def make_output(self):
'''
Dump Yaff parameters, Yaff system, plot energy contributions along
perturbation trajectories and dump perturbation trajectories to XYZ
files.
'''
if self.settings.fn_yaff is not None:
dump_yaff(self.valence, self.settings.fn_yaff)
if self.settings.fn_charmm22_prm is not None:
dump_charmm22_prm(self.valence, self.settings.fn_charmm22_prm)
if self.settings.fn_charmm22_psf is not None:
dump_charmm22_psf(self.system, self.valence, self.settings.fn_charmm22_psf)
if self.settings.fn_sys is not None:
self.system.to_file(self.settings.fn_sys)
if self.settings.plot_traj is not None and self.settings.plot_traj.lower() in ['Ehc3', 'final', 'all']:
self.plot_trajectories(do_valence=True, suffix='_Ehc3')
if self.settings.xyz_traj:
self.write_trajectories()
def make_output(self):
'''
Dump Yaff parameters, Yaff system, plot energy contributions along
perturbation trajectories and dump perturbation trajectories to XYZ
files.
'''
fn_yaff = self.kwargs.get('fn_yaff', None)
if fn_yaff is None:
fn_yaff = 'pars_cov%s.txt' % (self.kwargs.get('suffix', ''))
self.valence.dump_yaff(fn_yaff)
fn_charmm22_prm = self.kwargs.get('fn_charmm22_prm')
if fn_charmm22_prm is not None:
dump_charmm22_prm(self.valence, fn_charmm22_prm)
fn_charmm22_psf = self.kwargs.get('fn_charmm22_psf')
if fn_charmm22_psf is not None:
dump_charmm22_psf(self.system, self.valence, fn_charmm22_psf)
fn_sys = self.kwargs.get('fn_sys', None)
if fn_sys is None:
fn_sys = 'system%s.chk' % (self.kwargs.get('suffix', ''))
self.system.to_file(fn_sys)
self.plot_trajectories(do_valence=True)