def get_energy_by(gl, atomidx_list, energykey):
"""
input is a list of tuples of atom indexes:
[(1,2), (3,4,5), (4,5,6,9)]
in this case a distance, an angle and a dihedral
the output is a list of lists containing the value of the metric for
each scan_pt (or opt_pt if optimization)
and a list with the energy (energytype ONIOM?)
"""
metrics = []
# ENERGIES: if scan: last opt in each step; if opt: last scan_pt
if len(gl.bytedict['Converged?']) > 1:
energies = [e[-1] for e in gl.energies[energykey]]
for atomidx in atomidx_list:
metric = []
for byteS in gl.bytedict['orientation:']:
xyz = gl.read_coordinates(atomidx, byteS[-1])
metric.append(geom.anymetric(xyz))
metrics.append(metric)
else:
energies = gl.energies[energykey][-1]
for atomidx in atomidx_list:
metric = []
for byte in gl.bytedict['orientation:'][-1]:
xyz = gl.read_coordinates(atomidx, byte)
metric.append(geom.anymetric(xyz))
metrics.append(metric)
return metrics, energies
def get_energy_by(gl, atomidx_list, energykey):
"""
input is a list of tuples of atom indexes:
[(1,2), (3,4,5), (4,5,6,9)]
in this case a distance, an angle and a dihedral
the output is a list of lists containing the value of the metric for
each scan_pt (or opt_pt if optimization)
and a list with the energy (energytype ONIOM?)
"""
metrics = []
# ENERGIES: if scan: last opt in each step; if opt: last scan_pt
if len(gl.bytedict['Converged?']) > 1:
energies = [e[-1] for e in gl.energies[energykey]]
for atomidx in atomidx_list:
metric = []
for byteS in gl.bytedict['orientation:']:
xyz = gl.read_coordinates(atomidx, byteS[-1])
metric.append(geom.anymetric(xyz))
metrics.append(metric)
else:
energies = gl.energies[energykey][-1]
for atomidx in atomidx_list:
metric = []
for byte in gl.bytedict['orientation:'][-1]:
xyz = gl.read_coordinates(atomidx, byte)
metric.append(geom.anymetric(xyz))
metrics.append(metric)
return metrics, energies
def process_coords(self, gl, user_coords):
metrics = []
for coord in user_coords:
metric = []
for b in gl.bytedict['orientation:'][-1]: # last scan point
xyz = gl.read_coordinates(coord, b)
metric.append(geom.anymetric(xyz))
metrics.append(metric)
return metrics
