########## Main ###########
myfile = open('mol_remain.txt', 'r')
res_targ = []
for line in myfile:
res_targ.append([int(i) for i in line.split()])
traj_name, traj0, topology = comm.load_traj()
para = comm.load_para()
#res_targ, res_name = comm.select_groups(traj0)
massind, chargeind = comm.load_atomic(res_targ, topology, para)
bin_size = comm.bin_size
dt = comm.dt
nframe = comm.args.nframe - 1
xyz_pre = comm.calc_xyz_com(res_targ, traj0, topology, para)
vc = [[[] for row in range(nframe - nframe / 2 + 1)] for _ in res_targ]
base = [[[] for row in range(nframe - nframe / 2 + 1)] for _ in res_targ]
vel_ref = []
chunk_size = 100
for chunk_index, traj in enumerate(
md.iterload(traj_name, chunk=chunk_size, top='topol.pdb')):
for sub_ind, frame in enumerate(traj):
frame_ind = chunk_index * chunk_size + sub_ind
if frame_ind == 0:
continue
box = frame.unitcell_lengths[0, :]
xyz_com = comm.calc_xyz_com(res_targ, frame, topology, para)
vel = [[] for _ in res_targ]
for res_ind, xyz_res in enumerate(xyz_com):
vel[res_ind] = xyz_res[:, :2] - xyz_pre[res_ind][:, :2]
#!/Users/yuzhang/anaconda3/bin/python
# Filename: calc_com_OLC.py
# Description: This is a python script that calculates the center of mass
# coordinates of onion like carbon in an supercapacitor
# system
# Date: 11-22-2017 Created
import calc_common as comm
import mdtraj as md
print('Reading input file', comm.args.filename)
traj = md.load(comm.args.filename)
para = comm.load_para()
res_targ, res_name = comm.select_groups(traj)
xyz_com = comm.calc_xyz_com(res_targ, traj, traj.topology, para)
print('The center of the group:', )
for i in xyz_com:
print(i)
i = 0
avg = xyz_com[0][0]
for i in range(1, len(xyz_com)):
avg += xyz_com[i][0]
print(avg / (i + 1))
fsize = 28
########## Main ###########
traj_name, traj0, topology = comm.load_traj()
para = comm.load_para()
res_targ, res_name = comm.select_groups(traj0)
massind, chargeind = comm.load_atomic(res_targ, topology, para)
direction = comm.direction
bin_size = comm.bin_size
bound = comm.load_bound(traj0, direction)
n_all = [[[] for row in range(len(res_targ))] for row in range(4)]
chunk_size = 100
for chunk_index, traj in enumerate(md.iterload(traj_name, chunk = chunk_size, top = 'topol.pdb')):
for sub_ind, frame in enumerate(traj):
xyz_com = comm.calc_xyz_com(res_targ, frame, topology, para)
for j, item in enumerate(xyz_com):
for i in range(4):
n_all[i][j].append(0)
for xyz in item[:, direction]:
if xyz >= 1 and xyz <= 13:
n_all[0][j][-1] += 1
elif xyz > 13 and xyz < 20:
n_all[1][j][-1] += 1
elif xyz >= 20 and xyz<= 32:
n_all[2][j][-1] += 1
else:
n_all[3][j][-1] += 1
if sub_ind%10 == 9:
print 'Reading chunk', chunk_index+1, 'and frame',chunk_index*chunk_size+sub_ind+1
# if chunk_index == 0:
import calc_common as comm
lwidth = 4
fsize = 28
########## Main ###########
traj_name, traj0, topology = comm.load_traj()
para = comm.load_para()
res_targ, res_name = comm.select_groups(traj0)
massind, chargeind = comm.load_atomic(res_targ, topology, para)
direction = comm.direction
bin_size = comm.bin_size
bound = comm.load_bound(traj0, direction)
last_frame = md.load_frame('last_frame.xtc', 0, top = 'topol.pdb')
xyz_com = comm.calc_xyz_com(res_targ, last_frame, topology, para)
res_sel = [[], []]
x_t = [[], []]
if comm.args.rev == False:
rev = 0
else:
rev = 1
bound_sel = [0, 12, 19, 31] # boundaries for slit 1 and slit 2
for i in range(2):
jdg = (i+rev)%2
for j, xyz in enumerate(xyz_com[i][:, direction]):
if xyz >= bound_sel[2*jdg] and xyz <= bound_sel[2*jdg+1]:
res_sel[jdg].append(res_targ[i][j])
x_t[jdg].append([])
