def HLC_generic(A=0.009170, B=0.004455, C=0.009155, D=0.001947):
    '''calculate High Level Correction term
        from alpha and beta VALENCE electron count.
    '''
    global Ehlc
    
    say('HLC.')

    nClosed = nwchem.rtdb_get("scf:nclosed")
    nOpen = nwchem.rtdb_get("scf:nopen")
    nElec = nwchem.rtdb_get("scf:nelec")
    nFrozen = sum_core_orbitals()

    # According to Curtiss,
    # nBeta = num valence pairs
    # nAlpha = num unpaired or remaining valence electrons
    # subject to the constraint that nAlpha >= nBeta

    nBeta = nClosed - nFrozen

    nAlpha = nElec - (nFrozen * 2) - nBeta

    debug('\nclosed=%d open=%d frozen=%d nAlpha=%d nBeta=%d\n' %
        (nClosed,nOpen,nFrozen,nAlpha,nBeta))

    if nAlpha < nBeta:
        nAlpha, nBeta = nBeta, nAlpha

    if is_molecule():
        Ehlc = -(A * nBeta) - B * (nAlpha - nBeta)
    else:  # it's an atom, calc is different
        Ehlc = -(C * nBeta) - D * (nAlpha - nBeta)

    return False
def E_hlc ():
#   E_hlc =    High Level Correction

    global Ehlc

    # Correction coefficients in milli Hartrees
    # closed shell
    A   = 0.009472

    # open shell
    Ap  = 0.009769
    B   = 0.003179

    # atoms and atom ions
    C   = 0.009741
    D   = 0.002115

    # single electron pair species
    # e.g.: Li2, Na2, LiNa, BeH2, BeH+
    E   = 0.002379

    say('HLC.')

    nClosed = nwchem.rtdb_get("scf:nclosed")
    nOpen   = nwchem.rtdb_get("scf:nopen")
    nElec   = nwchem.rtdb_get("scf:nelec")
    nFrozen = sum_core_orbitals()

    # According to Curtiss,
    # nBeta = num valence pairs
    # nAlpha = num unpaired or remaining valence electrons
    # subject to the constraint that nAlpha >= nBeta

    nBeta   = nClosed - nFrozen
    nAlpha  = nElec - nFrozen - nClosed

    debug ('\nclosed=%d open=%d frozen=%d nAlpha=%d nBeta=%d\n' % \
            (nClosed,nOpen,nFrozen,nAlpha,nBeta))

    if nAlpha < nBeta:
        nAlpha,nBeta = nBeta,nAlpha

    # test for single (valence) electron pair species
    if (nOpen == 0) and (nClosed - nFrozen) == 1 and \
            (nAlpha == 1) and (nBeta == 1):
        hlc = E

    elif is_atom():
        hlc = -C * (nBeta) - D * (nAlpha-nBeta)

    elif Multiplicity > 1:
        hlc = -Ap * (nBeta) - B * (nAlpha-nBeta)

    else:                   # USUAL CASE: singlet, closed shell
        hlc = -A * (nBeta)

    Ehlc = hlc

    return False
Ejemplo n.º 3
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    def E_hlc(self):
        """E_hlc =    High Level Correction
        """

        # Correction coefficients in milli Hartrees
        # closed shell
        A   = 0.009472

        # open shell
        Ap  = 0.009769
        B   = 0.003179

        # atoms and atom ions
        C   = 0.009741
        D   = 0.002115

        # single electron pair species
        # e.g.: Li2, Na2, LiNa, BeH2, BeH+
        E   = 0.002379

        self.say('HLC.')

        nClosed = nwchem.rtdb_get("scf:nclosed")
        nOpen   = nwchem.rtdb_get("scf:nopen")
        nElec   = nwchem.rtdb_get("scf:nelec")
        self.nFrozen = self.sum_core_orbitals()

        # According to Curtiss,
        # nBeta = num valence pairs
        # nAlpha = num unpaired or remaining valence electrons
        # subject to the constraint that nAlpha >= nBeta

        self.nBeta   = nClosed - self.nFrozen
        self.nAlpha  = nElec - self.nFrozen - nClosed

        self.debug('\nclosed=%d open=%d frozen=%d nAlpha=%d nBeta=%d\n' % \
                   (nClosed, nOpen, self.nFrozen, self.nAlpha, self.nBeta))

        if self.nAlpha < self.nBeta:
            self.nAlpha, self.nBeta = self.nBeta, self.nAlpha
            #self.say('** a<->b swap: nAlpha=%d nBeta=%d\n' % (self.nAlpha,self.nBeta))

        # test for single (valence) electron pair species
        if (nOpen == 0) and (nClosed - self.nFrozen) == 1 and \
                (self.nAlpha == 1) and (self.nBeta == 1):
            hlc = E

        elif self.is_atom():
            hlc = -C * (self.nBeta) - D * (self.nAlpha - self.nBeta)

        elif self.multiplicity != "singlet":
            hlc = -Ap * (self.nBeta) - B * (self.nAlpha - self.nBeta)

        else:                   # USUAL CASE: singlet, closed shell
            hlc = -A * (self.nBeta)

        self.Ehlc = hlc
def set_atoms_list():
    global AtomsList
    global NumAtoms

    # rtdb_get() returns a string if only one atom
    #       or a list of atoms (i.e., tags).
    # Absent type handling,
    # len('CU') is the same as len(['C','U'])
    #
    tags = nwchem.rtdb_get("geometry:geometry:tags")
    tag_type = type(tags).__name__

    if type(tags).__name__ == 'str':
        AtomsList.append(tags)
        debug('AtomsList: %s\n' % tags)

    elif tag_type == 'list':
        AtomsList.extend(tags)
        if debug_flag:
            atmstr = ''
            for atm in tags:
                atmstr += ' ' + atm
            debug('AtomsList: %s\n' % atmstr)

    else:
        AtomsList = []

    NumAtoms = len(AtomsList)
    debug('NumAtoms=%d\n' % NumAtoms)
def init_g3mp2(charge=0, mult='singlet', use_qcisdt_f=False):
    '''say hello
    '''

    set_charge(charge)
    set_multiplicity(mult)

    if get_multiplicity() > 1:
        set_HFtype('uhf')
    else:
        set_HFtype('rhf')

    if use_qcisdt_f:
        use_qcisdt()
    else:
        use_ccsdt()

    if QCISDT_flag:
        ccstring = 'QCISD(T)'
    else:
        ccstring = 'CCSD(T)'

    title = nwchem.rtdb_get("title")
    say(" %s -- NWChem G3(MP2,%s) Composite Method\n" % (title, ccstring))

    return False
def set_atoms_list():
    global AtomsList
    global NumAtoms

    # rtdb_get() returns EITHER
    #       a string if only one atom, or
    #       a list of atoms (i.e., tags).
    #
    # Without type handling,
    # len('CU') is the same as len(['C','U'])
    #
    tags = nwchem.rtdb_get("geometry:geometry:tags")
    tag_type = type(tags).__name__

    if tag_type == "str":
        AtomsList.append(tags)
        debug("AtomsList: %s\n" % tags)

    elif tag_type == "list":
        AtomsList.extend(tags)
        if debug_flag:
            atmstr = ""
            for atm in tags:
                atmstr += " " + atm
            debug("AtomsList: %s\n" % atmstr)
    else:
        AtomsList = []

    NumAtoms = len(AtomsList)
    debug("NumAtoms=%d\n" % NumAtoms)
Ejemplo n.º 7
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    def init_g4mp2(self):
        """Say hello.
        """

        title = nwchem.rtdb_get("title")
        self.say(" %s -- NWChem G4(MP2) Composite Method\n" % (title))

        return False
Ejemplo n.º 8
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def get_theory():
    theory = nwchem.rtdb_get('task:theory').lower()
    if theory == 'dft':
        scf = nwchem.rtdb_get('dft:scftype').lower()
    else:
        scf = nwchem.rtdb_get('scf:scftype').lower()

    if theory == 'scf':
        return scf
    elif theory == 'dft':
        if scf == 'uhf':
            return 'uks'
        elif scf == 'rhf':
            return 'rks'

    # if here, it wasn't handled
    raise NotImplementedError('%s %s' % (theory, scf))
Ejemplo n.º 9
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def get_theory():
    theory = nwchem.rtdb_get('task:theory').lower()
    if theory == 'dft':
        scf = nwchem.rtdb_get('dft:scftype').lower()
    else:
        scf = nwchem.rtdb_get('scf:scftype').lower()

    if theory == 'scf':
        return scf
    elif theory == 'dft':
        if scf == 'uhf':
            return 'uks'
        elif scf =='rhf':
            return 'rks'

    # if here, it wasn't handled
    raise NotImplementedError('%s %s' % (theory, scf))
Ejemplo n.º 10
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    def geometry_hash(self):
        """Produce a hashed geometry identifier from the geometry in the
        RTDB. This is useful to generate file names for writing and reading
        geometry to/from disk.

        :return: sha1 hex digest of geometry
        :rtype : str
        """

        keys = [nwchem.rtdb_first()]
        while True:
            try:
                keys.append(nwchem.rtdb_next())
            except nwchem.NWChemError:
                break

        ckey = [k for k in keys if "coords" in k and "geometry" in k][0]
        tkey = [k for k in keys if "tags" in k and "geometry" in k][0]
        coords = nwchem.rtdb_get(ckey)
        tags = nwchem.rtdb_get(tkey)
        fused = " ".join([str(c) for c in coords]) + " ".join([str(t) for t in tags])
        result = hashlib.sha1(fused).hexdigest()

        return result
def init_g4mp2(charge=0, mult="singlet"):
    """say hello
    """

    set_charge(charge)
    set_multiplicity(mult)

    if get_multiplicity() > 1:
        set_HFtype("uhf")
    else:
        set_HFtype("rhf")

    title = nwchem.rtdb_get("title")
    say(" %s -- NWChem G4(MP2) Composite Method\n" % (title))

    return False
def init_g4mp2(charge=0,mult='singlet'):
    '''say hello
    '''

    set_charge(charge)
    set_multiplicity(mult)

    if get_multiplicity() > 1:
        set_HFtype('uhf')
    else:
        set_HFtype('rhf')

    title = nwchem.rtdb_get("title")
    say(" %s -- NWChem G4(MP2) Composite Method\n" % (title))

    return False
Ejemplo n.º 13
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    def initialize_atoms_list(self):
        """Use NWChem's RTDB geometry to initialize self.atoms,
        e.g. CH3OH gives ['C','H','H','H','O''H']
        """

        # rtdb_get() returns a string if only one atom
        #       or a list of atoms (i.e., tags).
        # Absent type handling,
        # len('CU') is the same as len(['C','U'])
        tags = nwchem.rtdb_get("geometry:geometry:tags")
        if type(tags) == str:
            self.atoms.append(tags)
            self.debug('AtomsList: %s\n' % tags)
        else:
            self.atoms.extend(tags)
            if self.debug_flag:
                atmstr=''
                for atm in tags:
                    atmstr += ' '+atm
                self.debug('AtomsList: %s\n' % atmstr)

        self.debug('NumAtoms={0}\n'.format(len(self.atoms)))
Ejemplo n.º 14
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def get_scftype():
    if nwchem.rtdb_get('task:theory').lower() == 'dft':
        return nwchem.rtdb_get('dft:scftype')
    else:
        return nwchem.rtdb_get('scf:scftype')
def get_spin_multiplicity():
    return nwchem.rtdb_get('dft:mult')
def get_dipole():
    return nwchem.rtdb_get('%s:dipole' % _PROPERTYGROUP)
Ejemplo n.º 17
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def prep():
    global _PROPERTYGROUP
    nwchem.rtdb_open('perm/mol.db', 'old')
    _PROPERTYGROUP = nwchem.rtdb_get('task:theory')
Ejemplo n.º 18
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def get_atomic_numbers():
    return map(int, nwchem.rtdb_get('geometry:geometry:charges'))
Ejemplo n.º 19
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def get_atom_names():
    return nwchem.rtdb_get('geometry:geometry:tags')
Ejemplo n.º 20
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def get_atom_names():
    return nwchem.rtdb_get('geometry:geometry:tags')
Ejemplo n.º 21
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def get_total_charge():
    return int(nwchem.rtdb_get('charge'))
Ejemplo n.º 22
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def get_converged():
    return 1 == nwchem.rtdb_get('%s:converged' % _PROPERTYGROUP)
def get_functional():
    return nwchem.rtdb_get('dft:xc_spec')
Ejemplo n.º 24
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def get_symmetry():
    return nwchem.rtdb_get('geometry:geometry:group name')
Ejemplo n.º 25
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def get_basis():
    return nwchem.rtdb_get('basis:ao basis:star bas type')
Ejemplo n.º 26
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def get_scftype():
    if nwchem.rtdb_get('task:theory').lower() == 'dft':
        return nwchem.rtdb_get('dft:scftype')
    else:
        return nwchem.rtdb_get('scf:scftype')
Ejemplo n.º 27
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def get_potential_energy():
    return nwchem.rtdb_get('%s:energy' % _PROPERTYGROUP)
def HF_zpe():
    ''' run hessian on equilibrium geometry
        get zero point energy.
                                                                          n
       note: linear tri-atomics and larger
       give high ZPE values in NWChem @ HF/6-31G*
    '''

    global Ezpe
    global Ethermal
    global Hthermal
    global AtomsList

    #AUKCAL = 627.5093314   # bogus
    AUKCAL = kCalPerHartree
    c = 2.99792458E+10
    h = 6.62606957E-27
    kgas = 1.3806488E-16     # cgs units
    Rgas = 1.9872041 / 1000.0 / AUKCAL     # atomic units

    temperature = T298

    say("zpe.")

    if is_atom():
        Ezpe = 0.0
        Ethermal = 1.5 * Rgas * temperature
        Hthermal = Ethermal + (Rgas * temperature)
        # Ethermal = 0.001416      # 3/2 * RT
        # Hthermal = 0.002360      # Ethermal + kT
        return False

    # run hessian on equilibrium geometry
    # ignore ZPE, calculate it from vibrations list
    zpe, vibs, intens = nwchem.task_freq("scf")

    # Handroll the ZPE because NWChem's zpe accumulates
    # truncation error from 3 sigfig physical constants.

    vibsum = 0.0
    for freq in vibs:
        if (freq > 0.1):
            vibsum += freq

    cm2Ha = 219474.6    # cm-1 to Hartree conversion
    Ezpe = vibsum / (2.0 * cm2Ha)

    # get total thermal energy, enthalpy
    eth = nwchem.rtdb_get("vib:ethermal")
    hth = nwchem.rtdb_get("vib:hthermal")
    debug("NWChem zpe,E,H thermal= %.6f, %.6f, %.6f\n" % (Ezpe,eth, hth))

    eth = 0.0
    hth = 0.0
    xdum = 0.0

    for freq in vibs:
        if (freq > 0.1):
            # freqency temperature in Kelvin from cm-1
            thetav = freq * (h * c / kgas)
            if (temperature > 0.0):
                xdum = math.exp(-thetav / temperature)
            else:
                xdum = 0.0

            xdum = xdum / (1.0 - xdum)
            eth = eth + thetav * (0.5 + xdum)

    # linear boolean is available only after task_freq('scf') runs
    # NWChem only writes the flag if molecule is linear

    eth = eth * Rgas

    try:
        is_linear = nwchem.rtdb_get("vib:linear")
    except:
        is_linear = False

    if (is_linear and QCISDT_flag):
        # translational(3/2RT) and rotation(2/2RT) thermal corrections
        eth = eth + 2.5 * Rgas * temperature
    else:
        # translational(3/2RT) and rotation(3/2RT) thermal corrections
        eth = eth + 3.0 * Rgas * temperature

    # Hthermal = eth+pV=eth+RT, since pV=RT
    hth = eth + Rgas * temperature
    debug("RgasT= %.9f, kT_298_perMol= %.9f\n" %
        (Rgas * temperature, kT_298_perMol))
    debug("Handrolled E,H thermal= %.6f, %.6f\n" % (eth, hth))

    Ethermal = eth
    Hthermal = hth

    return False
Ejemplo n.º 29
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def get_spin_multiplicity():
    try:
        return nwchem.rtdb_get('dft:mult')
    except SystemError:
        return None
Ejemplo n.º 30
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def get_atom_masses():
    return nwchem.rtdb_get('geometry:geometry:masses')
Ejemplo n.º 31
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def get_positions():
    return _reshape_atom_vector(nwchem.rtdb_get('geometry:geometry:coords'))
Ejemplo n.º 32
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def get_converged():
    return 1 == nwchem.rtdb_get('%s:converged' % _PROPERTYGROUP)
Ejemplo n.º 33
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def get_atom_masses():
    return nwchem.rtdb_get('geometry:geometry:masses')
Ejemplo n.º 34
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def get_forces():
    try:
        forces = nwchem.rtdb_get('%s:gradient' % _PROPERTYGROUP)
        return _reshape_atom_vector([-f for f in forces])
    except SystemError:
        return None
Ejemplo n.º 35
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def get_functional():
    try:
        return nwchem.rtdb_get('dft:xc_spec')
    except SystemError:
        return None
Ejemplo n.º 36
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def prep():
    global _PROPERTYGROUP

    nwchem.rtdb_open('perm/mol.db', 'old')

    _PROPERTYGROUP = nwchem.rtdb_get('task:theory')
Ejemplo n.º 37
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def get_dipole():
    try:
        return nwchem.rtdb_get('%s:dipole' % _PROPERTYGROUP)
    except SystemError:
        return None
Ejemplo n.º 38
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def get_atomic_numbers():
    return map(int, nwchem.rtdb_get('geometry:geometry:charges'))
Ejemplo n.º 39
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def get_potential_energy():
    return nwchem.rtdb_get('%s:energy' % _PROPERTYGROUP)
Ejemplo n.º 40
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def get_positions():
    return _reshape_atom_vector(nwchem.rtdb_get('geometry:geometry:coords'))
Ejemplo n.º 41
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def get_total_charge():
    return int(nwchem.rtdb_get('charge'))
Ejemplo n.º 42
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    def E_zpe(self):
        """Run hessian on equilibrium geometry, get zero point energy.
                                                                              n
        Note: linear tri-atomics and larger give high ZPE values in
        NWChem @ HF/6-31G*
        """

        self.say('ZPE.')

        AUKCAL  = 627.5093314
        c       = 2.99792458E+10
        h       = 6.62606957E-27
        kgas    = 1.3806488E-16     # cgs units
        Rgas    = 1.9872041/1000.0/AUKCAL     # atomic units

        temperature = 298.15

        if self.is_atom():
            self.Ezpe = 0.0
            self.Ethermal = 1.5 * Rgas * temperature # 3/2 * RT
            self.Hthermal = self.Ethermal + (Rgas * temperature)
            return False

        # run hessian on equilibrium geometry
        # ignore ZPE, calculate it from vibrations list
        zpe, vibs, intens = nwchem.task_freq("dft")

        # Handroll the ZPE because NWChem's zpe accumulates
        # truncation error from 3 sigfig physical constants.
        vibsum = 0.0
        for freq in vibs:
            if (freq > 0.1):
                vibsum += freq

        cm2Ha = 219474.6    # cm-1 to Hartree conversion
        self.Ezpe    = vibsum / (2.0 * cm2Ha)

        # shamelessly swipe code from NWCHEM/src/vib_wrtFreq.F
        eth = 0.0
        hth = 0.0
        xdum = 0.0

        for freq in vibs:
            if (freq > 0.1):
                thetav = freq * (h * c / kgas)    #freqency temperature in Kelvin from cm-1
                if (temperature > 0.0):
                    xdum   = math.exp(-thetav/temperature)
                else:
                    xdum = 0.0

                xdum = xdum / (1.0 - xdum)
                eth = eth + thetav * (0.5 + xdum)

        eth = eth * Rgas

        # linear boolean is available only after task_freq('scf') runs
        # NWChem only writes the flag if molecule is linear
        try:
            is_linear = nwchem.rtdb_get("vib:linear")
        except:
            is_linear = False

        if (is_linear):
            # translational(3/2RT) and rotation(2/2RT) thermal corrections
            eth = eth + 2.5 * Rgas * temperature
        else:
            # translational(3/2RT) and rotation(3/2RT) thermal corrections
            eth = eth + 3.0 * Rgas * temperature

        # Hthermal = eth+pV=eth+RT, since pV=RT
        hth = eth + Rgas * temperature
        self.debug("Handrolled E,H thermal= %.6f, %.6f\n" % (eth,hth))

        self.Ethermal = eth
        self.Hthermal = hth
            thetav = freq * (h * c / kgas)  # freqency temperature in Kelvin from cm-1
            if temperature > 0.0:
                xdum = math.exp(-thetav / temperature)
            else:
                xdum = 0.0

            xdum = xdum / (1.0 - xdum)
            eth = eth + thetav * (0.5 + xdum)

    eth = eth * Rgas

    # linear boolean is available only after task_freq('???') runs
    # NWChem only writes the flag if molecule is linear

    try:
        is_linear = nwchem.rtdb_get("vib:linear")
    except:
        is_linear = False

    if is_linear:
        # translational(3/2RT) and rotation(2/2RT) thermal corrections
        eth = eth + 2.5 * Rgas * temperature
    else:
        # translational(3/2RT) and rotation(3/2RT) thermal corrections
        eth = eth + 3.0 * Rgas * temperature

    # Hthermal = eth+pV=eth+RT, since pV=RT
    hth = eth + Rgas * temperature

    debug("ZPE,E,H thermal= %.6f, %.6f, %.6f\n" % (Ezpe, eth, hth))
Ejemplo n.º 44
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def get_basisname():
    return nwchem.rtdb_get('basis:ao basis:star bas type')
Ejemplo n.º 45
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def get_symmetry():
    return nwchem.rtdb_get('geometry:geometry:group name')
Ejemplo n.º 46
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def get_forces():
    try:
        forces = nwchem.rtdb_get('%s:gradient' % _PROPERTYGROUP)
        return _reshape_atom_vector([-f for f in forces])
    except:
        return None