def OnClickUpdate(self, e):
zwater, sig_water,sig_water_bar, d_water, Scale,specScale, beta, surface_new = param_unfold(self.nb.parameter,self.nb.parameter_usage,\
self.nb.surface, self.nb.MainControlPage.UBW_flag)
bulk = self.nb.bulk #shift_bulk(zwater, self.nb.bulk)
surface = RB_update(self.nb.rigid_bodies, surface_new,
self.nb.parameter, self.allrasd.cell)
for Rasd in self.allrasd.list:
Rasd.re_FNR ,Rasd.im_FNR = calcFNR(Rasd.Q,sig_water,sig_water_bar,d_water,zwater, self.allrasd.cell, bulk, surface, database,\
self.allrasd.g_inv, self.nb.MainControlPage.UBW_flag)
for item in range(len(self.allrasd.list)):
self.allrasd.list[item] = RASD_Fourier(self.allrasd, item)
self.datacontrol1[item].SetValue(
str(round(self.allrasd.list[item].AR, 3)))
self.datacontrol2[item].SetValue(
str(round(self.allrasd.list[item].PR, 3)))
def OnClickUpdate(self, e):
global_parms, surface_new = param_unfold(self.nb.parameter,self.nb.parameter_usage,self.nb.surface,\
self.nb.MainControlPage.UBW_flag, self.nb.MainControlPage.use_lay_el)
bulk = self.nb.bulk
surface = RB_update(self.nb.rigid_bodies, surface_new,
self.nb.parameter, self.allrasd.cell)
for Rasd in self.allrasd.list:
Rasd.re_FNR ,Rasd.im_FNR = calcFNR(Rasd.Q,global_parms, self.allrasd.cell, bulk, surface, database,\
self.allrasd.g_inv, self.nb.MainControlPage.UBW_flag,\
self.nb.MainControlPage.use_lay_el, str.lower(self.resel))
for item in range(len(self.allrasd.list)):
self.allrasd.list[item] = RASD_Fourier(self.allrasd, item)
self.datacontrol1[item].SetValue(
str(round(self.allrasd.list[item].AR, 3)))
self.datacontrol2[item].SetValue(
str(round(self.allrasd.list[item].PR, 3)))
def read_RSD(allrasd, bulk_tmp, surface_tmp, parameter, param_usage,
rigid_bodies, database, rasddata, use_bulk_water, dirname,
parent):
"""
read in data in RasdList of RasdAna objects for fitting
"""
if len(allrasd.E) == 0 and len(allrasd.f1) == 0:
dlg = wx.MessageDialog(parent, "Please read in f1f2 data first", "",
wx.OK | wx.STAY_ON_TOP)
if dlg.ShowModal() == wx.OK:
dlg.Destroy()
return allrasd
elif allrasd.E0 == 0:
dlg = wx.MessageDialog(parent, "Please specify Edge Energy first", "",
wx.OK | wx.STAY_ON_TOP)
if dlg.ShowModal() == wx.OK:
dlg.Destroy()
return allrasd
else:
zwater, sig_water, sig_water_bar, d_water, Scale, specScale, beta, surface_new = param_unfold(
parameter, param_usage, surface_tmp, use_bulk_water)
bulk = bulk_tmp #shift_bulk(zwater, bulk_tmp)
surface = RB_update(rigid_bodies, surface_new, parameter, allrasd.cell)
cell = allrasd.cell
g_inv = allrasd.g_inv
allrasd.ndata = 0
for dat in rasddata:
n = len(dat)
if dat[n - 1] == '\n':
dat = str.rstrip(dat, '\n')
Q = None
f = file(dirname + '/' + dat, 'r')
data = f.readlines()
f.close()
Rasd = RasdAna()
for i in range(len(data)):
if '#' not in data[i]:
tmp = str.rsplit(data[i])
if Q == None:
Q = Num.array([tmp[1], tmp[2], tmp[3]], float)
Rasd.Q = Q
Rasd.mod_Q = Num.dot(Num.dot(Q, g_inv), Q)**0.5
Rasd.re_FNR, Rasd.im_FNR = calcFNR(
Q, sig_water, sig_water_bar, d_water, zwater, cell,
bulk, surface, database, g_inv, use_bulk_water)
Rasd.E = Num.append(Rasd.E, int(round(float(tmp[0]))))
Rasd.F = Num.append(Rasd.F, float(tmp[4])**2)
Rasd.Ferr = Num.append(Rasd.Ferr, float(tmp[5])**2)
Rasd.Alpha = Num.append(Rasd.Alpha, float(tmp[6]))
Rasd.Beta = Num.append(Rasd.Beta, float(tmp[7]))
Rasd.E0 = allrasd.E0
for x in Rasd.E:
Rasd.Eorig = Num.append(Rasd.Eorig, x)
Rasd.abs_corr = Num.ones((len(Rasd.E)), float)
Rasd.ndata = len(Rasd.E)
Rasd.file = dat
allrasd.ndata = allrasd.ndata + Rasd.ndata
i = 0
Rasd.f1 = Num.ndarray((Rasd.ndata), float)
Rasd.f2 = Num.ndarray((Rasd.ndata), float)
for i in range(Rasd.ndata):
j = 0
for j in range(len(allrasd.E)):
if Rasd.E[i] == allrasd.E[j]:
Rasd.f1[i] = allrasd.f1[j]
Rasd.f2[i] = allrasd.f2[j]
allrasd.list.append(Rasd)
allrasd.dims = len(allrasd.list)
return allrasd
def createStructureRenderer(surface,cell,param,param_use,rigid_bodies,atom_styles):
global_parms, surface = \
param_unfold(param, param_use, surface, False, False)
surface = RB_update(rigid_bodies, surface, param, cell)
actors = []
M = calcM(cell)
supercell = []
for i in surface:
if i[10] > 0:
uxy = i[7] * (i[4] * i[5])**0.5
uxz = i[8] * (i[4] * i[6])**0.5
uyz = i[9] * (i[5] * i[6])**0.5
U = Num.array([[i[4],uxy,uxz],\
[uxy,i[5],uyz],\
[uxz,uyz,i[6]]],float)
Uinv = Num.linalg.inv(U)
supercell.append([i[0],Num.array([i[1],i[2],i[3]]),Uinv])
supercell.append([i[0],Num.array([i[1]+1,i[2],i[3]]),Uinv])
supercell.append([i[0],Num.array([i[1],i[2]+1,i[3]]),Uinv])
supercell.append([i[0],Num.array([i[1]+1,i[2]+1,i[3]]),Uinv])
#create an ellipsoid for every atom in supercell
for i in range(len(supercell)):
# create source
point = supercell[i][1]
[point] = aff2euk(M,[point])
Uinv = supercell[i][2]
if supercell[i][0] not in atom_styles.keys():
color = [1,1,1]
else:
color = atom_styles[supercell[i][0]]
actor = Ellipsoid(point, color, Uinv)
actors.append(actor)
# Create cell corner points
points = []
for i in [0.,1.]:
for j in [0.,1.]:
for k in [0.,1.]:
points.append([i,j,k])
points = aff2euk(M, points)
#create cell edge lines
line_id1 = [0,0,0,1,1,2,2,3,4,4,5,6]
line_id2 = [1,2,4,3,5,3,6,7,5,6,7,7]
for i in range(12):
line = vtk.vtkLineSource()
line.SetPoint1(points[line_id1[i]])
line.SetPoint2(points[line_id2[i]])
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(line.GetOutput())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(1,1,1) # (R,G,B)
actors.append(actor)
# create a renderer
ren = vtk.vtkRenderer()
# assign actors to the renderer
for actor in actors:
ren.AddActor(actor)
ren.SetBackground(0.0,0.0,0.0)
ren.GetActiveCamera().ParallelProjectionOn()
ren.ResetCamera()
ren.GetActiveCamera().Azimuth(180)
ren.GetActiveCamera().Elevation(270)
ren.ResetCameraClippingRange()
return ren
def read_RSD(allrasd, bulk_tmp, surface_tmp, parameter, param_usage,
rigid_bodies, database, rasddata, use_bulk_water, use_lay_el, el,
dirname, parent):
"""
read in data in RasdList of RasdAna objects for fitting
"""
if len(allrasd.E) == 0 and len(allrasd.f1) == 0:
dlg = wx.MessageDialog(parent, "Please read in f1f2 data first", "",
wx.OK | wx.STAY_ON_TOP)
if dlg.ShowModal() == wx.OK:
dlg.Destroy()
return allrasd
elif allrasd.E0 == 0:
dlg = wx.MessageDialog(parent, "Please specify Edge Energy first", "",
wx.OK | wx.STAY_ON_TOP)
if dlg.ShowModal() == wx.OK:
dlg.Destroy()
return allrasd
else:
global_parms, surface_new = param_unfold(parameter, param_usage,
surface_tmp, use_bulk_water,
use_lay_el)
bulk = bulk_tmp
surface = RB_update(rigid_bodies, surface_new, parameter, allrasd.cell)
cell = allrasd.cell
g_inv = allrasd.g_inv
allrasd.ndata = 0
allrasd.RMS = 0
f1 = interp1d(allrasd.E, allrasd.f1, 'cubic')
f2 = interp1d(allrasd.E, allrasd.f2, 'cubic')
for dat in rasddata:
n = len(dat)
if dat[n - 1] == '\n':
dat = str.rstrip(dat, '\n')
Q = None
f = file(dirname + '/' + dat, 'r')
data = f.readlines()
f.close()
Rasd = RasdAna()
for i in range(len(data)):
if '#' not in data[i]:
tmp = str.rsplit(data[i])
if Q == None:
Q = Num.array([tmp[1], tmp[2], tmp[3]], float)
Rasd.Q = Q
Rasd.mod_Q = Num.dot(Num.dot(Q, g_inv), Q)**0.5
Rasd.re_FNR, Rasd.im_FNR = calcFNR(
Q, global_parms, cell, bulk, surface, database,
g_inv, use_bulk_water, use_lay_el, el)
Rasd.E = Num.append(Rasd.E, float(tmp[0]))
Rasd.F = Num.append(Rasd.F, float(tmp[4])**2)
Rasd.f1 = Num.append(Rasd.f1, f1(Rasd.E[-1]))
Rasd.f2 = Num.append(Rasd.f2, f2(Rasd.E[-1]))
if float(tmp[5]) == 0:
Rasd.Ferr = Num.append(Rasd.Ferr, 1.0)
else:
Rasd.Ferr = Num.append(Rasd.Ferr, float(tmp[5])**2)
Rasd.Alpha = Num.append(Rasd.Alpha, float(tmp[6]))
Rasd.Beta = Num.append(Rasd.Beta, float(tmp[7]))
Rasd.E0 = allrasd.E0
for x in Rasd.E:
Rasd.Eorig = Num.append(Rasd.Eorig, x)
Rasd.abs_corr = Num.ones((len(Rasd.E)), float)
Rasd.ndata = len(Rasd.E)
Rasd.file = dat
allrasd.ndata = allrasd.ndata + Rasd.ndata
allrasd.list.append(Rasd)
allrasd.dims = len(allrasd.list)
allrasd.RMS = allrasd.RMS / allrasd.ndata
return allrasd