None):
@@ -1609,13 +1007,17 @@ def eval_xc1(xc_code, rho, spin=0, deriv=1, omega=None):
     '''
     out = _eval_xc(xc_code, rho, spin, deriv=deriv, omega=omega)
     xctype = xc_type(xc_code)
+    idx = _libxc_to_xcfun_indices(xctype, spin, deriv)
+    return out[idx]
+
+def _libxc_to_xcfun_indices(xctype, spin=0, deriv=1):
     if deriv <= 1:
-        return out
+        return slice(None)
     elif xctype == 'LDA' or xctype == 'HF':
-        return out
+        return slice(None)
     elif xctype == 'GGA':
         if spin == 0:
-            return out
+            return slice(None)
         else:
             idx = [numpy.arange(6)] # up to deriv=1
             for i in range(2, deriv+1):
@@ -1627,7 +1029,7 @@ def eval_xc1(xc_code, rho, spin=0, deriv=1, omega=None):
             idx = [numpy.arange(8)] # up to deriv=1
         for i in range(2, deriv+1):
             idx.append(_MGGA_SORT[(spin, i)])
-    return out[numpy.hstack(idx)]
+    return numpy.hstack(idx)
 
 def _eval_xc(xc_code, rho, spin=0, deriv=1, omega=None):
     assert deriv <= max_deriv_order(xc_code)
@@ -1657,7 +1059,7 @@ def _eval_xc(xc_code, rho, spin=0, deriv=1, omega=None):
         warnings.warn('Libxc functionals %s may have discrepancy to xcfun '
                       'library.\n' % problem_xc)
 
-    if any([needs_laplacian(fid) for fid in fn_ids]):
+    if any(needs_laplacian(fid) for fid in fn_ids):
         raise NotImplementedError('laplacian in meta-GGA method')
 
     nvar, xlen = xc_deriv._XC_NVAR[xctype, spin]
@@ -1762,19 +1164,43 @@ def define_xc_(ni, description, xctype='LDA', hyb=0, rsh=(0,0,0)):
     48.8525211046668
     '''
     if isinstance(description, str):
-        ni.eval_xc = lambda xc_code, rho, *args, **kwargs: \
-                eval_xc(description, rho, *args, **kwargs)
+        def _eval_xc(xc_code, rho, *args, **kwargs):
+            return eval_xc(description, rho, *args, **kwargs)
+        ni.eval_xc = _eval_xc
         ni.hybrid_coeff = lambda *args, **kwargs: hybrid_coeff(description)
         ni.rsh_coeff = lambda *args: rsh_coeff(description)
         ni._xc_type = lambda *args: xc_type(description)
 
     elif callable(description):
-        ni.eval_xc = description
+        ni.eval_xc = _eval_xc = description
         ni.hybrid_coeff = lambda *args, **kwargs: hyb
         ni.rsh_coeff = lambda *args, **kwargs: rsh
         ni._xc_type = lambda *args: xctype
+
     else:
         raise ValueError('Unknown description %s' % description)
+
+    def _eval_xc1(xc_code, rho, spin=0, deriv=1, omega=None):
+        libxc_out = _eval_xc(xc_code, rho, spin, deriv=deriv, omega=omega)
+        nvar, xlen = xc_deriv._XC_NVAR[xctype, spin]
+        outlen = lib.comb(xlen+deriv, deriv)
+        exc, vxc, fxc, kxc = libxc_out[:4]
+        out = [exc]
+        if vxc is not None:
+            out.extend([x for x in vxc if x is not None])
+        if fxc is not None:
+            out.extend([fxc[i] for i in [0, 1, 2, 6, 4, 9]])
+        if kxc is not None:
+            out.extend([x for x in kxc if x is not None])
+        if spin == 1:
+            # Returns of eval_xc are structured as [grid_id,deriv_component]
+            # for each term in libxc_out. Change the shape to [deriv_comp, grid_id]
+            out = [x.T for x in out]
+        out = numpy.vstack(out)[:outlen]
+        assert len(out) == outlen
+        idx = _libxc_to_xcfun_indices(xctype, spin, deriv)
+        return out[idx]
+    ni.eval_xc1 = _eval_xc1
     return ni
 
 def define_xc(ni, description, xctype='LDA', hyb=0, rsh=(0,0,0)):