def apply_tls(Utls, indexlist=None, srb=False):
"""
Uses the calculated TLS-Parameter to calculate the displacements
for all atoms based on those parameters.
"""
if srb:
pass
for i, atom in enumerate(fitted_atoms):
try:
atom.adp['cart_ext'] = Utls[i * 6:i * 6 + 6]
atom.adp['cart_sum'] = atom.adp['cart_int'] + atom.adp['cart_ext']
atom.adp['frac_ext'] = cg.rotate_adp3(atom.adp['cart_ext'],
data[useData].cart2fracmatrix,
data[useData].cell)
atom.adp['frac_sum'] = cg.rotate_adp3(atom.adp['cart_sum'],
data[useData].cart2fracmatrix,
data[useData].cell)
atom.updated()
except ADPDataError:
atom.adp['cart_sum'] = atom.adp['cart_meas']
atom.adp['cart_ext'] = Utls[i * 6:i * 6 + 6]
atom.updated()
def apply_tls(Utls, indexlist=None, srb=False):
"""
Uses the calculated TLS-Parameter to calculate the displacements
for all atoms based on those parameters.
"""
if srb:
pass
# m=np.linalg.pinv(data['exp'].frac2cartmatrix)
for i in range(len(Utls) / 6):
data['exp'].atoms[i].adp['cart_ext'] = Utls[i * 6:i * 6 + 6]
data['exp'].atoms[i].adp['cart_sum'] = data['exp'].atoms[i].adp['cart_int'] \
+ data['exp'].atoms[i].adp['cart_ext']
#===============================================================================
# if not data['exp'].atoms[i].element == 'H':
#
# data['exp'].atoms[i].adp['cart_int']=data['exp'].atoms[i].adp['cart_sum']\
# -data['exp'].atoms[i].adp['cart_ext']
# data['exp'].atoms[i].adp['frac_int']=cg.rotate_adp3(data['exp']\
# .atoms[i].adp['cart_int'],\
# data['exp'].cart2fracmatrix,\
# data['exp'].cell)
#===============================================================================
data['exp'].atoms[i].adp['frac_ext'] = cg.rotate_adp3(data['exp']
.atoms[i].adp['cart_ext'],
data['exp'].cart2fracmatrix,
data['exp'].cell)
data['exp'].atoms[i].adp['frac_sum'] = cg.rotate_adp3(data['exp']
.atoms[i].adp['cart_sum'],
data['exp'].cart2fracmatrix,
data['exp'].cell)
def run(pluginManager):
data = pluginManager.get_variable('data')
printer = pluginManager.setup()
useData = pluginManager.arg('data')
dabapa = './APD_DABA_{:.1f}_.txt'.format(data.temperature)
database = open(dabapa, 'r').readlines()
read_database(data, database, invlist=[], readAll=True)
pseudoMols = [data[key] for key in data.keys() if key.startswith('pointMass_')]
data.give_molecule('periphery', [])
periphery = data['periphery']
for i, pm in enumerate(pseudoMols):
for datom in pm.atoms:
# printer('{} {}'.format(atom.cart, atom.adp['cart_int']))
atom = ATOM('X{}'.format(i), 'C', datom.cart, molecule=periphery)
atom.adp['cart_meas'] = datom.adp['cart_int']
periphery.atoms.append(atom)
printer('Generating Pseudo Molecule from point masses:')
for atom in periphery.atoms:
printer(str(atom))
data['pseudo'] = periphery
printer('\nGenerating rigid body vibration description via TLS fit against\nPseudo Molecule.')
options = {'correlate': True, 'data': 'pseudo'}
pluginManager.call('T2', options)
TLS = pluginManager.get_variable('TLS')
refMol = data[useData]
for atom in refMol.atoms:
generateADP(atom, TLS)
atom.adp['frac_int'] = rotate_adp3(atom.adp['cart_int'],
atom.molecule.cart2fracmatrix,
atom.molecule.cell)
atom.adp['cart_sum'] = atom.adp['cart_int'] + atom.adp['cart_ext']
atom.adp['frac_sum'] = atom.adp['frac_int'] + atom.adp['frac_ext']
atom.updated()
def generateADP(atom, TLS):
"""
Computes the ADP of an atom located at the cartesian coordinates 'cart' based on the parameters
'T', 'L' and 'S' encoding the rigid body movement of the atom.
:param atom:
:param TLS:
:return:
"""
x1, x2, x3 = atom.cart
TLS = np.array(TLS)
newADP = []
U11 = np.array([1, 0, 0, 0, 0, 0, 0, x3 * x3, x2 * x2, 0, 0, -2 * x2 * x3, 0, 0, 0, 0, 0, 2 * x3, 0, -2 * x2, 0])
U11 = np.dot(TLS, U11)
newADP.append(U11)
U22 = np.array([0, 1, 0, 0, 0, 0, x3 * x3, 0, x1 * x1, 0, -2 * x1 * x3, 0, 0, 0, 0, -2 * x3, 0, 0, 0, 0, 2 * x1])
U22 = np.dot(TLS, U22)
newADP.append(U22)
U33 = np.array([0, 0, 1, 0, 0, 0, x2 * x2, x1 * x1, 0, -2 * x1 * x2, 0, 0, 0, 0, 0, 0, 2 * x2, 0, -2 * x1, 0, 0])
U33 = np.dot(TLS, U33)
newADP.append(U33)
U12 = np.array([0, 0, 0, 1, 0, 0, 0, 0, -x1 * x2, -x3 * x3, x2 * x3, x1 * x3, -x3, x3, 0, 0, 0, 0, 0, x1, -x2])
U12 = np.dot(TLS, U12)
newADP.append(U12)
U13 = np.array([0, 0, 0, 0, 1, 0, 0, -x1 * x3, 0, x2 * x3, -x2 * x2, x1 * x2, x2, 0, -x2, 0, 0, -x1, x3, 0, 0])
U13 = np.dot(TLS, U13)
newADP.append(U13)
U23 = np.array([0, 0, 0, 0, 0, 1, -x2 * x3, 0, 0, x1 * x3, x1 * x2, -x1 * x1, 0, -x1, x1, x2, -x3, 0, 0, 0, 0])
U23 = np.dot(TLS, U23)
newADP.append(U23)
atom.adp['cart_ext'] = newADP
atom.adp['frac_ext'] = rotate_adp3(newADP,
atom.molecule.cart2fracmatrix,
atom.molecule.cell)
def apply_tls(Utls, indexlist=None, srb=False):
"""
Uses the calculated TLS-Parameter to calculate the displacements
for all atoms based on those parameters.
"""
if srb:
pass
# ===============================================================================
# for i in range(len(Utls)/6):
# data['exp'].atoms[i].adp['cart_ext']=Utls[i*6:i*6+6]
# data['exp'].atoms[i].adp['cart_sum']=data['exp'].atoms[i].adp['cart_int']\
# +data['exp'].atoms[i].adp['cart_ext']
#
#
# data['exp'].atoms[i].adp['frac_ext']=cg.rotate_adp3(data['exp']\
# .atoms[i].adp['cart_ext'],\
# data['exp'].cart2fracmatrix,\
# data['exp'].cell)
#
# data['exp'].atoms[i].adp['frac_sum']=cg.rotate_adp3(data['exp']\
# .atoms[i].adp['cart_sum'],\
# data['exp'].cart2fracmatrix,\
# data['exp'].cell)
#===============================================================================
for i, atom in enumerate(fitted_atoms):
if atom.get_element() == 'H':
atom.adp['cart_ext'] = Utls[i * 6:i * 6 + 6]
atom.adp['cart_sum'] = atom.adp['cart_int'] + atom.adp['cart_ext']
atom.adp['frac_ext'] = cg.rotate_adp3(atom.adp['cart_ext'],
data['exp'].cart2fracmatrix,
data['exp'].cell)
atom.adp['frac_sum'] = cg.rotate_adp3(atom.adp['cart_sum'],
data['exp'].cart2fracmatrix,
data['exp'].cell)
atom.updated()
else:
atom.adp['cart_sum'] = atom.adp['cart_meas']
atom.adp['cart_ext'] = Utls[i * 6:i * 6 + 6]
atom.updated()
