def calc_A_P_Q(Qmax, g_inv, surface_tmp, parameter, param_usage, use_bulk_water, use_lay_el):
global_parms, surface = param_unfold(parameter, param_usage, surface_tmp, use_bulk_water, use_lay_el)
natoms = len(surface)
occ_el, K, sig_el, sig_el_bar, d_el, d0_el, sig_water, sig_water_bar, d_water, zwater, Scale, specScale, beta = (
global_parms
)
A = []
P = []
L = Num.arange(0.1, Qmax, 0.01)
for l in L:
Q = Num.array([0, 0, l], float)
Q_ang = Num.array([0, 0, l * g_inv[2][2] ** 0.5], float)
re_Fq = 0
im_Fq = 0
for n in range(natoms):
R = Num.array([surface[n][1], surface[n][2], surface[n][3]], float)
U = Num.ndarray((3, 3), float)
U[0][0] = surface[n][4]
U[0][1] = U[1][0] = surface[n][7] * (surface[n][4] * surface[n][5]) ** 0.5
U[0][2] = U[2][0] = surface[n][8] * (surface[n][4] * surface[n][6]) ** 0.5
U[1][1] = surface[n][5]
U[1][2] = U[2][1] = surface[n][9] * (surface[n][5] * surface[n][6]) ** 0.5
U[2][2] = surface[n][6]
theta = surface[n][10]
re_Fq = re_Fq + (
theta
* Num.cos(2 * Num.pi * (Q[0] * R[0] + Q[1] * R[1] + Q[2] * R[2]))
* Num.exp(-2 * Num.pi ** 2 * Num.dot(Num.dot(Q_ang, U), Q_ang))
)
im_Fq = im_Fq + (
theta
* Num.sin(2 * Num.pi * (Q[0] * R[0] + Q[1] * R[1] + Q[2] * R[2]))
* Num.exp(-2 * Num.pi ** 2 * Num.dot(Num.dot(Q_ang, U), Q_ang))
)
if use_lay_el:
re_lay, im_lay = calc_F_lay_el(Q, occ_el, K, sig_el, sig_el_bar, d_el, d0_el, g_inv)
re_Fq = re_Fq + re_lay
im_Fq = im_Fq + im_lay
PR = Num.arctan(im_Fq / re_Fq) / (2 * Num.pi)
AR = re_Fq / Num.cos(2 * Num.pi * PR)
if AR < 0 and PR < 0.5 and PR > 0.0:
PR = PR + 0.5
AR = -AR
elif AR < 0 and PR > 0.5:
PR = PR - 0.5
AR = -AR
elif PR < 0 and AR > 0:
PR = PR + 1.0
elif AR < 0 and PR < 0 and PR > -0.5:
PR = PR + 0.5
AR = -AR
if PR > 1:
PR = PR - 1
A.append(AR)
P.append(PR)
return L, A, P
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 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 Rasd_difference(allrasd, surface_tmp, parameter, param_usage, use_bulk_water, Refine_Data):
allrasd.RMS = 0
allrasd.ndata = 0
zwater, sig_water,sig_water_bar, d_water, Scale,specScale, beta, surface = param_unfold(parameter,param_usage, surface_tmp, use_bulk_water)
natoms = len(surface)
for Rasd in allrasd.list:
if Rasd.use_in_Refine:
Q = Num.zeros((3),float)
Q[0] = allrasd.g_inv[0][0]**0.5 * Rasd.Q[0]
Q[1] = allrasd.g_inv[1][1]**0.5 * Rasd.Q[1]
Q[2] = allrasd.g_inv[2][2]**0.5 * Rasd.Q[2]
j = 0
re_Fq = 0
im_Fq = 0
for n in range(natoms):
R = Num.array([surface[n][1],surface[n][2],surface[n][3]],float)
U = Num.array([[surface[n][4],surface[n][7],surface[n][8]],[surface[n][7],surface[n][5],surface[n][9]],[surface[n][8],surface[n][9],surface[n][6]]],float)
theta = surface[n][10]
re_Fq = re_Fq + (theta * Num.cos(2*Num.pi*(Rasd.Q[0]*R[0]+Rasd.Q[1]*R[1]+Rasd.Q[2]*R[2])) * Num.exp(-2* Num.pi**2 * Num.dot(Num.dot(Q,U),Q)))
im_Fq = im_Fq + (theta * Num.sin(2*Num.pi*(Rasd.Q[0]*R[0]+Rasd.Q[1]*R[1]+Rasd.Q[2]*R[2])) * Num.exp(-2* Num.pi**2 * Num.dot(Num.dot(Q,U),Q)))
Rasd.re_FR = Rasd.f1 * re_Fq - Rasd.f2 * im_Fq
Rasd.im_FR = Rasd.f1 * im_Fq + Rasd.f2 * re_Fq
Rasd.re_Fq = re_Fq
Rasd.im_Fq = im_Fq
if Refine_Data:
vec = [Rasd.a, Rasd.b]
result = leastsq(Wiggle2, vec, args=(Rasd), Dfun = Jacobi2, col_deriv = 1)
vec = result[0]
Rasd.a, Rasd.b = vec
Rasd.F_calc = (Rasd.a+Rasd.b*(Rasd.E - Rasd.E0))*((Rasd.re_FNR + Rasd.re_FR)**2 + (Rasd.im_FNR + Rasd.im_FR)**2)
Rasd.delta_F = (Rasd.F - Rasd.F_calc)**2/Rasd.Ferr**2
Rasd.norm = (Rasd.a+ Rasd.b* (Rasd.E - Rasd.E0))*(Rasd.re_FNR**2 + Rasd.im_FNR**2)
Rasd.RMS = Num.sum(Rasd.delta_F)/Rasd.ndata
allrasd.RMS = allrasd.RMS + Num.sum(Rasd.delta_F)
allrasd.ndata = allrasd.ndata + Rasd.ndata
else:
PR = Num.arctan(Rasd.im_Fq/Rasd.re_Fq)/(2*Num.pi)
AR = Rasd.re_Fq /Num.cos(2*Num.pi*PR)
if AR < 0 and PR < 0.5 and PR > 0.:
PR = PR + 0.5
AR = -AR
elif AR < 0 and PR > 0.5:
PR = PR - 0.5
AR = -AR
elif PR < 0 and AR > 0:
PR = PR + 1.
elif AR < 0 and PR < 0 and PR > -0.5:
PR = PR + 0.5
AR = -AR
if PR > 1: PR = PR -1
Rasd.AR_refine = AR
Rasd.PR_refine = PR
Rasd.RMS = (Rasd.re_Fq / Num.cos(2*Num.pi*Rasd.PR) - Rasd.AR)**2 + (Rasd.im_Fq / Num.sin(2*Num.pi*Rasd.PR) - Rasd.AR)**2
allrasd.RMS = allrasd.RMS + Rasd.RMS
allrasd.ndata = allrasd.ndata + 1
allrasd.RMS = allrasd.RMS/allrasd.ndata
return allrasd
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 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 Rasd_difference(allrasd, surface_tmp, parameter, param_usage, use_bulk_water, Refine_Data, use_lay_el, fix_bckg = False):
allrasd.RMS = 0
allrasd.ndata = 0
global_parms, surface = param_unfold(parameter,param_usage, surface_tmp, use_bulk_water, use_lay_el)
natoms = len(surface)
occ_el, K,sig_el,sig_el_bar,d_el,d0_el,sig_water, sig_water_bar, d_water, zwater, Scale, specScale, beta= global_parms
for Rasd in allrasd.list:
if Rasd.use_in_Refine:
Q = Num.zeros((3),float)
Q[0] = allrasd.g_inv[0][0]**0.5 * Rasd.Q[0]
Q[1] = allrasd.g_inv[1][1]**0.5 * Rasd.Q[1]
Q[2] = allrasd.g_inv[2][2]**0.5 * Rasd.Q[2]
j = 0
re_Fq = 0
im_Fq = 0
for n in range(natoms):
R = Num.array([surface[n][1],surface[n][2],surface[n][3]],float)
U = Num.ndarray((3,3),float)
U[0][0] = surface[n][4]
U[0][1] = U[1][0] = surface[n][7]*(surface[n][4]*surface[n][5])**0.5
U[0][2] = U[2][0] = surface[n][8]*(surface[n][4]*surface[n][6])**0.5
U[1][1] = surface[n][5]
U[1][2] = U[2][1] = surface[n][9]*(surface[n][5]*surface[n][6])**0.5
U[2][2] = surface[n][6]
theta = surface[n][10]
re_Fq = re_Fq + (theta * Num.cos(2*Num.pi*(Rasd.Q[0]*R[0]+Rasd.Q[1]*R[1]+Rasd.Q[2]*R[2])) * Num.exp(-2* Num.pi**2 * Num.dot(Num.dot(Q,U),Q)))
im_Fq = im_Fq + (theta * Num.sin(2*Num.pi*(Rasd.Q[0]*R[0]+Rasd.Q[1]*R[1]+Rasd.Q[2]*R[2])) * Num.exp(-2* Num.pi**2 * Num.dot(Num.dot(Q,U),Q)))
if use_lay_el and Q[0] == 0 and Q[1] == 0:
re_lay, im_lay = calc_F_lay_el(Rasd.Q, occ_el, K, sig_el, sig_el_bar, d_el, d0_el, allrasd.g_inv)
re_Fq = re_Fq + re_lay
im_Fq = im_Fq + im_lay
Rasd.re_FR = Rasd.f1 * re_Fq - Rasd.f2 * im_Fq
Rasd.im_FR = Rasd.f1 * im_Fq + Rasd.f2 * re_Fq
Rasd.re_Fq = re_Fq
Rasd.im_Fq = im_Fq
if Refine_Data:
if not fix_bckg:
vec = [Rasd.a, Rasd.b]
result = leastsq(Wiggle2, vec, args=(Rasd), Dfun = Jacobi2, col_deriv = 1)
vec = result[0]
Rasd.a, Rasd.b = vec
Rasd.F_calc = (Rasd.a+Rasd.b*(Rasd.E - Rasd.E0))*((Rasd.re_FNR + Rasd.re_FR)**2 + (Rasd.im_FNR + Rasd.im_FR)**2)
Rasd.delta_F = ((Rasd.F - Rasd.F_calc)/Rasd.Ferr)**2
Rasd.norm = (Rasd.a+ Rasd.b* (Rasd.E - Rasd.E0))*(Rasd.re_FNR**2 + Rasd.im_FNR**2)
Rasd.RMS = Num.sum(Rasd.delta_F)/Rasd.ndata
allrasd.RMS = allrasd.RMS + Num.sum(Rasd.delta_F)
allrasd.ndata = allrasd.ndata + Rasd.ndata
else:
PR = Num.arctan(Rasd.im_Fq/Rasd.re_Fq)/(2*Num.pi)
AR = Rasd.re_Fq /Num.cos(2*Num.pi*PR)
if AR < 0 and PR < 0.5 and PR > 0.:
PR = PR + 0.5
AR = -AR
elif AR < 0 and PR > 0.5:
PR = PR - 0.5
AR = -AR
elif PR < 0 and AR > 0:
PR = PR + 1.
elif AR < 0 and PR < 0 and PR > -0.5:
PR = PR + 0.5
AR = -AR
if PR > 1: PR = PR -1
Rasd.AR_refine = AR
Rasd.PR_refine = PR
Rasd.RMS = (Rasd.re_Fq / Num.cos(2*Num.pi*Rasd.PR) - Rasd.AR)**2 + (Rasd.im_Fq / Num.sin(2*Num.pi*Rasd.PR) - Rasd.AR)**2
allrasd.RMS = allrasd.RMS + Rasd.RMS
allrasd.ndata = allrasd.ndata + 1
allrasd.RMS = allrasd.RMS/allrasd.ndata
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
def calc_A_P_Q(Qmax, g_inv, surface_tmp, parameter, param_usage,
use_bulk_water, use_lay_el):
global_parms, surface = param_unfold(parameter, param_usage, surface_tmp,
use_bulk_water, use_lay_el)
natoms = len(surface)
occ_el, K, sig_el, sig_el_bar, d_el, d0_el, sig_water, sig_water_bar, d_water, zwater, Scale, specScale, beta = global_parms
A = []
P = []
L = Num.arange(0.1, Qmax, 0.01)
for l in L:
Q = Num.array([0, 0, l], float)
Q_ang = Num.array([0, 0, l * g_inv[2][2]**0.5], float)
re_Fq = 0
im_Fq = 0
for n in range(natoms):
R = Num.array([surface[n][1], surface[n][2], surface[n][3]], float)
U = Num.ndarray((3, 3), float)
U[0][0] = surface[n][4]
U[0][1] = U[1][0] = surface[n][7] * (surface[n][4] *
surface[n][5])**0.5
U[0][2] = U[2][0] = surface[n][8] * (surface[n][4] *
surface[n][6])**0.5
U[1][1] = surface[n][5]
U[1][2] = U[2][1] = surface[n][9] * (surface[n][5] *
surface[n][6])**0.5
U[2][2] = surface[n][6]
theta = surface[n][10]
re_Fq = re_Fq + (
theta * Num.cos(2 * Num.pi *
(Q[0] * R[0] + Q[1] * R[1] + Q[2] * R[2])) *
Num.exp(-2 * Num.pi**2 * Num.dot(Num.dot(Q_ang, U), Q_ang)))
im_Fq = im_Fq + (
theta * Num.sin(2 * Num.pi *
(Q[0] * R[0] + Q[1] * R[1] + Q[2] * R[2])) *
Num.exp(-2 * Num.pi**2 * Num.dot(Num.dot(Q_ang, U), Q_ang)))
if use_lay_el:
re_lay, im_lay = calc_F_lay_el(Q, occ_el, K, sig_el, sig_el_bar,
d_el, d0_el, g_inv)
re_Fq = re_Fq + re_lay
im_Fq = im_Fq + im_lay
PR = Num.arctan(im_Fq / re_Fq) / (2 * Num.pi)
AR = re_Fq / Num.cos(2 * Num.pi * PR)
if AR < 0 and PR < 0.5 and PR > 0.:
PR = PR + 0.5
AR = -AR
elif AR < 0 and PR > 0.5:
PR = PR - 0.5
AR = -AR
elif PR < 0 and AR > 0:
PR = PR + 1.
elif AR < 0 and PR < 0 and PR > -0.5:
PR = PR + 0.5
AR = -AR
if PR > 1:
PR = PR - 1
A.append(AR)
P.append(PR)
return L, A, P
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
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 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)))