Source code for psi4.driver.inputparser

#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
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# The copyrights for code used from other parties are included in
# the corresponding files.
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# This file is part of Psi4.
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# Psi4 is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, version 3.
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# Psi4 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
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# You should have received a copy of the GNU Lesser General Public License along
# with Psi4; if not, write to the Free Software Foundation, Inc.,
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# @END LICENSE
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"""Module with functions to parse the input file and convert
Psithon into standard Python. Particularly, forms psi4
module calls that access the C++ side of Psi4.

"""

## Force Python 3 print syntax, if this is python 2.X
#if sys.hexversion < 0x03000000:
from __future__ import print_function
from __future__ import absolute_import

import re
import os
import sys
import uuid
from psi4.driver import pubchem
from psi4.driver.p4util.exceptions import *
from psi4.driver.p4util.util import set_memory
from psi4 import core

# globally available regex strings
pubchemre = re.compile(r'^(\s*pubchem\s*:\s*(.*)\n)$', re.MULTILINE | re.IGNORECASE)

# inputfile contents to be preserved from the processor
literals = {}

# experimental - whether to run py statements as they're parsed from psithon
runalso = False


def bad_option_syntax(line):
    """Function to report bad syntax to screen and output file."""
    message = ('Unsupported syntax:\n\n%s\n\n' % (line))
    raise TestComparisonError(message)


def process_word_quotes(matchobj):
    """Function to determine if argument needs wrapping in quotes as string."""
    dollar = matchobj.group(2)
    val = matchobj.group(3)
    if dollar:
        # This is a python variable, make sure that it starts with a letter
        if re.match(r'^[A-Za-z][\w]*', val):
            return val
        else:
            message = ("Invalid Python variable: %s" % (val))
            raise TestComparisonError(message)
    elif re.match(r'^-?\d+\.?\d*(?:[Ee]-?\d+)?$', val):
        # This must be a number, don't wrap it in quotes
        return val
    elif re.match(r'^\'.*\'$', val) or re.match(r'^\".*\"$', val):
        # This is already wrapped in quotes, do nothing
        return val
    else:
        # This must be a string
        return "\"%s\"" % (val)


def quotify(string, isbasis=False):
    """Function to wrap anything that looks like a string in quotes
    and to remove leading dollar signs from python variables. When *basis*
    is True, allows commas, since basis sets may have commas and are assured to
    not involve arrays.

    """
    # This wraps anything that looks like a string in quotes, and removes leading
    # dollar signs from python variables
    if isbasis:
        wordre = re.compile(r'(([$]?)([-+()*.,\w\"\'/\\]+))')
    else:
        wordre = re.compile(r'(([$]?)([-+()*.\w\"\'/\\]+))')
    string = wordre.sub(process_word_quotes, string)
    return string

def dequotify(string):
    if string[0] == '"' and string[-1] == '"':
        return string[1:-1]
    else:
        return string


def process_option(spaces, module, key, value, line):
    """Function to process a line with set or in a set block
    into global/local domain and keyword/value.

    """
    module = module.upper()
    key = key.upper()
    isbasis = True if 'BASIS' in key else False
    value = quotify(value.strip(), isbasis=isbasis)

    if module == "GLOBALS" or module == "GLOBAL" or module == "" or module.isspace():
        # If it's really a global, we need slightly different syntax
        if runalso:
            core.set_global_option(key, dequotify(value))
        return "%score.set_global_option(\"%s\", %s)\n" % (spaces, key, value)
    else:
        # It's a local option, so we need the module name in there too
        if runalso:
            core.set_local_option(module, key, dequotify(value))
        return "%score.set_local_option(\"%s\", \"%s\", %s)\n" % (spaces, module, key, value)


def process_set_command(matchobj):
    """Function to process match of all individual ``set (module_list)
    key {[value_list] or $value or value}``.

    """
    result = ""
    module_string = ""
    if matchobj.group(2):
        module_string = matchobj.group(2)
    for module in module_string.split(","):
        result += process_option(matchobj.group(1), module, matchobj.group(3), matchobj.group(4), matchobj.group(0))
    return result


def process_set_commands(matchobj):
    """Function to process match of ``set name? { ... }``."""
    spaces = matchobj.group(1)
    commands = matchobj.group(3)
    command_lines = re.split('\n', commands)
    # Remove trailing newline from each line
    map(lambda x: x.strip(), command_lines)
    result = ""
    module_string = ""
    command = ""
    if matchobj.group(2):
        module_string = matchobj.group(2)
    for module in module_string.split(","):
        for line in command_lines:
            # Chomp the trailing newline and accumulate
            command += line
            if not check_parentheses_and_brackets(command, 0):
                # If the brackets don't match up, we need to move on to the next line
                # and keep going, until they do match. Only then do we process the command
                continue
            # Ignore blank/empty lines
            if not line or line.isspace():
                continue
            matchobj = re.match(r'^\s*(\w+)[\s=]+(.*?)$', command)
            # Is the syntax correct? If so, process the line
            if matchobj:
                result += process_option(spaces, module, matchobj.group(1), matchobj.group(2), command)
                # Reset the string
                command = ""
            else:
                bad_option_syntax(command)
    return result


def process_from_file_command(matchobj):
    """Function that process a match of ``from_file`` in molecule block."""
    string = matchobj.group(2)
    mol=core.mol_from_file(string,1)
    tempmol=[line for line in mol.split('\n') if line.strip() != '']
    mol2=set(tempmol)
    mol=""
    for i in mol2:
           mol+=i
           mol+="\n"
    return mol


[docs]def process_pubchem_command(matchobj): """Function to process match of ``pubchem`` in molecule block.""" string = matchobj.group(2) if re.match(r'^\s*[0-9]+\s*$', string): # This is just a number - must be a CID pcobj = pubchem.PubChemObj(int(string), '', '') try: return pcobj.getMoleculeString() except Exception as e: return e.message else: # Search pubchem for the provided string try: results = pubchem.getPubChemResults(string) except Exception as e: return e.message # N.B. Anything starting with PubchemError will be handled correctly by the molecule parser # in libmints, which will just print the rest of the string and exit gracefully. if not results: # Nothing! return "PubchemError\n\tNo results were found when searching PubChem for %s.\n" % (string) elif len(results) == 1: # There's only 1 result - use it return results[0].getMoleculeString() else: # There are multiple results. Print and exit msg = "\tPubchemError\n" msg += "\tMultiple pubchem results were found. Replace\n\n\t\tpubchem:%s\n\n" % (string) msg += "\twith the Chemical ID number or exact name from one of the following and re-run.\n\n" msg += "\t Chemical ID IUPAC Name\n\n" for result in results: msg += "%s" % (result) if result.name().lower() == string.lower(): #We've found an exact match! return result.getMoleculeString() return msg
def process_molecule_command(matchobj): """Function to process match of ``molecule name? { ... }``.""" spaces = matchobj.group(1) name = matchobj.group(2) geometry = matchobj.group(3) geometry = pubchemre.sub(process_pubchem_command, geometry) from_filere = re.compile(r'^(\s*from_file\s*:\s*(.*)\n)$', re.MULTILINE | re.IGNORECASE) geometry = from_filere.sub(process_from_file_command,geometry) molecule = spaces if name != "": if sys.version_info >= (3, 0): if not name.isidentifier(): raise ValidationError('Molecule name not valid Python identifier: ' + name) else: if not re.match(r'^[^\d\W]\w*\Z', name): raise ValidationError('Molecule name not valid Python identifier: ' + name) molecule += 'core.efp_init()\n' # clear EFP object before Molecule read in molecule += spaces if name != "": molecule += '%s = ' % (name) molecule += 'geometry("""%s"""' % (geometry) if name != "": molecule += ',"%s"' % (name) molecule += ")\n" molecule += '%score.IO.set_default_namespace("%s")' % (spaces, name) return molecule def process_literal_blocks(matchobj): """Function to process match of ``literals_psi4_yo-...``.""" return literals[matchobj.group(1)] def process_cfour_command(matchobj): """Function to process match of ``cfour name? { ... }``.""" spaces = matchobj.group(1) name = matchobj.group(2) cfourblock = matchobj.group(3) literalkey = str(uuid.uuid4())[:8] literals[literalkey] = cfourblock return "%score.set_global_option(\"%s\", \"\"\"%s\n\"\"\")\n" % \ (spaces, 'LITERAL_CFOUR', 'literals_psi4_yo-' + literalkey) def process_extract_command(matchobj): """Function to process match of ``extract_subsets``.""" spaces = matchobj.group(1) name = matchobj.group(2) result = matchobj.group(0) result += '%s%s.set_name("%s")' % (spaces, name, name) result += "\n%score.set_active_molecule(%s)" % (spaces, name) result += '\n%score.IO.set_default_namespace("%s")' % (spaces, name) return result def process_print_command(matchobj): """Function to process match of ``print`` and transform it to ``core.print_out()``. """ spaces = matchobj.group(1) string = matchobj.group(2) return "%score.print_out(str(%s))\n" % (spaces, str(string)) def process_memory_command(matchobj): """Function to process match of ``memory ...``.""" spaces = str(matchobj.group(1)) sig = str(matchobj.group(2)) units = str(matchobj.group(3)) mem_in_bytes = set_memory(sig + units, execute=False) return "%score.set_memory_bytes(%d)\n" % (spaces, mem_in_bytes) def basname(name): """Imitates BasisSet.make_filename() without the gbs extension""" return name.lower().replace('+', 'p').replace('*', 's').replace('(', '_').replace(')', '_').replace(',', '_') def process_basis_block(matchobj): """Function to process match of ``basis name? { ... }``.""" spaces = matchobj.group(1) basistype = matchobj.group(2).upper() name = matchobj.group(3) name = ('anonymous' + str(uuid.uuid4())[:8]) if name == '' else name cleanbas = basname(name).replace('-', '') # further remove hyphens so can be function name command_lines = re.split('\n', matchobj.group(4)) symbol_re = re.compile(r'^\s*assign\s+(?P<symbol>[A-Z]{1,3})\s+(?P<basis>[-+*\(\)\w]+)\s*$', re.IGNORECASE) label_re = re.compile(r'^\s*assign\s+(?P<label>(?P<symbol>[A-Z]{1,3})(?:(_\w+)|(\d+))?)\s+(?P<basis>[-+*\(\)\w]+)\s*$', re.IGNORECASE) all_re = re.compile(r'^\s*assign\s+(?P<basis>[-+*\(\)\w]+)\s*$', re.IGNORECASE) basislabel = re.compile(r'\s*\[\s*([-*\(\)\w]+)\s*\]\s*') result = """%sdef basisspec_psi4_yo__%s(mol, role):\n""" % (spaces, cleanbas) result += """%s basstrings = {}\n""" % (spaces) # Start by looking for assign lines, and remove them leftover_lines = [] for line in command_lines: if symbol_re.match(line): m = symbol_re.match(line) result += """%s mol.set_basis_by_symbol("%s", "%s", role=role)\n""" % \ (spaces, m.group('symbol'), m.group('basis')) elif label_re.match(line): m = label_re.match(line) result += """%s mol.set_basis_by_label("%s", "%s", role=role)\n""" % \ (spaces, m.group('label'), m.group('basis')) elif all_re.match(line): m = all_re.match(line) result += """%s mol.set_basis_all_atoms("%s", role=role)\n""" % \ (spaces, m.group('basis')) else: # Ignore blank lines and accumulate remainder if line and not line.isspace(): leftover_lines.append(line.strip()) # Now look for regular basis set definitions basblock = list(filter(None, basislabel.split('\n'.join(leftover_lines)))) if len(basblock) == 1: if len(result.split('\n')) == 3: # case with no [basname] markers where whole block is contents of gbs file result += """%s mol.set_basis_all_atoms("%s", role=role)\n""" % \ (spaces, name) result += """%s basstrings['%s'] = \"\"\"\n%s\n\"\"\"\n""" % \ (spaces, basname(name), basblock[0]) else: message = ("Conflicting basis set specification: assign lines present but shells have no [basname] label.""") raise TestComparisonError(message) else: # case with specs separated by [basname] markers for idx in range(0, len(basblock), 2): result += """%s basstrings['%s'] = \"\"\"\n%s\n\"\"\"\n""" % \ (spaces, basname(basblock[idx]), basblock[idx + 1]) result += """%s return basstrings\n""" % (spaces) result += """{}qcdb.libmintsbasisset.basishorde['{}'] = {}\n""" \ .format(spaces, name.upper(), 'basisspec_psi4_yo__' + cleanbas) result += """%score.set_global_option(\"%s\", \"%s\")""" % (spaces, basistype, name) return result def process_pcm_command(matchobj): """Function to process match of ``pcm name? { ... }``.""" spacing = str(matchobj.group(1)) # Ignore.. name = str(matchobj.group(2)) # Ignore.. block = str(matchobj.group(3)) # Get input to PCMSolver # Setup unique scratch directory and move in, as done for other add-ons psioh = core.IOManager.shared_object() psio = core.IO.shared_object() os.chdir(psioh.get_default_path()) pcm_tmpdir = 'psi.' + str(os.getpid()) + '.' + psio.get_default_namespace() + \ 'pcmsolver.' + str(uuid.uuid4())[:8] if os.path.exists(pcm_tmpdir) is False: os.mkdir(pcm_tmpdir) os.chdir(pcm_tmpdir) with open('pcmsolver.inp', 'w') as handle: handle.write(block) import pcmsolver pcmsolver.parse_pcm_input('pcmsolver.inp') return "" # The file has been written to disk; nothing needed in Psi4 input def process_external_command(matchobj): """Function to process match of ``external name? { ... }``.""" spaces = str(matchobj.group(1)) name = str(matchobj.group(2)) if not name or name.isspace(): name = "extern" block = str(matchobj.group(3)) lines = re.split('\n', block) extern = "%sqmmm = QMMM()\n" % (spaces) NUMBER = "((?:[-+]?\\d*\\.\\d+(?:[DdEe][-+]?\\d+)?)|(?:[-+]?\\d+\\.\\d*(?:[DdEe][-+]?\\d+)?))" # Comments are all removed by this point # 0. Remove blank lines re_blank = re.compile(r'^\s*$') lines2 = [] for line in lines: mobj = re_blank.match(line) if mobj: pass else: lines2.append(line) lines = lines2 # 1. Look for units [ang|bohr|au|a.u.] defaults to ang re_units = re.compile(r'^\s*units?[\s=]+((ang)|(angstrom)|(bohr)|(au)|(a\.u\.))$\s*', re.IGNORECASE) units = 'ang' lines2 = [] for line in lines: mobj = re_units.match(line) if mobj: unit = mobj.group(1) if unit in ['bohr', 'au', 'a.u.']: units = 'bohr' else: units = 'ang' else: lines2.append(line) lines = lines2 # 2. Look for basis basisname, defaults to cc-pvdz # 3. Look for df_basis_scf basisname, defaults to cc-pvdz-jkfit re_basis = re.compile(r'\s*basis[\s=]+(\S+)\s*$', re.IGNORECASE) re_df_basis = re.compile(r'\s*df_basis_scf[\s=]+(\S+)\s*$', re.IGNORECASE) basis = 'cc-pvdz' df_basis_scf = 'cc-pvdz-jkfit' lines2 = [] for line in lines: mobj = re_basis.match(line) if mobj: basis = mobj.group(1) else: mobj = re_df_basis.match(line) if mobj: df_basis_scf = mobj.group(1) else: lines2.append(line) lines = lines2 # 4. Look for charge lines Z x y z, convert according to unit convention charge_re = re.compile(r'^\s*' + NUMBER + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$') lines2 = [] for line in lines: mobj = charge_re.match(line) if mobj: if units == 'ang': extern += '%sqmmm.addChargeAngstrom(%s,%s,%s,%s)\n' % (spaces, mobj.group(1), mobj.group(2), mobj.group(3), mobj.group(4)) if units == 'bohr': extern += '%sqmmm.addChargeBohr(%s,%s,%s,%s)\n' % (spaces, mobj.group(1), mobj.group(2), mobj.group(3), mobj.group(4)) else: lines2.append(line) lines = lines2 # 5. Look for diffuse regions, which are XYZ molecules seperated by the usual -- lines spacer_re = re.compile(r'^\s*--\s*$') frags = [] frags.append([]) for line in lines: mobj = spacer_re.match(line) if mobj: if len(frags[len(frags) - 1]): frags.append([]) else: frags[len(frags) - 1].append(line) extern += '%sextern_mol_temp = core.get_active_molecule()\n' % (spaces) mol_re = re.compile(r'\s*\S+\s+' + NUMBER + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$') lines = [] for frag in frags: if not len(frag): continue extern += '%sexternal_diffuse = geometry("""\n' % (spaces) extern += '%s0 1\n' % (spaces) for line in frag: if not mol_re.match(line): lines.append(line) else: extern += '%s%s\n' % (spaces, line) extern += '%sunits %s\n' % (spaces, units) extern += '%ssymmetry c1\n' % (spaces) extern += '%sno_reorient\n' % (spaces) extern += '%sno_com\n' % (spaces) extern += '%s""")\n' % (spaces) extern += "%sdiffuse = Diffuse(external_diffuse,'%s','%s')\n" % (spaces, basis, df_basis_scf) extern += '%sdiffuse.fitScf()\n' % (spaces) extern += '%sqmmm.addDiffuse(diffuse)\n' % (spaces) extern += '\n' extern += '%score.set_active_molecule(extern_mol_temp)\n' % (spaces) # 6. If there is anything left, the user messed up if len(lines): print('Input parsing for external {}: Extra line(s) present:') for line in lines: raise TestComparisonError(line) # Return is actually an ExternalPotential, not a QMMM extern += '%sqmmm.populateExtern()\n' % (spaces) extern += '%s%s = qmmm.extern\n' % (spaces, name) extern += '%score.set_global_option_python("EXTERN", extern)\n' % (spaces) return extern def check_parentheses_and_brackets(input_string, exit_on_error): """Function to check that all parenthesis and brackets in *input_string* are paired. On that condition, *exit_on_error* =1, otherwise 0. """ # This returns 1 if the string's all matched up, 0 otherwise import collections # create left to right parenthesis mappings lrmap = {"(": ")", "[": "]", "{": "}"} # derive sets of left and right parentheses lparens = set(lrmap.keys()) rparens = set(lrmap.values()) parenstack = collections.deque() all_matched = 1 for ch in input_string: if ch in lparens: parenstack.append(ch) elif ch in rparens: opench = "" try: opench = parenstack.pop() except IndexError: # Run out of opening parens all_matched = 0 if exit_on_error: message = ("Input error: extra %s" % (ch)) raise TestComparisonError(message) if lrmap[opench] != ch: # wrong type of parenthesis popped from stack all_matched = 0 if exit_on_error: message = ("Input error: %s closed with a %s" % (opench, ch)) raise TestComparisonError(message) if len(parenstack) != 0: all_matched = 0 if exit_on_error: message = ("Input error: Unmatched %s" % (parenstack.pop())) raise TestComparisonError(message) return all_matched def parse_multiline_array(input_list): """Function to squash multiline arrays into a single line until all parentheses and brackets are fully paired. """ line = input_list.pop(0) # Keep adding lines to the current one, until all parens match up while not check_parentheses_and_brackets(line, 0): thisline = input_list.pop(0).strip() line += thisline return "%s\n" % (line) def process_multiline_arrays(inputfile): """Function to find array inputs that are spread across multiple lines and squash them into a single line. """ # This function takes multiline array inputs, and puts them on a single line # Start by converting the input to a list, splitting at newlines input_list = inputfile.split("\n") set_re = re.compile(r'^(\s*?)set\s+(?:([-,\w]+)\s+)?(\w+)[\s=]+\[.*', re.IGNORECASE) newinput = "" while len(input_list): line = input_list[0] if set_re.match(line): # We've found the start of a set matrix [ .... line - hand it off for more checks newinput += parse_multiline_array(input_list) else: # Nothing to do - just add the line to the string newinput += "%s\n" % (input_list.pop(0)) return newinput
[docs]def process_input(raw_input, print_level=1): """Function to preprocess *raw input*, the text of the input file, then parse it, validate it for format, and convert it into legitimate Python. *raw_input* is printed to the output file unless *print_level* =0. Does a series of regular expression filters, where the matching portion of the input is replaced by the output of the corresponding function (in this module) call. Returns a string concatenating module import lines, a copy of the user's .psi4rc files, a setting of the scratch directory, a dummy molecule, and the processed *raw_input*. """ # Check if the infile is actually an outfile (yeah we did) psi4_id = re.compile(r'Psi4: An Open-Source Ab Initio Electronic Structure Package') if re.search(psi4_id, raw_input): input_lines = raw_input.split("\n") input_re = re.compile(r'^\s*?\=\=> Input File <\=\=') input_start = -1 for line_count in range(len(input_lines)): line = input_lines[line_count] if re.match(input_re, line): input_start = line_count + 3 break stop_re = re.compile(r'^-{74}') input_stop = -1 for line_count in range(input_start, len(input_lines)): line = input_lines[line_count] if re.match(stop_re, line): input_stop = line_count break if input_start == -1 or input_stop == -1: message = ('Cannot extract infile from outfile.') raise TestComparisonError(message) raw_input = '\n'.join(input_lines[input_start:input_stop]) raw_input += '\n' # Echo the infile on the outfile if print_level > 0: core.print_out("\n ==> Input File <==\n\n") core.print_out("--------------------------------------------------------------------------\n") core.print_out(raw_input) core.print_out("--------------------------------------------------------------------------\n") core.flush_outfile() #NOTE: If adding mulitline data to the preprocessor, use ONLY the following syntax: # function [objname] { ... } # which has the regex capture group: # # r'^(\s*?)FUNCTION\s*(\w*?)\s*\{(.*?)\}', re.MULTILINE | re.DOTALL | re.IGNORECASE # # your function is in capture group #1 # your objname is in capture group #2 # your data is in capture group #3 # Sections that are truly to be taken literally (spaces included) # Must be stored then subbed in the end to escape the normal processing # Process "cfour name? { ... }" cfour = re.compile(r'^(\s*?)cfour[=\s]*(\w*?)\s*\{(.*?)\}', re.MULTILINE | re.DOTALL | re.IGNORECASE) temp = re.sub(cfour, process_cfour_command, raw_input) # Return from handling literal blocks to normal processing # Nuke all comments comment = re.compile(r'(^|[^\\])#.*') temp = re.sub(comment, '', temp) # Now, nuke any escapes from comment lines comment = re.compile(r'\\#') temp = re.sub(comment, '#', temp) # Check the brackets and parentheses match up, as long as this is not a pickle input file #if not re.search(r'pickle_kw', temp): # check_parentheses_and_brackets(temp, 1) # First, remove everything from lines containing only spaces blankline = re.compile(r'^\s*$') temp = re.sub(blankline, '', temp, re.MULTILINE) # Look for things like # set matrix [ # [ 1, 2 ], # [ 3, 4 ] # ] # and put them on a single line temp = process_multiline_arrays(temp) # Process all "set name? { ... }" set_commands = re.compile(r'^(\s*?)set\s*([-,\w]*?)[\s=]*\{(.*?)\}', re.MULTILINE | re.DOTALL | re.IGNORECASE) temp = re.sub(set_commands, process_set_commands, temp) # Process all individual "set (module_list) key {[value_list] or $value or value}" # N.B. We have to be careful here, because \s matches \n, leading to potential problems # with undesired multiline matches. Better the double-negative [^\S\n] instead, which # will match any space, tab, etc., except a newline set_command = re.compile(r'^(\s*?)set\s+(?:([-,\w]+)[^\S\n]+)?(\w+)(?:[^\S\n]|=)+((\[.*\])|(\$?[-+,*()\.\w]+))\s*$', re.MULTILINE | re.IGNORECASE) temp = re.sub(set_command, process_set_command, temp) # Process "molecule name? { ... }" molecule = re.compile(r'^(\s*?)molecule[=\s]*(\S*?)\s*\{(.*?)\}', re.MULTILINE | re.DOTALL | re.IGNORECASE) temp = re.sub(molecule, process_molecule_command, temp) # Process "external name? { ... }" external = re.compile(r'^(\s*?)external[=\s]*(\w*?)\s*\{(.*?)\}', re.MULTILINE | re.DOTALL | re.IGNORECASE) temp = re.sub(external, process_external_command, temp) # Process "pcm name? { ... }" pcm = re.compile(r'^(\s*?)pcm[=\s]*(\w*?)\s*\{(.*?)^\}', re.MULTILINE | re.DOTALL | re.IGNORECASE) temp = re.sub(pcm, process_pcm_command, temp) # Then remove repeated newlines multiplenewlines = re.compile(r'\n+') temp = re.sub(multiplenewlines, '\n', temp) # Process " extract" extract = re.compile(r'(\s*?)(\w+)\s*=\s*\w+\.extract_subsets.*', re.IGNORECASE) temp = re.sub(extract, process_extract_command, temp) # Process "print" and transform it to "core.print_out()" #print_string = re.compile(r'(\s*?)print\s+(.*)', re.IGNORECASE) #temp = re.sub(print_string, process_print_command, temp) # Process "memory ... " memory_string = re.compile(r'(\s*?)memory\s+(\d*\.?\d+)\s*([KMGTPBE]i?B)', re.IGNORECASE) temp = re.sub(memory_string, process_memory_command, temp) # Process "basis name? { ... }" basis_block = re.compile(r'^(\s*?)(basis|df_basis_scf|df_basis_mp2|df_basis_cc|df_basis_sapt)[=\s]*(\w*?)\s*\{(.*?)\}', re.MULTILINE | re.DOTALL | re.IGNORECASE) temp = re.sub(basis_block, process_basis_block, temp) # Process literal blocks by substituting back in lit_block = re.compile(r'literals_psi4_yo-(\d*\d)') temp = re.sub(lit_block, process_literal_blocks, temp) future_imports = [] def future_replace(m): future_imports.append(m.group(0)) return '' future_string = re.compile('^from __future__ import .*$', flags=re.MULTILINE) temp = re.sub(future_string, future_replace, temp) # imports imports = '\n'.join(future_imports) + '\n' imports += 'import psi4\n' imports += 'from psi4 import *\n' imports += 'from psi4.core import *\n' imports += 'from psi4.driver.diatomic import anharmonicity\n' imports += 'from psi4.driver.gaussian_n import *\n' imports += 'from psi4.driver.aliases import *\n' imports += 'from psi4.driver.driver_cbs import *\n' imports += 'from psi4.driver.wrapper_database import database, db, DB_RGT, DB_RXN\n' imports += 'from psi4.driver.wrapper_autofrag import auto_fragments\n' imports += 'from psi4.driver.constants.physconst import *\n' imports += 'psi4_io = core.IOManager.shared_object()\n' # psirc (a baby PSIthon script that might live in ~/.psi4rc) psirc_file = os.path.expanduser('~') + os.path.sep + '.psi4rc' if os.path.isfile(psirc_file): fh = open(psirc_file) psirc = fh.read() fh.close() psirc = psirc.replace('psi4.IOManager', 'psi4.core.IOManager') else: psirc = '' # Override scratch directory if user specified via env_var scratch = '' scratch_env = core.get_environment('PSI_SCRATCH') if len(scratch_env): scratch += 'psi4_io.set_default_path("%s")\n' % (scratch_env) blank_mol = 'geometry("""\n' blank_mol += '0 1\nH\nH 1 0.74\n' blank_mol += '""","blank_molecule_psi4_yo")\n' temp = imports + psirc + scratch + blank_mol + temp # Move up the psi4.core namespace for func in dir(core): temp = temp.replace("psi4." + func, "psi4.core." + func) # Move pseudonamespace for physconst into proper namespace from psi4.driver.p4util import constants for pc in dir(constants.physconst): if not pc.startswith('__'): temp = temp.replace('psi_' + pc, 'psi4.constants.' + pc) return temp
if __name__ == "__main__": result = process_input(""" molecule h2 { H H 1 R R = .9 } set basis 6-31G** """) print("Result\n==========================") print(result)