def on_copy_button_clicked_handler(self, *arg):
try:
v1 = float(self.vx_entry.get_text())
except:
msg().error("Wrong x-field in Vector.")
try:
v2 = float(self.vy_entry.get_text())
except:
msg().error("Wrong y-field in Vector.")
try:
v3 = float(self.vz_entry.get_text())
except:
msg().error("Wrong z-field in Vector.")
v = Vector(v1, v2, v3)
if self.system is not None:
if self.system.INITIAL_STRUCTURE is not None:
s = self.system.INITIAL_STRUCTURE
s.setCarthesian()
sel = Selection(self.group_entry.get_text(), s)
l = []
for i in sel.getAtoms():
if i >= 0 and i < len(s):
l.append((s.speciesIndex(i), s[i] + v))
for i, v in l:
s.appendAtom(i, v)
msg().status("OK")
systemlist().notifySystemChanged()
else:
msg().error("No initial structure in the current system.")
else:
msg().error("No system selected.")
def rotate(self):
try:
v1 = float(eval(self.vx_entry.get_text()))
except:
msg().error("Invalid x-field in axis.")
try:
v2 = float(eval(self.vy_entry.get_text()))
except:
msg().error("Invalid y-field in axis.")
try:
v3 = float(eval(self.vz_entry.get_text()))
except:
msg().error("Invalid z-field in axis.")
v = Vector(v1, v2, v3)
try:
o1 = float(eval(self.fromx_entry.get_text()))
except:
msg().error("Invalid x-field in center.")
try:
o2 = float(eval(self.fromy_entry.get_text()))
except:
msg().error("Invalid y-field in center.")
try:
o3 = float(eval(self.fromz_entry.get_text()))
except:
msg().error("Invalid z-field in center.")
o = Vector(o1, o2, o3)
try:
a = float(eval(self.angle_entry.get_text()))
except:
msg().error("Invalid angle.")
a *= pi / 180.0
n = v.normal()
if self.system is not None:
if self.system.INITIAL_STRUCTURE is not None:
s = self.system.INITIAL_STRUCTURE
s.setCarthesian()
sel = Selection(self.group_entry.get_text(), s)
for i, nx, ny, nz in sel:
d = nx * s.basis[0] + ny * s.basis[1] + nz * s.basis[2]
if i >= 0 and i < len(s):
r = s[i] + d - o
s[i] = cos(a) * r + (
(n * r) *
(1 - cos(a))) * n + sin(a) * r.cross(n) + o - d
msg().status("OK")
systemlist().notifySystemChanged()
else:
msg().error("No initial structure in the current system.")
else:
msg().error("No system selected.")
def readVacGen(self):
self.select_atoms = self.sel.getAtoms()
# print self.select_atoms
# selectedatoms=string.split(self.xml.get_widget("sel_entry").get_text())
# self.select_status=0
# self.select_atoms=[]
# try:
# for i in range(len(selectedatoms)):
# self.select_atoms.append(int(selectedatoms[i]))
# self.select_status=1
# except ValueError:
# self.select_status=0
# self.select_atoms=[]
# #else:
# print 'selected are:',selectedatoms
system = self.system
self.world[0].subtitle = ""
if len(self.sel):
if system is not None:
s = system.INITIAL_STRUCTURE
st = self.sel.encode(s)
self.world[0].subtitle = "Selected atoms:%s" % st
msg().status("VAC")
yield 1
if system is not None:
name = system.current("NAME")
if name is not None:
self.world[0].subtitle = "(%s)" % name
t0 = time.clock()
natoms = None
if self.multi:
totalnumconfigs = 0
systems = systemlist()
for s in systems:
cs = s.CSTRUCTURE_SEQUENCE_L
if cs is not None:
totalnumconfigs += len(cs)
natoms = len(cs[0]) # number of atoms in single config
try:
initconfigs = int(
self.xml.get_widget(
"init_entry").get_text()) # configs to be skipped
except:
initconfigs = 0
allcarts = zeros((totalnumconfigs - initconfigs, natoms, 3),
Float)
t1 = time.clock()
indx = 0
for si in range(len(systems)):
ss = systems[si].CSTRUCTURE_SEQUENCE_L
if ss is not None:
msg().message('t(parsing): %f' % (t1 - t0))
if initconfigs > (len(ss)):
initconfigs -= (len(ss))
continue
#if si!=0:initconfigs+=1
numconfigs = len(ss) # total number of configs
for i in range(initconfigs, numconfigs):
if indx % 50 == 0:
msg().status(
"Reading %s positions (%f s)" %
(systems[si].NAME, time.clock() - t1))
msg().step(indx, len(allcarts))
yield 1
ss[i].setCarthesian()
ssi = map(array, ss[i])
allcarts[indx] = ssi #ss[i] #.positions
indx += 1
msg().step(0, 1)
initconfigs = 0
else:
s = system
ss = s.CSTRUCTURE_SEQUENCE_L
t1 = time.clock()
msg().message('t(parsing): %f' % (t1 - t0))
numconfigs = len(ss) # total number of configs
natoms = len(ss[0]) # number of atoms in single config
try:
initconfigs = int(
self.xml.get_widget(
"init_entry").get_text()) # configs to be skipped
except:
initconfigs = 0
allcarts = zeros((numconfigs - initconfigs, natoms, 3), Float)
for i in range(initconfigs, numconfigs):
indx = i - initconfigs
if indx % 50 == 0:
msg().status("Reading positions (%f s)" %
(time.clock() - t1))
msg().step(indx, numconfigs - initconfigs)
yield 1
ss[i].setCarthesian()
allcarts[indx] = ss[i] #.positions
msg().step(0, 1)
velocities = zeros((len(allcarts) - 2, len(allcarts[0]), 3), Float)
msg().status("Calculating velocities")
yield 1
if len(self.select_atoms) > 0:
pattern = zeros((len(allcarts[0]), 3))
for i in self.select_atoms:
pattern[i] = 1
else:
pattern = ones((len(allcarts[0]), 3))
allcarts = allcarts * pattern
for i in range(1, len(allcarts) - 1):
velocities[i - 1] = (allcarts[i + 1] - allcarts[i - 1]
) #*pattern
if i % 100 == 0:
msg().step(i, len(allcarts) - 1)
yield 1
msg().step(0, 1)
t2 = time.clock()
msg().message('t(velocities): %f' % (t2 - t1))
msg().status('Calculating VAC')
yield 1
scheduleFirst(self.giveVacGen(velocities)) ###???????
yield 1
t3 = time.clock()
msg().message('t(vac):%f' % (t3 - t2))
else:
self.vac = []
msg().step(0, 1)
msg().status("OK")
self.xml.get_widget("win_lab").set_sensitive(True)
self.xml.get_widget("winopt").set_sensitive(True)
self.xml.get_widget("filter_button").set_sensitive(True)
self.xml.get_widget("fft_button").set_sensitive(True)
self.freq = []
self.updateGraph()
def changePositions(self):
sel=self.sel
if len(sel)==0:
msg().status("No atoms selected.")
return
if len(sel)>1:
try:
l1=float(eval(self.l1_entry.get_text()))
print "l1",l1
except:
msg().error("Error parsing length 1 in sub-Z-matrix")
return
if len(sel)>2:
try:
l2=float(eval(self.l2_entry.get_text()))
print "l2",l2
except:
msg().error("Error parsing length 2 in sub-Z-matrix")
return
try:
a2=float(eval(self.a2_entry.get_text()))
print "a2",a2
except:
msg().error("Error parsing angle 1 in sub-Z-matrix")
return
if len(sel)>3:
try:
l3=float(eval(self.l3_entry.get_text()))
print "l3",l3
except:
msg().error("Error parsing length 3 in sub-Z-matrix")
return
try:
a3=float(eval(self.a3_entry.get_text()))
print "a3",a3
except:
msg().error("Error parsing angle 2 in sub-Z-matrix")
return
try:
d3=float(eval(self.d3_entry.get_text()))
print "d3",d3
except:
msg().error("Error parsing dihedral angle in sub-Z-matrix")
return
s=self.system.INITIAL_STRUCTURE
if s is not None:
s.setCarthesian()
else:
msg().error("No initial structure available.")
if len(sel)>=2:
i,nx,ny,nz=sel[0]
v1=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[1]
v2=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
dv=v2-v1
l=(v1-v2).length()
if l!=0.0:
s[i]=v1+(l1/l)*dv-s.basis[0]*nx-s.basis[1]*ny-s.basis[2]*nz
else:
msg().status("Atoms have the same position, moving in X-direction")
s[i]=v1+Vector(l1,0.0,0.0)-s.basis[0]*nx-s.basis[1]*ny-s.basis[2]*nz
if len(sel)>=3:
i0,nx0,ny0,nz0=sel[0]
a=s[i0]+s.basis[0]*nx0+s.basis[1]*ny0+s.basis[2]*nz0
i1,nx1,ny1,nz1=sel[1]
b=s[i1]+s.basis[0]*nx1+s.basis[1]*ny1+s.basis[2]*nz1
i2,nx2,ny2,nz2=sel[2]
c=s[i2]+s.basis[0]*nx2+s.basis[1]*ny2+s.basis[2]*nz2
l=(a-b).length()
dv=(b-a)
angle=(a-b).angle(c-b)*180.0/pi
if l==0.0:
msg().status("First two atoms have the same position, moving in X-direction")
dv=Vector(1.0,0.0,0.0)
l=1.0
try:
n1=(c-b).cross(a-b).normal()
except:
msg().status("First three atoms do not define a plane, using Z-axis for rotation.")
try:
n1=Vector(0.0,-dv[2],dv[1]).normal()
except:
n1=Vector(0.0,0.0,1.0)
s[i2]=rot(b,n1,b-(l2/l)*dv,a2*pi/180.0)-s.basis[0]*nx2-s.basis[1]*ny2-s.basis[2]*nz2
if len(sel)>=4:
i0,nx0,ny0,nz0=sel[0]
a=s[i0]+s.basis[0]*nx0+s.basis[1]*ny0+s.basis[2]*nz0
i1,nx1,ny1,nz1=sel[1]
b=s[i1]+s.basis[0]*nx1+s.basis[1]*ny1+s.basis[2]*nz1
i2,nx2,ny2,nz2=sel[2]
c=s[i2]+s.basis[0]*nx2+s.basis[1]*ny2+s.basis[2]*nz2
i3,nx3,ny3,nz3=sel[3]
d=s[i3]+s.basis[0]*nx3+s.basis[1]*ny3+s.basis[2]*nz3
try:
n1=(c-b).cross(a-b).normal()
except:
msg().status("First three atoms do not define a plane, using Z-axis.")
try:
n1=Vector(0.0,-dv[2],dv[1]).normal()
except:
n1=Vector(0.0,0.0,1.0)
l=(b-c).length()
dv=(c-b)
angle=(b-c).angle(d-c)*180.0/pi
if l==0.0:
msg().status("Second and third have the same position, using X-direction")
dv=Vector(1.0,0.0,0.0)
l=1.0
newd=rot(c,n1,c-(l3/l)*dv,a3*pi/180.0)
s[i3]=rot(c,c-b,newd,(180+d3)*pi/180.0)-s.basis[0]*nx3-s.basis[1]*ny3-s.basis[2]*nz3
systemlist().notifySystemChanged()