.gitignore

data/

1a.ipynb

README.md

SURF Related Code

andrey_plot_data.csv

andrey_plot_data2.csv

andrey_plot_data3.csv

andrey_plots.ipynb

fipy_hackathon_1a.py

import fipy as fp
import numpy as np


def calc_dt(elapsed_time, dt, dt_old, dump_to_file, dump_times):
    if dump_to_file:
        dt = dt_old
        dt = dt * 1.1
        dump_to_file = False
    else:
        dt_old = dt
        dt = dt * 1.1
        # import ipdb; ipdb.set_trace()

        if len(dump_times) > 0:
            if (elapsed_time + dt) >= dump_times[0]:
                dt = dump_times[0] - elapsed_time
                dump_to_file = True
                del dump_times[0]

    return dt, dt_old, dump_times, dump_to_file

mesh = fp.PeriodicGrid2D(nx=50, ny=50, dx=0.5, dy=0.5)

c_alpha = 0.05
c_beta = 0.95
A = 2.0
kappa = 2.0
c_m = (c_alpha + c_beta) / 2.
B = A / (c_alpha - c_m)**2
D = D_alpha = D_beta = 2. / (c_beta - c_alpha)
c_0 = 0.45
q = np.sqrt((2., 3.))
epsilon = 0.01

c_var = fp.CellVariable(mesh=mesh, name=r"$c$", hasOld=True)

r = np.array((mesh.x, mesh.y))
c_var[:] = c_0 + epsilon * np.cos((q[:, None] * r).sum(0))

f_0_var = -A + 3*B*(c_var - c_m)**2 + 3*c_alpha*(c_var - c_alpha)**2 + 3*c_beta*(c_var - c_beta)**2

eqn = fp.TransientTerm(coeff=1.) == fp.DiffusionTerm(D * f_0_var) - fp.DiffusionTerm((D, kappa))

dump_times = [1.0, 3.0, 10.0]
elapsed_time = 0.0
steps = 0
dt = 0.01
dt_old = dt
total_sweeps = 2
tolerance = 1e-1
total_steps = 1000
dump_to_file = False

c_var[:] = c_0 + epsilon * np.cos((q[:, None] * r).sum(0))

c_var.updateOld()

from fipy.solvers.pysparse import LinearLUSolver as Solver

solver = Solver()

viewer = fp.Viewer(c_var)
while steps < total_steps:
    res0 = eqn.sweep(c_var, dt=dt, solver=solver)

    for sweeps in range(total_sweeps):
        res = eqn.sweep(c_var, dt=dt, solver=solver)

        print ' '
        print 'steps',steps
        print 'res',res
        print 'sweeps',sweeps
        print 'dt',dt
        print 'elapsed_time',elapsed_time


    if res < res0 * tolerance:
       
        steps += 1
        elapsed_time += dt

        if dump_to_file or steps % 10 == 0:
            np.savez('data_time-{0:.2f}_step-{1}.npz'.format(elapsed_time, str(steps).rjust(6, '0')),
                     c_var_array=np.array(c_var),
                     dt=dt,
                     steps=steps,
                     dx=c_var.mesh.dx,
                     dy=c_var.mesh.dy,
                     nx=c_var.mesh.nx,
                     ny=c_var.mesh.ny)

        dt, dt_old, dump_times, dump_to_file = calc_dt(elapsed_time, dt, dt_old, dump_to_file, dump_times)
        
        if steps % 1 == 0:
             viewer.plot('image{0}.png'.format(steps))
        c_var.updateOld()
    else:
        dt *= 0.8
        c_var[:] = c_var.old
        
        

free_energy_data.py

free_energy = [319.05536555635217, 318.96438404155111, 318.85827371179801,
         318.71177373639324, 317.3219931305095, 316.22675804754704,
         295.78674209013434, 293.44627548708797, 211.40914803231527,
         208.41914842277987, 184.07819540377673, 157.6414742534354,
         141.88608832893073, 136.77337503257573, 133.71312209978609,
         127.58635844028647, 122.8374065325492, 119.16606229714193,
         118.78040433709215, 114.84309746833861, 111.34382147809778,
         108.24803669260983, 105.75239041730647, 103.71046239404524,
         101.97686552768381, 100.41632806551529, 99.000944323339809,
         98.062543186938484, 97.650657656399233, 96.338157774767453,
         95.060383342577524, 93.778737345945359, 92.541863652252403,
         91.316727231027372, 90.100423299725151, 88.968461413824443,
         87.842955553658754, 86.74665883153709, 85.682141228050554,
         84.712858378886253, 83.769491279435556, 82.894708924309612,
         82.655783014582696, 82.08071595321239, 81.275738106363065,
         80.509692134445601, 79.763652610028359, 79.035931322104034,
         78.3409747692927, 77.660718477553502, 77.021685501786848,
         76.391555947590462, 75.807516475135884, 75.26342079114319,
         74.774789672803109, 74.300896831535212, 73.885739267106359,
         73.500143350575996, 73.123721016366019, 72.724017840341332,
         71.336502663943619, 70.662011555353288, 70.14874914162877,
         69.648117704895569, 69.151078128894753, 68.655941412113975,
         68.150734452141052, 67.657065213717743, 67.173909300193074,
         66.700760333677067, 66.236780044275463, 65.770936768584292,
         65.322888774827476, 64.871775807830289, 64.42666369356796,
         63.986396411740678, 63.550207450705777, 63.356119554960934,
         63.142286634509176, 62.703650807604141, 62.265455735066851,
         61.845580584780436, 61.414356780694675, 60.979830802554787,
         60.540640169017465, 60.09615836272333, 59.625003205952424,
         59.136912487404366, 58.622668253292993, 58.076092825947931,
         57.511977733344196, 56.933778748660423, 56.388579621140295,
         55.903103020110628, 55.485459969119923, 55.115288999704688,
         54.791591650395063, 54.489064026758335, 54.201911345719701,
         53.926377661114167, 53.671007239980398, 53.421976431099964,
         53.404497705757443, 53.19025008498398, 52.961040553224393,
         52.734233322894369, 52.518726045763657, 52.304161420369716,
         52.094626349927239, 51.889484546264299, 51.688330863926453,
         51.490728667712482, 51.291940811913115, 51.100329785187967,
         50.907111420711871, 50.716264680604105, 50.527505384618017,
         50.340711366599393, 50.15567549903858, 49.9680742070002,
         49.785952985841782, 49.609132814672734, 49.429433063356115,
         49.254603064523685, 49.076725078339557, 48.899547150192184,
         48.726737790570873, 48.554535098467419, 48.382686228235826,
         48.211010515305269, 48.039496594166678, 47.871813281492763,
         47.70398459936073, 47.535990663956035, 47.367661568224214,
         47.2025653086612, 47.036953802466009, 46.874349445463082,
         46.710875190170235, 46.550131558008268, 46.38833439850557,
         46.228789112175939, 46.067953064373725, 45.909087120213378,
         45.752011134066073, 45.596566767405996]

times = [0.13579476910000005, 0.5115909044841459, 0.9834705943388384,
         1.3586287667261558, 3.656963750138521, 4.895047518160528,
         8.841230413398128, 9.723205265987877, 18.547952522872556, 20.0,
         35.604002802866354, 56.326058286931065, 81.49446245368492,
         98.15872394616721, 109.15048609186623, 139.29256370812854,
      169.90967703817265, 198.02954049264576, 200.0, 232.1359693001254,
      264.76927133595655, 299.43879063599235, 333.887965292291,
      368.89371899071307, 402.9086144414274, 437.46375200693103,
      471.7960821459092, 496.4650166925172, 507.2659250382838,
      543.2903386698891, 580.7161301470529, 618.7621781684207,
      656.5519299340673, 694.9418780296073, 733.9469339871172,
      771.917751288336, 809.6016986336526, 847.899206586326,
      885.1225150997656, 919.7303015278968, 954.1382509190979,
      987.5480657797514, 997.1340508466747, 1018.8568805676563,
      1050.1594059988522, 1081.2785014426784, 1111.4988007532493,
      1141.5270327603312, 1171.3793020250491, 1200.3693642171852,
      1228.5381042519812, 1255.9255756202272, 1281.9357781838296,
      1305.571905422934, 1327.0777579042024, 1347.4948973268256,
      1364.8477820207972, 1379.9249960301584, 1393.952287514081,
      1406.6840503377355, 1429.5778411088318, 1462.430026071029,
      1495.032270727919, 1528.165777048673, 1561.8210081009065,
      1596.7934465388464, 1632.336224104293, 1667.6359625035539,
      1702.7113508558966, 1738.3534356892442, 1772.9866505514756,
      1808.1699279963257, 1843.1263478432468, 1877.8750776760708,
      1912.3861979886753, 1946.6779803737927, 1981.5237988884555,
      1998.5797212878279, 2013.6978666570374, 2047.9013418447785,
      2081.8709359275617, 2114.878131926784, 2147.689219027201,
      2180.275946080464, 2212.655565827135, 2245.5583277948517,
      2278.997676097163, 2312.964024724117, 2348.2469616008334,
      2385.731444772843, 2425.5548439298445, 2469.8179930941615,
      2517.9320223407394, 2569.013729350479, 2620.9004782508114,
      2673.6113192609087, 2725.982287023123, 2778.0420980055396,
      2830.9223656858726, 2884.6425050537027, 2938.016263337607,
      2991.072906863795, 2996.1910873612665, 3042.6324477909316,
      3094.682952434612, 3147.5601500412413, 3200.096401752393,
      3252.320514665971, 3304.1875225436825, 3355.7248858920425,
      3408.0949140752546, 3458.982578107559, 3510.6784662684177,
      3562.0410254769254, 3613.09841926252, 3663.8066859606115,
      3714.192672592935, 3765.3927218103872, 3815.143523813018,
      3865.6844937150427, 3915.8995814406, 3963.625079766833,
      4012.1085790747984, 4060.2794625325364, 4108.1641435843,
      4155.721392348748, 4202.976387570378, 4248.911732798931,
      4294.532975169813, 4339.864268426892, 4385.927957975926,
      4429.692006770498, 4473.177909979701, 4517.366394385568,
      4560.304098002526, 4602.019735083428, 4644.409352007381,
      4684.68274915826, 4724.700185813392, 4764.483123884174,
      4803.117032704666, 4841.505400916371, 4878.821729873659,
      4915.066609111439, 4951.077785668906, 4985.303581627125]