def run(mybgf, t, chunk, sel=""):
"""
This function performs the calculation.
Output:
- int t: timestep
- list result: found hbonds
- bgf.BgfFile mybgf: BgfFile with update coordinates
- string sel: a selection
"""
mybgf = update_coord(chunk, mybgf, mytrj.pbc[t], scaled=yes_scale)
mybgf = bt.periodicMoleculeSort(mybgf, mybgf.CRYSTX, fragments=atom_frags, ff_file=ff_file, silent=True)
if not sel:
sel = calculate_sel_kwac(mybgf) # for Kwac's confined water molecules in MoS2 nanoslit
elif sel == "all":
sel = "" # for water
if sel:
sel_O_atoms = [atom.aNo for atom in mybgf.a if eval(sel) and 'O' in atom.ffType]
else:
sel_O_atoms = [atom.aNo for atom in mybgf.a if 'O' in atom.ffType]
result = hbonds(mybgf, selection=sel)
if verbose:
mybgf.saveBGF(str(t) + ".bgf")
return t, sel_O_atoms, result
def run_hb(mybgf, t, chunk):
mybgf = update_coord(chunk, mybgf, mytrj.pbc[t], scaled=yes_scale)
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
fragments=atom_frags,
ff_file=ff_file,
silent=True)
'''
#sel = "atom.chain == 'I'" # for test
# find inwater boundary for selection
swr = 3.270615945/2
gwr = 3.057430885/2
margin = 5.0
gwa_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWA' in atom.rName")
gwb_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWB' in atom.rName")
if type == "gra":
avg_z1 = bt.atoms_average(mybgf, 'atom.z', selection="'C_R' in atom.ffType and 'GRA' in atom.rName") # gra bottom
avg_z2 = bt.atoms_average(mybgf, 'atom.z', selection="'C_R' in atom.ffType and 'GRB' in atom.rName") # gra top
actual_distance = avg_z2 - avg_z1
elif type == "mos":
avg_s3a_z2 = bt.atoms_average(mybgf, 'atom.z', selection="'S_3a' in atom.ffType and atom.rNo == 2") # mos2 top
avg_s3b_z1 = bt.atoms_average(mybgf, 'atom.z', selection="'S_3b' in atom.ffType and atom.rNo == 1") # mos2 bottom
actual_distance = avg_s3a_z2 - avg_s3b_z1
inwater_x = mybgf.CRYSTX[0]
inwater_y = gwb_y - gwa_y + 2 * gwr - 2 * margin
inwater_z = actual_distance - 2 * swr
sel = "atom.y > {gwa_y} + {margin} and atom.y < {gwb_y} - {margin}".format(**vars())
'''
sel = ""
hb = calc_hbonds(mybgf, selection=sel)
return t, hb
def analyze(bgf_file, trj_file, ff_file='', out_file=''):
'''analyze something within a timestep in a series of lammps trajectory.
'''
# variables
# inner functions
def get_line(file):
with open(file, 'r') as f:
for line in f:
yield line
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
# 2. Read LAMMPS Trajectory
#timesteps, N_HEADER, N_ATOMS = lt.getTrjInfo(trj_file)
mytrj = lt.lammpstrj(trj_file)
timesteps = mytrj.load()
N_HEADER = mytrj.nheader
N_ATOMS = mytrj.natoms[0]
N_BUFFER = N_HEADER + N_ATOMS
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
# 3. Determine dump style
dump_keywords = mytrj.dumpstyle
yes_scale = False
if 'xs' in dump_keywords:
yes_scale = True
# 4. Update coordinates from the snapshot
dump = get_line(trj_file)
for t in tqdm.tqdm(timesteps, ncols=120, desc="Analyzing"):
chunk = [next(dump) for i in range(N_BUFFER)]
t = int(chunk[1])
mybgf.CRYSTX = mytrj.pbc[t] + [90.0, 90.0, 90.0]
coords = chunk[9:]
for c in coords:
c = c.split(' ')
atom = mybgf.getAtom(int(c[0]))
if yes_scale:
atom.x = float(c[2]) * pbc[0]
atom.y = float(c[3]) * pbc[1]
atom.z = float(c[4]) * pbc[2]
else:
atom.x = float(c[2])
atom.y = float(c[3])
atom.z = float(c[4])
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
ff_file=ff_file,
silent=True)
def run(system, t, coords, sel=""):
"""
This function performs the analysis.
Input:
- bgf.BgfFile mybgf
- int t: a timestep written in LAMMPS trjectory
- list chunk: list of atom coordinates in LAMMPS trajectory
- str sel: a string to evaluate for selecting atoms
Output:
- int t: timestep
- list result: found hbonds
"""
assert isinstance(system, bgf.BgfFile), "Wrong object: should be an instance of bgf.BgfFile class."
assert isinstance(t, int), "Timestep should be int."
assert isinstance(coords, list), "coords should be a list."
# update the coordinates from trj to the BGF object
system = update_coord(coords, system, mytrj.pbc[t], scaled=yes_scale)
# wrap the coordinates into the pbc cell
system = bt.periodicMoleculeSort(system, system.CRYSTX, fragments=atom_frags, ff_file=ff_file, silent=True)
selected_atoms = [atom for atom in system.a if eval(sel)]
# do analysis here
out = [] # list to save results
# ...
# something something something
# ...
#
# blah blah blah
# ...
# save each trajectory as BGF file if verbose mode activated.
if verbose:
system.saveBGF(str(t) + ".bgf")
return t, out
def run(mybgf, t, chunk, sel=""):
"""
This function performs the calculation.
Output:
- int t: timestep
- list result: found hbonds
- bgf.BgfFile mybgf: BgfFile with update coordinates
- string sel: a selection
"""
mybgf = update_coord(chunk, mybgf, mytrj.pbc[t], scaled=yes_scale)
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
fragments=atom_frags,
ff_file=ff_file,
silent=True)
result = hbonds(mybgf, selection=sel)
if verbose:
mybgf.saveBGF(str(t) + ".bgf")
return t, result
def countWaterCNT(bgf_file, trj_file, silent=False):
# init
timestep = 0
l_timestep = []
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myDAT = open(bgf_file[:-4] + ".count.dat", "w")
myDAT.write("Time\tHeight\tRadius\tNumber\n")
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_MtOH_C = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Carbons in MeOH
if "MET" in atom.rName and "C" in atom.aName:
aNo_MtOH_C.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# for every shot in the trajectory file update BGF and manipulate
myDUMP = dump.dump(trj_file, 0) # sequential reading
while 1:
aNo_MtOH_C_in_CNT = copy.deepcopy(aNo_MtOH_C)
# 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
time = myDUMP.next()
sys.stdout.write('\r' + "Reading timestep.. " + str(time))
sys.stdout.flush()
#print("Timestep: " + str(time))
if time == -1:
break
nu.shutup()
myDUMP.sort()
nu.say()
l_timestep = myDUMP.time() # timesteps are 'appended' incrementally
atoms = myDUMP.viz(len(l_timestep) - 1)[
2] # atom coordinate info: id,type,x,y,z for each atom as 2d array
box = myDUMP.viz(len(l_timestep) -
1)[1] # [xlo, ylo, zlo, xhi, yhi, zhi]
box = [float(i) for i in box]
boxsize = [box[3] - box[0], box[4] - box[1],
box[5] - box[1]] # simbox size
myBGF.CRYSTX = [
boxsize[0], boxsize[1], boxsize[2], myBGF.CRYSTX[3],
myBGF.CRYSTX[4], myBGF.CRYSTX[5]
]
#print("l_atoms " + str(len(atoms)))
# update the coordinates in the bgf file
for atom in atoms:
bgfatom = myBGF.getAtom(atom[0])
bgfatom.x = float(atom[2])
bgfatom.y = float(atom[3])
bgfatom.z = float(atom[4])
"""
# com of CNT
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
"""
myBGF = bgftools.periodicMoleculeSort(myBGF)
#print(Mx, My, Mz)
# transpose for "all atoms in BGF"
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" transform
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])
# 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
#print(Mx, My, Mz)
# transpose for "all atoms in BGF"
for atom in myBGF.a:
atom.x -= Mx
atom.y -= My
atom.z -= Mz
""" ### THIS PART (UPDATING LAMMPSTRJ) DOES NOT WORK ###
myDUMP.aselect.all(time) # all atoms should be selected to be changed
myDUMP.tselect.one(time)
coordx = []; coordy = []; coordz = []
for atom in myBGF.a:
coordx.append(atom.x)
coordy.append(atom.y)
coordz.append(atom.z)
myDUMP.setv("xu", coordx)
myDUMP.setv("yu", coordy)
myDUMP.setv("zu", coordz)
"""
""" ### CHECKING ORIGIN by adding an atom at (0, 0, 0) and is okay. 110914 inkim
origin = bgf.BgfAtom()
origin.aTag = 0
origin.aName = "ORIG"
origin.ffType = "Ar"
origin.chain = "A"
origin.x = 0.0
origin.y = 0.0
origin.z = 0.0
origin.rName = "ORG"
myBGF.addAtom(origin)
"""
# for CNT atoms, calculate some properties
min_x_CNT = 0.0
max_x_CNT = 0.0
radius_CNT = 0.0
height_CNT = 0.0
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
radius_CNT += math.sqrt(atom.y**2 +
atom.z**2) # average radius of CNT
radius_CNT = radius_CNT / N_CNT
height_CNT = max_x_CNT - min_x_CNT
# determine whether C in MtOH is in the CNT Cylinder
for aNo in aNo_MtOH_C:
atom = myBGF.getAtom(aNo)
dist = math.sqrt(atom.y**2 + atom.z**2)
if atom.x > min_x_CNT \
and atom.x < max_x_CNT \
and dist < radius_CNT:
pass
else:
aNo_MtOH_C_in_CNT.remove(aNo)
#print("Height of CNT: " + str(height_CNT) + " " + str(min_x_CNT) + " " + str(max_x_CNT))
#print("Average radius of CNT: " + str(radius_CNT))
#print("Average number of methanols in CNT: " + str(len(aNo_MtOH_C_in_CNT)))
myDAT.write(str(time) + "\t")
myDAT.write(str("{0:<8.3f}".format(height_CNT)))
myDAT.write(str("{0:<8.3f}".format(radius_CNT)))
myDAT.write(str(len(aNo_MtOH_C_in_CNT)) + "\n")
# write output
myBGF.saveBGF(bgf_file[:-4] + "." + str(time) + ".bgf")
#myDUMP.write(trj_file.split(".")[0] + "_mod." + trj_file.split(".")[1])
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 densityProfile(bgf_file,
trj_file,
out_file,
interval,
avg_timestep,
direction='z',
ff_file='',
silent=False):
nu.warn(
"LAMMPS trajectory with NPT simulations will give you the wrong result."
)
### init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
vector = [0, 0, 1]
# the axis of interest. in the acetone-water case, z direction.
atominfo = bgftools.atom_mass # atom data extracted from ff_file
result = dict()
axis = 0
# 1: x-axis, 2: y-axis, 3: z-axis
### direction
if "x" in direction:
axis = 0
elif "y" in direction:
axis = 1
elif "z" in direction:
axis = 2
else:
nu.die("Error on reading direction.")
### open files
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
f_out_file = open(out_file + ".dat", 'w')
f_avg_out_file = open(out_file + ".average.dat", 'w')
f_pickle = open(out_file + ".pickle", 'w')
f_avg_pickle = open(out_file + ".average.pickle", 'w')
### read residues from bgf_file:: residue is replaced by ffTypes
residue = set()
# kind of residues in BGF file
dict_residue = dict()
# stores residue numbers per each residue. RES1: [1, 2, ..], RES2: [6, 7, ..]
for i in myBGF.a:
rname = string.strip(i.ffType)
residue.add(rname)
output = ""
for i in residue:
output += i + " "
if not silent:
print("Found " + str(len(residue)) + " residues in BGF file: " +
str(output))
residue = list(residue)
residue.append('TOTAL')
for index, i in enumerate(residue):
dict_residue[i] = index
n_residue = len(residue) # number of residues (including total)
if ff_file:
bgftools.update_mass(ff_file)
### read trajectory file
# how many steps to go?
#l_timestep = lt.getTrjInfo(trj_file)
#mytrj = trj.lammpstrj(trj_file)
mytrj = Trj(trj_file)
l_timestep = mytrj.load()
n_timestep = len(l_timestep)
if not silent:
print("\nThe trajectory contains %d timesteps." % n_timestep)
# 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])
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(' ')
### 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) + ")")
sys.stdout.flush()
processed_step += 1
### 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, myBGF.CRYSTX, silent=True)
### DONE for updating trj on BGF file ###
### Do whatever I want: density profile
### upper and lower bound
min = -3.0
max = boxsize[axis] + 3.0
### make a bin
bin = np.arange(math.floor(min), math.ceil(max), interval)
### for every atoms, get atom coordinate and its type
positions = []
# atom positions. [ res1, res2, ..., total ]
masses = []
# used for a weight for histogram. [ res1, res2, ..., total ]
hist = []
bin_edges = []
for i in range(n_residue):
positions.append([])
masses.append([])
hist.append([])
bin_edges.append([])
for atom in myBGF.a:
coord = [atom.x, atom.y, atom.z]
# total
positions[-1].append(coord[axis])
masses[-1].append(atominfo[atom.ffType])
# residues
positions[dict_residue[atom.ffType.strip()]].append(coord[axis])
masses[dict_residue[atom.ffType.strip()]].append(
atominfo[atom.ffType])
### calculate volume
area = 0
if axis == 0:
area = boxsize[1] * boxsize[2]
elif axis == 1:
area = boxsize[0] * boxsize[2]
elif axis == 2:
area = boxsize[0] * boxsize[1]
vol = area * interval
### histogram
for i in range(n_residue):
hist[i], bin_edges[i] = np.histogram(positions[i],
bins=bin,
weights=masses[i])
hist[i] = hist[i] / 6.022 / vol * 10 # density
### store
temp = dict()
for i in range(n_residue):
temp2 = dict()
temp2['HIST'] = hist[i]
temp2['BIN_EDGES'] = bin_edges[i]
temp[residue[i]] = temp2
result[timestep] = temp
### end of loop: check elapsed time
t2 = time.time() # time mark
elapsed_time = t2 - t1
### calculate average values
if not silent: print("\nAveraging the last %d timesteps.." % avg_timestep)
avg_timesteps = l_timestep[-avg_timestep:]
avg_hist = []
avg_bin_edges = []
for i in range(n_residue):
avg_hist.append(
np.zeros(len(result[l_timestep[-avg_timestep]]['TOTAL']['HIST'])))
#avg_bin_edges.append(np.zeros(len(result[-avg_timestep]['TOTAL']['BIN_EDGES'])));
for t in avg_timesteps:
for r in result[t]:
avg_hist[dict_residue[r]] += result[t][r]['HIST']
for i in range(n_residue):
avg_hist[i] /= len(avg_timesteps) # normalize
temp_avg = dict()
# residue --- HIST, BIN_EDGES
for i in residue:
temp2 = dict()
temp2['HIST'] = avg_hist[dict_residue[i]]
temp2['BIN_EDGES'] = bin_edges[0]
temp_avg[i] = temp2
### write up a average data to file
output = str(avg_timestep) + "\n"
for r in temp_avg:
output += str(r) + "\n"
for index, i in enumerate(temp_avg[r]['HIST']):
output += str(
temp_avg[r]['BIN_EDGES'][index]) + "\t" + str(i) + "\n"
output += "\n"
f_avg_out_file.write(output)
### write up a whole data to file
output = ""
tkey = result.keys()
tkey.sort()
for t in tkey:
output += str(t) + "\n"
rkey = result[t].keys()
rkey.sort()
for r in rkey:
output += str(r) + "\n"
for index, i in enumerate(result[t][r]['HIST']):
output += str(
result[t][r]['BIN_EDGES'][index]) + "\t" + str(i) + "\n"
output += "\n"
output += "\n"
f_out_file.write(output)
### write up a pickle object
if not silent: print("Writing pickle object..")
pickle.dump(result, f_pickle)
f_pickle.close()
pickle.dump(temp, f_avg_pickle)
f_avg_pickle.close()
### return
print('')
return 1
def myfunction(bgf_file, trj_file, n_step, out_file, 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
# environments
myBGF = bgf.BgfFile(bgf_file) # load BGF
myTRJ = open(trj_file) # load LAMMPS trj
myTRJ.seek(0)
out_file = "myfunction.dat"
f_out_file = open(out_file, 'w') # data will be recorded here
f_out_file.write(str(sys.argv) + "\n")
curr_dir = os.path.abspath(".")
temp_dir = curr_dir + "/data/"
if not os.path.isdir(temp_dir): os.makedirs(temp_dir)
print("* Current directory: " + curr_dir)
print("* Temp directory: " + temp_dir)
# variables
pass
# scan LAMMPS trj to count how many shots in the file
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.")
# prepare something with BGF file
for atom in myBGF.a:
# do something
pass
### Read trajectory file header
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 ')
# launch LAMMPS trj file
dumpatom = get_line(trj_file)
### loop over trj and do the analysis
processed_step = 0
# counter
t1 = t2 = 0
elapsed_time = 0
# timer: calculate ETA
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()
# stop analysis if requested n_step reached
if processed_step == n_step:
break
# Read a shot from the trj 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])
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])
# pbc wrap if required
myBGF = bgftools.periodicMoleculeSort(myBGF, 0, myBGF.CRYSTX)
### do some analysis
"""
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"""
### record data
output = str(timestep) + '\t' + str(123) + '\n'
f_out_file.write(output)
### update timer
sys.stdout.flush()
t2 = time.time() # time mark
elapsed_time = t2 - t1
processed_step += 1
print('')
f_out_file.close()
print("numbers of water molecules are written in " + out_file + " ..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
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 getHBond(bgf_file, trj_file, selection='', silent=False):
# init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
hbond_dat = dict()
d_crit = 3.5
a_crit = 30.0
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myPickle_file = bgf_file[:-4] + ".hbond.pickle"
myDAT = open(bgf_file[:-4] + ".hbond.count.dat", "w")
myDAT.write(str(sys.argv) + "\n")
# 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.")
# 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_timestep - 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()
### 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 = ""
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?")
pbc = myBGF.CRYSTX[:3]
# apply periodic condition
myBGF = bgftools.periodicMoleculeSort(myBGF, myBGF.CRYSTX, silent=True)
### myBGF update complete! ###
# get donor and acceptor
# donors: O in ACT
A = []
D = []
for atom in myBGF.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die(
"There are no atoms which can make H_bond (especially O atoms)!"
)
### find hydrogen bonds
# for all pairs of OC-HW
sys.stdout.write('Hbonds.. ')
sys.stdout.flush()
hbonds = []
donors = []
acceptors = []
hydrogens = []
angles = []
distances = []
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z])
for a_atom in A:
a = np.array([a_atom.x, a_atom.y, a_atom.z])
dist = nu.dist(d, a)
#dist = bgf.distance(d_atom, a_atom)
if 0.001 < dist < d_crit:
# check H angle
for ano in d_atom.CONECT:
h_atom = myBGF.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
theta = np.degrees(arccos(theta))
#theta = bgf.angle(h_atom, d_atom, a_atom, radians=False)
if theta < a_crit:
hbonds.append([d_atom.aNo, a_atom.aNo])
donors.append(d_atom.aNo)
acceptors.append(a_atom.aNo)
hydrogens.append(h_atom.aNo)
distances.append(dist)
angles.append(theta)
#n_hbond += 1
#print("%s %s" % (d_atom.rNo, a_atom.rNo))
hbond_dat[timestep] = hbonds
sys.stdout.write(
'Done ')
sys.stdout.flush()
print("")
for i in zip(donors, acceptors, hydrogens, distances, angles):
print i
sys.exit(0)
myDAT.write("%d %d\n" % (timestep, len(hbonds)))
# 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
pickle_f = open(myPickle_file, 'w')
pickle.dump(hbond_dat, pickle_f)
print('')
myDAT.close()
return 1
def getHbond(bgf_file, trj_file, ff_file='', selection='', out_file=''):
'''analyze something within a timestep in a series of lammps trajectory.
'''
# variables
result = dict()
# inner functions
def get_line(file):
with open(file, 'r') as f:
for line in f:
yield line
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
atom_frags = bt.getMoleculeList(mybgf)
# 2. Read LAMMPS Trajectory
mytrj = lt.lammpstrj(trj_file)
mytrj.load()
timesteps = sorted(mytrj.timesteps)
N_HEADER = mytrj.nheader
N_ATOMS = mytrj.natoms[timesteps[0]]
N_BUFFER = N_HEADER + N_ATOMS
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
# 3. Determine dump style
dump_keywords = mytrj._dump_style
yes_scale = False
if 'xs' in dump_keywords:
yes_scale = True
# 4. Update coordinates from the snapshot
dump = get_line(trj_file)
for t in tqdm.tqdm(timesteps, ncols=120, desc="Analyzing HBonds"):
chunk = [next(dump) for i in range(N_BUFFER)]
mybgf = update_coord(chunk, mybgf, mytrj.pbc[t], scaled=yes_scale)
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
fragments=atom_frags,
ff_file=ff_file,
silent=True)
### collect data
def calc_hbonds():
# variables
A = []
D = []
hbonds = []
d_crit = 3.5
a_crit = 30.0
for atom in mybgf.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die(
"There are no atoms which can make H_bond (O atoms so far)!"
)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A,
d,
r=d_crit,
pbc=mytrj.pbc[t],
k=6)
donors = [d_atom.aNo] + d_atom.CONECT
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y,
a_atom.z]) # acceptor coord
acceptors = [a_atom.aNo] + a_atom.CONECT
for ano in d_atom.CONECT:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
theta = np.degrees(arccos(theta))
if theta < a_crit: # HBond exists
dist = nu.pbc_dist(a, d, mytrj.pbc[t])
dist_ah = nu.pbc_dist(d, h, mytrj.pbc[t])
# E_vdw
sigma_r = O_sigma / dist
sigma_r_6 = sigma_r**6
sigma_r_12 = sigma_r**12
E_vdw = 4.0 * O_epsilon * (sigma_r_12 - sigma_r_6)
# E_vdw in kcal/mol
# E_coul
E_coul = 0.0
for i, j in itertools.product(donors, acceptors):
atom1 = mybgf.getAtom(i)
atom2 = mybgf.getAtom(j)
a1 = [atom1.x, atom1.y, atom1.z]
a2 = [atom2.x, atom2.y, atom2.z]
dist_ij = nu.pbc_dist(a1, a2, mytrj.pbc[t])
E_coul += 332.06371 * atom1.charge * atom2.charge / dist_ij # E_coul in kcal/mol
# E_hbond
E_hbond = E_coul + E_vdw # E_hbond = E_vdw + E_coul
# update for v4
# angle between H-O-H plane and O..O vector
H1 = mybgf.getAtom(d_atom.CONECT[0])
h1 = [H1.x, H1.y, H1.z] # H1
H2 = mybgf.getAtom(d_atom.CONECT[1])
h2 = [H2.x, H2.y, H2.z] # H2
p = d - h1
q = d - h2
n = np.cross(
p, q) # normal vector of the H1-O-H2 plane
m = a - d
# O..O vector
alpha = np.dot(n, m) / norm(n) / norm(m)
alpha = np.degrees(
arcsin(alpha)
) # angle between H-O-H plane and O..O vector
#hbonds.append([d_atom.aNo, a_atom.aNo, d, a, dist, theta, [E_coul, E_vdw, E_hbond]]) # v2
#hbonds.append([d_atom.aNo, a_atom.aNo, d, a, dist, theta, [E_coul, E_vdw, E_hbond], dist_ah]) # v3
hbonds.append([
d_atom.aNo, a_atom.aNo, d, a, dist, theta,
[E_coul, E_vdw, E_hbond], dist_ah, alpha
]) # v4
return hbonds
hbonds = calc_hbonds()
result[t] = hbonds
#break; # tester
# 5. Analyze
if not out_file:
out_file = trj_file + ".hbonds.v4"
pickle_file = out_file + ".pickle"
with open(pickle_file, 'wb') as f:
pickle.dump(result, f, protocol=pickle.HIGHEST_PROTOCOL)
print("Success to save the result to a pickle file %s" % pickle_file)
def trj2data(dat_file, trj_file, step, skipVelocity, silent=False):
# init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
### LAMMPS Data
dat_atoms = []
if not silent: print("== Step 1. Loading LAMMPS Data")
if not os.path.exists(dat_file):
nu.die("Please check the LAMMPS data file.")
f_dat_file = open(dat_file)
temp = f_dat_file.read().split('\n')
dat_atom_start = temp.index('Atoms')
dat_atom_end = temp.index('Bonds')
dat_atoms = temp[dat_atom_start + 1:dat_atom_end]
f_dat_file.close()
### LAMMPS Trajectory
# how many steps to go?
if not silent: print("== Step 2. Loading LAMMPS Trajectory")
n_timestep = len(lt.getTrjInfo(trj_file))
print("The trajectory contains " + str(n_timestep) + " timesteps.")
# 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
if not silent: print("== Step 3. Reading LAMMPS Trajectory")
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) + ")")
sys.stdout.flush()
processed_step += 1
### if step is specified, then save only for that step.
if step != "":
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'
flagVelocity = False
if 'vx' in keywords or 'vy' in keywords or 'vz' in keywords:
flagVelocity = True
# 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])
if not skipVelocity:
if flagVelocity == True:
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)
#myBGF.saveBGF(bgf_file[:-4] + "." + str(timestep) + ".trjupdated.bgf")
### myBGF update complete! ###
### update LAMMPS data file ###
myDAT = open(dat_file)
myNewDAT = open(dat_file + "." + str(timestep), 'w')
linecount = 0
while 1:
line = myDAT.readline()
if not line:
break
if linecount == 0:
output = line.strip(
"\n") + " and updated with timestep " + str(
timestep) + " in " + trj_file + "\n"
linecount += 1
myNewDAT.write(output)
continue
if "xlo " in line:
output = "\t" + " {0:>10.6f} {1:>10.6f}".format(
0.0, boxsize[0]) + " xlo xhi\n"
myNewDAT.write(output)
continue
elif "ylo " in line:
output = "\t" + " {0:>10.6f} {1:>10.6f}".format(
0.0, boxsize[1]) + " ylo yhi\n"
myNewDAT.write(output)
continue
elif "zlo " in line:
output = "\t" + " {0:>10.6f} {1:>10.6f}".format(
0.0, boxsize[2]) + " zlo zhi\n"
myNewDAT.write(output)
continue
if not "Atoms" in line:
myNewDAT.write(line)
else:
myNewDAT.write("Atoms\n\n")
for i in dat_atoms:
if len(i) == 0:
continue
parse = i.split()
atomNo = int(parse[0])
molNo = int(parse[1])
atomTypeNo = int(parse[2])
atom = myBGF.getAtom(atomNo)
if atom.aNo != atomNo or atom.rNo != molNo:
nu.die(
"BGF and data file mismatch. Please check both files."
)
else:
output = "{0:>8} {1:>8} {2:>8} {3:10.5f} {4:10.5f} {5:10.5f} {6:10.5f} {7:12.8f} {8:12.8f} {9:12.8f}".format(
atom.aNo, atom.rNo, atomTypeNo, atom.charge,
atom.x, atom.y, atom.z, atom.vx, atom.vy,
atom.vz) + "\n"
myNewDAT.write(output)
# consume
for i in range(len(dat_atoms)):
line = myDAT.readline()
myNewDAT.write("\n")
t2 = time.time() # time mark
elapsed_time = t2 - t1
print('')
return 1
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 getHbond(bgf_file, trj_file, ff_file='', selection='', out_file=''):
'''analyze something within a timestep in a series of lammps trajectory.
'''
# variables
result = dict()
# inner functions
def get_line(file):
with open(file, 'r') as f:
for line in f:
yield line
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
# 2. Read LAMMPS Trajectory
#timesteps, N_HEADER, N_ATOMS = lt.getTrjInfo(trj_file)
mytrj = lt.lammpstrj(trj_file)
timesteps = mytrj.load()
N_HEADER = mytrj.nheader
N_ATOMS = mytrj.natoms[timesteps[0]]
N_BUFFER = N_HEADER + N_ATOMS
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
# 3. Determine dump style
dump_keywords = mytrj.dumpstyle
yes_scale = False
if 'xs' in dump_keywords:
yes_scale = True
# 4. Update coordinates from the snapshot
dump = get_line(trj_file)
for t in tqdm.tqdm(timesteps, ncols=120, desc="Analyzing HBonds"):
chunk = [next(dump) for i in range(N_BUFFER)]
mybgf.CRYSTX = mytrj.pbc[t] + [90.0, 90.0, 90.0]
coords = chunk[9:]
for c in coords:
c = c.split(' ')
atom = mybgf.getAtom(int(c[0]))
if yes_scale:
atom.x = float(c[2]) * pbc[0]
atom.y = float(c[3]) * pbc[1]
atom.z = float(c[4]) * pbc[2]
else:
atom.x = float(c[2])
atom.y = float(c[3])
atom.z = float(c[4])
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
ff_file=ff_file,
silent=True)
### collect data
def calc_hbonds():
# variables
A = []
D = []
hbonds = []
d_crit = 3.5
a_crit = 30.0
for atom in mybgf.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die(
"There are no atoms which can make H_bond (O atoms so far)!"
)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A,
d,
r=d_crit,
pbc=mytrj.pbc[t],
k=6)
donors = [d_atom.aNo] + d_atom.CONECT
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y,
a_atom.z]) # acceptor coord
acceptors = [a_atom.aNo] + a_atom.CONECT
for ano in d_atom.CONECT:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
theta = np.degrees(arccos(theta))
if theta < a_crit:
dist = nu.pbc_dist(a, d, mytrj.pbc[t])
dist_dh = nu.pbc_dist(d, h, mytrj.pbc[t])
# E_vdw
sigma_r = O_sigma / dist
sigma_r_6 = sigma_r**6
sigma_r_12 = sigma_r**12
E_vdw = 4.0 * O_epsilon * (sigma_r_12 - sigma_r_6)
# Evdw in kcal/mol
# E_coul
E_coul = 0.0
for i, j in itertools.product(donors, acceptors):
atom1 = mybgf.getAtom(i)
atom2 = mybgf.getAtom(j)
a1 = [atom1.x, atom1.y, atom1.z]
a2 = [atom2.x, atom2.y, atom2.z]
dist_ij = nu.pbc_dist(a1, a2, mytrj.pbc[t])
E_coul += 332.06371 * atom1.charge * atom2.charge / dist_ij
#E_coul /= 2.0
E_hbond = E_coul + E_vdw # E_hbond = E_vdw + E_coul
#print("e_coul: %f, e_coul2: %f, E_coul: %f, E_vdw: %f, E_hbond: %f, O-O dist: %f, O-H dist: %f" % (e_coul, e_coul2, E_coul, E_vdw, E_hbond, dist, dist_a_dh))
#print("E_coul: %f, E_vdw: %f, E_hbond: %f, O-O dist: %f" % (E_coul, E_vdw, E_hbond, dist))
#hbonds.append([d_atom.aNo, a_atom.aNo, d, a, dist, theta, [E_coul, E_vdw, E_hbond]])
hbonds.append([
d_atom.aNo, a_atom.aNo, d, a, dist, theta,
[E_coul, E_vdw, E_hbond], dist_dh
])
return hbonds
hbonds = calc_hbonds()
result[t] = hbonds
#break; # tester
# 5. Analyze
if not out_file:
out_file = trj_file + ".hbonds.v2"
pickle_file = out_file + ".pickle"
with open(pickle_file, 'wb') as f:
pickle.dump(result, f, protocol=pickle.HIGHEST_PROTOCOL)
print("Success to save the result to a pickle file %s" % pickle_file)
'''
def getHbond(bgf_file,
trj_file,
ff_file='',
selection='',
out_file='',
nsamples=0):
'''analyze something within a timestep in a series of lammps trajectory.
'''
# variables
result = dict()
# inner functions
def get_line(file):
with open(file, 'r') as f:
for line in f:
yield line
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
# 2. Read LAMMPS Trajectory
#timesteps, N_HEADER, N_ATOMS = lt.getTrjInfo(trj_file)
mytrj = lt.lammpstrj(trj_file)
timesteps = mytrj.load()
if nsamples:
requested_timesteps = timesteps[-nsamples:]
else:
requested_timesteps = timesteps
N_HEADER = mytrj.nheader
N_ATOMS = mytrj.natoms[timesteps[0]]
N_BUFFER = N_HEADER + N_ATOMS
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
A = []
D = []
if not selection:
for atom in mybgf.a:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
# 3. Determine dump style
dump_keywords = mytrj.dumpstyle
# 4. Update coordinates from the snapshot
dump = get_line(trj_file)
for t in tqdm.tqdm(timesteps, ncols=120, desc="Analyzing HBonds"):
chunk = [next(dump) for i in range(N_BUFFER)]
t = int(chunk[1])
if not t in requested_timesteps:
continue
mybgf.CRYSTX = mytrj.pbc[t] + [90.0, 90.0, 90.0]
coords = chunk[9:]
for c in coords:
c = c.split(' ')
atom = mybgf.getAtom(int(c[0]))
atom.x = float(c[2])
atom.y = float(c[3])
atom.z = float(c[4])
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
ff_file=ff_file,
silent=True)
### collect data
def calc_hbonds():
hbonds = []
d_crit = 3.6
if selection:
for atom in mybgf.a:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A,
d,
r=d_crit,
pbc=mytrj.pbc[t],
k=6)
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y,
a_atom.z]) # acceptor coord
dist = nu.pbc_dist(a, d, mytrj.pbc[t])
if dist > 2.0:
for ano in d_atom.CONECT:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
#theta = np.degrees(arccos(theta))
if -0.17364817766693034885171662676931 < theta < 1.0:
hbonds.append([dist, np.degrees(theta)])
return hbonds
hbonds = calc_hbonds()
result[t] = hbonds
#break; # tester
# 5. Analyze
if not out_file:
out_file = trj_file + ".hbonds_pmf"
pickle_file = out_file + ".pickle"
with open(pickle_file, 'wb') as f:
pickle.dump(result, f, protocol=pickle.HIGHEST_PROTOCOL)
print("Success to save the result to a pickle file %s" % pickle_file)
def count_layer(bgf_file, trj_file, ff_file='', out_file='', prefix=''):
'''measures confined density of graphene interlayer
'''
# variables
result = dict()
r_vdw_C = 3.38383824 / 2
# inner functions
def get_line(file):
with open(file, 'r') as f:
for line in f:
yield line
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
# 2. Read LAMMPS Trajectory
mytrj = lt.lammpstrj(trj_file)
timesteps = mytrj.load()
N_HEADER = mytrj.nheader
N_ATOMS = mytrj.natoms[0]
N_BUFFER = N_HEADER + N_ATOMS
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
# 3. Determine dump style
dump_keywords = mytrj.dumpstyle
yes_scale = False
if 'xs' in dump_keywords:
yes_scale = True
# Mass
wat_ano = []
for atom in mybgf.a:
if atom.chain == "I":
wat_ano.append(atom.aNo)
mass = bt.getMass(mybgf, wat_ano, ff_file=ff_file)
# 4. Update coordinates from the snapshot
dump = get_line(trj_file)
for t in tqdm.tqdm(timesteps, ncols=120, desc="Counting Atoms"):
chunk = [next(dump) for i in range(N_BUFFER)]
t = int(chunk[1])
mybgf.CRYSTX = mytrj.pbc[t] + [90.0, 90.0, 90.0]
coords = chunk[9:]
for c in coords:
c = c.split(' ')
atom = mybgf.getAtom(int(c[0]))
if yes_scale:
atom.x = float(c[2]) * pbc[0]
atom.y = float(c[3]) * pbc[1]
atom.z = float(c[4]) * pbc[2]
else:
atom.x = float(c[2])
atom.y = float(c[3])
atom.z = float(c[4])
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
ff_file=ff_file,
silent=True)
### collect data
def density():
# variables
density = dict()
# height
avg_gra_z1 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_2G' in atom.ffType and atom.rNo == 1")
avg_gra_z2 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_2G' in atom.ffType and atom.rNo == 2")
dist = avg_gra_z2 - avg_gra_z1
eff_dist = avg_gra_z2 - avg_gra_z1 - 2 * r_vdw_C
# volume
x = mytrj.pbc[t][0]
y = mytrj.pbc[t][1]
volume = x * y * dist
eff_volume = x * y * eff_dist
# density
density = mass / 6.022 / volume * 10
eff_density = mass / 6.022 / eff_volume * 10
return [
x, y, dist, mass, volume, eff_volume, eff_dist, density,
eff_density
]
density = density()
result[t] = density
# 5. Analyze
timesteps = sorted(result.keys())
with open(prefix + '.trj.density.dat', 'w') as f:
output = "#x\ty\tdist\tmass\tvolume\teff_volume\teff_dist\tdensity\teff_density\n"
for t in timesteps:
output += "%d " % t
output += " ".join("%8.3f" % float(i) for i in result[t])
f.write(output)
def hard_work(mybgf, chunk):
mybgf = update_coord(chunk, mybgf, mytrj.pbc[t], scaled=yes_scale)
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
fragments=atom_frags,
ff_file=ff_file,
silent=True)
'''
# find inwater boundary
swr = 3.270615945/2
gwr = 3.057430885/2
margin = 5.0
gwa_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWA' in atom.rName")
gwb_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWB' in atom.rName")
if type == "gra":
avg_z1 = bt.atoms_average(mybgf, 'atom.z', selection="'C_R' in atom.ffType and 'GRA' in atom.rName") # gra bottom
avg_z2 = bt.atoms_average(mybgf, 'atom.z', selection="'C_R' in atom.ffType and 'GRB' in atom.rName") # gra top
actual_distance = avg_z2 - avg_z1
elif type == "mos":
avg_s3a_z2 = bt.atoms_average(mybgf, 'atom.z', selection="'S_3a' in atom.ffType and atom.rNo == 2") # mos2 top
avg_s3b_z1 = bt.atoms_average(mybgf, 'atom.z', selection="'S_3b' in atom.ffType and atom.rNo == 1") # mos2 bottom
actual_distance = avg_s3a_z2 - avg_s3b_z1
inwater_x = pbc[0]
inwater_y = gwb_y - gwa_y + 2 * gwr - 2 * margin
inwater_z = actual_distance - 2 * swr
selection = "atom.y > {gwa_y} + {margin} and atom.y < {gwb_y} - {margin}".format(**vars())
'''
### collect data
def calc_hbonds():
# variables
A = []
D = []
hbonds = []
d_crit = 3.5
a_crit = 30.0
for atom in mybgf.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die(
"There are no atoms which can make H_bond (O atoms so far)!"
)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A,
d,
r=d_crit,
pbc=mytrj.pbc[t],
k=6)
donors = [d_atom.aNo] + d_atom.CONECT
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y,
a_atom.z]) # acceptor coord
acceptors = [a_atom.aNo] + a_atom.CONECT
for ano in d_atom.CONECT:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
theta = np.degrees(arccos(theta))
if theta < a_crit: # HBond exists
dist = nu.pbc_dist(a, d, mytrj.pbc[t])
dist_ah = nu.pbc_dist(d, h, mytrj.pbc[t])
# E_vdw
sigma_r = O_sigma / dist
sigma_r_6 = sigma_r**6
sigma_r_12 = sigma_r**12
E_vdw = 4.0 * O_epsilon * (sigma_r_12 -
sigma_r_6)
# E_vdw in kcal/mol
# E_coul
E_coul = 0.0
for i, j in itertools.product(
donors, acceptors):
atom1 = mybgf.getAtom(i)
atom2 = mybgf.getAtom(j)
a1 = [atom1.x, atom1.y, atom1.z]
a2 = [atom2.x, atom2.y, atom2.z]
dist_ij = nu.pbc_dist(a1, a2, mytrj.pbc[t])
E_coul += 332.06371 * atom1.charge * atom2.charge / dist_ij # E_coul in kcal/mol
# E_hbond
E_hbond = E_coul + E_vdw # E_hbond = E_vdw + E_coul
# update for v4
# angle between H-O-H plane and O..O vector
H1 = mybgf.getAtom(d_atom.CONECT[0])
h1 = [H1.x, H1.y, H1.z] # H1
H2 = mybgf.getAtom(d_atom.CONECT[1])
h2 = [H2.x, H2.y, H2.z] # H2
p = d - h1
q = d - h2
n = np.cross(
p, q) # normal vector of the H1-O-H2 plane
m = a - d
# O..O vector
alpha = np.dot(n, m) / norm(n) / norm(m)
alpha = np.degrees(
arcsin(alpha)
) # angle between H-O-H plane and O..O vector
hbonds.append([
d_atom.aNo, a_atom.aNo, d, a, dist, theta,
[E_coul, E_vdw, E_hbond], dist_ah, alpha
]) # v4
return hbonds
hb = calc_hbonds()
return hb
def densityProfile(bgf_file,
trj_file,
ff_file,
out_file,
direction,
cnt_direction,
interval,
avg_timestep,
silent=False):
nu.warn(
"LAMMPS trajectory with NPT simulations will give you the wrong result."
)
### init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
vector = [0, 0, 1]
# the axis of interest. in the acetone-water case, z direction.
atominfo = dict()
# atom data extracted from ff_file
result = dict()
axis = 0
# 1: x-axis, 2: y-axis, 3: z-axis
### direction
if "x" in direction:
axis = 0
elif "y" in direction:
axis = 1
elif "z" in direction:
axis = 2
else:
nu.die("Error on reading direction.")
### CNT direction
if "x" in cnt_direction:
cnt_direction = 0
elif "y" in cnt_direction:
cnt_direction = 1
elif "z" in cnt_direction:
cnt_direction = 2
else:
nu.die("Error on reading CNT direction.")
### open files
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
f_out_file = open(out_file + ".dat", 'w')
f_avg_out_file = open(out_file + ".average.dat", 'w')
f_pickle = open(out_file + ".pickle", 'w')
f_avg_pickle = open(out_file + ".average.pickle", 'w')
### read residues from bgf_file
residue = set()
# kind of residues in BGF file
dict_residue = dict()
# stores residue numbers per each residue. RES1: [1, 2, ..], RES2: [6, 7, ..]
for i in myBGF.a:
rname = string.strip(i.rName)
residue.add(rname)
output = ""
for i in residue:
output += i + " "
if not silent:
print("Found " + str(len(residue)) + " residues in BGF file: " +
str(output))
residue = list(residue)
residue.append('TOTAL')
for index, i in enumerate(residue):
dict_residue[i] = index
n_residue = len(residue) # number of residues (including total)
### if no CNT the die
if "CNT" not in residue:
nu.die(
"It seems that the BGF file does not contain any CNT atoms. Exiting."
)
### 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)
### read mass from ff_file
try:
parse = ff_file.split(" ")
except:
nu.die(
"Error occurred when reading the force field file.. Check your " +
str(ff_file))
else:
if not silent:
print("Found " + str(len(parse)) + " Cerius2 Force Fields.")
for i in parse:
FF = dreiding.loadFF(i)
temp_atominfo = dreiding.loadAtomTypes(FF)
atominfo.update(temp_atominfo)
### read trajectory file
# how many steps to go?
n_timestep = len(lt.getTrjInfo(trj_file))
if not silent:
print("The trajectory contains " + str(n_timestep) + " timesteps.")
# 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]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = line[8].strip('ATOMS ')
initial_boxsize = copy.deepcopy(boxsize)
# 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])
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(' ')
### if the box size changes, then stop (only takes NVT trajectory)
for i in range(3):
if abs(initial_boxsize[i] - boxsize[i]) > 0.1:
nu.die(
"Simulation box change detected in the trajectory file. NVT trajectory is required to continue."
)
### 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) + ")")
sys.stdout.flush()
processed_step += 1
### 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)
### DONE for updating trj on BGF file ###
### Do whatever I want: density profile
### find the CNT center
radius_CNT = 0
cntx = cnty = cntz = 0
natoms_CNT = len(aNo_CNT)
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
cntx += atom.x
cnty += atom.y
cntz += atom.z
cntx /= natoms_CNT
cnty /= natoms_CNT
cntz = natoms_CNT
### make a bin
diagonal_length = 0.0
box_height = boxsize[cnt_direction]
radial_bin_length = 0.0
x_length = boxsize[0] / 2
y_length = boxsize[1] / 2
z_length = boxsize[2] / 2
if cnt_direction == 0:
diagonal_length = math.sqrt(boxsize[1]**2 + boxsize[2]**2) / 2
radial_bin_length = min(diagonal_length, y_length, z_length)
elif cnt_direction == 1:
diagonal_length = math.sqrt(boxsize[0]**2 + boxsize[2]**2) / 2
radial_bin_length = min(diagonal_length, x_length, z_length)
elif cnt_direction == 2:
diagonal_length = math.sqrt(boxsize[0]**2 + boxsize[1]**2) / 2
radial_bin_length = min(diagonal_length, y_length, z_length)
# choose the shortest length among diagonal and half size of the box length
#radial_bin_length = min(diagonal_length, boxsize[0]/2, boxsize[1]/2, boxsize[2]/2)
bin = np.arange(0.0, math.ceil(radial_bin_length), interval)
### for every atoms, get atom coordinate and its type
positions = []
# atom positions. [ res1, res2, ..., total ]
masses = []
# used for a weight for histogram. [ res1, res2, ..., total ]
hist = []
bin_edges = []
for i in range(n_residue):
positions.append([])
masses.append([])
hist.append([])
bin_edges.append([])
for atom in myBGF.a:
coord = [atom.x, atom.y, atom.z]
dist = 0
# calculate radial distance from CNT center to atom
if cnt_direction == 0:
dist = math.sqrt((atom.y - cnty)**2 + (atom.z - cntz)**2)
elif cnt_direction == 1:
dist = math.sqrt((atom.x - cntx)**2 + (atom.z - cntz)**2)
elif cnt_direction == 2:
dist = math.sqrt((atom.x - cntx)**2 + (atom.y - cnty)**2)
# total
positions[-1].append(dist)
masses[-1].append(atominfo[atom.ffType]['MASS'])
# residues
positions[dict_residue[atom.rName.strip()]].append(dist)
masses[dict_residue[atom.rName.strip()]].append(
atominfo[atom.ffType]['MASS'])
### histogram
for i in range(n_residue):
hist[i], bin_edges[i] = np.histogram(positions[i],
bins=bin,
weights=masses[i])
### divide by volume for density
vol = []
for j in range(len(hist[0])):
vol.append(math.pi *
(bin_edges[0][j + 1]**2 - bin_edges[0][j]**2) *
box_height)
for i in range(n_residue):
hist[i] = hist[i] / 6.022 / vol * 10.0 # density
### store
temp = dict()
for i in range(n_residue):
temp2 = dict()
temp2['HIST'] = hist[i]
temp2['BIN_EDGES'] = bin_edges[i]
temp[residue[i]] = temp2
result[timestep] = temp
### end of loop: check elapsed time
t2 = time.time() # time mark
elapsed_time = t2 - t1
### calculate average values
if not silent:
print("\nAveraging the last " + str(avg_timestep) + " timesteps..")
avg_timesteps = l_timestep[-avg_timestep:]
avg_hist = []
avg_bin_edges = []
for i in range(n_residue):
avg_hist.append(
np.zeros(len(result[l_timestep[-avg_timestep]]['TOTAL']['HIST'])))
#avg_bin_edges.append(np.zeros(len(result[-avg_timestep]['TOTAL']['BIN_EDGES'])));
for t in avg_timesteps:
for r in result[t]:
avg_hist[dict_residue[r]] += result[t][r]['HIST']
for i in range(n_residue):
avg_hist[i] /= len(avg_timesteps) # normalize
temp_avg = dict()
# residue --- HIST, BIN_EDGES
for i in residue:
temp2 = dict()
temp2['HIST'] = avg_hist[dict_residue[i]]
temp2['BIN_EDGES'] = bin_edges[0]
temp_avg[i] = temp2
### write up a average data to file
output = str(avg_timestep) + "\n"
for r in temp_avg:
output += str(r) + "\n"
for index, i in enumerate(temp_avg[r]['HIST']):
output += str(
temp_avg[r]['BIN_EDGES'][index]) + "\t" + str(i) + "\n"
output += "\n"
f_avg_out_file.write(output)
### write up a whole data to file
output = ""
tkey = result.keys()
tkey.sort()
for t in tkey:
output += str(t) + "\n"
rkey = result[t].keys()
rkey.sort()
for r in rkey:
output += str(r) + "\n"
for index, i in enumerate(result[t][r]['HIST']):
output += str(
result[t][r]['BIN_EDGES'][index]) + "\t" + str(i) + "\n"
output += "\n"
output += "\n"
f_out_file.write(output)
### write up a pickle object
if not silent: print("Writing pickle object..")
pickle.dump(result, f_pickle)
f_pickle.close()
pickle.dump(temp, f_avg_pickle)
f_avg_pickle.close()
### return
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)
# 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 countWaterCNT(bgf_file, trj_file, ff_file, n_step, do_hbonds, 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
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myDAT = open(bgf_file[:-4] + ".calcDensity.count.dat", "w")
myDAT2 = open(bgf_file[:-4] + ".calcDensity.hbond.dat", "w")
myDAT3 = open(bgf_file[:-4] + ".calcDensity.configuration.dat", "w")
myDAT.write(str(sys.argv) + "\n")
myDAT.write("Time\tmin_X\tmax_X\tHeight\tRadius\tNumber\tVolume\tEff_volume\tExact_mass\tMass\tExact_den\tMtOH_den\tExact_eff_den\tMtOH_eff_den\tn_hbond\n")
# how many steps to go?
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.")
print("The script will proceed for the last " + str(n_step) + " timesteps.")
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_MtOH_C = []
aNo_MtOH_all = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Carbons in MeOH
if "MET" in atom.rName and "C" in atom.aName:
aNo_MtOH_C.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists MtOH properly
if len(aNo_MtOH_C) == 0:
nu.die("No MtOH 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()
processed_step += 1;
if processed_step == n_step:
break;
aNo_MtOH_C_atoms = []
aNo_atoms_in_CNT = []
### 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 = ""
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, True)
### myBGF update complete! ###
aNo_MtOH_C_in_CNT = copy.deepcopy(aNo_MtOH_C)
### Realign whole system to x axis
sys.stdout.write(' Realigning.. ')
sys.stdout.flush()
# 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; radius_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
### Rotate y or z to x axis
Tyx = numpy.array([[0, -1, 0], [1, 0, 0], [0, 0, 1]])
Tzx = numpy.array([[0, 0, -1], [0, 1, 0], [1, 0, 0]])
if CNT_orientation == "y":
for atom in myBGF.a:
u = numpy.matrix([atom.x, atom.y, atom.z]).T
Tu = Tyx*u
atom.x = float(Tu[0])
atom.y = float(Tu[1])
atom.z = float(Tu[2])
min_x_CNT = min_y_CNT;
max_x_CNT = max_y_CNT;
elif CNT_orientation == "z":
for atom in myBGF.a:
u = numpy.matrix([atom.x, atom.y, atom.z]).T
Tu = Tzx*u
atom.x = float(Tu[0])
atom.y = float(Tu[1])
atom.z = float(Tu[2])
min_x_CNT = min_z_CNT;
max_x_CNT = max_z_CNT;
### get MtOHs in CNT
sys.stdout.write('Density.. ')
sys.stdout.flush()
# 1. aNo_atoms_in_CNT: exact atoms within CNT
for atom in myBGF.a:
ano = atom.aNo
dist = math.sqrt(atom.y**2 + atom.z**2)
if not "CNT" in atom.rName and atom.x > min_x_CNT and atom.x < max_x_CNT and dist < radius_CNT:
# inside
aNo_atoms_in_CNT.append(ano)
else:
# outside
pass;
# 2. aNo_MtOH_C_atoms: molecules which C atom is within CNT
for aNo in aNo_MtOH_C:
atom = myBGF.getAtom(aNo)
dist = math.sqrt(atom.y**2 + atom.z**2)
if atom.x > min_x_CNT and atom.x < max_x_CNT and dist < radius_CNT:
# inside of the CNT
pass;
else:
"""
# delete atoms
delete_list = [];
dummy = bgftools.getmolecule(myBGF, myBGF.getAtom(aNo), delete_list)
for i in delete_list:
aNo_MtOH_C_not_in_CNT.append(myBGF.a2i[i])
"""
# outside of the CNT
aNo_MtOH_C_in_CNT.remove(aNo)
for aNo in aNo_MtOH_C_in_CNT:
anos = [];
dummy = bgftools.getmolecule(myBGF, myBGF.getAtom(aNo), anos)
for i in anos:
aNo_MtOH_C_atoms.append(i)
# calculate volume of CNT
# radius: average radius - can't be applied in bent CNTs
# height: maximum height of CNT
# volume: radius**2 + height
volume = (radius_CNT**2) * height_CNT * PI
eff_volume = (radius_CNT - vdw_r_C)**2 * height_CNT * PI
# calculate mass in CNT
MtOH_exact_mass = bgftools.getMass(myBGF, aNo_atoms_in_CNT, ff_file)
MtOH_MtOH_C_mass = bgftools.getMass(myBGF, aNo_MtOH_C_atoms, ff_file)
# calculate density: mass / 6.022 / vol * 10
vol_exact_density = MtOH_exact_mass / 6.022 / volume * 10;
vol_MtOH_density = MtOH_MtOH_C_mass / 6.022 / volume * 10;
# calculate effective density ( radius - r_vdw )
eff_vol_exact_density = MtOH_exact_mass / 6.022 / eff_volume * 10;
eff_vol_MtOH_density = MtOH_MtOH_C_mass / 6.022 / eff_volume * 10;
### Check MET status
output = "";
MeOH_align = [];
# find O in MET: MeOH_align = [C.x, O.x]
for ano in aNo_MtOH_C_in_CNT:
atom = myBGF.getAtom(ano)
for i in atom.CONECT:
atom2 = myBGF.getAtom(i)
if "O" in atom2.ffType:
MeOH_align.append([atom.x, atom2.x])
MeOH_align.sort(key=sortkey)
# print MET align status
for i in MeOH_align:
if i[0] > i[1]:
# C-O: 1
output += "1 "
else:
# O-C: 0
output += "0 "
# n_hbond
n_hbond = 0;
"""
# how many 10 or 01 (hydrogen bonds) in output?
count += output.count("1 0")
count += output.count("0 1")
"""
hbond_C_pairs = "";
hbond_OH_pairs = [];
if do_hbonds:
### find hydrogen bonds
### criteria: r(O..O) <= 3.5, r(O..HO) <= 2.6, A(HO-O..O) <= 30' (ref: Haughney et al., JPC 1987)
### acceptor donor donor acceptor
# for all pairs of MtOH molecules
sys.stdout.write('Hbonds.. ')
sys.stdout.flush()
C_pairs = itertools.permutations(aNo_MtOH_C_in_CNT, 2)
# count how many iterations on the permutations:
#c_perm = 0;
#for i in C_pairs:
# c_perm += 1;
#print(str(len(aNo_MtOH_C_in_CNT)) + " " + str(c_perm))
for p in C_pairs:
(ano1, ano2) = p
# Donor part
# get C1
C1 = myBGF.getAtom(ano1)
# get O1
for i in C1.CONECT:
temp_atom = myBGF.getAtom(i)
if "O" in temp_atom.ffType[0]:
O1 = temp_atom
# get H1
for i in O1.CONECT:
temp_atom = myBGF.getAtom(i)
if "H" in temp_atom.ffType[0]:
H1 = temp_atom
# Acceptor part
# get C2
C2 = myBGF.getAtom(ano2)
# get O2
for i in C2.CONECT:
temp_atom = myBGF.getAtom(i)
if "O" in temp_atom.ffType[0]:
O2 = temp_atom
# get H2
for i in O2.CONECT:
temp_atom = myBGF.getAtom(i)
if "H" in temp_atom.ffType[0]:
H2 = temp_atom
"""
# H1 and O2 should be inside the CNT
dist = math.sqrt(H1.y**2 + H1.z**2)
if H1.x > min_x_CNT and H1.x < max_x_CNT and dist < radius_CNT:
continue;
dist = math.sqrt(O2.y**2 + O2.z**2)
if O2.x > min_x_CNT and O2.x < max_x_CNT and dist < radius_CNT:
continue;
"""
## determine hbond
# calculate r(O1..O2)
crit_1 = bgf.distance(O1, O2);
# calculate r(O1..H2)
crit_2 = bgf.distance(O2, H1);
# calculate A(O1-H2..O2)
crit_3 = bgf.angle(H1, O1, O2);
#if crit_1 <= 3.5 and crit_2 <= 2.6 and crit_3 <= 30:
if crit_1 <= 3.5 and crit_3 <= 30:
# Hbond!!
n_hbond += 1;
OH_pair = [O2.aNo, H1.aNo];
hbond_OH_pairs.append(OH_pair)
#hbond_C_pairs += str(ano1) + "-" + str(ano2) + "\t"
else:
continue;
hbond_pairs = hbond_OH_pairs
#temp = nu.removeRepeat(hbond_OH_pairs)
#hbond_pairs = nu.removeReverse(temp)
sys.stdout.write('Done ')
sys.stdout.flush()
myDAT.write(str(timestep) + "\t")
myDAT.write(str("{0:<8.3f}".format(min_x_CNT)) + "\t")
myDAT.write(str("{0:<8.3f}".format(max_x_CNT)) + "\t")
myDAT.write(str("{0:<8.3f}".format(height_CNT)) + "\t")
myDAT.write(str("{0:<8.3f}".format(radius_CNT)) + "\t")
myDAT.write(str(len(aNo_MtOH_C_in_CNT)) + "\t")
myDAT.write(str("{0:<8.3f}".format(volume)) + "\t")
myDAT.write(str("{0:<8.3f}".format(eff_volume)) + "\t")
myDAT.write(str("{0:<8.3f}".format(MtOH_exact_mass)) + "\t")
myDAT.write(str("{0:<8.3f}".format(MtOH_MtOH_C_mass)) + "\t")
myDAT.write(str("{0:<8.3f}".format(vol_exact_density)) + "\t")
myDAT.write(str("{0:<8.3f}".format(vol_MtOH_density)) + "\t")
myDAT.write(str("{0:<8.3f}".format(eff_vol_exact_density)) + "\t")
myDAT.write(str("{0:<8.3f}".format(eff_vol_MtOH_density) + "\t"))
myDAT.write(str(len(hbond_pairs)) + "\n")
myDAT2.write(str(hbond_pairs) + "\n")
myDAT3.write(str(output) + "\n")
#myDAT.write(str(aNo_MtOH_C_in_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('')
myDAT.close()
myDAT2.close()
return 1
def countWaterCNT(bgf_file,
trj_file,
d_crit=3.5,
selection='',
nsample=0,
silent=False):
### init
# constants
deg_109p47 = math.radians(109.47)
# variables
timestep = 0
l_timestep = []
line = []
n_header = 0
avg_angles = []
avg_diheds = []
bin = np.arange(0.0, 181.0, 1.0)
t1 = 0
t2 = 0
# clock
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myDAT = open(bgf_file[:-4] + ".AOP.dat", "w")
myDAT.write("#timestep\tAOP\tF4\n")
# how many steps to go?
#mytrj = lt.lammpstrj(trj_file)
mytrj = Trj(trj_file)
l_timestep = mytrj.load()
n_timestep = len(l_timestep)
l_timestep.sort()
requested_timesteps = l_timestep[-nsample:]
print(
"Using neighboring water distance criteria %4.1f A (should be consistent with the coordination number)"
% d_crit)
print("The trajectory contains " + str(n_timestep) + " timesteps.")
# 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 * (len(requested_timesteps) -
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()
### 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 not timestep in requested_timesteps:
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 = ""
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
# apply periodic condition
myBGF = bgftools.periodicMoleculeSort(myBGF, myBGF.CRYSTX, silent=True)
### myBGF update complete! ###
# get water OW
O = []
anos_O = []
for atom in myBGF.a:
if selection:
if "O" in atom.ffType and eval(selection):
O.append(atom)
anos_O.append(atom.aNo)
else:
if "O" in atom.ffType:
O.append(atom)
anos_O.append(atom.aNo)
if not len(O):
nu.die("There are no O atoms which satisfies %s!" % selection)
### calculate AOP and F4
sys.stdout.write('AOP..... ')
sys.stdout.flush()
coords = []
anos = []
for atom in O:
coords.append([atom.x, atom.y, atom.z])
anos.append(atom.aNo)
pbc = np.array(myBGF.CRYSTX[:3])
coords = np.array(coords)
tree = pkdtree.PeriodicKDTree(
pbc, coords) # KDtree for distance calculation
# analyze local water structures for a timestep
n_neighbors = []
angles = []
diheds = []
for atom in O:
# local variables
# find neighbors
neighbors = []
# list of O atoms near centerO
centerO = np.array([atom.x, atom.y, atom.z])
d, ndx = tree.query(centerO, k=6)
index = np.where((d >= 1e-4) & (d <= d_crit)) # discard self
for i in ndx[index]:
neighbors.append(myBGF.getAtom(anos[i]))
# calculate O1-O-O2 angle
for i, j in itertools.combinations(neighbors, 2):
if not "O" in i.ffType or not "O" in j.ffType:
nu.die("Wrong atom found.")
x = [i.x, i.y, i.z]
y = [j.x, j.y, j.z]
pbc_dist = nu.pbc_dist(x, y, pbc)
dist = nu.dist(x, y)
if abs(pbc_dist - dist) > 0.1:
continue
# discard atoms over pbc boundaries
# angle
angle = nu.angle(x, centerO, y, radians=False)
angles.append(angle)
n_neighbors.append(
len(neighbors)) # number of neighboring water molecules
# calculate dihedral
for i in neighbors:
# find aNos of H located farthest among all combinations
hO_anos = atom.CONECT
hi_anos = i.CONECT
max_dist_pair = []
max_dist = 0.0
for k, l in itertools.product(hO_anos, hi_anos):
h1 = myBGF.getAtom(k) # H atom connected with atom
h2 = myBGF.getAtom(l) # H atom connected with i
dist = bgf.distance(h1, h2)
if dist > max_dist:
max_dist = dist
max_dist_pair = [
h1, h2
] # now we have two H atoms in maximum distance connected with atom and i
# dihedral angle
phi = bgf.dihedral(max_dist_pair[0],
atom,
i,
max_dist_pair[1],
radians=False)
diheds.append(phi)
hist_angle, _ = np.histogram(angles, bins=bin, normed=True)
hist_dihed, _ = np.histogram(diheds, bins=bin, normed=True)
avg_angles.append(hist_angle)
avg_diheds.append(hist_dihed)
sys.stdout.write(
'Done ')
sys.stdout.flush()
# write output
processed_step += 1
t2 = time.time() # time mark
elapsed_time = t2 - t1
avg_angles = np.mean(np.array(avg_angles), axis=0)
avg_diheds = np.mean(np.array(avg_diheds), axis=0)
#print(avg_diheds)
myDAT.write("#angles population\n")
for index, i in enumerate(avg_angles):
myDAT.write("%8.2f %8.5f\n" % (_[index], avg_angles[index]))
myDAT.write("\n\n")
myDAT.write("#diheds population\n")
for index, i in enumerate(avg_diheds):
myDAT.write("%8.2f %8.5f\n" % (_[index], avg_diheds[index]))
myDAT.close()
print('')
return 1
def dipole(bgf_file, trj_file, ff_file, out_file, avg_timestep, silent=False):
### init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
vector = [0, 0, 1]
# the axis of interest. in the acetone-water case, z direction.
atominfo = dict()
# atom data extracted from ff_file
result = dict()
axis = 2
# for orientational distribution of dipole moments. 1: x-axis, 2: y-axis, 3: z-axis
### unit conversion for debye
elementary_q = 1.602176487e-19 # elementary charge in C
debye_conv = 3.33564e-30 # 1 Debye in C*m
k = elementary_q * 1e-10 / debye_conv
### open files
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myOUT = open(out_file + ".dat", 'w')
#myOUT2 = open(out_file + ".angle.dat", 'w')
myRESULT = open(out_file + ".pickle", 'w')
myRESULT2 = open(out_file + ".histo.pickle", 'w')
### read residues from bgf_file
residueNames = set()
# kind of residues in BGF file
residueNumbers = set()
dict_residue = dict()
# stores residue numbers per each residue. RES1: [1, 2, ..], RES2: [6, 7, ..]
for i in myBGF.a:
rname = string.strip(i.rName)
residueNames.add(rname)
rno = i.rNo
residueNumbers.add(rno)
temp = ""
for i in residueNames:
temp += i + " "
dict_residue[i] = []
if not silent:
print("Found " + str(len(residueNames)) + " residues in BGF file: " +
str(temp))
### bookkeep residue numbers for each residue
molecules = bgftools.getMoleculeList(myBGF)
for molecule in molecules:
# get an atom
atom = myBGF.getAtom(molecule[0])
atomresname = string.strip(atom.rName)
atomresno = atom.rNo
# check if all molecule has same residue name and numbers
for ano in molecule:
atom2 = myBGF.getAtom(ano)
temp_rno = atom2.rNo
temp_rname = string.strip(atom2.rName)
if temp_rno != atomresno or temp_rname != atomresname:
nu.die(
"Different residue name or residue number in a same molecule: "
+ str(atom2.aNo))
# record resid for resnames
dict_residue[atomresname].append(atom.rNo)
### read mass from ff_file
try:
parse = ff_file.split(" ")
except:
nu.die(
"Error occurred when reading the force field file.. Check your " +
str(ff_file))
else:
if not silent:
print("Found " + str(len(parse)) + " Cerius2 Force Fields.")
for i in parse:
FF = dreiding.loadFF(i)
temp_atominfo = dreiding.loadAtomTypes(FF)
atominfo.update(temp_atominfo)
### read trajectory file
# how many steps to go?
wc_trj_file = popen("grep -A 1 TIMESTEP " + trj_file).read()
wc_trj_file = wc_trj_file.split()
l_timestep = []
for i in wc_trj_file:
if "ITEM" in i or "TIME" in i or "--" in i:
pass
else:
l_timestep.append(i)
l_timestep = [int(i) for i in l_timestep]
l_timestep.sort()
n_timestep = len(l_timestep)
if not silent:
print("The trajectory contains " + str(n_timestep) + " timesteps.")
l_requested_timesteps = l_timestep[-avg_timestep:] # requested timesteps
if not silent:
print("Only requested the last " + str(avg_timestep) + " timesteps. ")
# 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])
if not timestep in l_requested_timesteps:
continue
#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(' ')
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (len(l_requested_timesteps) -
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) + ")")
sys.stdout.flush()
processed_step += 1
### 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)
### DONE for updating trj on BGF file ###
### Now Dipole Moment Calculation
# list of all molecules in BGF
dipole_moments = dict()
abs_dipole_moments = dict()
angles = dict()
temp_dict = dict()
output_dipole = str(timestep) + "\t"
output_abs_dipole = str(timestep) + "\t"
output_angle = str(timestep) + "\t"
### find bin for orientational distribution of dipole moment
min = 100000
max = -100000
for atom in myBGF.a:
coord = [atom.x, atom.y, atom.z]
if coord[axis] < min:
min = coord[axis]
if coord[axis] > max:
max = coord[axis]
if boxsize[axis] > max:
max = boxsize[axis]
if 0 < min:
min = 0
bins = np.arange(math.floor(min), math.ceil(max), 1.0)
binned_rNo = dict()
for r in residueNames:
binned_rNo[r] = [[] for b in bins]
# space for binned residue numbers (= molecules)
binned_mu = copy.deepcopy(binned_rNo)
### For every molecule
for molecule in molecules:
n_atom = len(molecule) # number of atoms in the molecule
residue_no = myBGF.getAtom(molecule[0]).rNo
# residue number of the molecule
residue_name = myBGF.getAtom(molecule[0]).rName
# residue name of the molecule
m = bgftools.getMass(myBGF, molecule, ff_file)
# molecule mass
cm = [0, 0, 0]
# center of mass
mu = [0, 0, 0]
# dipole moment
coord = [0, 0, 0]
# atom x, y, z
for aNo in molecule:
atom = myBGF.getAtom(aNo)
coord = [atom.x, atom.y, atom.z]
# error if residue numbers are different
if atom.rNo != residue_no:
nu.die(
"Residue numbers in a same molecule are not consistent. Please check your BGF file."
)
# error if mass is unreadable
ffType = string.strip(atom.ffType)
try:
aMass = atominfo[ffType]['MASS']
except:
nu.die("Cannot read the atom type " + str(atom.ffType) +
" in the data file.")
# calculate CM
for index, i in enumerate(coord):
cm[index] += i * aMass
cm = [i / m for i in cm]
# center of mass
#print(str(residue_no) + '\t' + str(cm))
# REMARK: it seems to be okay without this process.
"""
# translate the molecule to CM
for aNo in molecule:
atom = myBGF.getAtom(aNo)
atom.x -= cm[0]
atom.y -= cm[1]
atom.z -= cm[2]
"""
# calculate dipole moment sum(qi * di)
mu_i = []
for aNo in molecule:
atom = myBGF.getAtom(aNo)
coord = [atom.x, atom.y, atom.z]
mu_i.append([i * atom.charge * k for i in coord])
# sum up
mu = [0, 0, 0]
for i in mu_i:
mu[0] += i[0]
mu[1] += i[1]
mu[2] += i[2]
# for acetone case
#len_mu = math.sqrt(dot(mu, mu))
#len_vector = math.sqrt(dot(vector, vector))
len_mu = math.sqrt(dot(mu, mu))
len_vector = 1.0
#angle = dot(mu, vector) / ( len_mu * len_vector )
angle = mu[2] / (len_mu * len_vector) # for ACETONE case
# results
dipole_moments[residue_no] = mu
abs_dipole_moments[residue_no] = len_mu
angles[residue_no] = angle
### Orientational distribution of dipole moments
# binning according to molecule's CM and store to binned_rNo
for index, bin in enumerate(bins):
try:
if bin < cm[axis] and bins[index + 1] > cm[axis]:
binned_rNo[residue_name][index].append(residue_no)
except:
continue
# binning is perfect so far!
residueNumbers = list(residueNumbers)
residueNames = list(residueNames)
residueNumbers.sort()
temp_dict = dict()
temp_dict2 = dict()
temp_dict2['MU'] = dipole_moments
temp_dict2['ABSMU'] = abs_dipole_moments
temp_dict2['ANGLES'] = angles
temp_dict['TOTAL'] = temp_dict2
### paperworks per residue
for resname in residueNames:
temp_dict2 = dict()
res_dipole_moments = dict()
res_abs_dipole_moments = dict()
res_angles = dict()
# load residue numbers per residue type
resnumbers = dict_residue[resname]
for rno in resnumbers:
res_dipole_moments[rno] = dipole_moments[rno]
res_abs_dipole_moments[rno] = abs_dipole_moments[rno]
res_angles[rno] = angles[rno]
temp_dict2['MU'] = res_dipole_moments
temp_dict2['ABSMU'] = res_abs_dipole_moments
temp_dict2['ANGLES'] = res_angles
temp_dict2['BIN'] = bins
# for analyze
#temp_dict2['RNO_DISTR'] = binned_rNo[resname]
temp_dict2['DISTR_ANGLES'] = binned_mu[resname]
temp_dict2['DISTR_ABSMU'] = binned_mu[resname]
# write dipole moments
for index, item in enumerate(binned_rNo[resname]):
if len(item) == 0:
continue
for i in item:
temp_dict2['DISTR_ANGLES'][index].append(
temp_dict2['ANGLES'][i])
#temp_dict2['DISTR_ABSMU'][index].append(temp_dict2['ABSMU'][i])
temp_dict[resname] = temp_dict2
# result: timestep - residue - MU, ANGLES, NATOMS
result[timestep] = temp_dict
t2 = time.time() # time mark
elapsed_time = t2 - t1
### Averaging orientational distribution of dipole moments over timesteps
#del temp_dict1
del temp_dict2
temp_dict1 = dict()
# angles with keys: bin
temp_dict2 = dict()
# |mu| with keys: bin
# append
for r in residueNames:
temp_dict1[r] = dict()
temp_dict2[r] = dict()
for t in l_requested_timesteps:
for index, b in enumerate(result[t][r]['BIN']):
if not temp_dict1[r].has_key(b):
temp_dict1[r][b] = []
if not temp_dict2[r].has_key(b):
temp_dict2[r][b] = []
# append averaged values
avg, std = meanstdv(result[t][r]['DISTR_ANGLES'][index])
temp_dict1[r][b].append(avg)
for i in result[t][r]['DISTR_ANGLES'][index]:
temp_dict2[r][b].append(i)
#for i in result[t][r]['DISTR_ABSMU'][index]:
# temp_dict2[b].append(i)
# average
avg_angles = dict()
avg_absmu = dict()
avg_angles_stdev = dict()
avg_absmu_stdev = dict()
for r in residueNames:
avg_angles[r] = dict()
avg_absmu[r] = dict()
avg_angles_stdev[r] = dict()
avg_absmu_stdev[r] = dict()
temp = temp_dict1[r].keys()
temp.sort()
for i in temp:
avg_angles[r][i], avg_angles_stdev[r][i] = meanstdv(
temp_dict1[r][i])
avg_absmu[r][i], avg_absmu_stdev[r][i] = meanstdv(temp_dict2[r][i])
# print for average
print("")
print("Averaged " + str(avg_timestep) + " timesteps out of " +
str(n_timestep))
for r in residueNames:
print(r)
for i in temp:
#print(str(i) + '\t' + str(temp_dict1[i]))
print(
str(i) + '\t' + str(avg_angles[r][i]) + '\t' +
str(avg_angles_stdev[r][i]))
print("")
# save for debug
output = ""
for r in residueNames:
for i in temp:
output += str(i) + '\t' + str(temp_dict1[r][i]) + '\n'
myOUT.write(output)
myOUT.close()
# save the pickle object
pkl.dump(result, myRESULT)
myRESULT.close()
pkl.dump(temp_dict2, myRESULT2)
myRESULT2.close()
print('')
return 1
def getHbond(bgf_file, trj_file, ff_file='', selection='', out_file='', n=0):
'''analyze something within a timestep in a series of lammps trajectory.
'''
# variables
result = dict()
# inner functions
def get_line(file):
with open(file, 'r') as f:
for line in f:
yield line
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
atom_frags = bt.getMoleculeList(mybgf)
# 2. Read LAMMPS Trajectory
mytrj = lt.lammpstrj(trj_file)
timesteps = mytrj.load()
N_HEADER = mytrj.nheader
N_ATOMS = mytrj.natoms[timesteps[0]]
N_BUFFER = N_HEADER + N_ATOMS
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
# 3. Determine dump style
dump_keywords = mytrj.dumpstyle
yes_scale = False
if 'xs' in dump_keywords:
yes_scale = True
# 4. Update coordinates from the snapshot
dump = get_line(trj_file)
requested_t = sorted(timesteps)[-n:]
for t in tqdm.tqdm(timesteps,
ncols=120,
desc="Analyzing HBonds",
miniters=1):
chunk = [next(dump) for i in range(N_BUFFER)]
if not t in requested_t:
continue
mybgf = update_coord(chunk, mybgf, mytrj.pbc[t], scaled=yes_scale)
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
fragments=atom_frags,
ff_file=ff_file,
silent=True)
### collect data
def calc_hbonds():
# variables
A = []
D = []
hbond_angles = []
d_crit = 3.5
a_crit = 30.0
for atom in mybgf.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die(
"There are no atoms which can make H_bond (O atoms so far)!"
)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A, d, r=d_crit, k=6)
neigh_hbonded_coord = []
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y,
a_atom.z]) # acceptor coord
if bt.is_hbonded(mybgf, d_atom, a_atom):
neigh_hbonded_coord.append(a)
for i, j in itertools.combinations(neigh_hbonded_coord, 2):
angle = nu.angle(i, d, j, radians=False)
hbond_angles.append(angle)
return hbond_angles
hbonds = calc_hbonds()
result[t] = hbonds
#break; # tester
# 5. Analyze
if not out_file:
out_file = trj_file + ".hbonds.angles."
pickle_file = out_file + ".pickle"
with open(pickle_file, 'wb') as f:
pickle.dump(result, f, protocol=pickle.HIGHEST_PROTOCOL)
print("Success to save the result to a pickle file %s" % pickle_file)
def getHbond(bgf_file, trj_file, ff_file='', selection='', out_file=''):
'''analyze something within a timestep in a series of lammps trajectory.
'''
# variables
result = dict()
# inner functions
def get_line(file):
with open(file, 'r') as f:
for line in f:
yield line
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
# 2. Read LAMMPS Trajectory
#timesteps, N_HEADER, N_ATOMS = lt.getTrjInfo(trj_file)
mytrj = lt.lammpstrj(trj_file)
timesteps = mytrj.load()
N_HEADER = mytrj.nheader
N_ATOMS = mytrj.natoms[timesteps[0]]
N_BUFFER = N_HEADER + N_ATOMS
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
# 3. Determine dump style
dump_keywords = mytrj.dumpstyle
yes_scale = False
if 'xs' in dump_keywords:
yes_scale = True
# 4. Update coordinates from the snapshot
dump = get_line(trj_file)
for t in tqdm.tqdm(timesteps, ncols=120, desc="Analyzing HBonds"):
chunk = [next(dump) for i in range(N_BUFFER)]
t = int(chunk[1])
mybgf.CRYSTX = mytrj.pbc[t] + [90.0, 90.0, 90.0]
coords = chunk[9:]
for c in coords:
c = c.split(' ')
atom = mybgf.getAtom(int(c[0]))
if yes_scale:
atom.x = float(c[2]) * pbc[0]
atom.y = float(c[3]) * pbc[1]
atom.z = float(c[4]) * pbc[2]
else:
atom.x = float(c[2])
atom.y = float(c[3])
atom.z = float(c[4])
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
ff_file=ff_file,
silent=True)
### collect data
def calc_hbonds():
# variables
A = []
D = []
hbonds = []
d_crit = 3.5
a_crit = 30.0
for atom in mybgf.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die(
"There are no atoms which can make H_bond (O atoms so far)!"
)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z])
neigh_anos = bt.get_neighbors_aNo(A,
d,
r=d_crit,
pbc=mytrj.pbc[t])
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
h = bt.is_hbonded2(mybgf, d_atom,
a_atom) # returns hbonded H coord
if len(h) != 0:
a = np.array([a_atom.x, a_atom.y, a_atom.z])
dist = nu.pbc_dist(a, d, mytrj.pbc[t])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
theta = np.degrees(arccos(theta))
hbonds.append(
[d_atom.aNo, a_atom.aNo, d, a, dist, theta])
return hbonds
hbonds = calc_hbonds()
result[t] = hbonds
#break; # tester
# 5. Analyze
if not out_file:
out_file = trj_file + ".hbonds.new2"
pickle_file = out_file + ".pickle"
with open(pickle_file, 'wb') as f:
pickle.dump(result, f, protocol=pickle.HIGHEST_PROTOCOL)
print("Success to save the result to a pickle file %s" % pickle_file)
def countWaterCNT(bgf_file, trj_file, step, doSave, silent=False):
# init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myDAT = open(bgf_file[:-4] + ".count.dat", "w")
myDAT.write("Time\tmin_X\tmax_X\tHeight\tRadius\tNumber\n")
# 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_MtOH_C = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Carbons in MeOH
if "MET" in atom.rName and "C" in atom.aName:
aNo_MtOH_C.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) + ")")
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! ###
aNo_MtOH_C_in_CNT = copy.deepcopy(aNo_MtOH_C)
# 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])
"""
# 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
# transpose for "all atoms in BGF": move COM of CNT as origin
for atom in myBGF.a:
atom.x -= Mx
atom.y -= My
atom.z -= Mz
"""
# 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_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
# determine whether C in MtOH is in the CNT Cylinder
if doSave:
myBGF2 = copy.deepcopy(myBGF)
for aNo in aNo_MtOH_C:
atom = myBGF.getAtom(aNo)
if CNT_orientation == "x":
dist = math.sqrt(atom.y**2 + atom.z**2)
if atom.x > min_x_CNT and atom.x < max_x_CNT and dist < radius_CNT:
# inside of the CNT
pass
else:
# delete atoms
delete_list = []
dummy = bgftools.getmolecule(myBGF, myBGF.getAtom(aNo),
delete_list)
for i in delete_list:
aNo_MtOH_C_not_in_CNT.append(myBGF.a2i[i])
# outside of the CNT
aNo_MtOH_C_in_CNT.remove(aNo)
elif CNT_orientation == "y":
dist = math.sqrt(atom.x**2 + atom.z**2)
if atom.y > min_y_CNT and atom.y < max_y_CNT and dist < radius_CNT:
pass
else:
# delete atoms
delete_list = []
dummy = bgftools.getmolecule(myBGF, myBGF.getAtom(aNo),
delete_list)
for i in delete_list:
aNo_MtOH_C_not_in_CNT.append(myBGF.a2i[i])
# outside of the CNT
aNo_MtOH_C_in_CNT.remove(aNo)
elif CNT_orientation == "z":
dist = math.sqrt(atom.x**2 + atom.y**2)
if atom.z > min_z_CNT and atom.z < max_z_CNT and dist < radius_CNT:
pass
else:
# delete atoms
delete_list = []
dummy = bgftools.getmolecule(myBGF, myBGF.getAtom(aNo),
delete_list)
for i in delete_list:
aNo_MtOH_C_not_in_CNT.append(myBGF.a2i[i])
# outside of the CNT
aNo_MtOH_C_in_CNT.remove(aNo)
myBGF2.delAtoms(aNo_MtOH_C_not_in_CNT)
myBGF2.renumber()
myDAT.write(str(timestep) + "\t")
myDAT.write(str("{0:<8.3f}".format(min_x_CNT)))
myDAT.write(str("{0:<8.3f}".format(max_x_CNT)))
myDAT.write(str("{0:<8.3f}".format(min_y_CNT)))
myDAT.write(str("{0:<8.3f}".format(max_y_CNT)))
myDAT.write(str("{0:<8.3f}".format(min_z_CNT)))
myDAT.write(str("{0:<8.3f}".format(max_z_CNT)))
myDAT.write(str("{0:<8.3f}".format(height_CNT)))
myDAT.write(str("{0:<8.3f}".format(radius_CNT)))
myDAT.write(str(len(aNo_MtOH_C_in_CNT)) + "\n")
#myDAT.write(str(aNo_MtOH_C_in_CNT) + "\n")
# write output
if doSave:
myBGF2.saveBGF(bgf_file[:-4] + "." + str(timestep) + ".bgf")
t2 = time.time() # time mark
elapsed_time = t2 - t1
print('')
return 1
def countWaterCNT(bgf_file, trj_file, out_file, 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
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myNewTRJ = open(out_file, 'w')
# 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_MtOH_all = []
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
# check if there exists MtOH properly
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
d_atomtype = dict()
# dict for writing atom types
# check flag for atom informations: the first shot will be treated, and will be skipped after.
firsttimeFlag = 0
while 1:
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (n_timestep - 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()
processed_step += 1
### 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 = ""
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?")
### for the first shot, record atom types
if firsttimeFlag == 0:
d_atomtype[int(atomcoord[0])] = atomcoord[1]
### myBGF update complete! ###
### Realign whole system to x axis
sys.stdout.write(' Realigning.. ')
sys.stdout.flush()
# 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])
### update crystx information: note that CNT is along x-axis. # is this right?? 20130619
if boxsize[0] > boxsize[1] and boxsize[0] > boxsize[2]:
boxsize = [boxsize[0], boxsize[1], boxsize[2]]
elif boxsize[1] > boxsize[0] and boxsize[1] > boxsize[2]:
boxsize = [boxsize[1], boxsize[0], boxsize[2]]
elif boxsize[2] > boxsize[0] and boxsize[2] > boxsize[1]:
boxsize = [boxsize[2], boxsize[0], boxsize[1]]
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
# transpose to the center of box
for atom in myBGF.a:
atom.x += (boxsize[0] / 2)
atom.y += (boxsize[1] / 2)
atom.z += (boxsize[2] / 2)
# apply periodic condition
myBGF = bgftools.periodicMoleculeSort(myBGF, 0)
### Write LAMMPS trjectory
output = "ITEM: TIMESTEP\n"
output += str(timestep) + "\n"
output += "ITEM: NUMBER OF ATOMS\n"
output += str(natom_bgf) + "\n"
output += "ITEM: BOX BOUNDS pp pp pp\n"
output += "0 " + str(boxsize[0]) + "\n"
output += "0 " + str(boxsize[1]) + "\n"
output += "0 " + str(boxsize[2]) + "\n"
output += "ITEM: ATOMS id type xu yu zu\n"
for atom in myBGF.a:
output += str(atom.aNo) + " " + d_atomtype[atom.aNo] + " " + str(
atom.x) + " " + str(atom.y) + " " + str(atom.z) + "\n"
myNewTRJ.write(output)
t2 = time.time() # time mark
elapsed_time = t2 - t1
myNewTRJ.close()
print('')
return 1
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 getHBond(bgf_file,
trj_file,
out_file,
direction,
interval,
avg_timestep,
silent=False):
nu.warn(
"LAMMPS trajectory with NPT simulations will give you the wrong result."
)
### init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
vector = [0, 0, 1]
# the axis of interest. in the acetone-water case, z direction.
atominfo = dict()
# atom data extracted from ff_file
result = dict()
axis = 0
# 1: x-axis, 2: y-axis, 3: z-axis
### direction
if "x" in direction:
axis = 0
elif "y" in direction:
axis = 1
elif "z" in direction:
axis = 2
else:
nu.die("Error on reading direction.")
### open files
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
f_out_file = open(out_file + ".dat", 'w')
f_avg_out_file = open(out_file + ".average.dat", 'w')
f_pickle = open(out_file + ".pickle", 'w')
f_avg_pickle = open(out_file + ".average.pickle", 'w')
### read residues from bgf_file
residue = set()
# kind of residues in BGF file
dict_residue = dict()
# stores residue numbers per each residue. RES1: [1, 2, ..], RES2: [6, 7, ..]
for i in myBGF.a:
rname = string.strip(i.rName)
residue.add(rname)
output = ""
for i in residue:
output += i + " "
if not silent:
print("Found " + str(len(residue)) + " residues in BGF file: " +
str(output))
residue = list(residue)
residue.append('TOTAL')
for index, i in enumerate(residue):
dict_residue[i] = index
n_residue = len(residue) # number of residues (including total)
### read trajectory file
# 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.")
# 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])
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(' ')
### 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) + ")")
sys.stdout.flush()
processed_step += 1
### 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)
### DONE for updating trj on BGF file ###
### Do whatever I want: density profile
### list up O in ACT
### list up H in WAT
### for every pair, get hbond dist
### if it's less than 2.4A, then count++
### return
print('')
return 1
