'ignored_bond_types': [1, 2, 6, 9, 10, 15], # no h-bonds
'ignored_angle_types': [4, 5, 6, 8, 11, 12, 13, 14, 15, 17, 18,
23, 24, 27, 29] # no h-bonds
}
try:
kwargs['multip'] = multip
except NameError:
kwargs['multip'] = 1.0
clay_idcs = set()
for idx in range(9):
clay_idcs.update(set(range(1 + idx*5380, 721 + idx*5380)))
orientation_agg = {}
for idx, fname in enumerate(fnames):
print(idx + 1, '/', len(fnames))
current_orientation = single_z_profile(DatafileContent(fname),
clay_idcs=clay_idcs)
for k, v in current_orientation.items():
try:
orientation_agg[k][0] += v[0]
orientation_agg[k][1] += v[1]
except KeyError:
orientation_agg[k] = [v[0], v[1]]
xs = sorted(orientation_agg.keys())
ys = [orientation_agg[x][0] / orientation_agg[x][1] for x in xs]
xs = [x / multip for x in xs]
exspressiveness_abs_sum = 0
exspressiveness_sq_sum = 0
for y in ys:
raise NotImplementedError()
elif system_name == 'pa6x20':
from utils.monomers_cms import monomers_cms
from plotters.plot_data import plot_data
data_dir = ('/media/anton/Seagate Expansion Drive/'
'md_new_data/pa6x20/3507904_500K_pz100/datafiles')
fnames = [
'{0}/pa6x20.{1}.data'.format(data_dir, idx * 50000)
for idx in range(1, 51)
]
clay_idcs = set()
else:
print('Unknown system name:', sys.argv[1])
sys.exit()
dfc_start = DatafileContent(fnames[0])
dfc_end = DatafileContent(fnames[-1])
lx = dfc_start.xhi - dfc_start.xlo
ly = dfc_start.yhi - dfc_start.ylo
lz = dfc_start.zhi - dfc_start.zlo
start_positions = {
a['atom_id']: {
'x': a['x'] + a['nx'] * lx,
'y': a['y'] + a['ny'] * ly,
'z': a['z'] + a['nz'] * lz
}
for a in dfc_start.atoms
}
end_positions = {
a['atom_id']: {
'x': a['x'] + a['nx'] * lx,
8: 1.007970, # ho
9: 14.006700, # n4
10: 12.011150, # c2
11: 12.011150, # c3
12: 1.007970, # h
13: 1.007970, # hn
14: 12.011150, # c'
15: 15.999400, # o'
16: 14.006700, # n2
17: 14.006700, # n
}
density_agg = {}
for idx, fname in enumerate(fnames):
print(idx + 1, '/', len(fnames))
new_profile = single_z_profile_partial(DatafileContent(fname),
**kwargs)
for k, v in new_profile.items():
try:
density_agg[k]['clay'] += v['clay']
density_agg[k]['modifier'] += v['modifier']
density_agg[k]['polymer'] += v['polymer']
except KeyError:
try:
density_agg[k]['clay'] = v['clay']
density_agg[k]['modifier'] = v['modifier']
density_agg[k]['polymer'] = v['polymer']
except KeyError:
density_agg[k] = {
'clay': v['clay'],
'modifier': v['modifier'],
'10chains/2.2 - More relaxation 500 (wiggle)/'
'1785842 - relaxation')
fnames = [
'{0}/co.{1}.data'.format(data_dir, idx * 50000)
for idx in range(1, 51)
]
clay_idcs = set()
for idx in range(9):
clay_idcs.update(set(range(1 + idx * 5380, 721 + idx * 5380)))
kwargs = {'clay_idcs': clay_idcs, 'multip': multip}
plot_kwargs = {
'out_fname': 'atoms_mob_L.eps',
}
profile_agg = {}
f = open('logs/atomic_mobility_L', 'w')
dfc_last = DatafileContent(fnames[0])
dfc_next = DatafileContent(fnames[-1])
profile = atomic_mobility_profile(dfc_last, dfc_next, **kwargs)
xs = sorted(profile.keys())
ys = [profile[x][0] / profile[x][1] for x in xs]
plot_data(xs, ys=ys, **plot_kwargs)
elif system_name == 'S': # Too small data
raise NotImplementedError()
elif system_name == 'mix':
raise NotImplementedError()
elif system_name == 'seg':
raise NotImplementedError()
elif system_name == 'pa6x20':
from utils.monomers_cms import monomers_cms
from plotters.plot_data import plot_data
data_dir = ('/media/anton/Seagate Expansion Drive/'
6: 14.0067,
7: 14.0067,
8: 12.0112
}
kwargs = {
'masses': masses,
}
try:
kwargs['multip'] = multip
except NameError:
kwargs['multip'] = 1.0
plot_kwargs = {
'out_fname': 'dp_comp_pa6x20w.pdf',
'x_limits': [0, 45],
'y_limits': [0, 1.5]
}
else:
print('Unknown system name:', sys.argv[1])
sys.exit()
density_agg = Counter()
for idx, fname in enumerate(fnames):
print(idx + 1, '/', len(fnames))
density_agg += single_z_profile(DatafileContent(fname), **kwargs)
xs = sorted(density_agg.keys())
ys = [density_agg[x]/len(fnames) for x in xs]
xs = [x / multip for x in xs]
plot_data(xs, ys=ys, **plot_kwargs)
11: 12.011150, # c3
12: 1.007970, # h
13: 1.007970, # hn
14: 12.011150, # c'
15: 15.999400, # o'
16: 14.006700, # n2
17: 14.006700, # n
}
plot_kwargs = {
'out_fname': 'mon_mob_L.eps',
}
plot_log_kwargs = {
'out_fname': 'mon_mob_L_log.eps',
}
starting = monomers_cms(DatafileContent(fnames[0]), masses,
monomer_idx)
f = open('logs/monomers_mobility_L', 'w')
xs = []
ys = []
for idx, fname in enumerate(fnames):
dfc = DatafileContent(fname)
lx = dfc.xhi - dfc.xlo
ly = dfc.yhi - dfc.ylo
lz = dfc.zhi - dfc.zlo
time = idx * 50 # ps
current = monomers_cms(dfc, masses, monomer_idx)
delta = 0
for k in current.keys():
dx = abs(current[k]['x_cm'] - starting[k]['x_cm'])
dy = abs(current[k]['y_cm'] - starting[k]['y_cm'])