Python Molecule.init_with_xyz方法代码示例

# 需要导入模块: from molecule import Molecule [as 别名]
# 或者: from molecule.Molecule import init_with_xyz [as 别名]
def harvest_zmat(zmat):
    """Parses the contents of the Cfour ZMAT file into array and
    coordinate information. The coordinate info is converted into a
    rather dinky Molecule (no fragment, but does read charge, mult,
    unit). Return qcdb.Molecule. Written for findif zmat* where
    geometry always Cartesian and Bohr.

    """
    zmat = zmat.splitlines()[1:]  # skip comment line
    Nat = 0
    readCoord = True
    isBohr = ''
    charge = 0
    mult = 1
    molxyz = ''
    cgeom = []
    for line in zmat:
        if line.strip() == '':
            readCoord = False
        elif readCoord:
            lline = line.split()
            molxyz += line + '\n'
            Nat += 1
        else:
            if line.find('CHARGE') > -1:
                idx = line.find('CHARGE')
                charge = line[idx + 7:]
                idxc = charge.find(',')
                if idxc > -1:
                    charge = charge[:idxc]
                charge = int(charge)
            if line.find('MULTIPLICITY') > -1:
                idx = line.find('MULTIPLICITY')
                mult = line[idx + 13:]
                idxc = mult.find(',')
                if idxc > -1:
                    mult = mult[:idxc]
                mult = int(mult)
            if line.find('UNITS=BOHR') > -1:
                isBohr = ' bohr'

    molxyz = '%d%s\n%d %d\n' % (Nat, isBohr, charge, mult) + molxyz
    mol = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)

    return mol

# 需要导入模块: from molecule import Molecule [as 别名]
# 或者: from molecule.Molecule import init_with_xyz [as 别名]
def jajo2mol(jajodic):
    """Returns a Molecule from entries in dictionary *jajodic* extracted
    from JAINDX and JOBARC.

    """
    map = jajodic['MAP2ZMAT']
    elem = jajodic['ATOMCHRG']
    coord = jajodic['COORD   ']
    Nat = len(elem)

    molxyz = '%d bohr\n\n' % (Nat)
    # TODO chgmult, though not really necessary for reorientation
    for at in range(Nat):
        posn = map[at] - 1
        el = 'GH' if elem[posn] == 0 else z2el[elem[posn]]
        posn *= 3
        molxyz += '%s %21.15f %21.15f %21.15f\n' % (el, coord[posn], coord[posn + 1], coord[posn + 2])
    mol = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)

    return mol

# 需要导入模块: from molecule import Molecule [as 别名]
# 或者: from molecule.Molecule import init_with_xyz [as 别名]
def harvest_GRD(grd):
    """Parses the contents *grd* of the Cfour GRD file into the gradient
    array and coordinate information. The coordinate info is converted
    into a rather dinky Molecule (no charge, multiplicity, or fragment),
    but this is these coordinates that govern the reading of molecule
    orientation by Cfour. Return qcdb.Molecule and gradient array.

    """
    grd = grd.splitlines()
    Nat = int(grd[0].split()[0])
    molxyz = '%d bohr\n\n' % (Nat)

    grad = []
    for at in range(Nat):
        mline = grd[at + 1].split()
        el = 'GH' if int(float(mline[0])) == 0 else z2el[int(float(mline[0]))]
        molxyz += '%s %16s %16s %16s\n' % (el, mline[-3], mline[-2], mline[-1])
        lline = grd[at + 1 + Nat].split()
        grad.append([float(lline[-3]), float(lline[-2]), float(lline[-1])])
    mol = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)

    return mol, grad

# 需要导入模块: from molecule import Molecule [as 别名]
# 或者: from molecule.Molecule import init_with_xyz [as 别名]

#.........这里部分代码省略.........
    mobj = re.search(
        r'\s+' + r'Molecular gradient' + r'\s*' +
        r'\s+' + r'------------------' + r'\s*' +
        r'\s+' + r'\n' +
        r'(?:(?:\s+[A-Z]+\s*#\d+\s+[xyz]\s+[-+]?\d+\.\d+\s*\n)+)' +  # optional, it seems
        r'\n\n' +  # optional, it seems
        r'((?:\s+[A-Z]+\s*#\d+\s+\d?\s+[-+]?\d+\.\d+\s+[-+]?\d+\.\d+\s+[-+]?\d+\.\d+\s*\n)+)' +
        r'\n\n' +
        r'\s+' + 'Molecular gradient norm',
        outtext, re.MULTILINE)
    if mobj:
        print('matched molgrad')
        atoms = []
        psivar_grad = []
        for line in mobj.group(1).splitlines():
            lline = line.split()
            atoms.append(lline[0])
            #psivar_gradient.append([Decimal(lline[-3]), Decimal(lline[-2]), Decimal(lline[-1])])
            psivar_grad.append([float(lline[-3]), float(lline[-2]), float(lline[-1])])

    # Process geometry
    mobj = re.search(
#        r'\s+(?:-+)\s*' +
#        r'^\s+' + r'Z-matrix   Atomic            Coordinates (in bohr)' + r'\s*' +
        r'^\s+' + r'Symbol    Number           X              Y              Z' + r'\s*' +
        r'^\s+(?:-+)\s*' +
        r'((?:\s+[A-Z]+\s+[0-9]+\s+[-+]?\d+\.\d+\s+[-+]?\d+\.\d+\s+[-+]?\d+\.\d+\s*\n)+)' +
        r'^\s+(?:-+)\s*',
        outtext, re.MULTILINE)
    if mobj:
        print('matched geom')
        molxyz = '%d bohr\n\n' % len(mobj.group(1).splitlines())
        for line in mobj.group(1).splitlines():
            lline = line.split()
            molxyz += '%s %16s %16s %16s\n' % (lline[0], lline[-3], lline[-2], lline[-1])
        # Rather a dinky Molecule as no ghost, charge, or multiplicity
        psivar_coord = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)

    # Process atom geometry
    mobj = re.search(
        r'^\s+' + r'@GETXYZ-I,     1 atoms read from ZMAT.' + r'\s*' +
        r'^\s+' + r'[0-9]+\s+([A-Z]+)\s+[0-9]+\s+' + NUMBER + r'\s*',
        outtext, re.MULTILINE)
    if mobj:
        print('matched atom')
        # Dinky Molecule
        molxyz = '1 bohr\n\n%s 0.0 0.0 0.0\n' % (mobj.group(1))
        psivar_coord = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)

    # Process error codes
    mobj = re.search(
        r'^\s*' + r'--executable ' + r'(\w+)' + r' finished with status' + r'\s+' + r'([1-9][0-9]*)',
        outtext, re.MULTILINE)
    if mobj:
        print('matched error')
        psivar['CFOUR ERROR CODE'] = mobj.group(2)

    # Process CURRENT energies (TODO: needs better way)
    if 'SCF TOTAL ENERGY' in psivar:
        psivar['CURRENT REFERENCE ENERGY'] = psivar['SCF TOTAL ENERGY']
        psivar['CURRENT ENERGY'] = psivar['SCF TOTAL ENERGY']

    if 'MP2 TOTAL ENERGY' in psivar and 'MP2 CORRELATION ENERGY' in psivar:
        psivar['CURRENT CORRELATION ENERGY'] = psivar['MP2 CORRELATION ENERGY']
        psivar['CURRENT ENERGY'] = psivar['MP2 TOTAL ENERGY']

    if 'MP3 TOTAL ENERGY' in psivar and 'MP3 CORRELATION ENERGY' in psivar:
        psivar['CURRENT CORRELATION ENERGY'] = psivar['MP3 CORRELATION ENERGY']
        psivar['CURRENT ENERGY'] = psivar['MP3 TOTAL ENERGY']

    if 'MP4 TOTAL ENERGY' in psivar and 'MP4 CORRELATION ENERGY' in psivar:
        psivar['CURRENT CORRELATION ENERGY'] = psivar['MP4 CORRELATION ENERGY']
        psivar['CURRENT ENERGY'] = psivar['MP4 TOTAL ENERGY']

#    if ('%s TOTAL ENERGY' % (mobj.group('fullCC')) in psivar) and \
#       ('%s CORRELATION ENERGY' % (mobj.group('fullCC')) in psivar):
#        psivar['CURRENT CORRELATION ENERGY'] = psivar['%s CORRELATION ENERGY' % (mobj.group('fullCC')]
#        psivar['CURRENT ENERGY'] = psivar['%s TOTAL ENERGY' % (mobj.group('fullCC')]

    if 'CC2 TOTAL ENERGY' in psivar and 'CC2 CORRELATION ENERGY' in psivar:
        psivar['CURRENT CORRELATION ENERGY'] = psivar['CC2 CORRELATION ENERGY']
        psivar['CURRENT ENERGY'] = psivar['CC2 TOTAL ENERGY']

    if 'CCSD TOTAL ENERGY' in psivar and 'CCSD CORRELATION ENERGY' in psivar:
        psivar['CURRENT CORRELATION ENERGY'] = psivar['CCSD CORRELATION ENERGY']
        psivar['CURRENT ENERGY'] = psivar['CCSD TOTAL ENERGY']

    if 'CCSD(T) TOTAL ENERGY' in psivar and 'CCSD(T) CORRELATION ENERGY' in psivar:
        psivar['CURRENT CORRELATION ENERGY'] = psivar['CCSD(T) CORRELATION ENERGY']
        psivar['CURRENT ENERGY'] = psivar['CCSD(T) TOTAL ENERGY']

    if 'CC3 TOTAL ENERGY' in psivar and 'CC3 CORRELATION ENERGY' in psivar:
        psivar['CURRENT CORRELATION ENERGY'] = psivar['CC3 CORRELATION ENERGY']
        psivar['CURRENT ENERGY'] = psivar['CC3 TOTAL ENERGY']

    if 'CCSDT TOTAL ENERGY' in psivar and 'CCSDT CORRELATION ENERGY' in psivar:
        psivar['CURRENT CORRELATION ENERGY'] = psivar['CCSDT CORRELATION ENERGY']
        psivar['CURRENT ENERGY'] = psivar['CCSDT TOTAL ENERGY']

    return psivar, psivar_coord, psivar_grad