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How to use iRun method in fMBT

Best Python code snippet using fMBT_python

test_odassl.py

Source:test_odassl.py

1from scipy import *2import odassl as od3g=13.7503716373294544 # gravitation constant such that the period is 24def tolerance_set(irun,tol):5    rtol=atol=tol*ones((5,))6    if irun == 1 or irun == 3:7       rtol[4]=atol[4]=1.e78    elif irun == 0:                                                                9       rtol[2:]=atol[2:]=1.e7                                                    10    info=111    return rtol,atol,info            12def res1(t,p,pp):13    ires=0                                                                                                                      14    delta=empty((5,))                                                      15    # kinematics                                                                               16    delta[0:2] = [pp[0] - p[2], pp[1] - p[3]]                                                                         17    # dynamics                                                  18    delta[2:4] =  [pp[2] + p[4]*p[0], pp[3]+p[4]*p[1]+g]                                             19    # lambda constraint                                                              20    delta[4] = p[2]**2 + p[3]**2 - (p[0]**2 + p[1]**2)*p[4] - p[1]*g                                          21    return delta, ires22def res2(t,p,pp):23    ires=0                                                                      24    delta=empty((5,))                                                      25    # kinematics                                                                               26    delta[0:2] = [pp[0] - p[2], pp[1] - p[3]]                                                                         27    # dynamics                                                  28    delta[2:4] =  [pp[2] + p[4]*p[0], pp[3]+p[4]*p[1]+g]                                             29    # velocity constraint                                                              30    delta[4] = p[0]*p[2] + p[1]*p[3]                                          31    return delta, ires32def res3(t,p,pp):33    ires=0                                                                      34    delta=empty((5,))   35    #print t,p,pp                                                   36    # kinematics                                                                               37    delta[0:2] = [pp[0] - p[2], pp[1] - p[3]]                                                                         38    # dynamics                                                  39    delta[2:4] =  [pp[2] + p[4]*p[0], pp[3]+p[4]*p[1]+g]                                             40    # position constraint                                                              41    delta[4] = p[0]**2 + p[1]**2 - 1.0                                           42    return delta, ires43def resStab2(t,p,pp):44    ires=0                                                                      45    delta=empty((neq,))   46    #print t,p,pp                                                   47    # kinematics                                                                               48    delta[0:2] = [pp[0] - p[2], pp[1] - p[3]]                                                                         49    # dynamics                                                  50    delta[2:4] =  [pp[2] + p[4]*p[0], pp[3]+p[4]*p[1]+g]51    # velocity constraint  52    delta[4] = p[0]*p[2] + p[1]*p[3]                                            53    # position constraint                                                              54    delta[5] = p[0]**2 + p[1]**2 - 1.0                                           55    return delta, ires    56def resStab1(t,p,pp):57    ires=0                                                                      58    delta=empty((neq,))   59    #print t,p,pp                                                   60    # kinematics                                                                               61    delta[0:2] = [pp[0] - p[2], pp[1] - p[3]]                                                                         62    # dynamics                                                  63    delta[2:4] =  [pp[2] + p[4]*p[0], pp[3]+p[4]*p[1]+g]64    # lambda constraint65    delta[4] = p[2]**2 + p[3]**2 - (p[0]**2 + p[1]**2)*p[4] - p[1]*g66    # velocity constraint  67    delta[6] = p[0]*p[2] + p[1]*p[3]                                            68    # position constraint                                                              69    delta[5] = p[0]**2 + p[1]**2 - 1.0                                           70    return delta, ires    71p=empty(5)72pp=empty(5)73rwork=empty((1000,))74iwork=empty((200,),dtype=int32)  75                                                  76ny = 5                                                                    77tol= 1.e-5       78res=[res3,res2,res1, resStab2, resStab1]                                                 79for irun, task in enumerate(['INDEX-3', 'INDEX-2',80             'INDEX-1', 81             'STAB. INDEX-2','STAB. INDEX-1']):82     83     info=zeros((15,),dtype=int32)                                                                                         84     # initial conditions                                                                                                                                               85     p[0] = 1.0                                                             86     p[1] = -sqrt(1.0 - p[0]**2)                                           87     p[2:] = 0.0                                                                                                                         88     pp[0:2] = p[2:4]                                                           89     pp[2:5] = [-p[4]*p[0], -g-p[4]*p[1],0.]                                                                                                                        90     # other initialisations                                                                                                                                                                        91     t,th = 0., 2.0                                                            92                                                             93     rtol,atol,info[1] = tolerance_set(irun,tol)                                                                             94     ny=len(p)95     if irun <= 2:                                                                    96        neq=ny                                 97     elif irun==3:  # stab index 2                                                                   98        neq=ny+1                                        99     elif irun==4:  # stab index 1100        neq=ny+2                                                                 101#          INTEGRATION LOOP                                                     102     for i in range(50):103         tout=t+th                        104         t,y,yprime,tout,info,idid,rwork,iwork = od.odassl(res[irun],neq,ny,t,p,pp,tout,info,rtol,atol,105                                                         rwork,iwork,res[irun])                                                                                106         if idid<0:                              107            print task+':  ', idid                                                  108            break                                                         109         else:                                                                110            print '{0}  : t= {1: >8.2f}  p={2[0]: >-12.8f} {2[1]: > 12.8f} {2[2]: >-12.8f} {2[3]: >-12.8f} {2[4]: >-12.8f}'.format(task, t, p)                            ...

minidisc_masses.py

Source:minidisc_masses.py

1import matplotlib as mpl2mpl.use('Agg')3import matplotlib.pyplot as plt4import pandas as pd5import numpy as np6from scipy import interpolate7data_dir = "../analysis_out/"8norad_folder = "norad_prod"9rad_folder = "rad_prod"10sim_name_bases = ["small_ecc","small_circ"]11rad_format = "rad_{}_full"12rad_format_earlier = "rad_{}_earlier"13data_file_format = data_dir+"disc_components_{}_{}.txt"14t_orbit = 13.7e-3 # Myr15m_bh = 2.e316t_offset = 0.0002128*0.9778e9/1.e617norad_data_unprocessed = [pd.read_csv(data_file_format.format(norad_folder,sim_name_bases[irun]),sep=' ') for irun in [0,1]]18rad_data = [pd.read_csv(data_file_format.format(rad_folder,rad_format.format(sim_name_bases[irun])),sep=' ') for irun in [0,1]]19rad_data_earlier = [pd.read_csv(data_file_format.format(rad_folder,rad_format_earlier.format(sim_name_bases[irun])),sep=' ') for irun in [0,1]]20# interpolate norad_data to make timing consistent21norad_data = []22for df in norad_data_unprocessed:23    dt = df["t"].iloc[-1]-df["t"].iloc[-2]24    interp_t = np.arange(0,df["t"].iloc[-1],dt)25    new_df = pd.DataFrame()26    new_df["t"] = interp_t27    new_df["m1"] = interpolate.interp1d(df["t"],df["m1"])(interp_t)28    new_df["m2"] = interpolate.interp1d(df["t"],df["m2"])(interp_t)29    norad_data.append(new_df)30# yticks = [0,5e-4,1e-3,3e-3,5e-3,1e-2]31fig,sp = plt.subplots(1,2,figsize=(9,3),sharex=True,sharey=True,constrained_layout=True)32for irun in range(2):33    for idisc in [1,2]:34        for t,m,label in [(norad_data[irun]["t"], norad_data[irun][f"m{idisc}"], f"disc{idisc}"),35                          (rad_data[irun]["t"] + norad_data[irun]["t"].iloc[-1], rad_data[irun][f"m{idisc}"], None),36                          (rad_data_earlier[irun]["t"] + t_offset, rad_data_earlier[irun][f"m{idisc}"], None)37                          ]:38            sp[irun].plot(t / t_orbit, m / m_bh, label=label)39            # orbit_t = t/t_orbit40            # interp_t = np.arange(int(orbit_t[0]),orbit_t[-1],1)41        # sp[irun].plot(norad_data[irun]["t"]/t_orbit,norad_data[irun][f"m{idisc}"]/m_bh,label=f"disc{idisc}")42        # sp[irun].plot((rad_data[irun]["t"]+norad_data[irun]["t"].iloc[-1])/t_orbit,rad_data[irun][f"m{idisc}"]/m_bh)43        # sp[irun].plot((rad_data_earlier[irun]["t"]+t_offset)/t_orbit,rad_data_earlier[irun][f"m{idisc}"]/m_bh)44    # sp[irun].legend()45    sp[irun].minorticks_on()46    sp[irun].xaxis.set_minor_locator(plt.MultipleLocator(1))47    sp[irun].set_xlim([0,None])48    # sp[irun].set_ylim([0,1.e-2])49    sp[irun].set_ylim([0,0.003])50    # sp[irun].set_yscale('symlog',linthresh=1.e-3)51    # sp[irun].set_yticks(yticks)52    # sp[irun].set_yticklabels(yticks)53    sp[irun].set_xlabel(r"$t$ (orbits)")54sp[0].set_ylabel(r"$M_d/(M_1+M_2)$")55sp[0].set_title("Elliptical")56sp[1].set_title("Circular")...

torque_significance.py

Source:torque_significance.py

1import numpy as np2import h5py3from num2tex import num2tex4f = h5py.File("../analysis_out/tidy_torque.hdf5",'r')5def get_exponent(x):6    return np.floor(np.log10(np.abs(x))).astype(np.int)7def format_with_uncertainty(x,e,precision=1,significance=3):8    # fmt = fr"({{0:.{precision}f}} \pm {{1:.{precision}f}}) \times 10^{{{{{{2}}}}}}"9    #10    # exponents = np.minimum(get_exponent(x),get_exponent(e))11    # bases = x/10.**exponents12    # error_bases = e/10.**exponents13    # strout = fmt.format(bases,error_bases,exponents)14    round_factor = -np.floor(np.log10(e)).astype(np.int) + precision-115    x_round = np.round(x,round_factor)16    e_round = np.round(e,round_factor)17    if round_factor<0:18        strout = fr"{{{x_round:.0f}}} \pm {{{e_round:.0f}}}"19    else:20        strout_0 = fr"{{0:.{round_factor:0d}f}} \pm {{1:.{round_factor:0d}f}}"21        strout = strout_0.format(x_round,e_round)22    # strout = fr"{{{x:.3f}}} \pm {{{e:.3f}}}"23    # if np.abs(bases)>np.abs(error_bases):24    if np.abs(x) > significance*np.abs(e) :25            strout = r"$\mathbf{"+strout+r"}$"26    else:27        strout = r"$"+strout+r"$"28    # TODO: implement for arrays?29    return strout30stage_name = [r"norad\_all", r"norad\_eqm", r"rad\_early", r"rad\_late"]31torque_name = {"grav":r"$\tau_g$",32                "acc":r"$\tau_a$"33    }34run_indices = [0,0,1,2]35run_offsets = [0,20,0,0]36nruns = len(run_indices)37assert nruns==len(run_offsets)38# UNITS = L0/T (set in tidy_up_torque)39for plot_key in ["acc","grav"]:40    mu = np.zeros((2,2,nruns))41    sd = np.zeros((2,2,nruns))42    for isim in range(2):43        for bh in [1,2] :44            for irun,run_index in enumerate(run_indices):45                time = np.array(f[f"time_{run_index}_{isim}"])46                h5_key = f"BH_{plot_key}_J_{bh}_{run_index}_{isim}"47                angmom = -np.array(f[h5_key])48                torque = np.gradient(angmom,time)49                run_offset = run_offsets[irun]50                if run_offset>0:51                    torque = torque[(time>run_offset)]52                mu[isim,bh-1,irun] = np.mean(torque)53                sd[isim,bh-1,irun] = np.std(torque)/np.sqrt(len(torque))54    for irun in range(nruns):55        line = []56        for isim in range(2) :57            for bh in range(2) :58                line+=[format_with_uncertainty(mu[isim,bh,irun]*1e6,sd[isim,bh,irun]*1e6,precision=2)]59                # line+=[fr"${num2tex(mu[isim,bh,irun],precision=2):.2g} \pm {num2tex(sd[isim,bh,irun],precision=2):.0g}$"]60        if irun==1:61            key_str = torque_name[plot_key]+" & "62        else:63            key_str = "~ & "64        print(key_str+stage_name[irun]+" & "+r" & ".join(line)+r"\\")...

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