def run():
import select_peak_positions
import build_datafile_structure
import use_soh_for_3DFT
import inpkfd as ip
import logging as log
log.info("Path %s started.\n", __name__)
pos_est, gsqr_est = select_peak_positions.run(ip.gsqr_max, ip.negative_k,
ip.remove_000)
build_datafile_structure.run(pos_est)
use_soh_for_3DFT.run(pos_est, ip.source_location, ip.mass, ip.a_lattice,
ip.N_atoms, ip.k_steps, ip.run_soh)
#calc_peak_intensities.run()
#calc_debye_waller.run()
#plot.run()
log.info("Path %s finished.\n", __name__)
return
def run():
import inpkfd as ip
import select_peak_positions
import build_datafile_structure
import use_soh_for_3DFT
import calc_peak_intensities
import calc_debye_waller
import write_output_files
import plot_debye_waller
import plot_peaks
import logging as log
log.info("Path %s started.\n", __name__)
pos_est, gsqr_est = select_peak_positions.run(ip.gsqr_max, ip.negative_k,
ip.remove_000)
peak_str = build_datafile_structure.run(pos_est)
use_soh_for_3DFT.run(pos_est, ip.source_name, ip.timestep, ip.mass,
ip.a_lattice, ip.N_atoms, ip.k_steps, ip.run_soh,
ip.num_cores)
peak_centre, integrated_intensity = calc_peak_intensities.run(
pos_est, ip.source_name, ip.timestep)
debye_temperature, temperature, gsqr_per_angstrom, ln_intensity = calc_debye_waller.run(
peak_centre, integrated_intensity, ip.a_lattice, ip.mass,
ip.temperature, ip.uncompressed_debye_temperature,
ip.single_term_model_gamma_0_values,
ip.single_term_model_exponent_values,
ip.triple_term_model_gamma_0_values, ip.triple_term_model_constants)
write_output_files.run(debye_temperature, temperature, pos_est,
peak_centre, gsqr_per_angstrom,
integrated_intensity, ln_intensity)
plot_debye_waller.run(gsqr_per_angstrom, ln_intensity, pos_est,
ip.temperature, ip.mass)
if ip.make_final_peak_plots is True:
plot_peaks.run(peak_str, peak_centre, ip.source_name, ip.timestep)
log.info("Path %s finished.\n", __name__)
return
def run():
import inpkfd as ip
import select_peak_positions
import build_datafile_structure
import use_dynamic_peakfinding_for_3DFT
import calc_peak_intensities
import calc_debye_waller
import write_output_files
import plot_debye_waller
import plot_peaks
import find_compression_ratio
import fit_to_peak_centres
import overstep_peak_edges
import calc_md_temperature
import logging as log
log.info("Path %s started.\n", __name__)
current_md_temperature = ip.temperature
if ip.calc_md_temperature_from_dump_file is True:
current_md_temperature = calc_md_temperature.run(
ip.source_name, ip.temperature,
ip.calculated_temperature_dimensionality, ip.mass,
ip.velocity_columns, ip.number_velocity_bins)
raw_pos_est, raw_gsqr_est = select_peak_positions.run(
ip.gsqr_max, ip.negative_k, ip.remove_000, ip.crystal_type)
current_pos_est = raw_pos_est
current_gsqr_est = raw_gsqr_est
peak_str = build_datafile_structure.run(current_pos_est)
compression_ratio = find_compression_ratio.run(
ip.run_soh, ip.uncompressed_peak_positions,
ip.compression_ratio_undershoot, ip.compression_ratio_overshoot,
ip.source_name, ip.mass, ip.a_lattice, ip.lineout_k_steps, ip.timestep,
ip.soh_command)
fitted_pos_est = fit_to_peak_centres.run(
ip.run_soh, raw_pos_est, current_pos_est, current_gsqr_est,
compression_ratio, ip.source_name, ip.N_atoms, ip.mass, ip.a_lattice,
ip.k_steps_find_centre_1DFT, ip.k_steps_find_centre_3DFT, ip.timestep,
ip.soh_command, ip.make_plots_peak_centre_fit)
current_pos_est = fitted_pos_est
k_start_accurate, k_stop_accurate = overstep_peak_edges.run(
current_pos_est, ip.peak_edge_undershoot, ip.peak_edge_overshoot)
use_dynamic_peakfinding_for_3DFT.run(current_pos_est, raw_pos_est,
ip.source_name, ip.timestep, ip.mass,
ip.a_lattice, ip.k_steps, ip.run_soh,
k_start_accurate, k_stop_accurate,
ip.soh_command)
peak_centre, integrated_intensity = calc_peak_intensities.run(
raw_pos_est, ip.source_name, ip.timestep)
debye_temperature, xrd_temperature, model_debye_temperatures, gsqr_per_angstrom, ln_intensity, slope = calc_debye_waller.run(
peak_centre, integrated_intensity, ip.a_lattice, ip.mass,
current_md_temperature, ip.uncompressed_debye_temperature,
ip.single_term_model_gamma_0_values,
ip.single_term_model_exponent_values,
ip.triple_term_model_gamma_0_values, ip.triple_term_model_constants,
compression_ratio, ip.polynomial_coeff)
write_output_files.run(debye_temperature, xrd_temperature,
model_debye_temperatures, current_pos_est,
peak_centre, gsqr_per_angstrom,
integrated_intensity, ln_intensity, slope)
plot_debye_waller.run(gsqr_per_angstrom, ln_intensity, raw_pos_est,
current_md_temperature, ip.mass,
ip.uncompressed_peak_positions)
if ip.make_final_peak_plots is True:
plot_peaks.run(peak_str, peak_centre, ip.source_name, ip.timestep)
log.info("Path %s finished.\n", __name__)
return