def send_email(sid, iid, to, cc,
smtpserver='smtp.gmail.com:587'):
from_addr = "*****@*****.**"
login = "******"
password = "******"
subject = "SICP Application Received"
#to = "*****@*****.**"
sname, iname = adb.get_name(sid, iid)
message = """Hello,\nAn applicant, {}, has applied to your position {}. Please review this application on your home page.\n\nThank you,\nSICP Administration""".format(sname, iname)
msg = MIMEMultipart()
msg['From'] = from_addr
msg['To'] = to
msg['Subject'] = subject
msg.attach(MIMEText(message, 'plain'))
server = smtplib.SMTP(smtpserver)
server.ehlo()
server.starttls()
server.ehlo()
server.login(login, password)
text = msg.as_string()
problems = server.sendmail(from_addr, to, text)
server.quit()
def loadall(self, filename):
with open(filename, 'r') as hisfile:
spl_file = hisfile.readlines()
atoms, frames = [], []
pbc = (float(spl_file[1].split()[0]), float(spl_file[2].split()[1]),
float(spl_file[3].split()[2]))
nat = int(spl_file[0].split()[2])
splitted_traj = [
spl_file[line_n * (2 * nat + 4):line_n * (2 * nat + 4) +
(2 * nat + 4)]
for line_n in range(int(len(spl_file) / (2 * nat + 4)))
]
for at_n in range(nat):
atom = splitted_traj[0][4:][2 * at_n].split()[0]
if atom == 'OW' or atom == 'HW':
atom = atom[0]
atoms.append(periodic_table[db.get_name(atom)].atnum)
for frame in splitted_traj:
coordset = []
for at_n in range(nat):
coords = frame[4:][2 * at_n + 1].split()
coordset.append(np.array([float(coord) for coord in coords]))
frames.append(coordset)
return atoms, frames, nat, pbc
def wrap_h2o(self, frame):
def pbc(oxygen, hydrogen):
xx = np.linalg.norm(oxygen[0] - hydrogen[0])
yy = np.linalg.norm(oxygen[1] - hydrogen[1])
zz = np.linalg.norm(oxygen[2] - hydrogen[2])
delta = [xx, yy, zz]
delta = np.array([
delta[i] - round(delta[i] / self.pbc[i]) * self.pbc[i]
for i in range(3)
])
print(delta)
hydrogen = oxygen + delta
print(hydrogen)
return hydrogen
for at in range(self.nat):
if self.atoms[at] == 8:
self.frames[frame][at + 1] = pbc(self.frames[frame][at],
self.frames[frame][at + 1])
self.frames[frame][at + 2] = pbc(self.frames[frame][at],
self.frames[frame][at + 2])
with open('wrapped.xyz', 'a+') as output:
output.write(
F" {self.nat}\n {' '.join(self.energies[frame].split())}\n")
for at, coord in enumerate(self.frames[frame]):
label = periodic_table[db.get_name(self.atoms[at])].label
output.write(F'{label} {coord[0]} {coord[1]} {coord[2]}\n')
def mainloop(InnerFun, timeout=30, block=['None']):
people = db.get_contacts()
[people.remove(i) if i != 'None' else people for i in block]
while True:
try:
for contact in range(1, 18): #Tener al menos 18 contactos
db.extract_data(contact)
if db.newMsg() and db.get_name() in people: #CHAT FIJADO
hl.open_conversation(db.get_xpath_num(contact))
text = db.get_message()
response = InnerFun(text)
hl.write(response, db.get_xpath_num(contact))
hl.open_conversation(db.get_xpath_num(contact + 1))
except:
hl.refresh()
hl.wait_until_window(timeout)
people = db.get_contacts()
[people.remove(i) if i != 'None' else people for i in block]
def coordprint(self, frame, save=False):
if save:
with open('output.xyz', 'a+') as output:
output.write(
F" {self.nat}\n {' '.join(self.energies[frame].split())}\n"
)
for at, coord in enumerate(self.frames[frame]):
label = periodic_table[db.get_name(self.atoms[at])].label
output.write(
F'{label:<2} {coord[0]:13.8f} {coord[1]:13.8f} {coord[2]:13.8f}\n'
)
else:
print(F" {self.nat}\n {' '.join(self.energies[frame].split())}")
for at, coord in enumerate(self.frames[frame]):
label = periodic_table[db.get_name(self.atoms[at])].label
print(
F'{label:<2} {coord[0]:13.8f} {coord[1]:13.8f} {coord[2]:13.8f}'
)
def employerViewSpecificInt(iid):
if escape(session['type']) == 'employer':
cid = adb.get_cid(escape(session['uname']))
if adb.check_ci_ids(cid, iid):
studs = students_applied(iid)
sname, iname = adb.get_name(iid=iid)
return render_template('employerviewinternshipsiid.html', students=studs, iid=iid, posname=iname)
return redirect('/Employer')
def make_announcement(access):
if not database.valid_access(access):
return render_template("error.html", error="Page not found.")
elif access != session["access"] and not database.is_admin(session["access"]):
return redirect(url_for("unauthorized"))
name = request.form["name"]
text = request.form["statement"]
viewable = request.form["view"]
date = datetime.datetime.now()
poster = database.get_name(session["email"])
database.make_announcement(date=date, name=name, text=text, poster=poster, group=viewable)
return redirect(url_for("edit_all", access=access, editing="announce"))
def classinfo():
if not session.has_key('user'):
return redirect(url_for("about"))
username=session['user']
name=database.get_name(username)
osis=database.get_osis(username)
digits=database.get_id(username)
email=database.get_email(username)
schedule=database.get_schedule(username)
classes=database.get_class_info()
if request.method=='GET':
return render_template("class.html"
,name=name
,osis=osis
,digits=digits
,email=email
,classes=classes
,schedule=schedule
,get=True)
if request.method=="POST":
value=request.form['button']
value=value.split(" ")
index=int(value[1])-1
validate=True
if (str(value[0])=="set"):
period=classes[index][0]
clas=classes[index]
schedule=database.get_schedule(username)
if schedule[int(period)-1][1]=="free":
database.set_period(username,period,clas)
else:
validate=False
if (str(value[0])=="req"):
req=classes[index]
period=classes[index][0]
if database.has_lunch(username,period) or l_equal(schedule[int(period)-1],req):
validate=False
else:
database.post_request(username,req)
return render_template("class.html"
,name=name
,osis=osis
,digits=digits
,email=email
,classes=classes
,schedule=schedule
,validate=validate)
def atcount(self):
"""
Counts the atom frequency.
Returns
-------
atcount: dict
Dict with the atom labels as keys and the frequencies as values.
"""
at_cnt = {}
for at_typ in self.atomtypes:
cnt = 0
for atom in self.atoms:
if atom == at_typ:
cnt += 1
at_cnt[db.get_name(at_typ)] = cnt
del cnt
return at_cnt
def profile():
if not session.has_key('user'):
return redirect(url_for('about'))
username=session['user']
name=database.get_name(username)
osis=database.get_osis(username)
digits=database.get_id(username)
email=database.get_email(username)
schedule=database.get_schedule(username)
notif=database.get_notification(username)
if request.method=='GET':
return render_template("profile.html"
,name=name
,osis=osis
,digits=digits
,schedule=schedule
,email=email
,accept=notif["accept"]
,accepted=notif["accepted"]
)
elif request.method=="POST":
value=request.form["button"]
value=value.split(" ")
index=int(value[1])-1
if str(value[0])=="drop":
schedule=database.get_schedule(username)
clas=schedule[index]
if not (clas[1]=="free" or clas[1]=="Cafe"):
database.drop_period(username,clas[0])
schedule=database.get_schedule(username)
return render_template("profile.html"
,name=name
,osis=osis
,digits=digits
,schedule=schedule
,email=email
,accept=notif["accept"]
,accepted=notif["accepted"]
)
def visit(username=""):
if not session.has_key('user'):
return redirect(url_for('about'))
me=session['user']
if str(username)==str(me):
return redirect(url_for('profile'))
name=database.get_name(username)
osis=database.get_osis(username)
digits=database.get_id(username)
email=database.get_email(username)
schedule=database.get_schedule(username)
notif=database.get_notification(username)
if request.method=='GET':
return render_template("visit.html"
,name=name
,osis=osis
,digits=digits
,schedule=schedule
,email=email
,accept=notif["accept"]
,accepted=notif["accepted"]
)
def loadall(self, filename):
"""
Loads the XYZ trajectory file.
Parameters
----------
filename: str
Name of the XYZ file.
Returns
-------
atoms: list
List of int of the atomic numbers in order of appearance.
frames: list
List of np.arrays of the coordinates.
energies: list
List of str containing the comment line of the XYZ file.
nat: int
Number of atoms.
"""
with open(filename, 'r') as xyzfile:
spl_file = xyzfile.readlines()
atoms, frames, energies = [], [], []
nat = int(spl_file[0])
splitted_traj = [
spl_file[line_n * (nat + 2):line_n * (nat + 2) + (nat + 2)]
for line_n in range(int(len(spl_file) / (nat + 2)))
]
for at in splitted_traj[0][2:]:
atom = at.split()
atoms.append(periodic_table[db.get_name(atom[0])].atnum)
for frame in splitted_traj:
conf = self.XYZFrame(frame, en=True)
frames.append(conf.coordset)
energies.append(conf.energy)
return atoms, frames, energies, nat
from database import get_name name = get_name()
def cdf(xyzfile, atom1, atom2, atom3, r_range, th_range):
atom1 = get_name(atom1)
atom2 = get_name(atom2)
atom3 = get_name(atom3)
at1_cnt = xyzfile.atcount[atom1]
at2_cnt = xyzfile.atcount[atom2]
at3_cnt = xyzfile.atcount[atom3]
atom1 = periodic_table[atom1].atnum
atom2 = periodic_table[atom2].atnum
atom3 = periodic_table[atom3].atnum
triples = []
for at1_n, at1 in enumerate(xyzfile.atoms):
if at1 == atom1:
for at2_n, at2 in enumerate(xyzfile.atoms):
if at2 == atom2 and at2_n != at1_n:
# for at3_n, at3 in enumerate(xyzfile.atoms):
# if at3 == atom2 and at3_n != at1_n and at3_n != at2_n:
for at3_n, at3 in enumerate(xyzfile.atoms):
if at3 == atom3 and at3_n != at1_n and at3_n != at2_n:
triples.append((at1_n, at2_n, at3_n))
print("Triples generated.")
print(triples)
dists = []
angles = []
for frame in xyzfile.frames:
for triple in triples:
dx12 = frame[triple[0]][0] - frame[triple[1]][0]
dy12 = frame[triple[0]][1] - frame[triple[1]][1]
dz12 = frame[triple[0]][2] - frame[triple[1]][2]
dx13 = frame[triple[0]][0] - frame[triple[2]][0]
dy13 = frame[triple[0]][1] - frame[triple[2]][1]
dz13 = frame[triple[0]][2] - frame[triple[2]][2]
dx23 = frame[triple[1]][0] - frame[triple[2]][0]
dy23 = frame[triple[1]][1] - frame[triple[2]][1]
dz23 = frame[triple[1]][2] - frame[triple[2]][2]
############################
# Minimum Image Convention #
############################
dx13 = dx13 - round(dx12 / xyzfile.pbc[0]) * xyzfile.pbc[0]
dy13 = dy13 - round(dy12 / xyzfile.pbc[1]) * xyzfile.pbc[1]
dz13 = dz13 - round(dz12 / xyzfile.pbc[2]) * xyzfile.pbc[2]
dx12 = dx12 - round(dx12 / xyzfile.pbc[0]) * xyzfile.pbc[0]
dy12 = dy12 - round(dy12 / xyzfile.pbc[1]) * xyzfile.pbc[1]
dz12 = dz12 - round(dz12 / xyzfile.pbc[2]) * xyzfile.pbc[2]
############################
delta12 = dx12**2 + dy12**2 + dz12**2
delta13 = dx13**2 + dy13**2 + dz13**2
delta23 = dx23**2 + dy23**2 + dz23**2
d_12 = math.sqrt(delta12)
d_13 = math.sqrt(delta13)
d_23 = math.sqrt(delta23)
dists.append(d_12)
print(d_13, d_12, d_23)
angles.append(geom.cosrule(d_23, d_12, d_13, deg=True))
print("Distances and angles calculated.")
print(len(angles))
print(angles)
cdf, dist, angle = np.histogram2d(dists,
angles,
bins=(r_range[2], th_range[2]),
range=(r_range[:2], th_range[:2]))
# with open('before_norm.dat', 'w+') as outfile:
# for row in range(len(cdf)):
# for col in range(len(cdf[0])):
# outfile.write(F'{dist[row]} {angle[col]} {cdf[row][col]}\n')
#################
# Normalization #
#################
def volume(r_range, th_range):
th_range = list(map(lambda x: x * (math.pi / 180), th_range))
volume = (2 / 3) * math.pi * (pow(r_range[1], 3) - pow(
r_range[0], 3)) * (math.cos(th_range[0]) - math.cos(th_range[1]))
return volume
rho = at2_cnt / (xyzfile.pbc[0] * xyzfile.pbc[1] * xyzfile.pbc[2])
norm = 2 * xyzfile.nframes * at1_cnt * rho
# print(norm, xyzfile.nframes, at1_cnt, at2_cnt, rho, xyzfile.pbc)
plt_dist = []
plt_angle = []
plt_cdf = []
for row in range(len(cdf)):
for col in range(len(cdf[0])):
# cdf[row][col] /= (norm*volume((dist[row], dist[row + 1]), (angle[col], angle[col + 1])))
plt_dist.append(dist[row])
plt_angle.append(angle[col])
plt_cdf.append(cdf[row][col])
print("Normalized.")
#################
print(sum(plt_cdf))
# cdf = cdf.T
fig, ax = plt.subplots()
ax.scatter(plt_dist, plt_angle, c=plt_cdf) #, s=30)
# ax.imshow(cdf, interpolation='nearest', origin='low', extent=[dist[0], dist[-1], angle[0], angle[-1]])
plt.show()
def rdf(xyzfile, atom1, atom2, start, stop, nbins, outfile="out_rdf.dat"):
assert start >= 0, "The starting value of the rdf has to be positive."
assert stop > start, "The final value of the rdf has to be greater than the starting one."
#! ENTER PBC CONDITION, THROW ERROR
atom1 = get_name(atom1)
atom2 = get_name(atom2)
at1_cnt = xyzfile.atcount[atom1]
at2_cnt = xyzfile.atcount[atom2]
atom1 = periodic_table[atom1].atnum
atom2 = periodic_table[atom2].atnum
dr = (stop - start) / nbins
couples = corr_cpp.couples(xyzfile.atoms, atom1, atom2)
dists = corr_cpp.dists(xyzfile.frames, xyzfile.pbc, couples)
'''
couples = []
for at1_n, at1 in enumerate(xyzfile.atoms):
if at1 == atom1:
for at2_n, at2 in enumerate(xyzfile.atoms):
if at2 == atom2 and at2_n != at1_n: #this last bool checks for rdf with itself
couples.append((at1_n, at2_n))
dists = []
for frame in xyzfile.frames:
for couple in couples:
dx = frame[couple[0]][0] - frame[couple[1]][0]
dy = frame[couple[0]][1] - frame[couple[1]][1]
dz = frame[couple[0]][2] - frame[couple[1]][2]
############################
# Minimum Image Convention #
############################
dx = dx - round(dx / xyzfile.pbc[0]) * xyzfile.pbc[0]
dy = dy - round(dy / xyzfile.pbc[1]) * xyzfile.pbc[1]
dz = dz - round(dz / xyzfile.pbc[2]) * xyzfile.pbc[2]
############################
delta = dx**2 + dy**2 + dz**2
d_ij = math.sqrt(delta)
dists.append(d_ij)
'''
rdf = list(np.histogram(dists, nbins, range=(start, stop)))
#################
# Normalization #
#################
rho = at2_cnt / (xyzfile.pbc[0] * xyzfile.pbc[1] * xyzfile.pbc[2])
norm = 4 * math.pi * rho * dr * xyzfile.nframes * at1_cnt
if start == 0:
rdf[0] = list(
map(lambda x, y: x / (norm * y**2), rdf[0][1:], rdf[1][1:-1]))
else:
rdf[0] = list(map(lambda x, y: x / (norm * y**2), rdf[0], rdf[1][:-1]))
#################
with open(outfile, 'w+') as outfile:
for n in range(len(rdf[0])):
outfile.write(F'{rdf[1][n]} {rdf[0][n]}\n')
def tradingfloor():
if not session.has_key('user'):
return redirect(url_for("about"))
username=session['user']
name=database.get_name(username)
osis=database.get_osis(username)
digits=database.get_id(username)
email=database.get_email(username)
database.refresh_floor()
floor=database.get_floor()
if request.method=='GET':
return render_template("trading.html"
,name=name
,osis=osis
,digits=digits
,floor=floor
,email=email
,validate=False)
if request.method=='POST':
value=request.form["button"]
value=value.split(" ")
index=int(value[1])-1
req=floor[index]["request"]
period=int(req[0])-1
acceptername=username
postername=floor[index]['username']
schedule=database.get_schedule(username)[period]
validate=False
myself=False
illegaldel=False
try:
if not str(postername)==str(username):
if value[0]=="accept":
if l_equal(req,schedule):
database.accept_request(postername,acceptername,req)
return redirect(url_for("tradingfloor"))
else:
validate=True
elif value[0]=="delete":
validate=True
myself=False
illegaldel=True
else:
if value[0]=="accept":
validate=True
myself=True
else:
database.remove_request(username,req)
database.refresh_floor()
floor=database.get_floor()
return render_template("trading.html"
,name=name
,osis=osis
,digits=digits
,email=email
,floor=floor
,validate=validate
,myself=myself
,illegaldel=illegaldel)
except Exception:
return render_template("trading.html"
,name=name
,osis=osis
,digits=digits
,email=email
,floor=floor
,validate=True)
