def main():
sc = [0.05, 0.05, 10.0]
ns, ms = [], []
md1s, md2s = [], []
ints = []
end = '0'
while end == '0':
ns.append(int(input("Input N: ")))
ms.append(int(input("Input M: ")))
p = float(input("Enter parameter (tao): "))
md1s.append(
int(input("Outer integration mode (0 - Gauss, 1 - Simpson): ")))
md2s.append(
int(input("Inner integration mode (0 - Gauss, 1 - Simpson): ")))
lm = [[0, pi / 2], [0, pi / 2]]
ints.append(
inter.Integrator(lm, [ns[-1], ms[-1]], [md1s[-1], md2s[-1]]))
print("Result with {:.2f} as "
"a parameter is {:.7f}".format(p, ints[-1](p)))
end = input("Stop execution?: ")
plot.plot(ints, sc, ns, ms, md1s, md2s)
if not os.path.exists(newpath):
os.makedirs(newpath)
newpath = os.path.join(os.getcwd(), dataFileNameEigenVectors)
if not os.path.exists(newpath):
os.makedirs(newpath)
newpath = os.path.join(os.getcwd(), dataFileEnergy)
if not os.path.exists(newpath):
os.makedirs(newpath)
# simulation class sampler takes integrator class with chosen parameters as input
integrator = integrator.Integrator(model=mdl,
gamma=gamma,
temperature=temperature,
temperatureAlpha=temperatureAlpha,
dt=dt,
massScale=massScale,
gammaScale=gammaScale,
kappaScale=kappaScale)
## load initial condition from file
# IC = md.load('alanine_start_state_IC.h5')
# # remove first dimension - the intial condition has shape (1,nrParticles, spaceDimension) when taken from trajectory
# InitialPosition = np.squeeze(IC.xyz)
# integrator.x0 = InitialPosition * mdl.x_unit
general_sampler = sampler.Sampler(
model=mdl,
integrator=integrator,
algorithm=iAlgo,
diffusionMapMetric=diffMapMetric,
Returns
-------
Float for P/P_e
"""
Term1 = 4.0 / (math.pi**2)
Term2 = intg.get(f2, 0, math.pi / 2.0, 1e-6, alpha)**2
return Term1 * Term2
if __name__ == '__main__':
print("Solve for alpha")
intg = I.Integrator(I.gaussian2, I.gaussian4)
ListA = []
ListX = []
ListY = []
ListP = []
table = PrettyTable(["X_g/L", "alpha", "Y_b/L", "P/P_e"])
for XgOnL in (0.99, 0.95, 0.9, 0.5, 0):
ListX.append(XgOnL)
ListA.append(
solvebisect(optimiseXgOnL, 0.01, limit * math.pi, 1e-6, XgOnL,
intg))
ListY.append(getYbOnL(ListA[-1], intg))
ListP.append(getPOnPe(ListA[-1], intg))
type=int,
default=1,
help='Stride the trajectory modulo modnr.')
args = parser.parse_args()
# folder where the data is saved
dataFolderName = args.dataFolder
nrSteps = args.nrSteinSteps
steinStepSize = args.steinStepSize
modnr = args.modnr
# intialize sampler class together wuth the model
mdl = model.Model('Alanine')
intg = integrator.Integrator(model=mdl,
gamma=1.0 / unit.picosecond,
temperature=300 * unit.kelvin,
dt=2.0 * unit.femtosecond,
temperatureAlpha=300 * unit.kelvin)
smpl = sampler.Sampler(model=mdl,
integrator=intg,
algorithm=0,
dataFileName='Data')
# stein
st = stein.Stein(smpl, dataFolderName, modnr=modnr)
# change the stein step size
st.epsilon_step = unit.Quantity(steinStepSize, smpl.model.x_unit)**2
print('Running steinIS on ' + repr(len(st.qInit)) + ' points')
np.save(dataFolderName + '/stein_initial.npy', st.qInit)
#run stein
# X0=mdl.testsystem.positions.value_in_unit(mdl.x_unit)
temperature = T * unit.kelvin#300 * unit.kelvin
gamma = 1.0 / unit.picosecond
dt = 2.0 * unit.femtosecond
temperatureAlpha= (T)* unit.kelvin
# simulation class sampler takes integrator class with chosen parameters as input
integrator=integrator.Integrator( model=mdl, gamma=gamma, temperature=temperature, dt=dt, temperatureAlpha=temperatureAlpha)
smpl=sampler.Sampler(model=mdl, integrator=integrator, algorithm=0, dataFileName='Data')
newpath = os.path.join(os.getcwd(),simulationFolder)
if not os.path.exists(newpath):
os.makedirs(newpath)
X_FT = helpers.loadData(folderName+dataName+'/'+modelName+'/'+methodName+'/Traj/*.h5', mdl.testsystem.topology)
X_FT=X_FT[::modnr]
print('Data length is '+repr(len(X_FT)))
#compute collective variable
r=colective_variable(X_FT)