sys.exit(1) if filetype == '.cub': g = cube_helpers.Cube(args.points_file) elif filetype == '.esp': g = resp_helpers.G09_esp(args.points_file) # TODO: The colour span is calculated based on all values, but if only a slice # is plotted, the shown points may occupy only a narrow range. if args.color_range: color_span = args.color_range elif args.sym_color_range: color_limit = max(abs(np.nanmin(g.field.get_values())), abs(np.nanmax(g.field.get_values()))) color_span = [-color_limit, color_limit] else: color_span = [min(g.field.get_values()), max(g.field.get_values())] if args.slice_atoms: plane_eqn = graphs.plane_through_atoms(g.molecule, *args.slice_atoms) else: plane_eqn = args.slice_eqn graphs.plot_points( g.field, args.dimension, molecule=g.molecule, plane_eqn=plane_eqn, dist_thresh=args.slice_dist, axes_limits=[args.limits]*args.dimension, color_span=color_span, save_to=args.output)
min_rms, min_rrms, rep_esp_field = rms_and_rep(g.field, g.molecule, charge_type) rms_list.append(min_rms) print("\n", min_rms, file=fc) # Default given as extremal values of methane CHelpG color_span = check_color_span(g.field.values, color_span, default=[-0.0045, 0.011]) diff_field = difference(g.field, rep_esp_field) error_color_span = check_color_span(diff_field.values, error_color_span, default=[-0.0012, 0.019]) graphs.plot_points( g.field, 2, title=calc, molecule=g.molecule, plane_eqn=graphs.plane_through_atoms(g.molecule, 1, 2, 3), dist_thresh=0.5, axes_limits=[(-5, 5)]*2, color_span=color_span, save_to=path + calc[-6:] + '_V.pdf') graphs.plot_points( diff_field, 2, title=calc + " Errors", molecule=g.molecule, plane_eqn=graphs.plane_through_atoms(g.molecule, 1, 2, 3), dist_thresh=0.5, axes_limits=[(-5, 5)]*2, color_span=error_color_span, save_to=path + calc[-6:] + '_E.pdf') save_to = path + "RMS.pdf" calc_plot(calcs, rms_list, charge_type.upper() + " RMS value", set_lim=True, save_to=save_to) for atom in g.molecule: save_to = path + atom.atomic_number + str(atom.label) + "_charge.pdf"
min_rms, min_rrms, rep_esp_field = rms_and_rep(g.field, g.molecule, charge_type) rms_list.append(min_rms) print("\n", min_rms, file=fc) # Default given as extremal values of methane CHelpG color_span = check_color_span(g.field.values, color_span, default=[-0.0045, 0.011]) diff_field = difference(g.field, rep_esp_field) error_color_span = check_color_span(diff_field.values, error_color_span, default=[-0.0012, 0.019]) graphs.plot_points( g.field, 2, title=calc, molecule=g.molecule, plane_eqn=graphs.plane_through_atoms(g.molecule, 1, 2, 3), dist_thresh=0.5, axes_limits=[(-5, 5)]*2, color_span=color_span, save_to=path + calc[-6:] + '_V.pdf') graphs.plot_points( diff_field, 2, title=calc + " Errors", molecule=g.molecule, plane_eqn=graphs.plane_through_atoms(g.molecule, 1, 2, 3), dist_thresh=0.5, axes_limits=[(-5, 5)]*2, color_span=error_color_span, save_to=path + calc[-6:] + '_E.pdf') save_to = path + "RMS.pdf" calc_plot(calcs, rms_list, charge_type.upper() + " RMS value", set_lim=True, save_to=save_to) for atom in g.molecule: save_to = path + atom.identity + str(atom.label) + "_charge.pdf"