try:
qvol = ppu.read_dbin(str(dbin_path/f'{dbin_fname}'), nQ, nTheta)
except FileNotFoundError:
print(f'File {dbin_fname} Not Found: Skipping')
continue
qvol = qvol**(0.125)
# qvol[:,:,:] -= qvol[:,:,::-1]
r1r2 = ppu.extract_r1r2(qvol)
# r1r2 = ppu.convolve_gaussian(r1r2, 1.5,1.5)
ppu.plot_map(r1r2, title=f'{dbin_fname} r1r2',extent=[0,tmax,0,qmax], cmap='viridis', xlabel='Correlation Angle $\\theta$ [degrees]',ylabel='Correlation length $q$ [1/$\AA$]', save=f'{dbin_fname}_r1r2' )
sumax0 =np.sum(qvol, axis=0)
# sumax0 = ppu.convolve_gaussian(sumax0, 1.5,1.5)
ppu.plot_map(sumax0, title=f'{dbin_fname} sumax0',extent=[0,tmax,0,qmax], cmap='viridis', save=f'{dbin_fname}_sumax0')
#
#
# qsx, qsy = np.meshgrid(q_space,q_space)
#
# sumax2 =np.sum(qvol, axis=2)
#
# sumax2 = ppu.convolve_gaussian(sumax2, 1,1)
tscale, rscale = np.meshgrid(t_space, r_space)
try:
rvol = ppu.read_dbin(
str(padf_path / f'{padf_fname}_rmax{rmax}_nl{nl}_padf'),
nR, nTheta)
except FileNotFoundError:
print('File Not Found: Skipping')
continue
print(padf_fname, rvol.shape)
r1r2 = ppu.extract_r1r2(rvol * rscale**2)
ppu.plot_map(r1r2[:, :180],
title=f'{padf_fname} nl {nl} r1r2',
extent=[0, tmax, rmax, 0],
vmin=0,
cmap='gist_stern',
save=f'{padf_fname}_rmax{rmax}_nl{nl}_r1r2')
sumax0 = np.sum(rvol * rscale**2, axis=0)
ppu.plot_map(sumax0[:, :180],
title=f'{padf_fname} nl {nl} sumax0',
extent=[0, tmax, rmax, 0],
cmap='gist_stern',
vmin=0,
save=f'{padf_fname}_rmax{rmax}_nl{nl}_sumax0')
rsx, rsy = np.meshgrid(r_space, r_space)
sumax2 = np.sum(rvol, axis=2) * (rsx**(1.5)) * (rsy**(1.5))
r1r2 = r1r2[nrmin:ncropr, :cropt]
r1r2 = np.clip(r1r2, 0, np.max(r1r2))
r1r2 = r1r2**(0.5)
r1r2 = r1r2 - np.min(r1r2)
r1r2 = r1r2 / np.max(r1r2)
lps[f'{padf_fname[:4]}'] = []
for lp_dist in lp_dists:
lps[f'{padf_fname[:4]}'].append(r1r2[int((lp_dist / rmax) * nrmax), :])
ppu.plot_map(r1r2,
title=f'{padf_fname[:4].upper()} - PADF',
extent=[0, cropt, rmin, cropr],
cmap='viridis',
save=f'{padf_fname[:4]}_r1r2',
xlabel='$\\theta$ / $ ^{\circ}$',
ylabel='$r_1 = r_2$ / $\\AA$',
fig_size=(8, 5.5))
dists = [6, 2.2]
cols = ['orange', 'red']
for col, dist in zip(cols, dists):
plt.plot(t_space[90:179],
(dist / 2) / np.sin(np.radians(180 - t_space[90:179]) / 2),
'-.',
color=col,
label=f'{dist} \u00c5',
linewidth=3)
# plt.plot(t_space, (dist/2)/np.sin(np.radians(180-t_space)/2), color=col)
l = plt.legend(
qvol = ppu.read_dbin(str(dbin_path / f'{dbin_fname}'), nQ, nTheta)
except FileNotFoundError:
print(f'File {dbin_fname} Not Found: Skipping')
continue
r1r2 = ppu.extract_r1r2(qvol)
r1r2 = r1r2**(0.25)
r1r2 = ppu.convolve_gaussian(r1r2, 2, 2)
r1r2 -= np.min(r1r2)
r1r2 /= np.max(r1r2)
ppu.plot_map(r1r2,
aspect='auto',
title=f'{dbin_fname[:4].upper()} - $q$ Space Correlation',
extent=[0, tmax, 0, qmax],
xlabel='$\\theta$ / $ ^{\circ}$',
fig_size=(8, 5.5),
ylabel='$q_1=q_2$ / $\AA^{-1}$',
save=f'{dbin_fname[:4]}_q1q2',
cmap='viridis')
# plt.plot(t_space, 3.5175*t_space**(-1.038291), 'r,')
plt.xlim(0, 180)
plt.ylim(0, qmax)
plt.show()
tscale, rscale = np.meshgrid(t_space, r_space)
print(str(padf_path / f'{padf_fname}_{res_name}_padf'), nR, nTheta)
try:
rvol = ppu.read_dbin(
str(padf_path / f'{padf_fname}_{res_name}_padf'), nR, nTheta)
except FileNotFoundError:
print('File Not Found: Skipping')
continue
# rvol = rvol**(2)
r1r2 = ppu.extract_r1r2(rvol * rscale**2)
ppu.plot_map(r1r2[:, :180],
title=f'{padf_fname} r1r2 rbins nR{nR}',
extent=[0, tmax, 0, rmax],
vmin=0,
cmap='gist_stern',
save=f'{padf_fname}_r1r2_nR{nR}')
#
#
sumax0 = np.sum(rvol * rscale**2, axis=0)
ppu.plot_map(sumax0[:, :180],
title=f'{padf_fname} sumax0 nR{nR}',
extent=[0, tmax, 0, rmax],
vmin=0,
cmap='gist_stern',
save=f'{padf_fname}_sumax0_nR{nR}')
# extent=[0,tmax,0,rmax], cmap='gist_stern', vmin=0)
#
##JACK NORMAL
j_data = np.loadtxt('1al1_ex_rcor.dat')
j_data = np.flip(j_data.T, axis=1)
j_data = np.clip(j_data, 0 , np.max(j_data))
t_space = np.linspace(0,180, j_data.shape[1])
r_space = np.linspace(0,20, j_data.shape[0])
rmax = 20
rmin = 2.5
res = j_data.shape[0]/rmax
nrmin = round(rmin*res)
ppu.plot_map(j_data[nrmin:,:], extent=[0,180,rmin,20], vmax=15, xlabel='$\\theta$ / $ ^{\circ}$', ylabel ='$r_1 = r_2$ /$\AA$', cmap='viridis')
arc_dists = [1.7, 2.7, 4.1,6]#, 10]
cols = plt.cm.autumn(np.linspace(0,1, len(arc_dists)))
for col, arc_dist in zip(cols, arc_dists):
plt.plot(t_space, (arc_dist/2) /np.sin(np.radians(t_space/2)), '--',label=arc_dist, color=col)
plt.plot(t_space, (arc_dist/2) /np.sin(np.radians((180-t_space)/2)), '--', color=col)
plt.xlim(0,180)
plt.ylim(rmin, 20)
plt.legend()
tscale, rscale = np.meshgrid(t_space, r_space)
rxx, ryy = np.meshgrid(r_space, r_space)
try:
rvol = ppu.read_dbin(str(padf_path/f'{padf_fname}'), nrmax, ntheta)
except FileNotFoundError:
print(f'File Not Found: {padf_fname}')
continue
rvol = rvol[nrmin:ncropr,nrmin:ncropr, :cropt]
print('rvol', rvol.shape)
print('rxx', rxx.shape)
print('ryy', ryy.shape)
for theta in theta_lins:
rrtheta = rvol[:,:,theta]
rrtheta = np.clip(rrtheta, 0, np.max(rrtheta))
print(rrtheta.shape)
rrtheta = rrtheta*(rxx**1)
rrtheta = rrtheta*(ryy**1)
ppu.plot_map(rrtheta, extent=[0,cropr,0,cropr],
title=f'{padf_fname[:4].upper()} - $\\theta$={theta}$^\circ$',
save=f'{padf_fname[:4]}_rrtheta{theta}',cmap='viridis',
xlabel='$r$ / $\\AA$', ylabel='$r`$ / $\\AA$')
plt.show()
print(f'File Not Found: {padf_fname}')
continue
r1r2 = ppu.extract_r1r2(rvol)
# r1r2 *= rscale**2
r1r2 = r1r2[nrmin:ncropr, :cropt]
r1r2 = np.clip(r1r2, 0, np.max(r1r2))
r1r2 = r1r2 - np.min(r1r2)
r1r2 = r1r2 / np.max(r1r2)
ppu.plot_map(r1r2,
title=f'{padf_fname} r1r2',
extent=[0, cropt, rmin, cropr],
cmap='viridis',
save=f'{padf_fname}_r1r2',
xlabel='Correlation Angle $\\theta$ [degrees]',
ylabel='Correlation length $r$ [$\\AA$]')
iso_peaks = [
16.6, 10.1, 16.2, 15.2, 10.3, 9.8, 10.3, 15.4, 17.3, 20.4, 17.8, 11.7,
19.0
]
# colors = plt.cm.jet(np.linspace(0,1,len(theta_lins)))
#
#
# plt.figure()
# plt.title(f'{padf_fname}_r1r2_theta_lin')
# print(len(colors), len(theta_lins))
tscale, rscale = np.meshgrid(t_space, r_space)
try:
rvol = ppu.read_dbin(str(padf_path / f'{padf_fname}{rmax}_padf'),
nR, nTheta)
except FileNotFoundError:
print('File Not Found: Skipping')
continue
r1r2 = ppu.extract_r1r2(rvol) * rscale**2
r1r2 = np.clip(r1r2, 0, np.max(r1r2))**(0.125)
ppu.plot_map(r1r2[:nRs[0] - 1, :180],
title=f'{padf_fname}{rmax} r1r2',
extent=[0, tmax, 0, r_space[nRs[0] - 1]],
cmap='viridis',
save=f'{padf_fname}{rmax}r1r2')
multi *= r1r2[:nRs[0] - 1, :180]
ave += r1r2[:nRs[0] - 1, :180] / 3
#
#
# sumax0 =np.sum(rvol*rscale**2, axis=0)
#
# ppu.plot_map(sumax0[:,:180], title=f'{padf_fname} sumax0',
# extent=[0,tmax,0,rmax], cmap='gist_stern', vmin=0)
#
#
#