Create cp2k.py

basis_set_exchange/readers/cp2k.py

@@ -0,0 +1,130 @@
+# Copyright (c) 2017-2022 The Molecular Sciences Software Institute, Virginia Tech
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its
+# contributors may be used to endorse or promote products derived
+# from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+'''
+Reader for CP2K basis sets
+
+Written by Susi Lehtola, 2021
+'''
+
+import re
+from .. import lut
+from . import helpers
+
+# Shell entry: 'element names'
+element_shell_re = re.compile(r'^\s*(?P<sym>\w+)(?:\s+(?P<name>{}))+\s*$'.format(helpers.basis_name_re_str))
+# Number of blocks
+nblocks_re = re.compile(r'^\s*(?P<nblocks>\d+)\s*$')
+# Block entry: n lmin lmax nexp nshell(lmin) nshell(lmin+1) ... nshell(lmax-1) nshell(lmax)
+block_re = re.compile(r'^\s*(?P<n>\d+)\s+(?P<lmin>\d+)\s+(?P<lmax>\d+)\s+(?P<nprim>\d+)(?:\s+(?P<nshell>\d+))+\s*$')
+
+# Function type: spherical by default
+_func_type = 'gto_spherical'
+
+
+def _read_shell(basis_lines, bs_data):
+    '''Read in a shell from the input'''
+    # Read the shell entry
+    iline = 0
+    element_shell = helpers.parse_line_regex_dict(element_shell_re, basis_lines[iline], 'element (aliases)')
+    iline += 1
+
+    # Create entry
+    element_sym = element_shell['sym'][0]
+    element_Z = lut.element_Z_from_sym(element_sym, as_str=True)
+    if element_Z not in bs_data or 'electron_shells' not in bs_data[element_Z]:
+        element_data = helpers.create_element_data(bs_data, element_Z, 'electron_shells')
+    else:
+        element_data = bs_data[element_Z]
+
+    # Read the number of blocks
+    nblocks = helpers.parse_line_regex_dict(nblocks_re, basis_lines[iline], 'nblocks')['nblocks'][0]
+    iline += 1
+
+    # Read blocks
+    for iblock in range(nblocks):
+        block = helpers.parse_line_regex_dict(
+            block_re, basis_lines[iline],
+            'n lmin lmax nexp nshell(lmin) nshell(lmin+1) ... nshell(lmax-1) nshell(lmax)')
+        iline += 1
+
+        lmin = block['lmin'][0]
+        lmax = block['lmax'][0]
+        nprim = block['nprim'][0]
+        nshell = block['nshell']
+        assert (len(nshell) == lmax - lmin + 1)
+
+        # Total number of contractions is
+        ncontr = sum(nshell)
+
+        # Parse contractions
+        exps, coeffs = helpers.parse_primitive_matrix(basis_lines[iline:iline + nprim], nprim=nprim, ngen=ncontr)
+        iline += nprim
+
+        # Add the shells
+        for l in range(lmin, lmax + 1):
+            col_offset = sum(nshell[:l - lmin])
+            ncontr_l = nshell[l - lmin]
+            l_coeff = coeffs[:][col_offset:col_offset + ncontr_l]
+            func_type = helpers.function_type_from_am([l], 'gto', 'spherical')
+            shell = {
+                'function_type': func_type,
+                'region': '',
+                'angular_momentum': [l],
+                'exponents': exps,
+                'coefficients': l_coeff
+            }
+            element_data['electron_shells'].append(shell)
+
+
+def read_cp2k(basis_lines):
+    '''Reads basis set in CP2K format and converts it to a dictionary with
+       the usual BSE fields
+
+       Note that the CP2K format does not store all the fields we
+       have, so some fields are left blank
+
+    '''
+
+    # Removes comments
+    basis_lines = helpers.prune_lines(basis_lines, '!')
+
+    bs_data = {}
+
+    # Empty file?
+    if not basis_lines:
+        return bs_data
+
+    # split into element sections
+    element_sections = helpers.partition_lines(basis_lines, element_shell_re.match)
+    for es in element_sections:
+        _read_shell(es, bs_data)
+
+    return bs_data