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 countWater(bgf_file, trj_file, n_step, watercopy, ff_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)
global out_file
if out_file == "": out_file = "countWater5.profile"
print("The result will be recorded to the file " + out_file + " ...")
ftemp = open(out_file, 'w')
ftemp.write(str(sys.argv) + "\n")
ftemp.write("t" + '\t' + "n_O" + '\t' + "r_CNT" + '\t' + "std_r" + '\t' +
"min_x" + '\t' + "max_x" + '\t' + "min_y" + '\t' + "max_y" +
'\t' + "min_z" + '\t' + "max_z" + '\t' + "l_NT" + '\t' +
"replNum" + '\t' + "copyNum" + '\t' + "n_WAT" + '\t' +
"remark" + '\n')
curr_dir = os.path.abspath(".")
temp_dir = curr_dir + "/countWAT5/"
print(temp_dir)
if not os.path.isdir(temp_dir): os.makedirs(temp_dir)
### how many steps to go?
n_timestep = len(lt.getTrjInfo(trj_file))
if n_step == 0:
n_step = n_timestep
print(" ..The trajectory contains " + str(n_timestep) + " timesteps.")
print("The script will proceed for the first " + str(n_step) +
" timesteps.")
### read mass from ff_file
atominfo = dict()
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)
### extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
mass_CNT = []
for atom in myBGF.a:
# Carbons in CNT or atoms in BNNT
if "NT" in atom.rName:
aNo_CNT.append(atom.aNo)
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.")
mass_CNT.append(aMass)
# 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
myBGF = bgf.BgfFile(bgf_file)
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
timestep = int(chunk[1])
natoms = int(chunk[3])
boxsize = [
chunk[5].split(' ')[0], chunk[5].split(' ')[1],
chunk[6].split(' ')[0], chunk[6].split(' ')[1],
chunk[7].split(' ')[0], chunk[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
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:]
# load atom coordinates from chunk
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])
### convert atom coordinates to lists
CNT = []
WATER = []
for atom in myBGF.a:
if "NT" in atom.rName:
CNT.append([atom.x, atom.y, atom.z])
if "WAT" in atom.rName and "O" in atom.ffType:
WATER.append([atom.x, atom.y, atom.z])
CNT = np.array(CNT)
n_CNT = len(CNT) # CNT coordinates
WATER = np.array(WATER) # Water coordinates
WATERONLY = np.copy(WATER)
boxsize = np.array(boxsize)
### initialize for the moment of inertia and the center of mass calculation
U = 0
Ut = 0
Uv = 0
Ixx = 0
Ixy = 0
Ixz = 0
Iyx = 0
Iyy = 0
Iyz = 0
Izx = 0
Izy = 0
Izz = 0
Mx = 0
My = 0
Mz = 0
### transpose "all atoms in BGF": move COM of CNT as origin
Mx, My, Mz = np.average(CNT, axis=0, weights=mass_CNT) # CoM of CNT
COM = np.array([[Mx, My, Mz]])
CNT = CNT - COM + boxsize / 2.0 # move
WATER = WATER - COM + boxsize / 2.0
### apply PBC
WATER = np.mod(WATER, boxsize)
### save coordinates to BGF before rotation
myBGF2 = bgf.BgfFile()
for index, i in enumerate(CNT):
newatom = bgf.BgfAtom()
newatom.x, newatom.y, newatom.z = i
newatom.aNo = index
newatom.aName = 'C' + str(index)
newatom.rName = 'CNT'
newatom.ffType = 'C_'
newatom.chain = 'A'
newatom.rNo = 1
myBGF2.addAtom(newatom)
for index, i in enumerate(WATER):
newatom = bgf.BgfAtom()
newatom.x, newatom.y, newatom.z = i
newatom.aNo = index + n_CNT
newatom.aName = 'O'
newatom.rName = 'WAT'
newatom.ffType = 'OW'
newatom.chain = 'O'
newatom.rNo = 100
myBGF2.addAtom(newatom)
myBGF2.REMARK.append('TIMESTEP ' + str(timestep))
myBGF2.PERIOD = "111"
myBGF2.AXES = "ZYX"
myBGF2.SGNAME = "P 1 1 1"
myBGF2.CELLS = [-1, 1, -1, 1, -1, 1]
myBGF2.CRYSTX = [boxsize[0], boxsize[1], boxsize[2], 90.0, 90.0, 90.0]
myBGF2.saveBGF(temp_dir + bgf_file.split(".bgf")[0] + "." +
str(timestep) + ".bgf")
### move CM of CNT to origin
CNT = CNT - boxsize / 2.0
WATER = WATER - boxsize / 2.0
### how the CNT is lying across the periodic box?
for atom in CNT:
min_x_CNT, min_y_CNT, min_z_CNT = CNT.min(axis=0)
max_x_CNT, max_y_CNT, max_z_CNT = CNT.max(axis=0)
margin = 5.0
### copy water molecules
max_x_axis = int(round((max_x_CNT + margin) / boxsize[0]))
min_x_axis = int(round((min_x_CNT - margin) / boxsize[0]))
max_y_axis = int(round((max_y_CNT + margin) / boxsize[1]))
min_y_axis = int(round((min_y_CNT - margin) / boxsize[1]))
max_z_axis = int(round((max_z_CNT + margin) / boxsize[2]))
min_z_axis = int(round((min_z_CNT - margin) / boxsize[2]))
replNum = (min_x_axis, max_x_axis, min_y_axis, max_y_axis, min_z_axis,
max_z_axis)
copyNum = 0
remark = ""
if watercopy:
for x in range(min_x_axis, max_x_axis + 1):
remark += "x: "
if x != 0:
WATER2 = np.copy(WATERONLY)
dx = np.array([[boxsize[0] * x, 0, 0]])
WATER2 = WATER2 + dx
WATER = np.concatenate((WATER, WATER2))
copyNum += 1
remark += str(x) + " "
for y in range(min_y_axis, max_y_axis + 1):
remark += "y: "
if y != 0:
WATER2 = np.copy(WATERONLY)
dy = np.array([[0, boxsize[1] * y, 0]])
WATER2 = WATER2 + dy
WATER = np.concatenate((WATER, WATER2))
copyNum += 1
remark += str(y) + " "
for z in range(min_z_axis, max_z_axis + 1):
remark += "z: "
if z != 0:
WATER2 = np.copy(WATERONLY)
dz = np.array([[0, 0, boxsize[2] * z]])
WATER2 = WATER2 + dz
WATER = np.concatenate((WATER, WATER2))
copyNum += 1
remark += str(z) + " "
'''
### WATER distribution check
x_axis = np.linspace(WATER[:,0].min(), WATER[:,0].max(), 10)
y_axis = np.linspace(WATER[:,1].min(), WATER[:,1].max(), 10)
z_axis = np.linspace(WATER[:,2].min(), WATER[:,2].max(), 10)
x_hist, _ = np.histogram(WATER[:,0], x_axis, normed=True)
y_hist, _ = np.histogram(WATER[:,1], y_axis, normed=True)
z_hist, _ = np.histogram(WATER[:,2], z_axis, normed=True)
remark += " xdist: "
for i in x_hist:
remark += "{0:6.3f}".format(i)
remark += " ydist: "
for i in y_hist:
remark += "{0:6.3f}".format(i)
remark += " zdist: "
for i in z_hist:
remark += "{0:6.3f}".format(i)
'''
### MI of CNT calculation
for atom in CNT:
Ixx += (atom[1]**2 + atom[2]**2) / N_CNT
Iyy += (atom[0]**2 + atom[2]**2) / N_CNT
Izz += (atom[0]**2 + atom[1]**2) / N_CNT
Ixy -= (atom[0] * atom[1]) / N_CNT
Ixz -= (atom[0] * atom[2]) / N_CNT
Iyz -= (atom[1] * atom[2]) / N_CNT
I = np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz],
[Ixz, Iyz, Izz]]) # the moment of inertia tensor
eigval, eigvec = np.linalg.eig(
I) # eigval[0] is the minimum among the values.
U = np.matrix(eigvec)
Ut = U.T
### box rotation
for atom in CNT:
v = np.matrix([atom[0], atom[1], atom[2]]).T
Uv = Ut * v
atom[0] = float(Uv[2])
atom[1] = float(Uv[1])
atom[2] = float(Uv[0]) # CNT rotation
for atom in WATER:
v = np.matrix([atom[0], atom[1], atom[2]]).T
Uv = Ut * v
atom[0] = float(Uv[2])
atom[1] = float(Uv[1])
atom[2] = float(Uv[0]) # water rotation
### save coordinates to BGF after rotation
myBGF2 = bgf.BgfFile()
for index, i in enumerate(CNT):
newatom = bgf.BgfAtom()
newatom.x, newatom.y, newatom.z = i
newatom.aNo = index
newatom.aName = 'C' + str(index)
newatom.rName = 'CNT'
newatom.ffType = 'C_'
newatom.chain = 'A'
newatom.rNo = 1
myBGF2.addAtom(newatom)
for index, i in enumerate(WATER):
newatom = bgf.BgfAtom()
newatom.x, newatom.y, newatom.z = i
newatom.aNo = index + n_CNT
newatom.aName = 'O'
newatom.rName = 'WAT'
newatom.ffType = 'OW'
newatom.chain = 'O'
newatom.rNo = 100
myBGF2.addAtom(newatom)
myBGF2.REMARK.append('TIMESTEP ' + str(timestep))
myBGF2.PERIOD = "111"
myBGF2.AXES = "ZYX"
myBGF2.SGNAME = "P 1 1 1"
myBGF2.CELLS = [-1, 1, -1, 1, -1, 1]
myBGF2.CRYSTX = [boxsize[0], boxsize[1], boxsize[2], 90.0, 90.0, 90.0]
myBGF2.saveBGF(temp_dir + bgf_file.split(".bgf")[0] + "." +
str(timestep) + ".rot.bgf")
### CNT height
_, _, min_z_CNT = CNT.min(axis=0)
_, _, max_z_CNT = CNT.max(axis=0)
height_CNT = max_z_CNT - min_z_CNT
### CNT radius
x_CNT, y_CNT, z_CNT = np.mean(CNT, axis=0)
x_std_CNT, y_std_CNT, z_std_CNT = np.std(CNT, axis=0)
if x_std_CNT > 1.0 or y_std_CNT > 1.0:
remark += ""
### radius of CNT
l_r_CNT = []
for atom in CNT:
l_r_CNT.append(
math.sqrt((atom[0] - x_CNT)**2 + (atom[1] - y_CNT)**2))
r_CNT = np.mean(l_r_CNT)
std_r_CNT = np.std(l_r_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 < r_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
WAT_in_CNT = []
for atom in WATER:
dist_sq = (atom[0] - x_CNT)**2 + (atom[1] - y_CNT)**2
if min_z_CNT + margin <= atom[2] and atom[
2] <= max_z_CNT - margin and dist_sq < r_CNT**2:
WAT_in_CNT.append(atom)
n_WAT_in_CNT = len(WAT_in_CNT)
'''
### WATER bad contact check: copy-failure-proof: NEED CORRECTION
WAT1 = []; WAT2 = [];
for index1, i in enumerate(WAT_in_CNT):
for j in WATER[index1:]:
WAT1.append(i); WAT2.append(j);
WAT1 = np.array(WAT1); WAT2 = np.array(WAT2)
min_dists = np.min(np.dstack(((WAT1 - WAT2) % boxsize, (WAT2 - WAT1) % boxsize)), axis = 2)
dists = np.sqrt(np.sum(min_dists ** 2, axis = 1))
for d in dists:
if d > 0 and d < 1.0:
remark += "Bad contacts" + str(d)
continue;
'''
d = "{0:8.3f}"
e = "{0:6.1f}"
output = "{0:<10}".format(timestep) + str(
n_WAT_in_CNT
) + ' | ' + d.format(r_CNT) + d.format(std_r_CNT) + ' | ' + e.format(
boxsize[0]
) + e.format(boxsize[1]) + e.format(boxsize[2]) + ' | ' + e.format(
min_x_CNT) + e.format(max_x_CNT) + e.format(min_y_CNT) + e.format(
max_y_CNT) + e.format(min_z_CNT) + e.format(
max_z_CNT) + ' | ' + e.format(height_CNT) + ' | ' + str(
replNum) + '\t' + str(copyNum) + '\t' + str(
len(WATER)) + '\t' + str(remark) + '\n'
ftemp.write(output)
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 " + out_file + " ..Done.")
return 1
def getBestShot(bgf_file,
dat_file,
trj_file,
log_file,
ff_file,
keyword,
saveBgfFlag,
n_sample,
silent=False):
### init
timestep = 0
l_timestep = []
line = []
n_header = 0
yes_velocity = False
yes_image = False
mode = ""
t1 = 0
t2 = 0
# clock
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
### LAMMPS Trajectory
# how many steps to go?
if not silent: print("** Loading LAMMPS Trajectory **\n")
if not os.path.exists(trj_file):
nu.die("Please check the LAMMPS trajectory file.")
l_timestep = lt.getTrjInfo(trj_file)
n_timestep = len(l_timestep)
if not silent:
print("\nThe 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 ')
# Find modes
if 'vx' in keywords:
if not silent:
print("Found velocities information from the trajectory.")
yes_velocity = True
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'
if 'ix' in keywords or 'iy' in keywords or 'iz' in keywords:
yes_image = True
# scan trajectory to get timesteps
dumpatom = get_line(trj_file)
# get working path
workingpath = os.getcwd()
if not silent:
print(
'\n** Analyzing LAMMPS Log to find the timestep closest to the average "'
+ keyword + '" **\n')
# read keywords from log file
logdata = LAMMPS_getLogData.getLogData(log_file, "", keyword, silent=False)
logdata2 = []
for i in logdata:
if i[0] in l_timestep:
logdata2.append(i)
logdata2.sort(key=sortkey)
# truncate
if not silent:
print("Only the last " + str(n_sample) +
" snapshots will be used to calculate the average.")
logdata2 = logdata2[-n_sample:]
# average
temp_avg = 0
for i in logdata2:
temp_avg += float(i[1])
temp_avg /= len(logdata2)
# deviation
dev = []
for i in logdata2:
dev.append([i[0], abs(float(i[1]) - temp_avg)])
dev.sort(key=sortkeymin)
if not silent:
print("Found the timestep " + str(dev[0][0]) +
" has the value closest to the average " + keyword +
" (value: " + str(temp_avg) + ", deviation: " + str(dev[0][1]) +
")")
### REMARK: dev[0] has the smallest deviation from the average
# get trajectory
myTRJ.seek(0)
dumpatom = get_line(trj_file)
while 1:
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
# only treat the designated timestep
timestep = int(chunk[1])
if timestep != int(dev[0][0]):
continue
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."
)
# actual coordinate
coordinfo = chunk[9:]
info = hash()
# assume that coordinfo is similar to ['id', 'type', 'xs', 'ys', 'zs', 'ix', 'iy', 'iz']
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atomNo = int(atomcoord[0])
if mode == 'scaled':
info[atomNo]['x'] = float(atomcoord[2]) * boxsize[0]
info[atomNo]['y'] = float(atomcoord[3]) * boxsize[1]
info[atomNo]['z'] = float(atomcoord[4]) * boxsize[2]
elif mode == 'unwrapped':
info[atomNo]['x'] = float(atomcoord[2])
info[atomNo]['y'] = float(atomcoord[3])
info[atomNo]['z'] = float(atomcoord[4])
elif mode == 'normal':
# images
if yes_image:
ix_index = keywords.index('ix')
iy_index = keywords.index('iy')
iz_index = keywords.index('iz')
info[atomNo]['x'] = (int(atomcoord[ix_index]) *
boxsize[0]) + float(atomcoord[2])
info[atomNo]['y'] = (int(atomcoord[iy_index]) *
boxsize[1]) + float(atomcoord[3])
info[atomNo]['z'] = (int(atomcoord[iz_index]) *
boxsize[2]) + float(atomcoord[4])
else:
info[atomNo]['x'] = float(atomcoord[2])
info[atomNo]['y'] = float(atomcoord[3])
info[atomNo]['z'] = float(atomcoord[4])
# velocities
if yes_velocity:
vx_index = keywords.index('vx')
vy_index = keywords.index('vy')
vz_index = keywords.index('vz')
info[atomNo]['vx'] = float(atomcoord[vx_index])
info[atomNo]['vy'] = float(atomcoord[vy_index])
info[atomNo]['vz'] = float(atomcoord[vz_index])
print("")
if not silent:
print("** New system size: %12.6f %12.6f %12.6f" %
(boxsize[0], boxsize[1], boxsize[2]))
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
if saveBgfFlag:
myBGF.REMARK.append("From the " + str(timestep) + " of " +
trj_file + " in " + workingpath + " and " +
bgf_file + " by " + str(sys.argv[0]))
myBGF.REMARK.append(
"n_samples: %d / %s average: %8.3f / stdev of the snapshot: %8.3f"
% (n_sample, keyword, temp_avg, dev[0][1]))
new_bgf_filename = bgf_file[:-4] + "." + str(timestep) + ".bgf"
for atom in myBGF.a:
atom.x = info[atom.aNo]['x']
atom.y = info[atom.aNo]['y']
atom.z = info[atom.aNo]['z']
#myBGF = bgftools.periodicMoleculeSort(myBGF, 0, [], ff_file=ff_file, silent=True) # pbc wrap
myBGF.saveBGF(new_bgf_filename)
if not silent:
print("The snapshot is saved in BGF file " + new_bgf_filename)
if dat_file:
### LAMMPS Data
dat_atoms = []
if not silent: print("** Loading LAMMPS Data **\n")
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()
### update LAMMPS data file ###
myDAT = open(dat_file)
new_dat_filename = dat_file + "." + keyword + "." + str(timestep)
myNewDAT = open(new_dat_filename, '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} {7:10.5f} {8:10.5f} {9:10.5f}".format(
atom.aNo, atom.rNo, atomTypeNo, atom.charge,
atom.x, atom.y, atom.z, float(parse[7]),
float(parse[8]), float(parse[9])) + "\n"
myNewDAT.write(output)
# Write velocities
if yes_velocity:
myNewDAT.write("\n\nVelocities\n\n")
for i in dat_atoms:
if len(i) == 0:
continue
parse = i.split()
atomNo = int(parse[0])
output = "{0:>8} {1:12.8f} {2:12.8f} {3:12.8f}\n".format(
atomNo, info[atomNo]['vx'], info[atomNo]['vy'],
info[atomNo]['vz'])
myNewDAT.write(output)
# consume
for i in range(len(dat_atoms)):
line = myDAT.readline()
myNewDAT.write("\n")
if not silent:
print("The snapshot is saved in LAMMPS data file " +
new_dat_filename)
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 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 countWater(bgf_file, trj_file, n_step, n_water, 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)
global out_file
if out_file == "": out_file = "waterPosition.profile"
print("The result will be recorded to the file " + out_file + " ...")
ftemp = open(out_file, 'w')
ftemp.write(str(sys.argv) + "\n")
ftemp.write(str(os.path.abspath('.') + "\n"))
curr_dir = os.path.abspath(".")
### 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 first " + str(n_step) +
" timesteps.")
### extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
for atom in myBGF.a:
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName and "I" in atom.chain:
aNo_WAT_O.append(atom.aNo)
### Draw O atoms to trace
n_trace = n_water
if len(aNo_WAT_O) < n_water:
nu.die(
'Cannot draw %d molecules out of %d water molecules in the system!'
% (n_water, len(aNo_WAT_O)))
aNo_WAT_trace = random.sample(aNo_WAT_O, n_trace)
# convert aNo as rNo
_ = []
for i in aNo_WAT_trace:
_.append(myBGF.getAtom(i).rNo)
output = "resid " + ''.join("%d\t" % i for i in _) + '\n'
ftemp.write(output)
print(output)
### check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water 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
coord = dict()
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(' ')
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:]
# load atom coordinates from chunk
for atomline in coordinfo:
atomcoord = atomline.split(' ')
coord[int(atomcoord[0])] = [
float(atomcoord[2]),
float(atomcoord[3]),
float(atomcoord[4])
]
### convert atom coordinates to lists
WATER = []
for atom in myBGF.a:
if atom.aNo in aNo_WAT_trace:
WATER.append(coord[atom.aNo][2])
WATER = np.array(WATER) # chosen water coordinates
### write output
output = str(timestep) + "\t" + ''.join("%8.5f\t" % i
for i in WATER) + '\n'
ftemp.write(output)
sys.stdout.flush()
### time
t2 = time.time() # time mark
elapsed_time = t2 - t1
processed_step += 1
print('')
ftemp.close()
print("Numbers of water molecules are written in " + out_file + " ..Done.")
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
"""
asdflkjhasdlkfjadslkfjasdlkvjbaldskjfha;lsiefhja;lsejkfblnkdsjvb
"""
### 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 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 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, force_profile, silent=False):
"""
This calculates the profile of averaged velocity according to r.
NOTE: This is different from averaged velocity profile according to r.
"""
# const
PI = math.pi
vdw_r_C = 1.7
# init
timestep = 0
l_timestep = []
line = []
n_header = 0
output = ""
t1 = 0
t2 = 0
# clock
output += "t\tforce\tarea\tvz\tvisc\tsliplen\n"
l_radial_vz_profile = []
l_avg_data = []
l_result = []
l_avg_count = []
n_avg_count_step = 0
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
myOUT = open(trj_file + ".sliplength.profile", 'w')
# how many steps to go?
if not silent: print("Scanning trajectory file..")
l_timestep = lt.getTrjInfo(trj_file, silent=False)
n_timestep = len(l_timestep)
if not silent:
print("\nThe trajectory contains " + str(n_timestep) + " timesteps.")
# read force data from force profile
if not silent: print("Reading force profile..")
f_fp = open(force_profile)
force = dict()
while 1:
line = f_fp.readline()
if not line:
break
if line[0] == "#":
continue
parse = line.split()
step = int(parse[0])
force[step] = float(parse[1])
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
for atom in myBGF.a:
# Carbons in CNT
if "CNT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
t1 = t2 = 0
elapsed_time = 0
# Find header of the trajectory file
line = []
n_header = 0
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [
line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0],
line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# calculate properties
dumpatom = get_line(trj_file)
processed_step = 0
while 1:
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (n_timestep - processed_step)
### Read
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
timestep = int(chunk[1])
l_timestep.append(timestep)
natoms = int(chunk[3])
boxsize = [
chunk[5].split(' ')[0], chunk[5].split(' ')[1],
chunk[6].split(' ')[0], chunk[6].split(' ')[1],
chunk[7].split(' ')[0], chunk[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
sys.stdout.write('\r' + "Fetched timestep: " + str(timestep) +
" (Remaining time: " +
"{0:4.1f}".format(remaining_time) + " seconds, " +
"{0:4.1f} minutes".format(remaining_time / 60) + ")")
sys.stdout.flush()
if timestep == 0:
continue
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die(
"Number of atoms in trajectory file does not match with BGF file."
)
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.vx = float(atomcoord[5])
atom.vy = float(atomcoord[6])
atom.vz = float(atomcoord[7])
### myBGF update complete! ###
# calculate z-directional velocity of water molecules wrt r vcm = sum vi mi / sum mi
mass_O = 16.0000
mass_H = 1.008
mass_H2O = mass_O + 2 * mass_H # H2O mass
vz = []
# data container
# z velocity calculation
for ano in aNo_WAT_O:
atom = myBGF.getAtom(ano) # oxygen
vcmz = atom.vz * mass_O
for ano2 in atom.CONECT:
atom2 = myBGF.getAtom(ano2) # hydrogens
vcmz += atom2.vz * mass_H
vcmz /= mass_H2O
vz.append(vcmz * (10**5)) # velocity in A/fs -> m/s
avg_vz, _ = nu.meanstdv(vz)
f = force[timestep] * (6.95e9)
l = f / A / avg_vz # lambda
b = v / l * 1e9 # slip length
output += str(timestep) + "\t" + str(force[timestep]) + "\t" + str(
A) + "\t" + str(avg_vz) + "\t" + str(v) + "\t" + str(b) + "\n"
t2 = time.time() # time mark
elapsed_time = t2 - t1
processed_step += 1
myOUT.write(output)
myOUT.close()
print('')
return 1
def getVelocity(bgf_file, trj_file, n_step, silent=False):
# const
PI = math.pi
vdw_r_C = 1.7
# init
timestep = 0; l_timestep = []; line = []; n_header = 0;
t1 = 0; t2 = 0; # clock
l_data = []; # stores vz
l_avg_radius_CNT = [];
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
ftemp = open("countWater4.profile.test", 'w')
ftemp.write(str(sys.argv) + "\n")
curr_dir = os.path.abspath(".")
temp_dir = curr_dir + "/CountWAT5/"
print(temp_dir)
if not os.path.isdir(temp_dir): os.makedirs(temp_dir)
# how many steps to go?
n_timestep = len(lt.getTrjInfo(trj_file))
if n_step == 0:
n_step = n_timestep;
print(" ..The trajectory contains " + str(n_timestep) + " timesteps.")
print("The script will proceed for the last " + str(n_step) + " timesteps.")
# extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
for atom in myBGF.a:
# Carbons in CNT or atoms in BNNT
if "NT" in atom.rName:
aNo_CNT.append(atom.aNo)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
# check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
# Find header of the trajectory file
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break;
# INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0], line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# for every shot in the trajectory file update BGF and manipulate
dumpatom = get_line(trj_file)
processed_step = 0;
t1 = t2 = 0; elapsed_time = 0;
while 1:
### tester
if processed_step == 50:
break;
### Show progress
t1 = time.time();
remaining_time = elapsed_time * (n_step - processed_step)
sys.stdout.write('\r' + "Reading timestep.. " + str(timestep) + " (Remaining time: " + "{0:4.1f}".format(remaining_time) + " seconds, " + "{0:4.1f} minutes".format(remaining_time/60) + ")")
sys.stdout.flush()
if processed_step == n_step:
break;
### Read
myBGF = bgf.BgfFile(bgf_file)
try:
chunk = [next(dumpatom) for i in range(natoms+n_header)]
except StopIteration:
break;
timestep = int(chunk[1])
natoms = int(chunk[3])
boxsize = [chunk[5].split(' ')[0], chunk[5].split(' ')[1], chunk[6].split(' ')[0], chunk[6].split(' ')[1], chunk[7].split(' ')[0], chunk[7].split(' ')[1]];
boxsize = [float(i) for i in boxsize]; boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]), (boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
### update myBGF with trajectory information ###
natom_bgf = len(myBGF.a) # number of atoms in BGF file
if not natom_bgf == natoms:
nu.die("Number of atoms in trajectory file does not match with BGF file.")
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# modified for fast treatment
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
atom.vx = float(atomcoord[5])
atom.vy = float(atomcoord[6])
atom.vz = float(atomcoord[7])
### myBGF update complete! ###
### align CNT to z axis
# initialize for the moment of inertia and the center of mass calculation
U = 0; Ut = 0; Uv = 0;
Ixx = 0; Ixy = 0; Ixz = 0;
Iyx = 0; Iyy = 0; Iyz = 0;
Izx = 0; Izy = 0; Izz = 0;
Mx = 0; My = 0; Mz = 0;
# transpose "all atoms in BGF": move COM of CNT as origin
# com of CNT (important: only one CNT!)
Mx = 0; My = 0; Mz = 0;
min_x_CNT = 0.0; max_x_CNT = 0.0; min_y_CNT = 0.0; max_y_CNT = 0.0; min_z_CNT = 0.0; max_z_CNT = 0.0;
for atom in myBGF.a:
if "NT" in atom.rName:
Mx += atom.x / N_CNT
My += atom.y / N_CNT
Mz += atom.z / N_CNT
### before we proceed to calculate MI first check how the CNT is lying across the periodic box
if atom.x < min_x_CNT:
min_x_CNT = atom.x
if atom.x > max_x_CNT:
max_x_CNT = atom.x
if atom.y < min_y_CNT:
min_y_CNT = atom.y
if atom.y > max_y_CNT:
max_y_CNT = atom.y
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
max_x_axis = int(math.ceil(max_x_CNT/boxsize[0]))
min_x_axis = int(math.floor(min_x_CNT/boxsize[0]))
max_y_axis = int(math.ceil(max_y_CNT/boxsize[1]))
min_y_axis = int(math.floor(min_y_CNT/boxsize[1]))
max_z_axis = int(math.ceil(max_z_CNT/boxsize[2]))
min_z_axis = int(math.floor(min_z_CNT/boxsize[2]))
replNum = (min_x_axis, max_x_axis, min_y_axis, max_y_axis, min_z_axis, max_z_axis)
copyNum = 0
### copy water molecules
for x in range(min_x_axis, max_x_axis):
if x != 0:
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, boxsize[0]*x, 0, 0)
myBGF = myBGF.merge(myBGF2)
copyNum += 1
for y in range(min_y_axis, max_y_axis):
if y != 0:
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, 0, boxsize[1]*y, 0)
myBGF = myBGF.merge(myBGF2)
copyNum += 1
for z in range(min_z_axis, max_z_axis):
if z != 0:
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, 0, 0, boxsize[2]*z)
myBGF = myBGF.merge(myBGF2)
copyNum += 1
print(str(replNum) + " " + str(copyNum) + " natoms: " + str(len(myBGF.a)))
### now continute to MI calculation
# move atoms to box center
COM = nu.array([[Mx, My, Mz]])
CNT = CNT - COM
'''
for atom in myBGF.a:
atom.x -= Mx
atom.y -= My
atom.z -= Mz
'''
# calculate the moment of inertia (MI) and the center of mass (COM) of CNT from "myBGF"
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
Ixx += (atom.y**2 + atom.z**2) / N_CNT
Iyy += (atom.x**2 + atom.z**2) / N_CNT
Izz += (atom.x**2 + atom.y**2) / N_CNT
Ixy -= (atom.x * atom.y) / N_CNT
Ixz -= (atom.x * atom.z) / N_CNT
Iyz -= (atom.y * atom.z) / N_CNT
# the moment of inertia tensor
I = np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]])
# eigenvalue & eigenvector calculation
eigval, eigvec = np.linalg.eig(I) # eigval[0] is the minimum among the values.
# rearrange the U vector
U = np.matrix(eigvec)
Ut = U.T
# "myBGF" rotation
for atom in myBGF.a:
v = np.matrix([atom.x, atom.y, atom.z]).T
Uv = Ut * v
atom.x = float(Uv[2])
atom.y = float(Uv[1])
atom.z = float(Uv[0])
# for CNT atoms, calculate some properties
min_x_CNT = 1000.0; max_x_CNT = -1000.0; radius_CNT = 0.0; height_CNT = 0.0;
min_y_CNT = 1000.0; max_y_CNT = -1000.0;
min_z_CNT = 1000.0; max_z_CNT = -1000.0;
CNT_orientation = "-"
# move origin to box center
for atom in myBGF.a:
atom.x += boxsize[0]/2.0
atom.y += boxsize[1]/2.0
atom.z += boxsize[2]/2.0
#myBGF = bgftools.periodicMoleculeSort(myBGF, 0, myBGF.CRYSTX) ##### testestestest
### update PBC information
myBGF.PERIOD = "111"
myBGF.AXES = "ZYX"
myBGF.SGNAME = "P 1 1 1\n"
myBGF.CELLS = [-1, 1, -1, 1, -1, 1]
if myBGF.CRYSTX != []:
for i in range(0, 3):
myBGF.CRYSTX[i] = boxsize[i]
else:
for i in range(0, 3):
myBGF.CRYSTX.append(boxsize[i])
myBGF.CRYSTX += [90.0, 90.0, 90.0]
myBGF.saveBGF(temp_dir + bgf_file.split(".bgf")[0] + "." + str(timestep) + ".bgf")
l_radius_CNT = [];
l_x_CNT = [];
l_y_CNT = [];
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
# center of CNT
l_x_CNT.append(atom.x)
l_y_CNT.append(atom.y)
# height
if atom.z < min_z_CNT:
min_z_CNT = atom.z
if atom.z > max_z_CNT:
max_z_CNT = atom.z
x_CNT, a = nu.meanstdv(l_x_CNT)
y_CNT, a = nu.meanstdv(l_y_CNT)
z_diff = max_z_CNT - min_z_CNT
height_CNT = z_diff
# radius of CNT
for aNo in aNo_CNT:
atom = myBGF.getAtom(aNo)
l_radius_CNT.append( math.sqrt( (atom.x - x_CNT)**2 + (atom.y - y_CNT)**2 ))
radius_CNT, a = nu.meanstdv(l_radius_CNT)
l_avg_radius_CNT.append(radius_CNT)
### get water molecules in CNT
# inside the CNT := min_z_CNT <= z <= max_z_CNT and (x - (x_diff/2))**2 + (y - (y_diff/2))**2 < radius_CNT**2
# aNo_WAT_O_atoms: molecules which O atom is within CNT
# we don't need to calculate H atoms. Let's consider only O atoms
margin = 0.0; # water molecules far from the margin will be only considered
aNo_WAT_O_in_CNT = []
for aNo in aNo_WAT_O:
atom = myBGF.getAtom(aNo)
dist_sq = (atom.x - x_CNT)**2 + (atom.y - y_CNT)**2
if "WAT" in atom.rName and "O" in atom.ffType and min_z_CNT + margin <= atom.z and atom.z <= max_z_CNT - margin and dist_sq < radius_CNT**2:
aNo_WAT_O_in_CNT.append(aNo)
else:
pass;
#output = str(timestep) + '\t' + str(len(aNo_WAT_O_in_CNT)) + '\t' + str(radius_CNT) + '\t' + str(z_diff) + '\n'
output = str(timestep) + '\t' + str(len(aNo_WAT_O_in_CNT)) + '\t' + str(radius_CNT) + '\t' + str(boxsize[0]/2) + '\t' + str(boxsize[1]/2) + '\t' + str(min_z_CNT) + '\t' + str(max_z_CNT) + '\t' + str(z_diff) + '\t' + str(height_CNT) + '\t' + str(len(aNo_CNT)) + '\t' + str(replNum) + '\t' + str(copyNum) + '\n' # debug
ftemp.write(output)
#sys.stdout.write('Done ')
sys.stdout.flush()
t2 = time.time() # time mark
elapsed_time = t2 - t1;
processed_step += 1;
print('')
ftemp.close()
print("numbers of water molecules are written in countWater.profile ..Done.")
return 1
