def randomDisperse(bgf_file, size, number, out_file, silent=False):
"""
def randomDisperse():
Create a randomly distributed cubic with full of the monomers
Function Parameters:
bgf_file A string which contains a monomer information in a BGF format.
size
number
out_file
"""
# initialize
# open bgf
if not silent: print("reading monomer..")
cubicBGF = bgf.BgfFile()
#for atom in cubicBGF.a:
# cubicBGF.delAtom(cubicBGF.a2i[atom.aNo])
# repeat up to number:
if not silent: print("generating cubic box..")
for i in xrange(number):
# create three random numbers
x1 = random.uniform(0, size)
y1 = random.uniform(0, size)
z1 = random.uniform(0, size)
# move the monomer
addBGF = bgf.BgfFile(bgf_file)
headAtom = addBGF.a[0]
#delta = (headAtom.x - x1, headAtom.y - y1, headAtom.z - z1)
delta = (x1 - headAtom.x, y1 - headAtom.y, z1 - headAtom.z)
bgf.moveBGF(addBGF, delta[0], delta[1], delta[2])
# merge
cubicBGF = cubicBGF.merge(addBGF, True)
# make it periodic
cubicBGF.BIOGRF = "200"
cubicBGF.DESCRP = bgf_file[:-4]
cubicBGF.REMARK.insert(0, "Cubic generated by " + os.path.basename(sys.argv[0]) + " by " + os.environ["USER"] + " on " + time.asctime(time.gmtime()))
cubicBGF.FF = "FORCEFIELD DREIDING"
cubicBGF.PERIOD = "111"
cubicBGF.CRYSTX = [ size, size, size, 90.0, 90.0, 90.0 ]
cubicBGF.AXES = "ZYX"
cubicBGF.SGNAME = "P 1 1 1\n"
cubicBGF.CELLS = [-1, 1, -1, 1, -1, 1]
# save
if not silent: print("saving.. " + out_file)
cubicBGF.saveBGF(out_file)
def centerbgffileclass(myBGF, method="com_origin"):
new_x, new_y, new_z = bgftools.getCom(myBGF, "")
if len(myBGF.CRYSTX) > 2:
boxcenter = [(i / 2.0) for i in myBGF.CRYSTX[0:3]]
else:
boxsize = bgf.getBGFSize(myBGF, 0)
boxcenter = [(boxsize[1] - boxsize[0]) / 2,
(boxsize[3] - boxsize[2]) / 2,
(boxsize[5] - boxsize[4]) / 2]
if method == "com_origin":
bgf.moveBGF(myBGF, (-new_x), (-new_y), (-new_z))
elif method == "com_center":
dx = boxcenter[0] - new_x
dy = boxcenter[1] - new_y
dz = boxcenter[2] - new_z
bgf.moveBGF(myBGF, dx, dy, dz)
elif method == "box_origin":
dx = boxcenter[0]
dy = boxcenter[1]
dz = boxcenter[2]
bgf.moveBGF(myBGF, dx, dy, dz)
else:
bgf.moveBGF(myBGF, (-new_x), (-new_y), (-new_z))
return myBGF
def centerbgf(bgf_file, out_file, ff_file, method="com_origin", silent=False):
if silent == 1:
nu.shutup()
boxcenter = []
# open bgf
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("Reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
if not silent:
print("Moving the origin of the coordinate in " + bgf_file +
" and saving to " + out_file + ".")
if method != "box_origin":
new_x, new_y, new_z = bgftools.getCom(myBGF, ff_file)
if len(myBGF.CRYSTX) > 2:
boxcenter = [(i / 2.0) for i in myBGF.CRYSTX[0:3]]
else:
boxsize = bgf.getBGFSize(myBGF, 0) # [xlo, xhi, ylo, yhi, zlo, zhi]
boxcenter = [(boxsize[1] - boxsize[0]) / 2,
(boxsize[3] - boxsize[2]) / 2,
(boxsize[5] - boxsize[4]) / 2]
if method == "com_origin":
bgf.moveBGF(myBGF, (-new_x), (-new_y), (-new_z))
elif method == "com_center":
dx = boxcenter[0] - new_x
dy = boxcenter[1] - new_y
dz = boxcenter[2] - new_z
bgf.moveBGF(myBGF, dx, dy, dz)
elif method == "box_origin":
dx = boxcenter[0]
dy = boxcenter[1]
dz = boxcenter[2]
bgf.moveBGF(myBGF, dx, dy, dz)
else:
bgf.moveBGF(myBGF, (-new_x), (-new_y), (-new_z))
# save
if isinstance(out_file, str):
if not silent: print("Saving information to " + out_file + " ..")
myBGF.saveBGF(out_file)
return 1
else:
return myBGF
def addsolvent(bgf_file,
solvent_bgf,
size,
margin,
out_file,
ff_file,
silent=True):
### initialize
water = False
### load the solute bgf file
if not silent: print("Initializing..")
myBGF = bgf.BgfFile(bgf_file) # str
#solventBGF = bgf.BgfFile("/home/noische/scripts/dat/WAT/f3c_box.bgf") # F3C waterbox
if not silent: print("Loading the solvent file " + solvent_bgf + " ..")
solventBGF = bgf.BgfFile(solvent_bgf)
### Generate error when the solvent box is not periodic:
if not solventBGF.PERIOD:
nu.die(
"addSolvent: The solvent file is not periodic. Use a box full of solvent."
)
### Check the type of solvent
if not silent:
print("(the solvent box seems to be full of " +
os.path.basename(solvent_file)[:-4] + " )")
if "f3c" in solvent_bgf:
water = True # this flag is used to remove the bad contacts with the molecule.
if "spc" in solvent_bgf:
water = True # this flag is used to remove the bad contacts with the molecule.
if "tip" in solvent_bgf:
water = True # this flag is used to remove the bad contacts with the molecule.
### calculate the box size
if not silent: print("Analyzing box information..")
if len(myBGF.CRYSTX) > 2:
strsize = [myBGF.CRYSTX[0], myBGF.CRYSTX[1], myBGF.CRYSTX[2]]
else:
box = bgf.getBGFSize(myBGF, 0) # [xlo, xhi, ylo, yhi, zlo, zhi]
strsize = [box[1] - box[0], box[3] - box[2], box[5] - box[4]]
###
if size == "" and margin != "":
strsize = [
strsize[0] + 2 * margin[0], strsize[1] + 2 * margin[1],
strsize[2] + 2 * margin[2]
] # add margin on str size
elif size != "" and margin == "":
strsize = size
waterboxsize = solventBGF.CRYSTX[:3] # REMARK: This is a kind of constant.
copyNumber = [0, 0, 0]
for index, i in enumerate(copyNumber):
copyNumber[index] = math.ceil(
strsize[index] /
waterboxsize[index]) # how many times to replicate the water box
if not silent: print("Creating box information: " + str(strsize))
### replicate the solvent box
bigboxBGF = bgftools.replicateCell(solventBGF, copyNumber, True)
bigboxBGF.saveBGF("_replicate.bgf")
if not silent:
print("- Number of atoms in the created box: " + str(len(bigboxBGF.a)))
### trim the water box
if water:
if not silent:
print("Generating water box.. Calculating water molecules")
delatom = []
delwater = []
delwaterindex = []
for atom in bigboxBGF.a:
if atom.x > strsize[0] or atom.y > strsize[1] or atom.z > strsize[
2]:
delatom.append(atom.aNo)
for aNo in delatom:
water_molecule = bgftools.is_water(bigboxBGF, aNo)
if not water_molecule in delwater:
delwater.append(water_molecule)
delwater = nu.flatten(delwater)
delwater = nu.removeRepeat(delwater)
delwater.sort()
delwater.reverse()
for aNo in delwater:
delwaterindex.append(bigboxBGF.getAtomIndex(aNo))
del (delwater)
if not silent: print("Generating water box.. Trimming")
bigboxBGF.delAtoms(delwaterindex, False)
bigboxBGF.renumber()
elif not water:
if not silent:
print("Generating solvent box.. Extracting solvent molecules")
delatom = []
delsolvent = []
delsolventindex = []
for atom in bigboxBGF.a:
if atom.x > strsize[0] or atom.y > strsize[1] or atom.z > strsize[
2]:
delatom.append(atom.aNo)
for aNo in delatom:
molecule_list = []
molecule = bgftools.getmolecule(bigboxBGF, bigboxBGF.getAtom(aNo),
molecule_list)
for number in molecule_list:
if not number in delsolvent: delsolvent.append(number)
delsolvent = nu.flatten(delsolvent)
delsolvent = nu.removeRepeat(delsolvent)
delsolvent.sort()
delsolvent.reverse()
for aNo in delsolvent:
delsolventindex.append(bigboxBGF.getAtomIndex(aNo))
if not silent: print("Generating solvent box.. Trimming")
bigboxBGF.delAtoms(delsolventindex, False)
bigboxBGF.renumber()
### merge two structure
# REMARK: it is natural to have the periodic information of water box for the output BGF file.
# REMARK: HETATOM should be located on the first of the BGF file. So use dummy for merging.
if not silent: print("\nAdding trimmed solvent box to the structure..")
bigboxcenter = [strsize[0] / 2, strsize[1] / 2, strsize[2] / 2]
a, b, c = bgftools.getCom(myBGF, ff_file)
bgf.moveBGF(myBGF, bigboxcenter[0] - a, bigboxcenter[1] - b,
bigboxcenter[2] - c)
## remove bad contacts between solutes and solvents
if not silent: print("Atom distance calculation for contacts..")
delatom = []
delsolvent = []
delsolventindex = []
for atom1 in myBGF.a:
for atom2 in bigboxBGF.a:
# if the distance between atom1 and atom2 is less than 2.8, add to a delete list
dist_sq = (atom1.x - atom2.x)**2 + (atom1.y - atom2.y)**2 + (
atom1.z - atom2.z)**2
if dist_sq < 7.84:
delatom.append(atom2.aNo)
# delete bad atoms!
if not silent: print("Removing bad contacts..")
for aNo in delatom:
molecule_list = []
molecule = bgftools.getmolecule(bigboxBGF, bigboxBGF.getAtom(aNo),
molecule_list)
for number in molecule_list:
if not number in delsolvent: delsolvent.append(number)
delsolvent = nu.flatten(delsolvent)
delsolvent = nu.removeRepeat(delsolvent)
delsolvent.sort()
delsolvent.reverse()
for aNo in delsolvent:
delsolventindex.append(bigboxBGF.getAtomIndex(aNo))
bigboxBGF.delAtoms(delsolventindex, False)
bigboxBGF.renumber()
## compute stats for adding solvents
if not silent: print("\nComputing stats..")
mol_list = bgftools.getMoleculeList(bigboxBGF)
n_mol = len(mol_list)
n_atom = len(nu.flatten(mol_list))
if not silent:
print(
str(n_mol) + " molecules (" + str(n_atom) +
" atoms) will be added.")
## merge
bigboxBGF = myBGF.merge(bigboxBGF, True)
if not silent: print("Total atoms in the file: " + str(len(bigboxBGF.a)))
## some paperworking for periodic box
bigboxBGF.OTHER = solventBGF.OTHER
bigboxBGF.PERIOD = solventBGF.PERIOD
bigboxBGF.AXES = solventBGF.AXES
bigboxBGF.SGNAME = solventBGF.SGNAME
bigboxBGF.CRYSTX = solventBGF.CRYSTX
bigboxBGF.CELLS = solventBGF.CELLS
## adjust the size of the box
bigboxBGF.CRYSTX = [
strsize[0], strsize[1], strsize[2], solventBGF.CRYSTX[3],
solventBGF.CRYSTX[4], solventBGF.CRYSTX[5]
]
"""
### remove bad contacts and save
if water:
if not silent: print("Removing bad contacts: distance criteria is 2.8 A")
bigboxBGF = removebadcontacts(bigboxBGF, bigboxBGF, 2.8)
### renumber residue numbers
# RULE: all rNos for water molecules will be renumbered from 2. (for createLammpsInput.pl)
if not silent: print("Renumbering water molecules..")
max_rNo_in_hetatm = 0;
oxygen_list = bgftools.listOxygenAtoms(bigboxBGF)
### find the biggest rNo among HETATM
for atom in bigboxBGF.a:
if atom.aTag == 1:
if max_rNo_in_hetatm < atom.rNo: max_rNo_in_hetatm = atom.rNo
### update rNo in water molecules
rNo_for_water = max_rNo_in_hetatm + 500;
for aNo in oxygen_list:
water_aNo = bgftools.is_water(bigboxBGF, aNo) # get aNo in a water molecule by checking the oxygen atom
if water_aNo != []:
for atom_aNo in water_aNo:
bigboxBGF.getAtom(atom_aNo).rNo = rNo_for_water
rNo_for_water += 1
"""
### record BGF remarks
bigboxBGF.REMARK.insert(
0, "Solvents added by " + os.path.basename(sys.argv[0]) + " by " +
os.environ["USER"] + " on " + time.asctime(time.gmtime()))
bigboxBGF.REMARK.insert(0, "Solvents: " + str(solvent_file))
### save BGF
if not silent: print("Saving the file.. see " + str(out_file))
bigboxBGF.saveBGF(out_file)
return 1
def replicateCell(myBGF, multiplication, spaceFilling=True):
"""
replicateCell():
Requires a BgfFile class.
Returns a BgfFile class of the replicated structure of the given structure.
Options:
spaceFilling = True
Just copy the cell (x, y, z) times to the (x, y, z) coordinateas. Negative multiplication indices are allowed.
(1, 1, 1) with a cell gives 4 cells (i.e. replication to x, y, and z coordinates).
spaceFilling = False
Fill the space as a Cuboid form for a given times. Negative multiplication indices are NOT allowed.
(2, 1, 3) with a cell gives the 6 cells (i.e. cubiod). (1, 1, 1) with a cell gives the identical structure (nothing happens).
"""
copyTime = [
int(multiplication[0]),
int(multiplication[1]),
int(multiplication[2])
]
# the number of cells that will be copied
myBGFx = bgf.BgfFile()
myBGFy = bgf.BgfFile()
myBGFz = bgf.BgfFile()
boxsize = [0, 0, 0]
if len(myBGF.CRYSTX) > 2:
boxsize = [myBGF.CRYSTX[0], myBGF.CRYSTX[1], myBGF.CRYSTX[2]]
else:
box = bgf.getBGFSize(myBGF, 0) # [xlo, xhi, ylo, yhi, zlo, zhi]
boxsize = [box[1] - box[0], box[3] - box[2], box[5] - box[4]]
if spaceFilling:
if copyTime[0] != 0:
myBGF2 = copy.deepcopy(myBGF)
for n in range(0, copyTime[0] - 1):
bgf.moveBGF(myBGF2, boxsize[0], 0, 0)
myBGF = myBGF.merge(myBGF2, True)
if copyTime[1] != 0:
myBGF2 = copy.deepcopy(myBGF)
for n in range(0, copyTime[1] - 1):
bgf.moveBGF(myBGF2, 0, boxsize[1], 0)
myBGF = myBGF.merge(myBGF2, True)
if copyTime[2] != 0:
myBGF2 = copy.deepcopy(myBGF)
for n in range(0, copyTime[2] - 1):
bgf.moveBGF(myBGF2, 0, 0, boxsize[2])
myBGF = myBGF.merge(myBGF2, True)
# update the CRYSTX information
if len(myBGF.CRYSTX) > 2:
for index, number in enumerate(copyTime):
myBGF.CRYSTX[index] *= copyTime[index]
else:
# replication
if copyTime[0] != 0:
if copyTime[0] < 0: sign = -1
else: sign = 1
for n in range(0, abs(copyTime[0])):
if copyTime[0] < 0: n -= 1
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, boxsize[0] * (n + 1) * sign, 0, 0)
myBGFx = myBGFx.merge(myBGF2, True)
if copyTime[1] != 0:
if copyTime[0] < 0: sign = -1
else: sign = 1
for n in range(0, abs(copyTime[1])):
if copyTime[0] < 0: n -= 1
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, 0, boxsize[1] * (n + 1) * sign, 0)
myBGFy = myBGFy.merge(myBGF2, True)
if copyTime[2] != 0:
if copyTime[0] < 0: sign = -1
else: sign = 1
for n in range(0, abs(copyTime[2])):
if copyTime[0] < 0: n -= 1
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, 0, 0, boxsize[2] * (n + 1) * sign)
myBGFz = myBGFz.merge(myBGF2, True)
myBGF = myBGF.merge(myBGFx, True)
myBGF = myBGF.merge(myBGFy, True)
myBGF = myBGF.merge(myBGFz, True)
# update the CRYSTX information
if len(myBGF.CRYSTX) > 2:
for index, number in enumerate(copyTime):
myBGF.CRYSTX[index] += myBGF.CRYSTX[index] * copyTime[index]
return myBGF
def fourPEI(bgf_file, ff_file, suffix, out_file, monomers, Rg, directory, silent):
"""
def fourPEI(bgf_file, ff_file, suffix, out_file, monomers, Rg, directory, silent):
Runs a simulation which performs a crosslinking with given monomers.
Function Parameters:
bgf_file A string which contains a PEI information in a BGF format.
(e.g. "file1.bgf file2.bgf file3.bgf ...")
ff_file A string which contains a ForceField information.
(e.g. "~/ff/dreiding_den.par")
suffix A string which represents the job suffix. e.g. "tetramer"
out_file A string which represents the name of the output file.
monomers An integer which represents the number of PEIs that participates in a crosslinker.
If # of bgf_file < monomers, then additional PEI structure files will be added by looking up files from
"/home/noische/research/dendrimer/structure/600/minEnergyOrder". You can change this directory by changing
structure_dir variables in the script.
Rg A float which contains the distance between monomers.
directory A string which contains the pool of BGF files.
silent True/False flag for determining printing output messages.
"""
if monomers == 4:
pass;
elif monomers == 10:
pass;
elif monomers == 16:
pass;
elif monomers == 27:
pass;
elif monomers == 2:
pass;
else:
nu.die("Sorry, %s crosslinking is not yet provided." % str(monomers))
# variables
chosen_pei = []
extension = ".bgf"
log_file = suffix + ".log"
f_log_file = open(log_file, 'w')
f_log_file.write("fourPEI.py: version " + str(version) + "\n")
f_log_file.write("" + "\n")
f_log_file.write("Job started at " + time.asctime(time.gmtime()) + " on " + os.environ["HOSTNAME"] + " by " + os.environ["USER"] + "\n")
f_log_file.write("Command executed at " + os.getcwd() + "\n")
f_log_file.write("Requested options: " + str(sys.argv) + "\n")
f_log_file.write("" + "\n")
# CONSTANTS
#Rg = 6.0055 # average radius of gyration of PEI 600
#Rg = 8.4088 # don't know?
#Rg = 12.0100 # just feeling: actually Rg * 2
f_log_file.write("Using the PEI intermolecular distance " + str(Rg) + "\n")
# file preparation
#structure_dir = "/home/noische/research/dendrimer/structure/600/minEnergyOrder" # basic bgf repository
structure_dir = directory
curr_dir = os.path.abspath(".")
temp_dir = os.path.join(curr_dir, suffix)
pei_file = glob.glob(structure_dir + "/*.bgf") # only extracts bgf filename.ext
#pei_file = [os.path.basename(i) for i in glob.glob(structure_dir + "/*.bgf")] # only extracts bgf filename.ext
pei_name = [i.rstrip(".bgf\n")[0] for i in pei_file] # only extracts bgf filename
chosen_pei = bgf_file.split(" ")
if chosen_pei == ['']: chosen_pei = []
if len(chosen_pei) != monomers:
for file in chosen_pei:
if file in pei_file: pei_file.remove(file) # prevents repeated selections of monomer
for i in range(0, monomers - len(chosen_pei)):
a = random.choice(pei_file)
chosen_pei.append(a)
pei_file.remove(a) # prevents repeat. Now chosen_pei contains the files
# REMARK: chosen_pei = ['a.bgf', 'b.bgf', 'c.bgf', '/home/noische/research/dendrimer/structure/600/minEnergyOrder/600_E025.bgf']
# scratch preparation
if not os.path.isdir(temp_dir):
os.makedirs(temp_dir)
else:
#shutil.rmtree(temp_dir)
os.makedirs(temp_dir)
# copy files to the scratch
for file in chosen_pei:
shutil.copy(file, temp_dir)
# move to the scratch directory
os.chdir(temp_dir)
chosen_pei = [os.path.basename(i) for i in chosen_pei] # REMARK: ['a.bgf', 'b.bgf', 'c.bgf', '600_E018.bgf']
chosen_pei_name = [i.partition(".bgf")[0] for i in chosen_pei] # REMARK: ['a', 'b', 'c', '600_E018']
f_log_file.write("Structure file directory: " + structure_dir + "\n")
f_log_file.write("Current working directory: " + curr_dir + "\n")
f_log_file.write("Temp file directory: " + temp_dir + "\n")
f_log_file.write("Chosen PEI molecules: " + str(chosen_pei) + "\n")
if not silent: print(chosen_pei)
# open BGF structures as BgfFile
myBGF = [ bgf.BgfFile(i) for i in chosen_pei ]
# center BGF
for structure in myBGF:
structure = centerBGF.centerbgf(structure, 0, ff_file, "com_center", True)
# move BGF for tetrahedron
#moveBGF(myBGF[1], 0, Rg, Rg)
#moveBGF(myBGF[2], Rg, 0, Rg)
#moveBGF(myBGF[3], Rg, Rg, 0)
# move BGF for planar
if monomers == 4:
# Tetrahedron
bgf.moveBGF(myBGF[1], Rg, Rg, 0)
bgf.moveBGF(myBGF[2], Rg, 0, Rg)
bgf.moveBGF(myBGF[3], 0, Rg, Rg)
elif monomers == 10:
# Decahedron
bgf.moveBGF(myBGF[1], Rg, 0, 0)
bgf.moveBGF(myBGF[2], 2 * Rg, 0, 0)
bgf.moveBGF(myBGF[3], 0.5 * Rg, 0.86603 * Rg, 0)
bgf.moveBGF(myBGF[4], 1.5 * Rg, 0.86603 * Rg, 0)
bgf.moveBGF(myBGF[5], Rg, 1.73205 * Rg, 0)
bgf.moveBGF(myBGF[6], 0.5 * Rg, 0.28868 * Rg, 0.81650 * Rg)
bgf.moveBGF(myBGF[7], 1.5 * Rg, 0.28868 * Rg, 0.81650 * Rg)
bgf.moveBGF(myBGF[8], Rg, 1.15470 * Rg, 0.81650 * Rg)
bgf.moveBGF(myBGF[9], Rg, 0.57735 * Rg, 1.63300 * Rg)
elif monomers == 16:
"""
# < planar >
bgf.moveBGF(myBGF[1], 0, Rg, 0)
bgf.moveBGF(myBGF[2], 0, 2*Rg, 0)
bgf.moveBGF(myBGF[3], 0, 3*Rg, 0)
bgf.moveBGF(myBGF[4], Rg, 0, 0)
bgf.moveBGF(myBGF[5], Rg, Rg, 0)
bgf.moveBGF(myBGF[6], Rg, 2*Rg, 0)
bgf.moveBGF(myBGF[7], Rg, 3*Rg, 0)
bgf.moveBGF(myBGF[8], 2*Rg, 0, 0)
bgf.moveBGF(myBGF[9], 2*Rg, Rg, 0)
bgf.moveBGF(myBGF[10], 2*Rg, 2*Rg, 0)
bgf.moveBGF(myBGF[11], 2*Rg, 3*Rg, 0)
bgf.moveBGF(myBGF[12], 3*Rg, 0, 0)
bgf.moveBGF(myBGF[13], 3*Rg, Rg, 0)
bgf.moveBGF(myBGF[14], 3*Rg, 2*Rg, 0)
bgf.moveBGF(myBGF[15], 3*Rg, 3*Rg, 0)
"""
# L shaped box
bgf.moveBGF(myBGF[1], Rg, 2*Rg, 2*Rg)
bgf.moveBGF(myBGF[2], 0, Rg, 0)
bgf.moveBGF(myBGF[3], Rg, Rg, 0)
bgf.moveBGF(myBGF[4], 0, 2*Rg, 0)
bgf.moveBGF(myBGF[5], Rg, 2*Rg, 0)
bgf.moveBGF(myBGF[6], Rg, 0, Rg)
bgf.moveBGF(myBGF[7], Rg, Rg, Rg)
bgf.moveBGF(myBGF[8], Rg, 2*Rg, Rg)
bgf.moveBGF(myBGF[9], 0, 2*Rg, Rg)
bgf.moveBGF(myBGF[10], 0, Rg, Rg)
bgf.moveBGF(myBGF[11], 0, 0, Rg)
bgf.moveBGF(myBGF[12], Rg, 0, 2*Rg)
bgf.moveBGF(myBGF[13], Rg, Rg, 2*Rg)
bgf.moveBGF(myBGF[14], 0, 0, 2*Rg)
bgf.moveBGF(myBGF[15], 0, Rg, 2*Rg)
elif monomers == 27:
# cubic style crosslinking
bgf.moveBGF(myBGF[1], Rg, 0, 0)
bgf.moveBGF(myBGF[2], 2*Rg, 0, 0)
bgf.moveBGF(myBGF[3], 0, Rg, 0)
bgf.moveBGF(myBGF[4], Rg, Rg, 0)
bgf.moveBGF(myBGF[5], 2*Rg, Rg, 0)
bgf.moveBGF(myBGF[6], 0, 2*Rg, 0)
bgf.moveBGF(myBGF[7], Rg, 2*Rg, 0)
bgf.moveBGF(myBGF[8], 2*Rg, 2*Rg, 0)
bgf.moveBGF(myBGF[9], 0, 0, Rg)
bgf.moveBGF(myBGF[10], Rg, 0, Rg)
bgf.moveBGF(myBGF[11], 2*Rg, 0, Rg)
bgf.moveBGF(myBGF[12], 0, Rg, Rg)
bgf.moveBGF(myBGF[13], Rg, Rg, Rg)
bgf.moveBGF(myBGF[14], 2*Rg, Rg, Rg)
bgf.moveBGF(myBGF[15], 0, 2*Rg, Rg)
bgf.moveBGF(myBGF[16], Rg, 2*Rg, Rg)
bgf.moveBGF(myBGF[17], 2*Rg, 2*Rg, Rg)
bgf.moveBGF(myBGF[18], 0, 0, 2*Rg)
bgf.moveBGF(myBGF[19], Rg, 0, 2*Rg)
bgf.moveBGF(myBGF[20], 2*Rg, 0, 2*Rg)
bgf.moveBGF(myBGF[21], 0, Rg, 2*Rg)
bgf.moveBGF(myBGF[22], Rg, Rg, 2*Rg)
bgf.moveBGF(myBGF[23], 2*Rg, Rg, 2*Rg)
bgf.moveBGF(myBGF[24], 0, 2*Rg, 2*Rg)
bgf.moveBGF(myBGF[25], Rg, 2*Rg, 2*Rg)
bgf.moveBGF(myBGF[26], 2*Rg, 2*Rg, 2*Rg)
elif monomers == 2:
bgf.moveBGF(myBGF[1], Rg, 0, 0)
# change resnumber of monomers
for index, structure in enumerate(myBGF):
for atom in structure.a:
#atom.rNo = index + 1
#atom.rNo += (index + 1) * 10
atom.rNo += (index + 1) * 100
# merge BGF for any number of monomers
"""
myBGF[0] = myBGF[0].merge(myBGF[1], True)
myBGF[0] = myBGF[0].merge(myBGF[2], True)
myBGF[0] = myBGF[0].merge(myBGF[3], True)
"""
for i in range(1, monomers):
myBGF[0] = myBGF[0].merge(myBGF[i], True)
# record BGF properties
myBGF[0].REMARK.insert(0, "Crosslinked structures: " + str(chosen_pei))
myBGF[0].REMARK.insert(0, "Crosslinked by " + os.path.basename(sys.argv[0]) + " by " + os.environ["USER"] + " on " + time.asctime(time.gmtime()))
# save BGF
myBGF[0].saveBGF(suffix + ".bgf")
# crosslink
#if yes_crosslink:
# f_log_file.write("Entering crosslinking.\n")
# crosslink.crosslink(suffix + ".bgf", ff_file, suffix, nodes, criteria, t, out_file)
#else:
# f_log_file.write("-M option activated. Ignore crosslinking process.\n")
# file copy
shutil.copy(os.path.join(temp_dir, suffix + ".bgf"), curr_dir)
#os.system("cp -rp " + temp_dir + " " + curr_dir)
f_log_file.close()
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