#!/usr/bin/env python ######################################### import matplotlib.pyplot as plt # import numpy as np # from math import sqrt, radians, cos # ######################################### plt.rcParams.update({'font.size': 11}) from scipy.constants import golden_ratio, inch mm2inch = 1.0E-3 / inch energy = 96.8 # kJmol normal incidence # Laser-off rotation around y LO_S0_y = [] LO_S0_trap_y = [] LO_S0_weight_step_y = [] LO_S0_weight_terr_y = [] LO_S0_step_y = [] LO_S0_terr_y = [] LO_branch_terr_y = [] LO_branch_step_y = [] LO_branch_y = [] energy_rot_off_y = [] #v1 rotation around y v1_S0_y = [] v1_S0_trap_y = [] v1_S0_weight_step_y = [] v1_S0_weight_terr_y = [] v1_S0_step_y = [] v1_S0_terr_y = [] v1_branch_terr_y = [] v1_branch_step_y = [] v1_branch_y = [] energy_rot_v1_y = [] # Laser off rotation around x LO_S0_x = [] LO_S0_trap_x = [] LO_S0_weight_step_x = [] LO_S0_weight_terr_x = [] LO_S0_step_x = [] LO_S0_terr_x = [] LO_branch_terr_x = [] LO_branch_step_x = [] LO_branch_x = [] energy_rot_off_x = [] # v1 rotation around x v1_S0_x = [] v1_S0_trap_x = [] v1_S0_weight_step_x = [] v1_S0_weight_terr_x = [] v1_S0_step_x = [] v1_S0_terr_x = [] v1_branch_terr_x = [] v1_branch_step_x = [] v1_branch_x = [] energy_rot_v1_x = [] # Experimental data - rotating around y LO_expt_y_rot = [[0, 0.0753, 0.00753], # Angle, S0, err [-10, 0.0751, 0.00751], [-20, 0.0702, 0.00702], [-30, 0.0574, 0.00574], [-40, 0.0426, 0.005], [-50, 0.0228, 0.005]] LO_norm = [[58.2384, 0.01580, 0.005, 0.006, 0.002], # Energy, Expt S0, Expt err, AIMD S0, AIMD err [69.2488, 0.02685, 0.005, 0.019, 0.004], [79.532, 0.04285, 0.005, 0.040, 0.009], [92.5326, 0.06100, 0.005, 0.058, 0.010], [96.8281, 0.07530, 0.005, 0.069, 0.008], # Davide's values (0.07, 0.011) are for 500 trajectories [107.875, 0.09425, 0.005, 0.102, 0.014]] v1_norm = [[58.2384, 0.06825, 0.020, 0.030, 0.008], # Energy, Expt S0, Expt err, AIMD S0, AIMD err [69.2488, 0.08303, 0.012, 0.076, 0.012], [79.532, 0.08300, 0.030, 0.068, 0.011]] # Calculations - rotating around y LO_data_y = [[50, 1, 5, 1, 1, 134, 468, 509, 23, 1000.], [40, 3, 8, 2, 8, 78, 478, 488, 33, 1000.], # Angle, CH step, CD step, CH terr, CD terr, trapped, nearest step, nearest edge, nearest corner, total [30, 7, 25, 1, 4, 35, 481, 434, 85, 1000.], [20, 7, 29, 0, 3, 18, 527, 363, 110, 1000.], [10, 7, 46, 2, 5, 7, 545, 359, 96, 1000.], [0, 16, 49, 2, 2, 4, 545, 335, 120, 1000.], [-10, 21, 46, 0, 2, 1, 569, 333, 98, 1000.], [-20, 11, 42, 0, 0, 5, 563, 343, 94, 1000.], [-30, 12, 42, 0, 0, 17, 606, 301, 93, 1000.], [-40, 13, 37, 0, 0, 47, 651, 267, 82, 1000.], [-50, 7, 26, 0, 0, 120, 713, 240, 47, 1000.]] v1_data_y = [[40, 6, 3, 3, 0, 34, 257, 220, 23, 500.], [20, 20, 12, 6, 5, 11, 269, 190, 41, 500.], [0, 41, 19, 6, 1, 1, 269, 178, 52, 500.], [-20, 21, 21, 2, 0, 5, 281, 158, 59, 500.], [-40, 22, 14, 0, 0, 26, 317, 146, 37, 500.]] LO_data_y_TN_corr = [[50, 0.007, 0.003], [40, 0.019, 0.005], [30, 0.033, 0.006], [20, 0.040, 0.007], [10, 0.060, 0.009], [ 0, 0.069, 0.010], [-10, 0.064, 0.009], [-20, 0.049, 0.008], [-30, 0.059, 0.009], [-40, 0.044, 0.007], [-50, 0.032, 0.006]] # Calculations - rotating around x LO_data_x = [[20, 3, 24, 0, 1, 6, 525, 383, 92, 1000.], [0, 16, 49, 2, 2, 4, 545, 335, 120, 1000.]] v1_data_x = [[40, 12, 3, 0, 0, 10, 268, 189, 43, 500.], [20, 23, 17, 5, 2, 3, 281, 168, 52, 500.], [0, 41, 19, 6, 1, 1, 271, 178, 52, 500.]] LO_data_x_TN_corr = [[20, 0.027, 0.006], [ 0, 0.069, 0.010]] #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Sticking coefficients #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ def sticking(stick,tot,S0_array): S0 = (float(stick)/tot) err = sqrt((1-S0)*S0/tot) S0_array.append([S0, err]) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Branching ratios #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ def branching(CH,CD,branching_array): tot = CH+CD if tot !=0: CH_br = float(CH) / tot CD_br = float(CD) / tot if CH != 0 and CD !=0: err = sqrt((1.0-CH_br)*CH_br/tot) else: err = 1.0-0.32**(1./tot) else: err = 0 CH_br = 0 CD_br = 0 branching_array.append([CH_br, CD_br, err]) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Analysing data for rotation around the y axis #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ for i in range (len(LO_data_y)): # S0 for reaction stick = (LO_data_y[i][1] + LO_data_y[i][2] + LO_data_y[i][3] + LO_data_y[i][4]) sticking(stick, LO_data_y[i][9], LO_S0_y) # S0 for reaction + trapping trap = (stick + LO_data_y[i][5]) sticking(trap, LO_data_y[i][9], LO_S0_trap_y) # S0 for reaction on step and terrace sticking(LO_data_y[i][1]+LO_data_y[i][2], LO_data_y[i][9], LO_S0_step_y) sticking(LO_data_y[i][3]+LO_data_y[i][4], LO_data_y[i][9], LO_S0_terr_y) # S0 for reaction on step and terrace considering number of molecules that hit step and terrace sticking(LO_data_y[i][1]+LO_data_y[i][2], LO_data_y[i][6], LO_S0_weight_step_y) sticking(LO_data_y[i][3]+LO_data_y[i][4], LO_data_y[i][7], LO_S0_weight_terr_y) # Step to terrace branching ratio for reactivity branching(LO_data_y[i][1]+LO_data_y[i][2],LO_data_y[i][3]+LO_data_y[i][4],LO_branch_y) # CH and CD on steps branching(LO_data_y[i][1],LO_data_y[i][2], LO_branch_step_y) # CH and CD on terraces branching(LO_data_y[i][3],LO_data_y[i][4], LO_branch_terr_y) # Energy energy_rot_off_y.append(energy*cos(radians(LO_data_y[i][0]))*cos(radians(LO_data_y[i][0]))) for i in range (len(v1_data_y)): # S0 for reaction stick = (v1_data_y[i][1] + v1_data_y[i][2] + v1_data_y[i][3] + v1_data_y[i][4]) sticking(stick, v1_data_y[i][9], v1_S0_y) # S0 for reaction + trapping trap = (stick + v1_data_y[i][5]) sticking(trap, v1_data_y[i][9], v1_S0_trap_y) # S0 for reaction on step and terrace sticking(v1_data_y[i][1]+v1_data_y[i][2], v1_data_y[i][9], v1_S0_step_y) sticking(v1_data_y[i][3]+v1_data_y[i][4], v1_data_y[i][9], v1_S0_terr_y) # S0 for reaction on step and terrace considering number of molecules that hit step and terrace sticking(v1_data_y[i][1]+v1_data_y[i][2], v1_data_y[i][6], v1_S0_weight_step_y) sticking(v1_data_y[i][3]+v1_data_y[i][4], v1_data_y[i][7], v1_S0_weight_terr_y) # Step to terrace branching ratio for reactivity branching(v1_data_y[i][1]+v1_data_y[i][2],v1_data_y[i][3]+v1_data_y[i][4],v1_branch_y) # CH and CD on steps branching(v1_data_y[i][1],v1_data_y[i][2], v1_branch_step_y) # CH and CD on terraces branching(v1_data_y[i][3],v1_data_y[i][4], v1_branch_terr_y) # Energy energy_rot_v1_y.append(energy*cos(radians(v1_data_y[i][0]))*cos(radians(v1_data_y[i][0]))) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Analysing data for rotation around the x axis #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ for i in range (len(LO_data_x)): # S0 for reaction stick = (LO_data_x[i][1] + LO_data_x[i][2] + LO_data_x[i][3] + LO_data_x[i][4]) sticking(stick, LO_data_x[i][9], LO_S0_x) # S0 for reaction + trapping trap = (stick + LO_data_x[i][5]) sticking(trap, LO_data_x[i][9], LO_S0_trap_x) # S0 for reaction on step and terrace sticking(LO_data_x[i][1]+LO_data_x[i][2], LO_data_x[i][9], LO_S0_step_x) sticking(LO_data_x[i][3]+LO_data_x[i][4], LO_data_x[i][9], LO_S0_terr_x) # S0 for reaction on step and terrace considering number of molecules that hit step and terrace sticking(LO_data_x[i][1]+LO_data_x[i][2], LO_data_x[i][6], LO_S0_weight_step_x) sticking(LO_data_x[i][3]+LO_data_x[i][4], LO_data_x[i][7], LO_S0_weight_terr_x) # Step to terrace branching ratio for reactivity branching(LO_data_x[i][1]+LO_data_x[i][2],LO_data_x[i][3]+LO_data_x[i][4],LO_branch_x) # CH and CD on steps branching(LO_data_x[i][1],LO_data_x[i][2], LO_branch_step_x) # CH and CD on terraces branching(LO_data_x[i][3],LO_data_x[i][4], LO_branch_terr_x) # Energy energy_rot_off_x.append(energy*cos(radians(LO_data_x[i][0]))*cos(radians(LO_data_x[i][0]))) for i in range (len(v1_data_x)): # S0 for reaction stick = (v1_data_x[i][1] + v1_data_x[i][2] + v1_data_x[i][3] + v1_data_x[i][4]) sticking(stick, v1_data_x[i][9], v1_S0_x) # S0 for reaction + trapping trap = (stick + v1_data_x[i][5]) sticking(trap, v1_data_x[i][9], v1_S0_trap_x) # S0 for reaction on step and terrace sticking(v1_data_x[i][1]+v1_data_x[i][2], v1_data_x[i][9], v1_S0_step_x) sticking(v1_data_x[i][3]+v1_data_x[i][4], v1_data_x[i][9], v1_S0_terr_x) # S0 for reaction on step and terrace considering number of molecules that hit step and terrace sticking(v1_data_x[i][1]+v1_data_x[i][2], v1_data_x[i][6], v1_S0_weight_step_x) sticking(v1_data_x[i][3]+v1_data_x[i][4], v1_data_x[i][7], v1_S0_weight_terr_x) # Step to terrace branching ratio for reactivity branching(v1_data_x[i][1]+v1_data_x[i][2],v1_data_x[i][3]+v1_data_x[i][4],v1_branch_x) # CH and CD on steps branching(v1_data_x[i][1],v1_data_x[i][2], v1_branch_step_x) # CH and CD on terraces branching(v1_data_x[i][3],v1_data_x[i][4], v1_branch_terr_x) # Energy energy_rot_v1_x.append(energy*cos(radians(v1_data_x[i][0]))*cos(radians(v1_data_x[i][0]))) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Plots #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LO_data_y = np.transpose(LO_data_y) LO_S0_y = np.transpose(LO_S0_y) LO_expt_y_rot = np.transpose(LO_expt_y_rot) LO_S0_trap_y = np.transpose(LO_S0_trap_y) LO_branch_y = np.transpose(LO_branch_y) LO_branch_step_y = np.transpose(LO_branch_step_y) LO_branch_terr_y = np.transpose(LO_branch_terr_y) LO_norm = np.transpose(LO_norm) LO_S0_step_y = np.transpose(LO_S0_step_y) LO_S0_terr_y = np.transpose(LO_S0_terr_y) LO_S0_weight_step_y = np.transpose(LO_S0_weight_step_y) LO_S0_weight_terr_y = np.transpose(LO_S0_weight_terr_y) LO_data_y_TN_corr = np.transpose(LO_data_y_TN_corr) v1_data_y = np.transpose(v1_data_y) v1_S0_y = np.transpose(v1_S0_y) v1_S0_trap_y = np.transpose(v1_S0_trap_y) v1_branch_y = np.transpose(v1_branch_y) v1_branch_step_y = np.transpose(v1_branch_step_y) v1_branch_terr_y = np.transpose(v1_branch_terr_y) v1_norm = np.transpose(v1_norm) v1_S0_step_y = np.transpose(v1_S0_step_y) v1_S0_terr_y = np.transpose(v1_S0_terr_y) v1_S0_weight_step_y = np.transpose(v1_S0_weight_step_y) v1_S0_weight_terr_y = np.transpose(v1_S0_weight_terr_y) LO_data_x = np.transpose(LO_data_x) LO_S0_x = np.transpose(LO_S0_x) LO_S0_trap_x = np.transpose(LO_S0_trap_x) LO_branch_x = np.transpose(LO_branch_x) LO_branch_step_x = np.transpose(LO_branch_step_x) LO_branch_terr_x = np.transpose(LO_branch_terr_x) LO_S0_step_x = np.transpose(LO_S0_step_x) LO_S0_terr_x = np.transpose(LO_S0_terr_x) LO_S0_weight_step_x = np.transpose(LO_S0_weight_step_x) LO_S0_weight_terr_x = np.transpose(LO_S0_weight_terr_x) LO_data_x_TN_corr = np.transpose(LO_data_x_TN_corr) v1_data_x = np.transpose(v1_data_x) v1_S0_x = np.transpose(v1_S0_x) v1_S0_trap_x = np.transpose(v1_S0_trap_x) v1_branch_x = np.transpose(v1_branch_x) v1_branch_step_x = np.transpose(v1_branch_step_x) v1_branch_terr_x = np.transpose(v1_branch_terr_x) v1_S0_step_x = np.transpose(v1_S0_step_x) v1_S0_terr_x = np.transpose(v1_S0_terr_x) v1_S0_weight_step_x = np.transpose(v1_S0_weight_step_x) v1_S0_weight_terr_x = np.transpose(v1_S0_weight_terr_x) leiden_blue = (0,17/255,88/255) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Rotating around y #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # TO FLIP PLOTS! # fac = -1. angfit = np.array([float(i) for i in range(-60,60)]) cosfit = 0.069*np.cos(np.radians(angfit))*np.cos(np.radians(angfit)) ########################################################### ########################################################### ### ### ### TERRACE VS STEP BRANCHING ### ### ### ########################################################### ########################################################### # y rotation #~~~ MAKING ASYMMETRIC ERRORS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ low_err_step = np.array(LO_branch_y[2]) up_err_step = np.array(LO_branch_y[2]) low_err_terr = np.array(LO_branch_y[2]) up_err_terr = np.array(LO_branch_y[2]) for i in range (len(LO_branch_y[2])): if LO_branch_y[0][i]-low_err_step[i] < 0.:low_err_step[i] = 0 if LO_branch_y[1][i]-low_err_terr[i] < 0.:low_err_terr[i] = 0 if LO_branch_y[0][i]+up_err_step[i] > 1.: up_err_step[i] = 0 if LO_branch_y[1][i]+up_err_terr[i] > 1.: up_err_terr[i] = 0 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ plt.subplot(4,2,1) plt.bar(fac*LO_data_y[0], LO_branch_y[0], width = 4, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(fac*LO_data_y[0], LO_branch_y[1], width = -4, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.errorbar(fac*LO_data_y[0]+2, LO_branch_y[0], yerr=np.array([low_err_step,up_err_step]), linestyle='None', ecolor = 'black') plt.errorbar(fac*LO_data_y[0]-2, LO_branch_y[1], yerr=np.array([low_err_terr,up_err_terr]), linestyle='None', ecolor = 'black') plt.xlim(-55,55) plt.ylim(0,1.2) plt.xticks(np.arange(-40., 50., 20.0)) plt.ylabel('Fraction') plt.annotate('A $\\rm{\\phi_i} = 0$'u'\xb0 Laser-Off', xy = (-52,0.95), xytext=(-52,0.95)) #~~~ MAKING ASYMMETRIC ERRORS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ low_err_step = np.array(v1_branch_y[2]) up_err_step = np.array(v1_branch_y[2]) low_err_terr = np.array(v1_branch_y[2]) up_err_terr = np.array(v1_branch_y[2]) for i in range (len(v1_branch_y[2])): if v1_branch_y[0][i]-low_err_step[i] < 0.:low_err_step[i] = 0 if v1_branch_y[1][i]-low_err_terr[i] < 0.:low_err_terr[i] = 0 if v1_branch_y[0][i]+up_err_step[i] > 1.: up_err_step[i] = 0 if v1_branch_y[1][i]+up_err_terr[i] > 1.: up_err_terr[i] = 0 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ plt.subplot(4,2,3) plt.bar(fac*v1_data_y[0], v1_branch_y[0], width = 4, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(fac*v1_data_y[0], v1_branch_y[1], width = -4, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.errorbar(fac*v1_data_y[0]+2, v1_branch_y[0], yerr=np.array([low_err_step,up_err_step]), linestyle='None', ecolor = 'black') plt.errorbar(fac*v1_data_y[0]-2, v1_branch_y[1], yerr=np.array([low_err_terr,up_err_terr]), linestyle='None', ecolor = 'black') plt.xlim(-55,55) plt.ylim(0,1.2) plt.xticks(np.arange(-40., 50., 20.0)) plt.ylabel('Fraction') plt.annotate('B $\\rm{\\phi_i} = 0$'u'\xb0 $\\nu_1$=1', xy = (-52,0.95), xytext=(-52,0.95)) # x rotation #~~~ MAKING ASYMMETRIC ERRORS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ low_err_step = np.array(LO_branch_x[2]) up_err_step = np.array(LO_branch_x[2]) low_err_terr = np.array(LO_branch_x[2]) up_err_terr = np.array(LO_branch_x[2]) for i in range (len(LO_branch_x[2])): if LO_branch_x[0][i]-low_err_step[i] < 0.:low_err_step[i] = 0 if LO_branch_x[1][i]-low_err_terr[i] < 0.:low_err_terr[i] = 0 if LO_branch_x[0][i]+up_err_step[i] > 1.: up_err_step[i] = 0 if LO_branch_x[1][i]+up_err_terr[i] > 1.: up_err_terr[i] = 0 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ plt.subplot(4,2,5) plt.bar(LO_data_x[0], LO_branch_x[0], width = 2, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(LO_data_x[0], LO_branch_x[1], width = -2, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.errorbar(LO_data_x[0]+1, LO_branch_x[0], yerr=np.array([low_err_step,up_err_step]), linestyle='None', ecolor = 'black') plt.errorbar(LO_data_x[0]-1, LO_branch_x[1], yerr=np.array([low_err_terr,up_err_terr]), linestyle='None', ecolor = 'black') plt.xlim(-5,55) plt.ylim(0,1.2) plt.xticks(np.arange(0, 51, 10.0)) plt.ylabel('Fraction') lg = plt.legend(loc = 'upper right', numpoints = 1, prop={'size': 12}) lg.draw_frame(False) plt.annotate('C $\\rm{\\phi_i} = 90$'u'\xb0 Laser-Off', xy = (-3,0.95), xytext=(-3,0.95)) #~~~ MAKING ASYMMETRIC ERRORS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ low_err_step = np.array(v1_branch_x[2]) up_err_step = np.array(v1_branch_x[2]) low_err_terr = np.array(v1_branch_x[2]) up_err_terr = np.array(v1_branch_x[2]) for i in range (len(v1_branch_x[2])): if v1_branch_x[0][i]-low_err_step[i] < 0.:low_err_step[i] = 0 if v1_branch_x[1][i]-low_err_terr[i] < 0.:low_err_terr[i] = 0 if v1_branch_x[0][i]+up_err_step[i] > 1.: up_err_step[i] = 0 if v1_branch_x[1][i]+up_err_terr[i] > 1.: up_err_terr[i] = 0 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ plt.subplot(4,2,7) plt.bar(v1_data_x[0], v1_branch_x[0], width = 2, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(v1_data_x[0], v1_branch_x[1], width = -2, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.errorbar(v1_data_x[0]+1, v1_branch_x[0], yerr=np.array([low_err_step,up_err_step]), linestyle='None', ecolor = 'black') plt.errorbar(v1_data_x[0]-1, v1_branch_x[1], yerr=np.array([low_err_terr,up_err_terr]), linestyle='None', ecolor = 'black') plt.xlim(-5,55) plt.ylim(0,1.2) plt.xticks(np.arange(0, 51, 10.0)) plt.xlabel('$\\rm{\\theta_i}$ ('u'\xb0)') plt.ylabel('Fraction') plt.annotate('D $\\rm{\\phi_i} = 90$'u'\xb0 $\\nu_1$=1', xy = (-3,0.95), xytext=(-3,0.95)) plt.subplots_adjust(left=0.1, bottom=0.08, right=0.95, top=0.99, wspace=0.15, hspace=0.25) plt.savefig('Fig7.png',bbox_inches='tight',dpi=300) plt.show() ########################################################### ########################################################### ### ### ### SHADOWING NEAREST TRAJ ### ### ### ########################################################### ########################################################### # y rotation plt.subplot(4,2,1) plt.bar(fac*LO_data_y[0], LO_data_y[6]/LO_data_y[9], width = 4, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(fac*LO_data_y[0], LO_data_y[7]/LO_data_y[9], width = -4, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.bar(fac*LO_data_y[0], LO_data_y[8]/LO_data_y[9], width = -4, color = 'green', ecolor = 'black', align = 'center', label = 'Corner') plt.xlim(-55,55) plt.ylim(0,1.2) plt.xticks(np.arange(-40., 50., 20.0)) plt.ylabel('Fraction') plt.annotate('A $\\rm{\\phi_i} = 0$'u'\xb0 Laser-Off', xy = (-52,0.95), xytext=(-52,0.95)) plt.subplot(4,2,3) plt.bar(fac*v1_data_y[0], v1_data_y[6]/v1_data_y[9], width = 4, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(fac*v1_data_y[0], v1_data_y[7]/v1_data_y[9], width = -4, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.bar(fac*v1_data_y[0], v1_data_y[8]/v1_data_y[9], width = -4, color = 'green', ecolor = 'black', align = 'center', label = 'Corner') plt.xlim(-55,55) plt.ylim(0,1.2) plt.xticks(np.arange(-40., 50., 20.0)) plt.ylabel('Fraction') plt.annotate('B $\\rm{\\phi_i} = 0$'u'\xb0 $\\nu_1$=1', xy = (-52,0.95), xytext=(-52,0.95)) # x rotation plt.subplot(4,2,5) plt.bar(LO_data_x[0], LO_data_x[6]/LO_data_x[9], width = 2, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(LO_data_x[0], LO_data_x[7]/LO_data_x[9], width = -2, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.bar(LO_data_x[0], LO_data_x[8]/LO_data_x[9], width = -2, color = 'green', ecolor = 'black', align = 'center', label = 'Corner') plt.xlim(-5,55) plt.ylim(0,1.2) plt.xticks(np.arange(0, 51, 10.0)) lg = plt.legend(loc = 'best', numpoints = 1, prop={'size': 12}) lg.draw_frame(False) plt.ylabel('Fraction') plt.annotate('C $\\rm{\\phi_i} = 90$'u'\xb0 Laser-Off', xy = (-3,0.95), xytext=(-3,0.95)) plt.subplot(4,2,7) plt.bar(v1_data_x[0], v1_data_x[6]/v1_data_x[9], width = 2, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(v1_data_x[0], v1_data_x[7]/v1_data_x[9], width = -2, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.bar(v1_data_x[0], v1_data_x[8]/v1_data_x[9], width = -2, color = 'green', ecolor = 'black', align = 'center', label = 'Corner') plt.xlim(-5,55) plt.ylim(0,1.2) plt.xticks(np.arange(0, 51, 10.0)) plt.xlabel('$\\rm{\\theta_i}$ ('u'\xb0)') plt.ylabel('Fraction') plt.annotate('D $\\rm{\\phi_i} = 90$'u'\xb0 $\\nu_1$=1', xy = (-3,0.95), xytext=(-3,0.95)) plt.subplots_adjust(left=0.1, bottom=0.08, right=0.95, top=0.99, wspace=0.15, hspace=0.25) plt.savefig('Fig8.png',bbox_inches='tight', dpi=300) plt.show() ########################################################### ########################################################### ### ### ### WEIGHTED S0 ### ### ### ########################################################### ########################################################### # y rotation plt.subplot(4,2,1) plt.errorbar(fac*LO_data_y[0], LO_S0_weight_step_y[0], yerr = LO_S0_weight_step_y[1],marker = 'o', color = 'red', mec = 'red', markersize =5, linestyle = 'None', label = 'Step') plt.errorbar(fac*LO_data_y[0], LO_S0_weight_terr_y[0], yerr = LO_S0_weight_terr_y[1],marker = 'o', color = 'blue', mec = 'blue', markersize =5, linestyle = 'None', label = 'Terrace') plt.xlim(-55,55) plt.ylim(0,0.16) plt.xticks(np.arange(-40., 50., 20.0)) plt.yticks(np.arange(0.0, 0.2, 0.04)) plt.ylabel('S$_0$(site)') plt.annotate('A $\\rm{\\phi_i} = 0$'u'\xb0 Laser-Off', xy = (50,0.1), xytext=(-52,0.13)) plt.subplot(4,2,3) plt.errorbar(fac*v1_data_y[0], v1_S0_weight_step_y[0], yerr = v1_S0_weight_step_y[1], marker = 'o', color = 'red', mec = 'red', markersize =5, linestyle = 'None', label = 'Step') plt.errorbar(fac*v1_data_y[0], v1_S0_weight_terr_y[0], yerr = v1_S0_weight_terr_y[1], marker = 'o', color = 'blue', mec = 'blue', markersize =5, linestyle = 'None', label = 'Terrace') plt.xlim(-55,55) plt.ylim(0,0.25) plt.xticks(np.arange(-40., 50., 20.0)) plt.ylabel('S$_0$(site)') plt.annotate('B $\\rm{\\phi_i} = 0$'u'\xb0 $\\nu_1$=1', xy = (-52,0.20), xytext = (-52,0.20)) # x rotation plt.subplot(4,2,5) plt.errorbar(LO_data_x[0], LO_S0_weight_step_x[0], yerr = LO_S0_weight_step_x[1],marker = 's', color = 'red', mec = 'red', markersize =5, linestyle = 'None', label = 'Step') plt.errorbar(LO_data_x[0], LO_S0_weight_terr_x[0], yerr = LO_S0_weight_terr_x[1],marker = 's', color = 'blue', mec = 'blue', markersize =5, linestyle = 'None', label = 'Terrace') plt.errorbar(-LO_data_x[0], LO_S0_weight_step_x[0], yerr = LO_S0_weight_step_x[1],marker = 's', color = 'red', mec = 'red', markersize =5, linestyle = 'None') plt.errorbar(-LO_data_x[0], LO_S0_weight_terr_x[0], yerr = LO_S0_weight_terr_x[1],marker = 's', color = 'blue', mec = 'blue', markersize =5, linestyle = 'None') plt.xlim(-5,55) plt.ylim(0,0.16) plt.yticks(np.arange(0.0, 0.2, 0.04)) plt.xticks(np.arange(0, 51, 10.0)) plt.ylabel('S$_0$(site)') lg = plt.legend(loc = 'lower right', numpoints = 1, prop={'size': 12}) lg.draw_frame(False) plt.annotate('C $\\rm{\\phi_i} = 90$'u'\xb0 Laser-Off', xy = (23,0.1), xytext=(23,0.13)) plt.subplot(4,2,7) plt.errorbar(v1_data_x[0], v1_S0_weight_step_x[0], yerr = v1_S0_weight_step_x[1], marker = 's', color = 'red', mec = 'red', markersize =5, linestyle = 'None', label = 'Step') plt.errorbar(v1_data_x[0], v1_S0_weight_terr_x[0], yerr = v1_S0_weight_terr_x[1], marker = 's', color = 'blue', mec = 'blue', markersize =5, linestyle = 'None', label = 'Terrace') plt.errorbar(-v1_data_x[0], v1_S0_weight_step_x[0], yerr = v1_S0_weight_step_x[1], marker = 's', color = 'red', mec = 'red', markersize =5, linestyle = 'None') plt.errorbar(-v1_data_x[0], v1_S0_weight_terr_x[0], yerr = v1_S0_weight_terr_x[1], marker = 's', color = 'blue', mec = 'blue', markersize =5, linestyle = 'None') plt.xlim(-5,55) plt.ylim(0,0.25) plt.xticks(np.arange(0, 51, 10.0)) plt.xlabel('$\\rm{\\theta_i}$ ('u'\xb0)') plt.ylabel('S$_0$(site)') plt.annotate('D $\\rm{\\phi_i} = 90$'u'\xb0 $\\nu_1$=1', xy = (30,0.20), xytext = (30,0.20)) plt.subplots_adjust(left=0.1, bottom=0.08, right=0.95, top=0.99, wspace=0.15, hspace=0.25) plt.savefig('Fig9.png',bbox_inches='tight', dpi=300) plt.show() ########################################################### ########################################################### ### ### ### CH RATIO ### ### ### ########################################################### ########################################################### # y rotation #~~~ MAKING ASYMMETRIC ERRORS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ low_err_step = np.array(LO_branch_step_y[2]) up_err_step = np.array(LO_branch_step_y[2]) low_err_terr = np.array(LO_branch_terr_y[2]) up_err_terr = np.array(LO_branch_terr_y[2]) for i in range (len(LO_branch_step_y[2])): if LO_branch_step_y[0][i]-low_err_step[i] < 0.:low_err_step[i] = 0 if LO_branch_terr_y[0][i]-low_err_terr[i] < 0.:low_err_terr[i] = 0 if LO_branch_step_y[0][i]+up_err_step[i] > 1.: up_err_step[i] = 0 if LO_branch_terr_y[0][i]+up_err_terr[i] > 1.: up_err_terr[i] = 0 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # CH branching laser off (top) and v1 (bottom) plt.subplot(4,2,1) plt.bar(fac*LO_data_y[0], LO_branch_step_y[0], width = 4, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(fac*LO_data_y[0], LO_branch_terr_y[0], width = -4, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.errorbar(fac*LO_data_y[0]+2, LO_branch_step_y[0], yerr=np.array([up_err_step,low_err_step]), linestyle='None', ecolor = 'black') plt.errorbar(fac*LO_data_y[0]-2, LO_branch_terr_y[0], yerr=np.array([low_err_terr,up_err_terr]), linestyle='None', ecolor = 'black') plt.xlim(-55,55) plt.ylim(0,1.2) plt.xticks(np.arange(-40., 50., 20.0)) plt.ylabel('Fraction') plt.annotate('A $\\rm{\\phi_i} = 0$'u'\xb0 Laser-Off', xy = (-52,0.95), xytext = (-52,0.95)) lg = plt.legend(loc = 'upper right', numpoints = 1, prop={'size': 12}) lg.draw_frame(False) #~~~ MAKING ASYMMETRIC ERRORS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ low_err_step = np.array(v1_branch_step_y[2]) up_err_step = np.array(v1_branch_step_y[2]) low_err_terr = np.array(v1_branch_terr_y[2]) up_err_terr = np.array(v1_branch_terr_y[2]) for i in range (len(v1_branch_step_y[2])): if v1_branch_step_y[0][i]-low_err_step[i] < 0.:low_err_step[i] = 0 if v1_branch_terr_y[0][i]-low_err_terr[i] < 0.:low_err_terr[i] = 0 if v1_branch_step_y[0][i]+up_err_step[i] > 1.: up_err_step[i] = 0 if v1_branch_terr_y[0][i]+up_err_terr[i] > 1.: up_err_terr[i] = 0 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ plt.subplot(4,2,3) plt.plot([],[], 'w', label = '$\\rm{\\phi_i} = 0$'u'\xb0') plt.bar(fac*v1_data_y[0], v1_branch_step_y[0], width = 4, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(fac*v1_data_y[0], v1_branch_terr_y[0], width = -4, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.errorbar(fac*v1_data_y[0]+2, v1_branch_step_y[0], yerr=np.array([up_err_step,low_err_step]), linestyle='None', ecolor = 'black') plt.errorbar(fac*v1_data_y[0]-2, v1_branch_terr_y[0], yerr=np.array([low_err_terr,up_err_terr]), linestyle='None', ecolor = 'black') plt.xlim(-55,55) plt.ylim(0,1.2) plt.xticks(np.arange(-40., 50., 20.0)) plt.ylabel('Fraction') plt.annotate('B $\\rm{\\phi_i} = 0$'u'\xb0 $\\nu_1$=1', xy = (-52,0.95), xytext = (-52,0.95)) #~~~ MAKING ASYMMETRIC ERRORS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ low_err_step = np.array(LO_branch_step_x[2]) up_err_step = np.array(LO_branch_step_x[2]) low_err_terr = np.array(LO_branch_terr_x[2]) up_err_terr = np.array(LO_branch_terr_x[2]) for i in range (len(LO_branch_step_x[2])): if LO_branch_step_x[0][i]-low_err_step[i] < 0.:low_err_step[i] = 0 if LO_branch_terr_x[0][i]-low_err_terr[i] < 0.:low_err_terr[i] = 0 if LO_branch_step_x[0][i]+up_err_step[i] > 1.: up_err_step[i] = 0 if LO_branch_terr_x[0][i]+up_err_terr[i] > 1.: up_err_terr[i] = 0 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # x rotation plt.subplot(4,2,5) plt.bar(LO_data_x[0], LO_branch_step_x[0], width = 2, color = 'red', ecolor = 'black', align = 'edge', label = 'Step') plt.bar(LO_data_x[0], LO_branch_terr_x[0], width = -2, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terrace') plt.errorbar(LO_data_x[0]+1, LO_branch_step_x[0], yerr=np.array([up_err_step,low_err_step]), linestyle='None', ecolor = 'black') plt.errorbar(LO_data_x[0]-1, LO_branch_terr_x[0], yerr=np.array([low_err_terr,up_err_terr]), linestyle='None', ecolor = 'black') plt.xlim(-5,55) plt.ylim(0,1.2) plt.xticks(np.arange(0, 51, 10.0)) plt.ylabel('Fraction') plt.annotate('C $\\rm{\\phi_i} = 90$'u'\xb0 Laser-Off', xy = (-3,0.95), xytext = (-3,0.95)) #~~~ MAKING ASYMMETRIC ERRORS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ low_err_step = np.array(v1_branch_step_x[2]) up_err_step = np.array(v1_branch_step_x[2]) low_err_terr = np.array(v1_branch_terr_x[2]) up_err_terr = np.array(v1_branch_terr_x[2]) for i in range (len(v1_branch_step_x[2])): if v1_branch_step_x[0][i]-low_err_step[i] < 0.:low_err_step[i] = 0 if v1_branch_terr_x[0][i]-low_err_terr[i] < 0.:low_err_terr[i] = 0 if v1_branch_step_x[0][i]+up_err_step[i] > 1.: up_err_step[i] = 0 if v1_branch_terr_x[0][i]+up_err_terr[i] > 1.: up_err_terr[i] = 0 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ plt.subplot(4,2,7) plt.bar(v1_data_x[0], v1_branch_step_x[0], width = 2, color = 'red', ecolor = 'black', align = 'edge', label = 'Step rxn') plt.bar(v1_data_x[0], v1_branch_terr_x[0], width = -2, color = 'blue', ecolor = 'black', align = 'edge', label = 'Terr rxn') plt.errorbar(v1_data_x[0]+1, v1_branch_step_x[0], yerr=np.array([up_err_step,low_err_step]), linestyle='None', ecolor = 'black') plt.errorbar(v1_data_x[0]-1, v1_branch_terr_x[0], yerr=np.array([low_err_terr,up_err_terr]), linestyle='None', ecolor = 'black') plt.xlim(-5,55) plt.ylim(0,1.2) plt.xticks(np.arange(0, 51, 10.0)) plt.xlabel('$\\rm{\\theta_i}$ ('u'\xb0)') plt.ylabel('Fraction') plt.annotate('D $\\rm{\\phi_i} = 90$'u'\xb0 $\\nu_1$=1', xy = (-3,0.95), xytext = (-3,0.95)) plt.subplots_adjust(left=0.1, bottom=0.08, right=0.95, top=0.99, wspace=0.15, hspace=0.25) plt.savefig('Fig10.png',bbox_inches='tight', dpi=300) plt.show() #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # x rotation vs y rotation #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # AIMD laser off vs laser on cosfit = v1_S0_x[0][2]*np.cos(np.radians(angfit))*np.cos(np.radians(angfit)) plt.subplot(2,2,1) plt.plot(angfit,cosfit, 'k--') plt.plot([],[], 'ko', label = '$\\rm{\\phi_i} = 0$'u'\xb0') plt.errorbar(fac*LO_data_y[0],LO_S0_y[0], yerr=LO_S0_y[1], color='blue', marker='o', mec = 'blue', markersize = 5, linestyle='None') plt.errorbar(fac*v1_data_y[0], v1_S0_y[0], yerr=v1_S0_y[1], color='red', marker='o', mec = 'red', markersize = 5, linestyle='None') plt.plot([],[], 'ks', label = '$\\rm{\\phi_i} = 90$'u'\xb0') plt.errorbar(LO_data_x[0],LO_S0_x[0], yerr=LO_S0_x[1], color='blue', marker='s', mec = 'blue', markersize = 5, linestyle='None') plt.errorbar(v1_data_x[0], v1_S0_x[0], yerr=v1_S0_x[1], color='red', marker='s', mec = 'red', markersize = 5, linestyle='None') plt.errorbar(-LO_data_x[0],LO_S0_x[0], yerr=LO_S0_x[1], color='blue', marker='s', mec = 'blue', markersize = 5, linestyle='None') plt.errorbar(-v1_data_x[0], v1_S0_x[0], yerr=v1_S0_x[1], color='red', marker='s', mec = 'red', markersize = 5, linestyle='None') plt.xlim(-55,55) plt.ylim(0,0.16) plt.xticks(np.arange(-40., 50., 20.0)) plt.yticks(np.arange(0.,0.18,0.04)) plt.xlabel('$\\rm{\\theta_i}$ ('u'\xb0)') plt.ylabel('S$_0$') lg = plt.legend(loc = 'best', numpoints = 1, prop={'size': 11}) lg.draw_frame(False) plt.savefig('Fig5.png',bbox_inches='tight', dpi=300) plt.show()