def run(peak_str, peak_centre, source_name, timestep):
import units as un
print "Plotting each individual peak in kx, ky, and kz..."
directions = ["kx", "ky", "kz"]
constant_axes = [[1, 2], [0, 2], [0, 1]]
variable_axes = [0, 1, 2]
for i, current_peak_str in enumerate(peak_str):
data_filename = un.determine_accurate_soh_output_file_location(
current_peak_str, source_name, timestep)
soh_output = un.read_from_soh_output(data_filename)
centre_point = peak_centre[i]
for j, direction in enumerate(directions):
k, intensity = un.find_line_data_from_3DFT(constant_axes[j],
variable_axes[j],
centre_point,
soh_output)
plot_data_filename = "./data/" + current_peak_str + "/" + direction + ".dat"
plot_filename = "./data/" + current_peak_str + "/" + direction + ".png"
un.plot_pygnuplot(k, intensity, plot_filename, plot_data_filename)
return
def run(peak_str, peak_centre, source_name, timestep):
import units as un
import numpy as np
print "Plotting each peak in kx, ky, kz, and |G^2|..."
directions = ["kx", "ky", "kz"]
constant_axes = [[1, 2], [0, 2], [0, 1]]
variable_axes = [0, 1, 2]
for i, current_peak_str in enumerate(peak_str):
data_filename = un.determine_accurate_soh_output_file_location(
current_peak_str, source_name, timestep)
soh_output = un.read_from_soh_output(data_filename)
centre_point = peak_centre[i]
# This for loop plots the peak through kx, ky, and kz.
for j, direction in enumerate(directions):
k, intensity = un.find_line_data_from_3DFT(constant_axes[j],
variable_axes[j],
centre_point,
soh_output)
plot_data_filename = "./data/" + current_peak_str + "/" + direction + ".dat"
plot_filename = "./data/" + current_peak_str + "/" + direction + ".png"
un.plot_pygnuplot(k, intensity, plot_filename, plot_data_filename)
# This section plots every point in the 3DFT as intensity vs. G^2.
gsqr = list((np.array(soh_output[0])**2) +
(np.array(soh_output[1])**2) +
(np.array(soh_output[2])**2))
intensity = soh_output[3]
plot_data_filename = "./data/" + current_peak_str + "/I_vs_gsqr.dat"
plot_filename = "./data/" + current_peak_str + "/I_vs_gsqr_" + current_peak_str + ".png"
un.plot_pygnuplot(gsqr, intensity, plot_filename, plot_data_filename)
return
def run(pos, source_name, timestep):
import units as un
import logging as log
log.debug("Brick %s started.\n", __name__)
print "Calculating peak intensities..."
peak_centre = []
integrated_intensity = []
for i in pos:
peak_str = un.make_peak_str(i)
soh_output_file_location = un.determine_accurate_soh_output_file_location(
peak_str, source_name, timestep)
soh_output = un.read_from_soh_output(soh_output_file_location)
point_of_max_height = un.find_point_of_max_height(soh_output)
peak_centre.append(point_of_max_height)
dvol = un.calc_dvol(soh_output)
current_integrated_intensity = un.calc_integrated_intensity(
soh_output, dvol)
integrated_intensity.append(current_integrated_intensity)
log.debug("Brick %s finished.\n", __name__)
return peak_centre, integrated_intensity
def run(run_soh, lineout_directions, undershoot, overshoot, source, mass,
a_lattice, lineout_k_steps, timestep, soh_command):
import units as un
import os
print "Finding compression ratios..."
compression_ratio = [1.0, 1.0, 1.0]
direction_str = ["kx", "ky", "kz"]
if os.path.exists("./data/lineouts/"):
pass
else:
un.make_lineout_directory()
for i, direction in enumerate(lineout_directions):
k_start, k_stop = un.calc_lineout_k_start_stop(direction, undershoot,
overshoot)
soh_location = un.determine_soh_compression_finding_input_file_location(
direction_str[i])
un.write_soh_input_1DFT(source, soh_location,
"lineout_" + direction_str[i], mass, a_lattice,
k_start, k_stop, lineout_k_steps)
if run_soh is True:
for i, direction in enumerate(lineout_directions):
soh_location = un.determine_soh_compression_finding_input_file_location(
direction_str[i])
un.run_soh(soh_location, soh_command)
un.move_soh_output_to_lineout_folder(direction_str[i], source,
timestep)
for i, direction in enumerate(lineout_directions):
soh_location = un.determine_soh_1DFT_output_file_location(
direction_str[i], source, timestep)
soh_output = un.read_from_soh_output(soh_location)
un.plot_pygnuplot(
soh_output[i], soh_output[3],
os.getcwd() + "/data/lineouts/" + direction_str[i] +
"_lineout.png",
os.getcwd() + "/data/lineouts/" + direction_str[i] +
"_lineout.dat")
k_of_max_height = un.find_point_of_max_height(soh_output)
compression_ratio[i] = un.calc_compression_ratio(
k_of_max_height[i], lineout_directions[i][i])
return compression_ratio
def run(run_soh, raw_pos_est, pos_est, gsqr_est, compression_ratio, source_name, N_atoms, mass, a_lattice,
k_steps_find_centre_1D, k_steps_find_centre_3D, timestep, soh_command, plot):
import units as un
import copy
print "Fitting to peak centres..."
centre_guess_3DFT = copy.deepcopy(pos_est) # This list will contain the first guesses of peak centres gained from
# the three 1DFTs performed below. It is used as a first guess of the centre for the final 3DFT.
fitted_pos_est = copy.deepcopy(pos_est) # This list contains the final peak centres, determined from the final
# 3DFT. These are used as the input for peak centres when calculating the intensity of a full peak.
compressed_pos_est, compressed_gsqr_est = un.apply_compression_ratio_to_pos_est(pos_est, gsqr_est, compression_ratio)
offset = un.calc_k_offset_with_N_atoms(N_atoms)
for i, pos in enumerate(compressed_pos_est):
k_start = un.find_simple_k_start(pos, offset)
k_stop = un.find_simple_k_stop(pos, offset)
kx_start, kx_stop, ky_start, ky_stop, kz_start, kz_stop = un.calc_lineout_k_start_stop_along_xyz(k_start,
k_stop,
pos)
peak_str = un.make_peak_str(raw_pos_est[i])
input_file_location = un.determine_rough_soh_input_file_location(peak_str, "find_centre_kx_1DFT.in")
un.write_soh_input_1DFT(source_name, input_file_location, "find_centre_kx_" + peak_str, mass, a_lattice, kx_start, kx_stop, k_steps_find_centre_1D)
input_file_location = un.determine_rough_soh_input_file_location(peak_str, "find_centre_ky_1DFT.in")
un.write_soh_input_1DFT(source_name, input_file_location, "find_centre_ky_" + peak_str, mass, a_lattice, ky_start, ky_stop, k_steps_find_centre_1D)
input_file_location = un.determine_rough_soh_input_file_location(peak_str, "find_centre_kz_1DFT.in")
un.write_soh_input_1DFT(source_name, input_file_location, "find_centre_kz_" + peak_str, mass, a_lattice, kz_start, kz_stop, k_steps_find_centre_1D)
if run_soh is True:
for i, pos in enumerate(compressed_pos_est):
peak_str = un.make_peak_str(raw_pos_est[i])
input_file_location = un.determine_rough_soh_input_file_location(peak_str, "find_centre_kx_1DFT.in")
un.run_soh(input_file_location, soh_command)
un.move_soh_rough_output_to_peak_folder(peak_str, "find_centre_kx_" + peak_str, source_name, timestep)
input_file_location = un.determine_rough_soh_input_file_location(peak_str, "find_centre_ky_1DFT.in")
un.run_soh(input_file_location, soh_command)
un.move_soh_rough_output_to_peak_folder(peak_str, "find_centre_ky_" + peak_str, source_name, timestep)
input_file_location = un.determine_rough_soh_input_file_location(peak_str, "find_centre_kz_1DFT.in")
un.run_soh(input_file_location, soh_command)
un.move_soh_rough_output_to_peak_folder(peak_str, "find_centre_kz_" + peak_str, source_name, timestep)
for i, pos in enumerate(compressed_pos_est):
peak_str = un.make_peak_str(raw_pos_est[i])
appended_string = "find_centre_kx_" + peak_str
soh_output_file_location = un.determine_rough_soh_output_file_location(peak_str, source_name, timestep,
appended_string)
soh_output = un.read_from_soh_output(soh_output_file_location)
k_max = un.find_point_of_max_height(soh_output)
kx_centre = k_max[0]
if plot is True:
un.plot_pygnuplot(soh_output[0], soh_output[3], "./data/" + peak_str + "/find_centre_kx.png",
"./data/" + peak_str + "/find_centre_kx.dat")
appended_string = "find_centre_ky_" + peak_str
soh_output_file_location = un.determine_rough_soh_output_file_location(peak_str, source_name, timestep,
appended_string)
soh_output = un.read_from_soh_output(soh_output_file_location)
k_max = un.find_point_of_max_height(soh_output)
ky_centre = k_max[1]
if plot is True:
un.plot_pygnuplot(soh_output[1], soh_output[3], "./data/" + peak_str + "/find_centre_ky.png",
"./data/" + peak_str + "/find_centre_ky.dat")
appended_string = "find_centre_kz_" + peak_str
soh_output_file_location = un.determine_rough_soh_output_file_location(peak_str, source_name, timestep,
appended_string)
soh_output = un.read_from_soh_output(soh_output_file_location)
k_max = un.find_point_of_max_height(soh_output)
kz_centre = k_max[2]
if plot is True:
un.plot_pygnuplot(soh_output[2], soh_output[3], "./data/" + peak_str + "/find_centre_kz.png",
"./data/" + peak_str + "/find_centre_kz.dat")
centre_guess_3DFT[i] = [kx_centre, ky_centre, kz_centre]
# Now that the initial guesses have been determined using the 1DFTs above, a 3DFT is performed to get as close as
# possible to the centre of the peak.
dk = un.calc_dk_from_offset(offset, k_steps_find_centre_1D, k_steps_find_centre_1D, k_steps_find_centre_1D)
for i, pos in enumerate(centre_guess_3DFT):
k_start = un.find_simple_k_start(pos, dk)
k_stop = un.find_simple_k_stop(pos, dk)
peak_str = un.make_peak_str(raw_pos_est[i])
input_file_location = un.determine_rough_soh_input_file_location(peak_str, "find_centre_3DFT.in")
un.write_soh_input_3DFT(source_name, input_file_location, "find_centre_3DFT_" + peak_str, mass, a_lattice,
k_steps_find_centre_3D, k_start, k_stop)
if run_soh is True:
for i, pos in enumerate(centre_guess_3DFT):
peak_str = un.make_peak_str(raw_pos_est[i])
input_file_location = un.determine_rough_soh_input_file_location(peak_str, "find_centre_3DFT.in")
un.run_soh(input_file_location, soh_command)
un.move_soh_rough_output_to_peak_folder(peak_str, "find_centre_3DFT_" + peak_str, source_name, timestep)
for i, pos in enumerate(centre_guess_3DFT):
peak_str = un.make_peak_str(raw_pos_est[i])
appended_string = "find_centre_3DFT_" + peak_str
soh_output_file_location = un.determine_rough_soh_output_file_location(peak_str, source_name, timestep,
appended_string)
soh_output = un.read_from_soh_output(soh_output_file_location)
k_max = un.find_point_of_max_height(soh_output)
fitted_pos_est[i] = k_max
return fitted_pos_est
def run(run_soh, current_pos_est, raw_pos_est, source_name, timestep,
undershoot, overshoot, source, mass, a_lattice, k_steps, num_cores):
import units as un
import copy
import os
print "Fitting to peak edges..."
direction_str = ["kx", "ky", "kz"]
k_start_accurate = copy.deepcopy(current_pos_est)
k_stop_accurate = copy.deepcopy(current_pos_est)
for i, pos in enumerate(raw_pos_est):
peak_str = un.make_peak_str(pos)
for j, direction in enumerate(direction_str):
k_start, k_stop = un.calc_peak_edge_k_start_stop(
current_pos_est[i], undershoot[j], overshoot[j])
soh_location = un.determine_soh_edge_finding_input_file_location(
direction, peak_str)
un.write_soh_input_1DFT(source_name, soh_location,
peak_str + "_find_edges_" + direction,
mass, a_lattice, k_start, k_stop, k_steps)
if run_soh is True:
for i, pos in enumerate(raw_pos_est):
peak_str = un.make_peak_str(pos)
for j, direction in enumerate(direction_str):
soh_location = un.determine_soh_edge_finding_input_file_location(
direction, peak_str)
un.run_soh(soh_location, num_cores)
un.move_soh_rough_output_to_peak_folder(
peak_str, peak_str + "_find_edges_" + direction,
source_name, timestep)
for i, pos in enumerate(raw_pos_est):
peak_str = un.make_peak_str(pos)
for j, direction in enumerate(direction_str):
soh_location = un.determine_soh_edge_finding_output_file_location(
peak_str, direction, source, timestep)
soh_output = un.read_from_soh_output(soh_location)
un.plot_pygnuplot(
soh_output[j], soh_output[3],
os.getcwd() + "/data/" + peak_str + "/" + direction +
"_lineout.png",
os.getcwd() + "/data/" + peak_str + "/" + direction +
"_lineout.dat")
k_start_accurate[i][j], k_stop_accurate[i][
j] = un.find_k_start_stop_for_peak_from_first_minima(
soh_output[j], soh_output[3])
return k_start_accurate, k_stop_accurate