def analyzeData(d_cum_data):
l = []
for key in d_cum_data:
m, s = nu.meanstdv(d_cum_data[key])
l.append([key, m])
return l
def getSlipLength(bgf_file,
trj_file,
ff_file,
interval,
n_step,
n_avg_step,
silent=False):
"""
This calculates the profile of averaged velocity according to r.
NOTE: This is different from averaged velocity profile according to r.
"""
# const
PI = math.pi
vdw_r_C = 1.7
# init
timestep = 0
l_timestep = []
line = []
n_header = 0
output = ""
t1 = 0
t2 = 0
# clock
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myPkl = open(
trj_file + ".profile.r_ave_vel-s" + str(n_step) + "k" + str(n_skip) +
".pickle", 'w')
#f_dump = open(trj_file + ".profile.r_ave_vel.dump", 'w')
#dump = "";
# how many steps to go?
n_timestep = len(lt.getTrjInfo(trj_file, silent=False))
if n_step == 0:
n_step = n_timestep
if not silent:
print("The trajectory contains " + str(n_timestep) + " timesteps.")
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
# Find header of the trajectory file
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [
line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0],
line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# for every shot in the trajectory file update BGF and manipulate
dumpatom = get_line(trj_file)
processed_step = 0
t1 = t2 = 0
elapsed_time = 0
# calculate radius_CNT
avg_radius_CNT = 0.0
x_CNT = 0.0
y_CNT = 0.0
if not silent:
print(
"Calculating the average radius of CNT throughout the averaging steps"
)
while 1:
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (n_step - processed_step)
### Read
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
# skip if necessary
if processed_step <= n_skip:
processed_step += 1
continue
timestep = int(chunk[1])
l_timestep.append(timestep)
natoms = int(chunk[3])
boxsize = [
chunk[5].split(' ')[0], chunk[5].split(' ')[1],
chunk[6].split(' ')[0], chunk[6].split(' ')[1],
chunk[7].split(' ')[0], chunk[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
sys.stdout.write('\r' + "Fetched timestep: " + str(timestep) +
" (Remaining time: " +
"{0:4.1f}".format(remaining_time) + " seconds, " +
"{0:4.1f} minutes".format(remaining_time / 60) + ")")
sys.stdout.flush()
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
try:
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
except:
pass
# apply periodic condition
#myBGF = bgftools.periodicMoleculeSort(myBGF, 0, True)
### myBGF update complete! ###
# for CNT atoms, calculate some properties
min_x_CNT = 0.0
max_x_CNT = 0.0
radius_CNT = 0.0
height_CNT = 0.0
aNo_WAT_O_not_in_CNT = []
temp = []
min_y_CNT = 0.0
max_y_CNT = 0.0
min_z_CNT = 0.0
max_z_CNT = 0.0
CNT_orientation = ""
l_radius_CNT = []
l_x_CNT = []
l_y_CNT = []
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
# center of CNT
l_x_CNT.append(atom.x)
l_y_CNT.append(atom.y)
# height
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
x_CNT, a = nu.meanstdv(l_x_CNT)
y_CNT, a = nu.meanstdv(l_y_CNT)
z_diff = max_z_CNT - min_z_CNT
# radius of CNT
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
l_radius_CNT.append(
math.sqrt((atom.x - x_CNT)**2 + (atom.y - y_CNT)**2))
radius_CNT, a = nu.meanstdv(l_radius_CNT)
l_avg_radius_CNT.append(radius_CNT)
if processed_step > 3:
break
avg_radius_CNT, s = nu.meanstdv(l_avg_radius_CNT)
bins = np.arange(0.0, math.ceil(radius_CNT), interval)
l_radial_vz_profile = np.zeros(len(bins) - 1)
if not silent:
print("\nAveraged CNT radius: " + str(avg_radius_CNT) + " A")
if not silent: print("CNT center: " + str([x_CNT, y_CNT]))
# calculate properties
myTRJ.close()
myTRJ = open(trj_file)
myTRJ.seek(0)
dumpatom = get_line(trj_file)
processed_step = 0
r = []
vz = []
# data container
while 1:
data = dict()
# stores [r vz] for a timestep
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (n_step - processed_step)
### Read
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
if processed_step <= n_skip:
processed_step += 1
continue
timestep = int(chunk[1])
l_timestep.append(timestep)
natoms = int(chunk[3])
boxsize = [
chunk[5].split(' ')[0], chunk[5].split(' ')[1],
chunk[6].split(' ')[0], chunk[6].split(' ')[1],
chunk[7].split(' ')[0], chunk[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
sys.stdout.write('\r' + "Fetched timestep: " + str(timestep) +
" (Remaining time: " +
"{0:4.1f}".format(remaining_time) + " seconds, " +
"{0:4.1f} minutes".format(remaining_time / 60) + ")")
sys.stdout.flush()
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die(
"Number of atoms in trajectory file does not match with BGF file."
)
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
atom.vx = float(atomcoord[5])
atom.vy = float(atomcoord[6])
atom.vz = float(atomcoord[7])
try:
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
except:
pass
#nu.warn("Crystal information error: is this file not periodic?")
# apply periodic condition
myBGF = bgftools.periodicMoleculeSort(myBGF, 0, True)
### myBGF update complete! ###
# calculate z-directional velocity of water molecules wrt r vcm = sum vi mi / sum mi
atom = myBGF.getAtom(aNo_WAT_O[0])
mass_O = bgftools.getMass(myBGF, [aNo_WAT_O[0]], ff_file)
atom = myBGF.getAtom(atom.CONECT[0])
mass_H = bgftools.getMass(myBGF, [atom.aNo], ff_file)
mass_H2O = mass_O + 2 * mass_H # H2O mass
for ano in aNo_WAT_O:
atom = myBGF.getAtom(ano) # oxygen
# com & velocity calculation
cmx = atom.x * mass_O
cmy = atom.y * mass_O
vcmz = atom.vz * mass_O
for ano2 in atom.CONECT:
atom2 = myBGF.getAtom(ano2)
cmx += atom2.x * mass_H
cmy += atom2.y * mass_H
vcmz += atom2.vz * mass_H
cmx /= mass_H2O
cmy /= mass_H2O
vcmz /= mass_H2O
dist = math.sqrt((x_CNT - cmx)**2 + (y_CNT - cmy)**2)
r.append(dist)
vz.append(vcmz * 10**5) # LAMMPS real unit conversion for velocity
# timestep mark for starting average
if l_avg_count == []:
n_avg_count_step = timestep
l_avg_count.append(timestep)
# if the time has come.. average!
if len(l_avg_count) == n_avg_step or processed_step == n_timestep - 1:
if not silent:
print(" Averaging invoked at timestep " + str(timestep) +
" (" + str(len(l_avg_count)) + " points)")
# binning
vz = np.array(vz)
sum_vz = np.ma.array(np.histogram(r, bins, weights=vz)[0])
sum_vz2 = np.ma.array(np.histogram(r, bins, weights=vz * vz)[0])
n_vz = np.ma.array(np.histogram(r, bins)[0])
#mask_n = ma.masked_values(n_vz, 0)
mean = sum_vz / n_vz
std = np.sqrt(sum_vz2 / n_vz - mean * mean)
mean = np.ma.fix_invalid(mean, fill_value=0.0).data
std = np.ma.fix_invalid(std, fill_value=0.0).data
n_vz = np.ma.fix_invalid(n_vz, fill_value=0).data
if len(mean) != len(bins) - 1 or len(std) != len(bins) - 1:
nu.die("on numpy masked_array calculation!")
l_result.append([l_avg_count, bins, n_vz, mean, std])
# reset
r = []
vz = []
l_radial_vz_profile = np.zeros(len(bins) - 1)
l_avg_count = []
t2 = time.time() # time mark
elapsed_time = t2 - t1
processed_step += 1
#f_dump.write(dump)
pkl.dump(l_result, myPkl)
print('')
return 1
def getVelocity(bgf_file, trj_file, n_step, silent=False):
# const
PI = math.pi
vdw_r_C = 1.7
# init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
l_data = []
# stores vz
l_avg_radius_CNT = []
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
ftemp = open("countWater42.profile", 'w')
ftemp.write(str(sys.argv) + "\n")
curr_dir = os.path.abspath(".")
temp_dir = curr_dir + "/CountWAT42/"
if not os.path.isdir(temp_dir): os.makedirs(temp_dir)
# how many steps to go?
n_timestep = len(lt.getTrjInfo(trj_file))
if n_step == 0:
n_step = n_timestep
print(" ..The trajectory contains " + str(n_timestep) + " timesteps.")
print("The script will proceed for the last " + str(n_step) +
" timesteps.")
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
for atom in myBGF.a:
# Carbons in CNT or atoms in BNNT
if "NT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
# Find header of the trajectory file
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [
line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0],
line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# for every shot in the trajectory file update BGF and manipulate
dumpatom = get_line(trj_file)
processed_step = 0
t1 = t2 = 0
elapsed_time = 0
while 1:
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (n_step - processed_step)
sys.stdout.write('\r' + "Reading timestep.. " + str(timestep) +
" (Remaining time: " +
"{0:4.1f}".format(remaining_time) + " seconds, " +
"{0:4.1f} minutes".format(remaining_time / 60) + ")")
sys.stdout.flush()
if processed_step == n_step:
break
### Read
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
timestep = int(chunk[1])
natoms = int(chunk[3])
boxsize = [
chunk[5].split(' ')[0], chunk[5].split(' ')[1],
chunk[6].split(' ')[0], chunk[6].split(' ')[1],
chunk[7].split(' ')[0], chunk[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die(
"Number of atoms in trajectory file does not match with BGF file."
)
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
atom.vx = float(atomcoord[5])
atom.vy = float(atomcoord[6])
atom.vz = float(atomcoord[7])
if myBGF.CRYSTX != []:
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
else:
nu.warn("Crystal information error: is this file not periodic?")
for i in range(0, 3):
myBGF.CRYSTX.append(boxsize[i])
### myBGF update complete! ###
### align CNT to z axis
# initialize for the moment of inertia and the center of mass calculation
U = 0
Ut = 0
Uv = 0
Ixx = 0
Ixy = 0
Ixz = 0
Iyx = 0
Iyy = 0
Iyz = 0
Izx = 0
Izy = 0
Izz = 0
Mx = 0
My = 0
Mz = 0
# set COM of CNT as origin
Mx = 0
My = 0
Mz = 0
# Center of mass of CNT
for atom in myBGF.a:
if "NT" in atom.rName:
Mx += atom.x / N_CNT
My += atom.y / N_CNT
Mz += atom.z / N_CNT
for atom in myBGF.a:
atom.x -= Mx # move
atom.y -= My
atom.z -= Mz
# calculate the moment of inertia (MI) and the center of mass (COM) of CNT from "myBGF"
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
Ixx += (atom.y**2 + atom.z**2) / N_CNT
Iyy += (atom.x**2 + atom.z**2) / N_CNT
Izz += (atom.x**2 + atom.y**2) / N_CNT
Ixy -= (atom.x * atom.y) / N_CNT
Ixz -= (atom.x * atom.z) / N_CNT
Iyz -= (atom.y * atom.z) / N_CNT
# the moment of inertia tensor
I = np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]])
# eigenvalue & eigenvector calculation
eigval, eigvec = np.linalg.eig(
I) # eigval[0] is the minimum among the values.
# rearrange the U vector
U = np.matrix(eigvec)
Ut = U.T
# "myBGF" rotation
for atom in myBGF.a:
v = np.matrix([atom.x, atom.y, atom.z]).T
Uv = Ut * v
atom.x = float(Uv[2])
atom.y = float(Uv[1])
atom.z = float(Uv[0])
#dimension = np.matrix(boxsize).T
#boxsize_prime = np.array(np.dot(Ut, dimension).T)
boxsize_prime = np.transpose(
np.dot(Ut,
np.transpose(np.array(boxsize)))) # new pbc from jackjack5
print(boxsize)
print(boxsize_prime)
# move atoms to box center
for atom in myBGF.a:
atom.x -= boxsize_prime[0] / 2
atom.y -= boxsize_prime[1] / 2
atom.z -= boxsize_prime[2] / 2
myBGF.saveBGF(temp_dir + bgf_file.split(".bgf")[0] + "." +
str(timestep) + ".beforepbc.bgf")
myBGF = bgftools.periodicMoleculeSort(myBGF, 0, myBGF.CRYSTX)
myBGF.saveBGF(temp_dir + bgf_file.split(".bgf")[0] + "." +
str(timestep) + ".bgf")
# for CNT atoms, calculate some properties
min_x_CNT = 1000.0
max_x_CNT = -1000.0
radius_CNT = 0.0
height_CNT = 0.0
min_y_CNT = 1000.0
max_y_CNT = -1000.0
min_z_CNT = 1000.0
max_z_CNT = -1000.0
l_radius_CNT = []
l_x_CNT = []
l_y_CNT = []
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
# center of CNT
l_x_CNT.append(atom.x)
l_y_CNT.append(atom.y)
# height
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
x_CNT, a = nu.meanstdv(l_x_CNT)
y_CNT, a = nu.meanstdv(l_y_CNT)
z_diff = max_z_CNT - min_z_CNT
height_CNT = z_diff
# radius of CNT
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
l_radius_CNT.append(
math.sqrt((atom.x - x_CNT)**2 + (atom.y - y_CNT)**2))
radius_CNT, a = nu.meanstdv(l_radius_CNT)
l_avg_radius_CNT.append(radius_CNT)
### get water molecules in CNT
# inside the CNT := min_z_CNT <= z <= max_z_CNT and (x - (x_diff/2))**2 + (y - (y_diff/2))**2 < radius_CNT**2
# aNo_WAT_O_atoms: molecules which O atom is within CNT
# we don't need to calculate H atoms. Let's consider only O atoms
margin = 0.0
# water molecules far from the margin will be only considered
aNo_WAT_O_in_CNT = []
for aNo in aNo_WAT_O:
atom = myBGF.getAtom(aNo)
dist_sq = (atom.x - x_CNT)**2 + (atom.y - y_CNT)**2
if "WAT" in atom.rName and "O" in atom.ffType and min_z_CNT + margin <= atom.z and atom.z <= max_z_CNT - margin and dist_sq < radius_CNT**2:
aNo_WAT_O_in_CNT.append(aNo)
else:
pass
### record number of water molecules in CNT
#l_data.append([timestep, len(aNo_WAT_O_in_CNT), radius_CNT, z_diff])
#output = str(timestep) + '\t' + str(len(aNo_WAT_O_in_CNT)) + '\t' + str(radius_CNT) + '\t' + str(z_diff) + '\n'
output = str(timestep) + '\t' + str(
len(aNo_WAT_O_in_CNT)) + '\t' + str(radius_CNT) + '\t' + str(
min_z_CNT) + '\t' + str(max_z_CNT) + '\t' + str(
z_diff) + '\t' + str(height_CNT) + '\t' + str(
len(aNo_CNT)) + '\n' # debug
ftemp.write(output)
#sys.stdout.write('Done ')
sys.stdout.flush()
t2 = time.time() # time mark
elapsed_time = t2 - t1
processed_step += 1
print('')
ftemp.close()
print(
"numbers of water molecules are written in countWater.profile ..Done.")
return 1
def getVelocity(bgf_file, trj_file, n_step, silent=False):
# const
PI = math.pi
vdw_r_C = 1.7
# init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
l_data = []
# stores vz
l_avg_radius_CNT = []
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
# how many steps to go?
n_timestep = len(lt.getTrjInfo(trj_file))
if n_step == 0:
n_step = n_timestep
print("The trajectory contains " + str(n_timestep) + " timesteps.")
print("The script will proceed for the last " + str(n_step) +
" timesteps.")
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
# Find header of the trajectory file
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [
line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0],
line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# for every shot in the trajectory file update BGF and manipulate
dumpatom = get_line(trj_file)
processed_step = 0
t1 = t2 = 0
elapsed_time = 0
while 1:
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (n_step - processed_step)
sys.stdout.write('\r' + "Reading timestep.. " + str(timestep) +
" (Remaining time: " +
"{0:4.1f}".format(remaining_time) + " seconds, " +
"{0:4.1f} minutes".format(remaining_time / 60) + ")")
sys.stdout.flush()
if processed_step == n_step:
break
### Read
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
timestep = int(chunk[1])
natoms = int(chunk[3])
boxsize = [
chunk[5].split(' ')[0], chunk[5].split(' ')[1],
chunk[6].split(' ')[0], chunk[6].split(' ')[1],
chunk[7].split(' ')[0], chunk[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die(
"Number of atoms in trajectory file does not match with BGF file."
)
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
del (chunk)
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
atom.vx = float(atomcoord[5])
atom.vy = float(atomcoord[6])
atom.vz = float(atomcoord[7])
try:
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
except:
pass
#nu.warn("Crystal information error: is this file not periodic?")
# apply periodic condition
myBGF = bgftools.periodicMoleculeSort(myBGF, 0, True)
### myBGF update complete! ###
#aNo_WAT_O_in_CNT = copy.deepcopy(aNo_WAT_O)
# for CNT atoms, calculate some properties
min_x_CNT = 1000.0
max_x_CNT = -1000.0
radius_CNT = 0.0
height_CNT = 0.0
temp = []
min_y_CNT = 1000.0
max_y_CNT = -1000.0
min_z_CNT = 1000.0
max_z_CNT = -1000.0
CNT_orientation = ""
l_radius_CNT = []
l_x_CNT = []
l_y_CNT = []
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
# center of CNT
l_x_CNT.append(atom.x)
l_y_CNT.append(atom.y)
# height
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
x_CNT, a = nu.meanstdv(l_x_CNT)
y_CNT, a = nu.meanstdv(l_y_CNT)
z_diff = max_z_CNT - min_z_CNT
# radius of CNT
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
l_radius_CNT.append(
math.sqrt((atom.x - x_CNT)**2 + (atom.y - y_CNT)**2))
radius_CNT, a = nu.meanstdv(l_radius_CNT)
l_avg_radius_CNT.append(radius_CNT)
### get water molecules in CNT
# inside the CNT := min_z_CNT <= z <= max_z_CNT and (x - (x_diff/2))**2 + (y - (y_diff/2))**2 < radius_CNT**2
# aNo_WAT_O_atoms: molecules which O atom is within CNT
# we don't need to calculate H atoms. Let's consider only O atoms
margin = 0.0
# water molecules far from the margin will be only considered
aNo_WAT_O_in_CNT = []
for aNo in aNo_WAT_O:
atom = myBGF.getAtom(aNo)
dist_sq = (atom.x - x_CNT)**2 + (atom.y - y_CNT)**2
if "WAT" in atom.rName and "O" in atom.ffType and min_z_CNT + margin <= atom.z and atom.z <= max_z_CNT - margin and dist_sq < radius_CNT**2:
aNo_WAT_O_in_CNT.append(aNo)
else:
pass
### record number of water molecules in CNT
l_data.append([timestep, len(aNo_WAT_O_in_CNT), radius_CNT, z_diff])
#sys.stdout.write('Done ')
#sys.stdout.flush()
t2 = time.time() # time mark
elapsed_time = t2 - t1
processed_step += 1
print('')
ftemp = open("countWater.profile", 'w')
ftemp.write(str(sys.argv))
for i in l_data:
output = str(i[0]) + '\t' + str(i[1]) + '\t' + str(i[2]) + '\t' + str(
i[3]) + '\n'
ftemp.write(output)
ftemp.close()
print(
"numbers of water molecules are written in countWater.profile ..Done.")
return 1
def main():
filename = forceFile
v = read_value(filename)
nv = len(v)
t = numpy.arange(0, nv - 1, step)
result = []
result2 = []
output = ""
### calculate constants
reff = R - 0.5 * sOC
A = 2 * pi * reff * L
A *= 1e-20
C = 1 / kb / T / A
output += "Version " + str(version) + "\n"
output += "Parameters\n"
output += "R" + '\t' + str(R) + '\t' + \
"r_eff" + '\t' + str(reff) + '\t' + \
"area" + '\t' + str(A) + '\t' + \
"coeff" + '\t' + str(C) + '\n'
output += str("t") + '\t' + str("int fac") + '\t' + str("l") + '\t' + str(
"b") + '\n'
### calculate AC
print("Reading force file and calculating autocorrelation function..")
print(str(t))
for i in t:
if i + averageStep <= nv:
temp_v = v[i:i + averageStep]
temp_acs = ac(temp_v)
result.append(temp_acs)
### test for vac
for index, i in enumerate(result):
print "** timestep ", t[index]
a = scipy.integrate.cumtrapz(i, dx=2e-15) # integration
a2, _ = nu.meanstdv(a[averageACStep:])
a2 *= (6.95e-11)**2 # kcal/mol.m -> J/m
print "\t- integrated force AC=", a2
l = C * a2
print "\t- lambda=", l
b = u / l
print "\t- slip length (m)=", b
b *= 1e9
print "\t- slip length (nm)=", b
result2.append(b)
output += str(
t[index]) + '\t' + str(a2) + '\t' + str(l) + '\t' + str(b) + '\n'
### write output file
fname = outFilePrefix + ".a." + str(averageStep) + ".s." + str(
sampleStep) + ".n." + str(step) + ".t." + str(averageACStep)
f_out = open(fname + ".out", 'w')
f_out.write(str(sys.argv) + "\n")
f_out.write(output)
f_out.close()
### print averaged slip length
m, _ = nu.meanstdv(result2)
print "averaged slip length=", m, _
### write dump file
f_dump = open(fname + ".dump", 'w')
output = "\t"
# timesteps
for i in t:
output += str(i) + "\t"
output += "\n"
# result
for r, row in enumerate(result[0]):
output += str(r) + "\t"
for c, col in enumerate(result):
output += str(result[c][r]) + "\t"
output += "\n"
f_dump.write(output)
f_dump.close()
return 1
def getVelocity(bgf_file, trj_file, n_step, silent=False):
# const
PI = math.pi
vdw_r_C = 1.7
# init
timestep = 0; l_timestep = []; line = []; n_header = 0;
t1 = 0; t2 = 0; # clock
interval = 0.1;
l_data = []; # stores vz
l_avg_radius_CNT = [];
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
# how many steps to go?
wc_trj_file = popen("grep TIMESTEP " + trj_file + " | wc -l ").read()
n_timestep = int(wc_trj_file.split()[0]);
print("The trajectory contains " + str(n_timestep) + " timesteps.")
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
# Find header of the trajectory file
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break;
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0], line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# for every shot in the trajectory file update BGF and manipulate
dumpatom = get_line(trj_file)
processed_step = 0;
t1 = t2 = 0; elapsed_time = 0;
while 1:
### Show progress
sys.stdout.write('\r' + "Reading timestep.. " + str(timestep) )
sys.stdout.flush()
### Read
try:
chunk = [next(dumpatom) for i in range(natoms+n_header)]
except StopIteration:
break;
timestep = int(chunk[1])
natoms = int(chunk[3])
boxsize = [chunk[5].split(' ')[0], chunk[5].split(' ')[1], chunk[6].split(' ')[0], chunk[6].split(' ')[1], chunk[7].split(' ')[0], chunk[7].split(' ')[1]];
boxsize = [float(i) for i in boxsize]; boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]), (boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
if timestep != n_step:
continue;
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die("Number of atoms in trajectory file does not match with BGF file.")
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
atom.vx = float(atomcoord[5])
atom.vy = float(atomcoord[6])
atom.vz = float(atomcoord[7])
try:
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
except:
pass;
#nu.warn("Crystal information error: is this file not periodic?")
# apply periodic condition
myBGF = bgftools.periodicMoleculeSort(myBGF, 0, True)
### myBGF update complete! ###
#aNo_WAT_O_in_CNT = copy.deepcopy(aNo_WAT_O)
### align CNT to z axis
# initialize for the moment of inertia and the center of mass calculation
U = 0; Ut = 0; Uv = 0;
Ixx = 0; Ixy = 0; Ixz = 0;
Iyx = 0; Iyy = 0; Iyz = 0;
Izx = 0; Izy = 0; Izz = 0;
Mx = 0; My = 0; Mz = 0;
# transpose for "all atoms in BGF": move COM of CNT as origin
# com of CNT
Mx = 0; My = 0; Mz = 0;
for atom in myBGF.a:
if "CNT" in atom.rName:
Mx += atom.x / N_CNT
My += atom.y / N_CNT
Mz += atom.z / N_CNT
# move
for atom in myBGF.a:
atom.x -= Mx
atom.y -= My
atom.z -= Mz
# calculate the moment of inertia (MI) and the center of mass (COM) of CNT from "myBGF"
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
Ixx += (atom.y**2 + atom.z**2) / N_CNT
Iyy += (atom.x**2 + atom.z**2) / N_CNT
Izz += (atom.x**2 + atom.y**2) / N_CNT
Ixy -= (atom.x * atom.y) / N_CNT
Ixz -= (atom.x * atom.z) / N_CNT
Iyz -= (atom.y * atom.z) / N_CNT
# the moment of inertia tensor
I = np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]])
# eigenvalue & eigenvector calculation
eigval, eigvec = np.linalg.eig(I) # eigval[0] is the minimum among the values.
# rearrange the U vector
U = np.matrix(eigvec)
Ut = U.T
# "myBGF" rotation
for atom in myBGF.a:
v = np.matrix([atom.x, atom.y, atom.z]).T
Uv = Ut * v
atom.x = float(Uv[1])
atom.y = float(Uv[2])
atom.z = float(Uv[0])
# for CNT atoms, calculate some properties
min_x_CNT = 1000.0; max_x_CNT = -1000.0; radius_CNT = 0.0; height_CNT = 0.0; temp = [];
min_y_CNT = 1000.0; max_y_CNT = -1000.0;
min_z_CNT = 1000.0; max_z_CNT = -1000.0;
CNT_orientation = "";
l_radius_CNT = [];
l_x_CNT = [];
l_y_CNT = [];
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
# center of CNT
l_x_CNT.append(atom.x)
l_y_CNT.append(atom.y)
# height
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
x_CNT, a = nu.meanstdv(l_x_CNT)
y_CNT, a = nu.meanstdv(l_y_CNT)
z_diff = max_z_CNT - min_z_CNT
# radius of CNT
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
l_radius_CNT.append( math.sqrt( (atom.x - x_CNT)**2 + (atom.y - y_CNT)**2 ))
radius_CNT, a = nu.meanstdv(l_radius_CNT)
l_avg_radius_CNT.append(radius_CNT)
### get water molecules in CNT
# inside the CNT := min_z_CNT <= z <= max_z_CNT and (x - (x_diff/2))**2 + (y - (y_diff/2))**2 < radius_CNT**2
# aNo_WAT_O_atoms: molecules which O atom is within CNT
# we don't need to calculate H atoms. Let's consider only O atoms
margin = 0.0; # water molecules far from the margin will be only considered
aNo_WAT_O_in_CNT = []
aNo_WAT_O_not_in_CNT = []
myBGF2 = copy.deepcopy(myBGF)
# delete graphenes
for atom in myBGF2.a:
if "GRA" in atom.rName:
aNo_WAT_O_not_in_CNT.append(myBGF.a2i[atom.aNo])
# delete water molecules
for aNo in aNo_WAT_O:
atom = myBGF.getAtom(aNo)
dist_sq = (atom.x - x_CNT)**2 + (atom.y - y_CNT)**2
if "WAT" in atom.rName and "O" in atom.ffType and min_z_CNT + margin <= atom.z and atom.z <= max_z_CNT - margin and dist_sq < radius_CNT**2:
aNo_WAT_O_in_CNT.append(aNo)
else:
delete_list = [];
dummy = bgftools.getmolecule(myBGF, myBGF.getAtom(aNo), delete_list)
for i in delete_list:
aNo_WAT_O_not_in_CNT.append(myBGF.a2i[i])
myBGF2.delAtoms(aNo_WAT_O_not_in_CNT)
myBGF2.renumber()
myBGF2.saveBGF(bgf_file[:-4] + "." + str(timestep) + "." + str(len(aNo_WAT_O_in_CNT)) + ".bgf")
sys.stdout.write('Done ')
sys.stdout.flush()
print(len(aNo_WAT_O_in_CNT))
processed_step += 1;
print('')
return 1
def main():
usage = """This script averages the data which has rows in 'step number', usually from LAMMPS profile.
Usage: reduceText.py input output Nevery Nrepeat Nfreq
With (Nevery, Nrepeat, Nfreq) == (2, 6, 100), the following will be averaged:
[90, 92, 94, 96, 98, 100] --> 100
[190, 192, 194, 196, 198, 200] --> 200
...
"""
if len(sys.argv) < 2:
print("Usage: " + str(sys.argv[0]) +
" input output Nevery Nrepeat Nfreq")
sys.exit(0)
infile = sys.argv[1]
outfile = sys.argv[2]
n_every = int(sys.argv[3])
n_repeat = int(sys.argv[4])
n_freq = int(sys.argv[5])
ifs = open(infile)
ofs = open(outfile, 'w')
n_count = 0
# main counter
output = ""
temp = []
while 1:
line = ifs.readline()
if not line:
break
if line[0] == "#":
continue
parse = line.split()
step = int(parse[0])
value = float(parse[1])
n_count += 1
if n_count <= n_freq:
#temp.append(step); #test
temp.append(value)
else:
#temp.append(step); #test
#print(temp) #test
#print(temp[::n_every][-n_repeat:]) #test
temp.append(value)
m, _ = nu.meanstdv(temp[::n_every][-n_repeat:]) # average
if _ != 0.0:
output += str(parse[0]) + '\t' + str(m) + '\t' + str(_) + '\n'
else:
output += str(parse[0]) + '\t' + str(m) + '\n'
# initialize
temp = [0]
n_count = 1
ofs.write(output)
print("File is written in " + outfile + " ...")
def countWaterCNT(bgf_file, trj_file, fixed, silent):
# init
timestep = 0; l_timestep = []; line = []; n_header = 0; output = ""; radius_CNTs = [];
t1 = 0; t2 = 0; # clock
radius_CNT = 0.0;
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
# how many steps to go?
#wc_trj_file = popen("grep TIMESTEP " + trj_file + " | wc -l ").read()
#n_timestep = int(wc_trj_file.split()[0]);
n_timestep = len(lt.getTrjInfo(trj_file))
print("The trajectory contains " + str(n_timestep) + " timesteps.")
# extract aNos of CNT in the BGF file
aNo_CNT = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# Find header of the trajectory file
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break;
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0], line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# for every shot in the trajectory file update BGF and manipulate
dumpatom = get_line(trj_file)
processed_step = 0;
t1 = t2 = 0; elapsed_time = 0;
while 1:
try:
chunk = [next(dumpatom) for i in range(natoms+n_header)]
except StopIteration:
break;
timestep = int(chunk[1])
natoms = int(chunk[3])
boxsize = [chunk[5].split(' ')[0], chunk[5].split(' ')[1], chunk[6].split(' ')[0], chunk[6].split(' ')[1], chunk[7].split(' ')[0], chunk[7].split(' ')[1]];
boxsize = [float(i) for i in boxsize]; boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]), (boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
### Show progress
t1 = time.time();
remaining_time = elapsed_time * (n_timestep - processed_step)
sys.stdout.write('\r' + "Reading timestep.. " + str(timestep) + " (Elapsed time for the previous step: " + "{0:4.1f}".format(elapsed_time) + " seconds, Remaining time: " + "{0:4.1f}".format(remaining_time) + " seconds = " + "{0:4.1f} minutes".format(remaining_time/60) + ") " + str(radius_CNT))
sys.stdout.flush()
processed_step += 1;
### if step is specified, then save only for that step.
if step != 0:
if timestep == step:
pass;
else:
continue;
else:
pass;
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die("Number of atoms in trajectory file does not match with BGF file.")
mode = ""
if 'xs' in keywords or 'ys' in keywords or 'zs' in keywords:
mode = 'scaled'
elif 'x' in keywords or 'y' in keywords or 'z' in keywords:
mode = 'normal'
elif 'xu' in keywords or 'yu' in keywords or 'zu' in keywords:
mode = 'unwrapped'
# actual coordinate
coordinfo = chunk[9:]
# assume that coordinfo is similar to ['id', 'type', 'xs', 'ys', 'zs', 'ix', 'iy', 'iz']
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
if mode == 'scaled':
atom.x = float(atomcoord[2]) * boxsize[0]
atom.y = float(atomcoord[3]) * boxsize[1]
atom.z = float(atomcoord[4]) * boxsize[2]
elif mode == 'unwrapped':
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
elif mode == 'normal':
try:
ix_index = keywords.index('ix')
iy_index = keywords.index('iy')
iz_index = keywords.index('iz')
except ValueError:
nu.warn("No image information no the trajectory file. Will be treated as unwrapped.")
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
else:
atom.x = (int(atomcoord[ix_index]) * boxsize[0]) + float(atomcoord[2])
atom.y = (int(atomcoord[iy_index]) * boxsize[1]) + float(atomcoord[3])
atom.z = (int(atomcoord[iz_index]) * boxsize[2]) + float(atomcoord[4])
try:
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
except:
pass;
#nu.warn("Crystal information error: is this file not periodic?")
# apply periodic condition
myBGF = bgftools.periodicMoleculeSort(myBGF, 0)
#myBGF.saveBGF(bgf_file[:-4] + "." + str(timestep) + ".trjupdated.bgf")
### myBGF update complete! ###
if not fixed:
### rotate cnt to x axis
# initialize for the moment of inertia and the center of mass calculation
U = 0; Ut = 0; Uv = 0;
Ixx = 0; Ixy = 0; Ixz = 0;
Iyx = 0; Iyy = 0; Iyz = 0;
Izx = 0; Izy = 0; Izz = 0;
Mx = 0; My = 0; Mz = 0;
# transpose for "all atoms in BGF": move COM of CNT as origin
# com of CNT
Mx = 0; My = 0; Mz = 0;
for atom in myBGF.a:
if "CNT" in atom.rName:
Mx += atom.x / N_CNT
My += atom.y / N_CNT
Mz += atom.z / N_CNT
# move
for atom in myBGF.a:
atom.x -= Mx
atom.y -= My
atom.z -= Mz
# calculate the moment of inertia (MI) and the center of mass (COM) of CNT from "myBGF"
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
Ixx += (atom.y**2 + atom.z**2) / N_CNT
Iyy += (atom.x**2 + atom.z**2) / N_CNT
Izz += (atom.x**2 + atom.y**2) / N_CNT
Ixy -= (atom.x * atom.y) / N_CNT
Ixz -= (atom.x * atom.z) / N_CNT
Iyz -= (atom.y * atom.z) / N_CNT
# the moment of inertia tensor
I = numpy.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]])
# eigenvalue & eigenvector calculation
eigval, eigvec = numpy.linalg.eig(I) # eigval[0] is the minimum among the values.
# rearrange the U vector
U = numpy.matrix(eigvec)
Ut = U.T
# "myBGF" rotation
for atom in myBGF.a:
v = numpy.matrix([atom.x, atom.y, atom.z]).T
Uv = Ut * v
atom.x = float(Uv[0])
atom.y = float(Uv[1])
atom.z = float(Uv[2])
# for CNT atoms, calculate some properties
min_x_CNT = 0.0; max_x_CNT = 0.0; height_CNT = 0.0; aNo_MtOH_C_not_in_CNT = []; temp = [];
min_y_CNT = 0.0; max_y_CNT = 0.0;
min_z_CNT = 0.0; max_z_CNT = 0.0;
CNT_orientation = "";
# check the orientation of CNT
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
# minimum and maximum x coord of CNT: this will be the height of CNT
if atom.x < min_x_CNT:
min_x_CNT = atom.x
if atom.x > max_x_CNT:
max_x_CNT = atom.x
if atom.y < min_y_CNT:
min_y_CNT = atom.y
if atom.y > max_y_CNT:
max_y_CNT = atom.y
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
x_diff = max_x_CNT - min_x_CNT
y_diff = max_y_CNT - min_y_CNT
z_diff = max_z_CNT - min_z_CNT
if x_diff > y_diff and x_diff > z_diff:
# CNT is aligned along x axis
height_CNT = x_diff
CNT_orientation = "x"
elif y_diff > x_diff and y_diff > z_diff:
# CNT is aligned along y axis
height_CNT = y_diff
CNT_orientation = "y"
elif z_diff > x_diff and z_diff > y_diff:
# CNT is aligned along z axis
height_CNT = z_diff
CNT_orientation = "z"
if CNT_orientation == "x":
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
radius_CNT += math.sqrt(atom.y**2 + atom.z**2) # average radius of CNT
elif CNT_orientation == "y":
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
radius_CNT += math.sqrt(atom.x**2 + atom.z**2) # average radius of CNT
elif CNT_orientation == "z":
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
radius_CNT += math.sqrt(atom.x**2 + atom.y**2) # average radius of CNT
radius_CNT = radius_CNT / N_CNT
radius_CNTs.append(radius_CNT)
output += str(timestep) + '\t' + str(radius_CNT) + '\n'
#if not silent: print(str(timestep) + '\t' + str(radius_CNT) + '\n')
# write output
#myBGF.saveBGF(bgf_file[:-4] + "." + str(timestep) + ".bgf")
#myBGF2.saveBGF(bgf_file[:-4] + "." + str(timestep) + ".bgf")
t2 = time.time() # time mark
elapsed_time = t2 - t1;
#print(output)
m, s = nu.meanstdv(radius_CNTs)
output += "average: " + '\t' + str(m) + '\t' + str(s) + '\n'
print('')
print(output)
return 1
def getSlipLength(bgf_file,
trj_file,
ff_file,
n_step,
n_avg_step,
silent=False):
# const
PI = math.pi
vdw_r_C = 1.7
# init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
l_data = []
# stores [r vz]
l_F_N = []
l_F_N_inner = []
l_F_N_outer = []
# stores sum of friction force
l_result = []
l_avg_radius_CNT = []
n_avg_count = 0
n_avg_count_step = 0
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myPkl = open(trj_file + ".method2.pickle", 'w')
myOut = open(trj_file + ".method2.avg_vz.out", 'w')
myOut.write(str(n_avg_step) + " steps are averaged.\n")
myOut.write("AVG_STARTING_STEP\tAVG_vz\tF_N\tF_N_outer\tF_N_inner\n")
# how many steps to go?
if not silent: print("== Step 1. Loading LAMMPS Trajectory")
wc_trj_file = popen("grep TIMESTEP " + trj_file + " | wc -l ").read()
n_timestep = int(wc_trj_file.split()[0])
if n_step == 0:
n_step = n_timestep
print("The trajectory contains " + str(n_timestep) + " timesteps.")
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
# Find header of the trajectory file
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [
line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0],
line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip(
'ATOMS ') # assume ATOMS id type xu yu zu vx vy vz fx fy fz
# for every shot in the trajectory file update BGF and manipulate
dumpatom = get_line(trj_file)
processed_step = 0
t1 = t2 = 0
elapsed_time = 0
while 1:
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (n_step - processed_step)
sys.stdout.write('\r' + "Reading timestep.. " + str(timestep) +
" (Remaining time: " +
"{0:4.1f}".format(remaining_time) + " seconds, " +
"{0:4.1f} minutes".format(remaining_time / 60) + ")")
sys.stdout.flush()
if processed_step == n_step:
break
### Read
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
timestep = int(chunk[1])
l_timestep.append(timestep)
natoms = int(chunk[3])
boxsize = [
chunk[5].split(' ')[0], chunk[5].split(' ')[1],
chunk[6].split(' ')[0], chunk[6].split(' ')[1],
chunk[7].split(' ')[0], chunk[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die(
"Number of atoms in trajectory file does not match with BGF file."
)
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz fx fy fz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.x = float(atomcoord[2]) # coord
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
atom.vx = float(atomcoord[5]) # vel
atom.vy = float(atomcoord[6])
atom.vz = float(atomcoord[7])
if 'fx' in keywords:
atom.fx = float(atomcoord[8]) # force
atom.fy = float(atomcoord[9])
atom.fz = float(atomcoord[10])
try:
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
except:
pass
#nu.warn("Crystal information error: is this file not periodic?")
# apply periodic condition
myBGF = bgftools.periodicMoleculeSort(myBGF, 0, True)
### myBGF update complete! ###
# for CNT atoms, calculate some properties on CNT
min_x_CNT = 0.0
max_x_CNT = 0.0
radius_CNT = 0.0
height_CNT = 0.0
aNo_WAT_O_not_in_CNT = []
temp = []
min_y_CNT = 0.0
max_y_CNT = 0.0
min_z_CNT = 0.0
max_z_CNT = 0.0
CNT_orientation = ""
l_radius_CNT = []
l_x_CNT = []
l_y_CNT = []
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
# center of CNT
l_x_CNT.append(atom.x)
l_y_CNT.append(atom.y)
# height
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
# center of CNT
x_CNT, a = nu.meanstdv(l_x_CNT)
y_CNT, a = nu.meanstdv(l_y_CNT)
z_diff = max_z_CNT - min_z_CNT
# radius of CNT
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
l_radius_CNT.append(
math.sqrt((atom.x - x_CNT)**2 + (atom.y - y_CNT)**2))
radius_CNT, a = nu.meanstdv(l_radius_CNT)
l_avg_radius_CNT.append(radius_CNT)
### get water molecules in CNT
# inside the CNT := min_z_CNT <= z <= max_z_CNT and (x - (x_diff/2))**2 + (y - (y_diff/2))**2 < radius_CNT**2
margin = 0
# water molecules far from the margin will be only considered
aNo_WAT_O_in_CNT = []
for aNo in aNo_WAT_O:
atom = myBGF.getAtom(aNo)
dist_sq = (atom.x - x_CNT)**2 + (atom.y - y_CNT)**2
if "WAT" in atom.rName and min_z_CNT + margin <= atom.z and atom.z <= max_z_CNT - margin and dist_sq < radius_CNT**2:
aNo_WAT_O_in_CNT.append(aNo)
else:
pass
### find outer water layer and collect data
aNo_WAT_outer = []
for aNo in aNo_WAT_O_in_CNT:
atom = myBGF.getAtom(aNo)
r = math.sqrt((atom.x - x_CNT)**2 + (atom.y - y_CNT)**2)
# separate inner and outer water molecules # for (12, 12) outer is r >= 3
#if r >= 3: # 5 = 2 (depletion area) + 3 (outer shell)
if radius_CNT - r <= 5:
aNo_WAT_outer.append(aNo)
#l_data.append(atom.vz*10**5) # outer water velocity = v_slip, original velocity unit: A/fs = 10^5 m/s
# calculate z-directional velocity of water molecules vcm = sum vi mi / sum mi
atom = myBGF.getAtom(aNo_WAT_outer[0])
mass_O = bgftools.getMass(myBGF, [aNo_WAT_outer[0]], ff_file)
atom = myBGF.getAtom(atom.CONECT[0])
mass_H = bgftools.getMass(myBGF, [atom.aNo], ff_file)
mass_H2O = mass_O + 2 * mass_H # H2O mass
for aNo in aNo_WAT_outer:
atom = myBGF.getAtom(aNo) # oxygen
#vcmx = atom.vx * mass_O
#vcmy = atom.vy * mass_O
vcmz = atom.vz * mass_O
for ano in atom.CONECT:
atom2 = myBGF.getAtom(ano)
#vcmx += atom.vx * mass_O
#vcmy += atom.vy * mass_O
vcmz += atom.vz * mass_H
#vcmx /= mass_H2O
#vcmy /= mass_H2O
vcmz /= mass_H2O
l_data.append(vcmz * 10**5)
# calculate sum of forces on carbon atoms of CNT
F_N = 0.0
F_N_outer = 0.0
F_N_inner = 0.0
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
x, y = (atom.x - x_CNT, atom.y - y_CNT)
theta = 0
if y >= 0:
theta = math.acos(x / (math.sqrt(x**2 + y**2)))
else:
theta = -math.acos(x / (math.sqrt(x**2 + y**2)))
F_N += atom.fy * math.cos(theta) + atom.fx * math.sin(theta)
#F_N += abs(atom.fx * math.cos(theta) + atom.fy * math.sin(theta))
l_F_N.append(F_N)
# timestep mark for starting average
if n_avg_count == 0:
n_avg_count_step = timestep
n_avg_count += 1 # "Job's Done" counter
# if the time comes.. average!
if n_avg_count == n_avg_step:
a = analyzeData(l_data) # average vz
l_result.append(
[timestep, a]
) # note the the timestep here is not the timestep that the average started.
t, s = nu.meanstdv(l_F_N) # average force on CNT
myOut.write(
str(n_avg_count_step) + "\t" + str(a) + "\t" + str(t) + "\n")
# reset
l_data = []
n_avg_count = 0
l_F_N = []
sys.stdout.write(
'Done ')
sys.stdout.flush()
# ending for timestep treatment
t2 = time.time() # time mark
elapsed_time = t2 - t1
processed_step += 1
# write output
pkl.dump(l_result, myPkl)
print('')
return 1
def getSlipLength(bgf_file, trj_file, force_profile, silent=False):
"""
This calculates the profile of averaged velocity according to r.
NOTE: This is different from averaged velocity profile according to r.
"""
# const
PI = math.pi
vdw_r_C = 1.7
# init
timestep = 0
l_timestep = []
line = []
n_header = 0
output = ""
t1 = 0
t2 = 0
# clock
output += "t\tforce\tarea\tvz\tvisc\tsliplen\n"
l_radial_vz_profile = []
l_avg_data = []
l_result = []
l_avg_count = []
n_avg_count_step = 0
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myOUT = open(trj_file + ".sliplength.profile", 'w')
# how many steps to go?
if not silent: print("Scanning trajectory file..")
l_timestep = lt.getTrjInfo(trj_file, silent=False)
n_timestep = len(l_timestep)
if not silent:
print("\nThe trajectory contains " + str(n_timestep) + " timesteps.")
# read force data from force profile
if not silent: print("Reading force profile..")
f_fp = open(force_profile)
force = dict()
while 1:
line = f_fp.readline()
if not line:
break
if line[0] == "#":
continue
parse = line.split()
step = int(parse[0])
force[step] = float(parse[1])
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
t1 = t2 = 0
elapsed_time = 0
# Find header of the trajectory file
line = []
n_header = 0
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [
line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0],
line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# calculate properties
dumpatom = get_line(trj_file)
processed_step = 0
while 1:
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (n_timestep - processed_step)
### Read
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
timestep = int(chunk[1])
l_timestep.append(timestep)
natoms = int(chunk[3])
boxsize = [
chunk[5].split(' ')[0], chunk[5].split(' ')[1],
chunk[6].split(' ')[0], chunk[6].split(' ')[1],
chunk[7].split(' ')[0], chunk[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
sys.stdout.write('\r' + "Fetched timestep: " + str(timestep) +
" (Remaining time: " +
"{0:4.1f}".format(remaining_time) + " seconds, " +
"{0:4.1f} minutes".format(remaining_time / 60) + ")")
sys.stdout.flush()
if timestep == 0:
continue
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die(
"Number of atoms in trajectory file does not match with BGF file."
)
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.vx = float(atomcoord[5])
atom.vy = float(atomcoord[6])
atom.vz = float(atomcoord[7])
### myBGF update complete! ###
# calculate z-directional velocity of water molecules wrt r vcm = sum vi mi / sum mi
mass_O = 16.0000
mass_H = 1.008
mass_H2O = mass_O + 2 * mass_H # H2O mass
vz = []
# data container
# z velocity calculation
for ano in aNo_WAT_O:
atom = myBGF.getAtom(ano) # oxygen
vcmz = atom.vz * mass_O
for ano2 in atom.CONECT:
atom2 = myBGF.getAtom(ano2) # hydrogens
vcmz += atom2.vz * mass_H
vcmz /= mass_H2O
vz.append(vcmz * (10**5)) # velocity in A/fs -> m/s
avg_vz, _ = nu.meanstdv(vz)
f = force[timestep] * (6.95e9)
l = f / A / avg_vz # lambda
b = v / l * 1e9 # slip length
output += str(timestep) + "\t" + str(force[timestep]) + "\t" + str(
A) + "\t" + str(avg_vz) + "\t" + str(v) + "\t" + str(b) + "\n"
t2 = time.time() # time mark
elapsed_time = t2 - t1
processed_step += 1
myOUT.write(output)
myOUT.close()
print('')
return 1
def getVelocity(bgf_file, trj_file, n_step, silent=False):
# const
PI = math.pi
vdw_r_C = 1.7
# init
timestep = 0; l_timestep = []; line = []; n_header = 0;
t1 = 0; t2 = 0; # clock
l_data = []; # stores vz
l_avg_radius_CNT = [];
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
ftemp = open("countWater4.profile.test", 'w')
ftemp.write(str(sys.argv) + "\n")
curr_dir = os.path.abspath(".")
temp_dir = curr_dir + "/CountWAT5/"
print(temp_dir)
if not os.path.isdir(temp_dir): os.makedirs(temp_dir)
# how many steps to go?
n_timestep = len(lt.getTrjInfo(trj_file))
if n_step == 0:
n_step = n_timestep;
print(" ..The trajectory contains " + str(n_timestep) + " timesteps.")
print("The script will proceed for the last " + str(n_step) + " timesteps.")
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
for atom in myBGF.a:
# Carbons in CNT or atoms in BNNT
if "NT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
# Find header of the trajectory file
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break;
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0], line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# for every shot in the trajectory file update BGF and manipulate
dumpatom = get_line(trj_file)
processed_step = 0;
t1 = t2 = 0; elapsed_time = 0;
while 1:
### tester
if processed_step == 50:
break;
### Show progress
t1 = time.time();
remaining_time = elapsed_time * (n_step - processed_step)
sys.stdout.write('\r' + "Reading timestep.. " + str(timestep) + " (Remaining time: " + "{0:4.1f}".format(remaining_time) + " seconds, " + "{0:4.1f} minutes".format(remaining_time/60) + ")")
sys.stdout.flush()
if processed_step == n_step:
break;
### Read
myBGF = bgf.BgfFile(bgf_file)
try:
chunk = [next(dumpatom) for i in range(natoms+n_header)]
except StopIteration:
break;
timestep = int(chunk[1])
natoms = int(chunk[3])
boxsize = [chunk[5].split(' ')[0], chunk[5].split(' ')[1], chunk[6].split(' ')[0], chunk[6].split(' ')[1], chunk[7].split(' ')[0], chunk[7].split(' ')[1]];
boxsize = [float(i) for i in boxsize]; boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]), (boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die("Number of atoms in trajectory file does not match with BGF file.")
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
atom.vx = float(atomcoord[5])
atom.vy = float(atomcoord[6])
atom.vz = float(atomcoord[7])
### myBGF update complete! ###
### align CNT to z axis
# initialize for the moment of inertia and the center of mass calculation
U = 0; Ut = 0; Uv = 0;
Ixx = 0; Ixy = 0; Ixz = 0;
Iyx = 0; Iyy = 0; Iyz = 0;
Izx = 0; Izy = 0; Izz = 0;
Mx = 0; My = 0; Mz = 0;
# transpose "all atoms in BGF": move COM of CNT as origin
# com of CNT (important: only one CNT!)
Mx = 0; My = 0; Mz = 0;
min_x_CNT = 0.0; max_x_CNT = 0.0; min_y_CNT = 0.0; max_y_CNT = 0.0; min_z_CNT = 0.0; max_z_CNT = 0.0;
for atom in myBGF.a:
if "NT" in atom.rName:
Mx += atom.x / N_CNT
My += atom.y / N_CNT
Mz += atom.z / N_CNT
### before we proceed to calculate MI first check how the CNT is lying across the periodic box
if atom.x < min_x_CNT:
min_x_CNT = atom.x
if atom.x > max_x_CNT:
max_x_CNT = atom.x
if atom.y < min_y_CNT:
min_y_CNT = atom.y
if atom.y > max_y_CNT:
max_y_CNT = atom.y
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
max_x_axis = int(math.ceil(max_x_CNT/boxsize[0]))
min_x_axis = int(math.floor(min_x_CNT/boxsize[0]))
max_y_axis = int(math.ceil(max_y_CNT/boxsize[1]))
min_y_axis = int(math.floor(min_y_CNT/boxsize[1]))
max_z_axis = int(math.ceil(max_z_CNT/boxsize[2]))
min_z_axis = int(math.floor(min_z_CNT/boxsize[2]))
replNum = (min_x_axis, max_x_axis, min_y_axis, max_y_axis, min_z_axis, max_z_axis)
copyNum = 0
### copy water molecules
for x in range(min_x_axis, max_x_axis):
if x != 0:
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, boxsize[0]*x, 0, 0)
myBGF = myBGF.merge(myBGF2)
copyNum += 1
for y in range(min_y_axis, max_y_axis):
if y != 0:
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, 0, boxsize[1]*y, 0)
myBGF = myBGF.merge(myBGF2)
copyNum += 1
for z in range(min_z_axis, max_z_axis):
if z != 0:
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, 0, 0, boxsize[2]*z)
myBGF = myBGF.merge(myBGF2)
copyNum += 1
print(str(replNum) + " " + str(copyNum) + " natoms: " + str(len(myBGF.a)))
### now continute to MI calculation
# move atoms to box center
COM = nu.array([[Mx, My, Mz]])
CNT = CNT - COM
'''
for atom in myBGF.a:
atom.x -= Mx
atom.y -= My
atom.z -= Mz
'''
# calculate the moment of inertia (MI) and the center of mass (COM) of CNT from "myBGF"
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
Ixx += (atom.y**2 + atom.z**2) / N_CNT
Iyy += (atom.x**2 + atom.z**2) / N_CNT
Izz += (atom.x**2 + atom.y**2) / N_CNT
Ixy -= (atom.x * atom.y) / N_CNT
Ixz -= (atom.x * atom.z) / N_CNT
Iyz -= (atom.y * atom.z) / N_CNT
# the moment of inertia tensor
I = np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]])
# eigenvalue & eigenvector calculation
eigval, eigvec = np.linalg.eig(I) # eigval[0] is the minimum among the values.
# rearrange the U vector
U = np.matrix(eigvec)
Ut = U.T
# "myBGF" rotation
for atom in myBGF.a:
v = np.matrix([atom.x, atom.y, atom.z]).T
Uv = Ut * v
atom.x = float(Uv[2])
atom.y = float(Uv[1])
atom.z = float(Uv[0])
# for CNT atoms, calculate some properties
min_x_CNT = 1000.0; max_x_CNT = -1000.0; radius_CNT = 0.0; height_CNT = 0.0;
min_y_CNT = 1000.0; max_y_CNT = -1000.0;
min_z_CNT = 1000.0; max_z_CNT = -1000.0;
CNT_orientation = "-"
# move origin to box center
for atom in myBGF.a:
atom.x += boxsize[0]/2.0
atom.y += boxsize[1]/2.0
atom.z += boxsize[2]/2.0
#myBGF = bgftools.periodicMoleculeSort(myBGF, 0, myBGF.CRYSTX) ##### testestestest
### update PBC information
myBGF.PERIOD = "111"
myBGF.AXES = "ZYX"
myBGF.SGNAME = "P 1 1 1\n"
myBGF.CELLS = [-1, 1, -1, 1, -1, 1]
if myBGF.CRYSTX != []:
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
else:
for i in range(0, 3):
myBGF.CRYSTX.append(boxsize[i])
myBGF.CRYSTX += [90.0, 90.0, 90.0]
myBGF.saveBGF(temp_dir + bgf_file.split(".bgf")[0] + "." + str(timestep) + ".bgf")
l_radius_CNT = [];
l_x_CNT = [];
l_y_CNT = [];
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
# center of CNT
l_x_CNT.append(atom.x)
l_y_CNT.append(atom.y)
# height
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
x_CNT, a = nu.meanstdv(l_x_CNT)
y_CNT, a = nu.meanstdv(l_y_CNT)
z_diff = max_z_CNT - min_z_CNT
height_CNT = z_diff
# radius of CNT
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
l_radius_CNT.append( math.sqrt( (atom.x - x_CNT)**2 + (atom.y - y_CNT)**2 ))
radius_CNT, a = nu.meanstdv(l_radius_CNT)
l_avg_radius_CNT.append(radius_CNT)
### get water molecules in CNT
# inside the CNT := min_z_CNT <= z <= max_z_CNT and (x - (x_diff/2))**2 + (y - (y_diff/2))**2 < radius_CNT**2
# aNo_WAT_O_atoms: molecules which O atom is within CNT
# we don't need to calculate H atoms. Let's consider only O atoms
margin = 0.0; # water molecules far from the margin will be only considered
aNo_WAT_O_in_CNT = []
for aNo in aNo_WAT_O:
atom = myBGF.getAtom(aNo)
dist_sq = (atom.x - x_CNT)**2 + (atom.y - y_CNT)**2
if "WAT" in atom.rName and "O" in atom.ffType and min_z_CNT + margin <= atom.z and atom.z <= max_z_CNT - margin and dist_sq < radius_CNT**2:
aNo_WAT_O_in_CNT.append(aNo)
else:
pass;
#output = str(timestep) + '\t' + str(len(aNo_WAT_O_in_CNT)) + '\t' + str(radius_CNT) + '\t' + str(z_diff) + '\n'
output = str(timestep) + '\t' + str(len(aNo_WAT_O_in_CNT)) + '\t' + str(radius_CNT) + '\t' + str(boxsize[0]/2) + '\t' + str(boxsize[1]/2) + '\t' + str(min_z_CNT) + '\t' + str(max_z_CNT) + '\t' + str(z_diff) + '\t' + str(height_CNT) + '\t' + str(len(aNo_CNT)) + '\t' + str(replNum) + '\t' + str(copyNum) + '\n' # debug
ftemp.write(output)
#sys.stdout.write('Done ')
sys.stdout.flush()
t2 = time.time() # time mark
elapsed_time = t2 - t1;
processed_step += 1;
print('')
ftemp.close()
print("numbers of water molecules are written in countWater.profile ..Done.")
return 1
