def run_ode( FORMULA, FUNCTIONS, INPUTS, inits, params, T , fs, inputs = None, decimate=1 ,variable_length = False, stochastic = False, Tterm = 0, gpu = False, nthreads = 4 , dtype = np.float32, debug = False,seed =None,threads_per_block=32 ):
from gpuODE import ode, param_grid, funcs2code
PARAMETERS = params.keys()
odeRK4 = ode("ode")
odeRK4.setup(FORMULA, PARAMETERS, INPUTS)
Tt = T + Tterm
dt = 1.0/np.array(fs)
N = np.int32(Tt*fs)
Nterm = np.int32(Tterm*fs)
extra_funcs = funcs2code(FUNCTIONS, gpu = gpu)
odeRK4.extra_func = extra_funcs
odeRK4.generate_code(debug=debug, gpu = gpu,variable_length = variable_length, stochastic=stochastic, dtype = dtype)
odeRK4.compile()
if gpu==True:
time, out = odeRK4.run(inits, param_grid(**params) , dt, decimate = decimate, inputs=inputs, N = N, Nterm = Nterm,seed = seed,threads_per_block=threads_per_block)
return time, out
else:
import distributed_exploration as de
import timeit
from random import randint
seed_off = 0
#Modifications are needed to change the seed on differnet threads
def func(**args):
seedr = seed + randint(0,10000)
time,out = odeRK4.run(inits, args, dt ,decimate=decimate, inputs=inputs, N = N , Nterm = Nterm,seed = seedr)
return time, out
tic = timeit.default_timer()
out0 = de.explore_thread(func, param_grid(**params) ,nthreads=nthreads)
toc = timeit.default_timer()
Nm = int(T*fs)/decimate
M = len(out0)
out = {}
for j,k in enumerate(FORMULA.keys()):
out[k] = np.zeros((Nm,M))
for i,o in enumerate(out0):
for j,k in enumerate(FORMULA.keys()):
out[k][:,i] = o['out'][1][k].T[0,:N]
return toc-tic, out
# -*- coding: utf-8 -*-
from __future__ import division
from gpuODE import ode, param_grid
import pylab as pl
import numpy as np
vdp = ode("vdp")
PARAMETERS = ["mu"]
INPUTS = ["I"]
FORMULA = {"x": "mu*(x-x*x*x/3 -y)",
"y": "x/mu"}
vdp.setup(FORMULA, PARAMETERS, INPUTS)
vdp.generate_code(debug=False, stochastic = False, gpu = True, dtype = np.float32)
vdp.compile()
x0 = {'x':1,'y':0}
M = 32
mu = np.linspace(-1,10,M)
params = {'mu': mu}
Tterm = 0
T = 100 + Tterm
fs = 100
dt = 1/fs
N = int(T*fs)
# -*- coding: utf-8 -*-
from __future__ import division
from gpuODE import ode, param_grid
import pylab as pl
import numpy as np
#from utils import *
hr = ode("hr")
extra_func="""
__device__ float phi( float x,float a, float b)
{
return -a*x*x*x+b*x*x;
}
__device__ float psi( float x,float c, float d)
{
return c-d*x*x;
}
"""
PARAMETERS = ["a","b","c","d","r","s","xr","i"]
INPUTS = ["I"]
FORMULA = {'x':'y + phi( x ,a,b) - z + i + I + noise',
'y':'psi( x , c ,d )- y',
'z':'r*(s*(x - xr) - z )'}
hr.setup(FORMULA, PARAMETERS, INPUTS)
# -*- coding: utf-8 -*-
from __future__ import division
from gpuODE import ode, param_grid
import pylab as pl
import numpy as np
hopf = ode("hopf")
PARAMETERS = ["e","w"]
INPUTS = ["I1","I2"]
FORMULA = {"x": "w*y + w*e*x - (x*x+y*y)*x + I1",
"y": "-w*x + w*e*y - (x*x+y*y)*y + I2"}
hopf.setup(FORMULA, PARAMETERS, INPUTS)
hopf.generate_code(debug=False, stochastic = False, gpu = True, dtype = np.float32)
hopf.compile()
x0 = {'x':0,'y':0}
M1 = 128
ff = np.logspace(np.log10(100.0),np.log10(5000.0),M1)
w = 2*np.pi*ff
es = np.logspace(0,-2,5)
e = np.r_[-es,0,0.0005]
M2 = len(e)
INPUTS = []
FORMULA = {"w": "noise"}
x0 = {'w':0}
M = 2
params = {'d':np.ones(M)}
T = 0.001
fs = 1000
stochastic = True
gpu = False
PARAMETERS = params.keys()
odeRK4 = ode("ode")
odeRK4.setup(FORMULA, PARAMETERS, INPUTS)
Tterm = 0
decimate = 1
inputs = None
debug = True
nthreads = 1
T = T + Tterm
dt = 1.0/float(fs)
N = np.int32(T*fs)
Nterm = np.int32(Tterm*fs).min()
dtype = np.float32
variable_length = False
# -*- coding: utf-8 -*-
from __future__ import division
from gpuODE import ode, param_grid, funcs2code
import pylab as pl
import numpy as np
aplysia = ode("aplysia")
Vhna = 115.0
Vhk = -12.0
V_i = 30.0
V_k = -75.0
a = (Vhna-Vhk)/(V_i-V_k)
b = -(Vhna*V_k-V_i*Vhk )/(V_i-V_k)
params = {'a' :a,
'b' :b,
'g_i':4.0,
'g_t':0.01,
'g_k':0.3,
'g_p':0.03,
'g_l':0.003,
'K_p':0.5,
'K_c':0.008,
'rho':0.0001,
'V_i':V_i,
'V_k':V_k,
'V_l':-40.0,
# -*- coding: utf-8 -*-
from __future__ import division
from gpuODE import ode, param_grid
import pylab as pl
import numpy as np
#from utils import *
osc = ode("osc")
INPUTS = ["I"]
PARAMETERS = ["e","w"]
FORMULA = {"x": "w*y + w*e*x",
"y": "-w*x + w*e*y"}
osc.setup(FORMULA, PARAMETERS, INPUTS)
osc.generate_code(debug=False, stochastic = False, gpu = True, variable_length = True, dtype = np.float32)
osc.compile()
x0 = {'x':1,'y':0}
M = 32
freq_list = np.linspace(10,1000,M)
w_list = 2*np.pi*freq_list
params = {'w':w_list,
'e':-0.1}