Python Optimisation_settings Exemples

Exemple #1

Fichier : full_analysis.py Projet : pombredanne/relax

# The frame order models to use.
MODELS = [
    'rigid',
    'rotor',
    'iso cone',
    'pseudo-ellipse',
    'iso cone, torsionless',
    'pseudo-ellipse, torsionless',
    'double rotor'
]

# The number of Monte Carlo simulations to be used for error analysis at the end of the protocol.
MC_NUM = 10

# Rigid model optimisation setup.
OPT_RIGID = Optimisation_settings()
OPT_RIGID.add_grid(inc=21, zoom=0)
OPT_RIGID.add_grid(inc=21, zoom=1)
OPT_RIGID.add_grid(inc=21, zoom=2)
OPT_RIGID.add_grid(inc=21, zoom=3)
OPT_RIGID.add_min(min_algor='simplex')

# PCS subset optimisation setup.
OPT_SUBSET = Optimisation_settings()
OPT_SUBSET.add_grid(inc=11, zoom=0, sobol_max_points=100)
OPT_SUBSET.add_grid(inc=11, zoom=1, sobol_max_points=100)
OPT_SUBSET.add_grid(inc=11, zoom=2, sobol_max_points=100)
OPT_SUBSET.add_min(min_algor='simplex', func_tol=1e-2, sobol_max_points=100)

# Full data set optimisation setup.
OPT_FULL = Optimisation_settings()

Exemple #2

Fichier : refinement.py Projet : pombredanne/relax

# The frame order models to use.
MODELS = [
    'rigid',
    'rotor',
    'iso cone',
    'pseudo-ellipse',
    'iso cone, torsionless',
    'pseudo-ellipse, torsionless',
    'double rotor'
]

# The number of Monte Carlo simulations to be used for error analysis at the end of the protocol.
MC_NUM = 10

# Full data set optimisation setup.
OPT_FULL = Optimisation_settings()
OPT_FULL.add_min(min_algor='simplex', func_tol=1e-4, quad_int=True)

# Monte Carlo simulation optimisation setup.
OPT_MC = Optimisation_settings()
OPT_MC.add_min(min_algor='simplex', func_tol=1e-3, quad_int=True)


# Set up the base data pipes.
#############################

# The data pipe bundle to group all data pipes.
PIPE_BUNDLE = "Frame Order (%s)" % asctime(localtime())


# Execution.

Exemple #3

Fichier : auto_analysis_to_rigid.py Projet : pombredanne/relax

    'rigid',
    'free rotor',
    'rotor',
    'iso cone, torsionless',
    'iso cone, free rotor',
    'iso cone',
    'pseudo-ellipse, torsionless',
    'pseudo-ellipse',
    'double rotor'
]

# The number of Monte Carlo simulations to be used for error analysis at the end of the protocol.
MC_NUM = 3

# Rigid model optimisation setup.
OPT_RIGID = Optimisation_settings()
OPT_RIGID.add_grid(inc=8, zoom=0)
OPT_RIGID.add_min(min_algor='simplex', func_tol=1e-2, max_iter=20)

# PCS subset optimisation setup.
OPT_SUBSET = Optimisation_settings()
OPT_SUBSET.add_grid(inc=2, sobol_max_points=1)
OPT_SUBSET.add_min(min_algor='simplex', func_tol=1e-2, max_iter=5, sobol_max_points=1)

# Full data set optimisation setup.
OPT_FULL = Optimisation_settings()
OPT_FULL.add_grid(inc=2, sobol_max_points=1)
OPT_FULL.add_min(min_algor='simplex', func_tol=1e-2, max_iter=5, sobol_max_points=1)

# Monte Carlo simulation optimisation setup.
OPT_MC = Optimisation_settings()

Exemple #4

    'rigid',
    'free rotor',
    'rotor',
    'iso cone, torsionless',
    'iso cone, free rotor',
    'iso cone',
    'pseudo-ellipse, torsionless',
    'pseudo-ellipse',
    'double rotor'
]

# The number of Monte Carlo simulations to be used for error analysis at the end of the protocol.
MC_NUM = 100

# Rigid model optimisation setup.
OPT_RIGID = Optimisation_settings()
OPT_RIGID.add_grid(inc=11, zoom=0, num_int_pts=50)
OPT_RIGID.add_grid(inc=11, zoom=1, num_int_pts=50)
OPT_RIGID.add_grid(inc=11, zoom=2, num_int_pts=50)
OPT_RIGID.add_min(min_algor='simplex', func_tol=1e-2)

# PCS subset optimisation setup.
OPT_SUBSET = Optimisation_settings()
OPT_SUBSET.add_grid(inc=11, num_int_pts=100)
OPT_SUBSET.add_min(min_algor='simplex', func_tol=1e-2, num_int_pts=100)

# Full data set optimisation setup.
OPT_FULL = Optimisation_settings()
OPT_FULL.add_grid(inc=11, num_int_pts=100)
OPT_FULL.add_min(min_algor='simplex', func_tol=1e-2, num_int_pts=100)
OPT_FULL.add_min(min_algor='simplex', func_tol=1e-3, num_int_pts=1000)

Exemple #5

Fichier : refinement.py Projet : tlinnet/relax

from auto_analyses.frame_order import Frame_order_analysis, Optimisation_settings

# Analysis variables.
#####################

# The frame order models to use.
MODELS = [
    'rigid', 'rotor', 'iso cone', 'pseudo-ellipse', 'iso cone, torsionless',
    'pseudo-ellipse, torsionless', 'double rotor'
]

# The number of Monte Carlo simulations to be used for error analysis at the end of the protocol.
MC_NUM = 10

# Full data set optimisation setup.
OPT_FULL = Optimisation_settings()
OPT_FULL.add_min(min_algor='simplex', func_tol=1e-4, quad_int=True)

# Monte Carlo simulation optimisation setup.
OPT_MC = Optimisation_settings()
OPT_MC.add_min(min_algor='simplex', func_tol=1e-3, quad_int=True)

# Set up the base data pipes.
#############################

# The data pipe bundle to group all data pipes.
PIPE_BUNDLE = "Frame Order (%s)" % asctime(localtime())

# Execution.
############

Exemple #6

Fichier : auto_analysis_to_rigid.py Projet : tlinnet/relax

# Analysis variables.
#####################

# The frame order models to use.
MODELS = [
    'rigid', 'free rotor', 'rotor', 'iso cone, torsionless',
    'iso cone, free rotor', 'iso cone', 'pseudo-ellipse, torsionless',
    'pseudo-ellipse', 'double rotor'
]

# The number of Monte Carlo simulations to be used for error analysis at the end of the protocol.
MC_NUM = 3

# Rigid model optimisation setup.
OPT_RIGID = Optimisation_settings()
OPT_RIGID.add_grid(inc=8, zoom=0)
OPT_RIGID.add_min(min_algor='simplex', func_tol=1e-2, max_iter=20)

# PCS subset optimisation setup.
OPT_SUBSET = Optimisation_settings()
OPT_SUBSET.add_grid(inc=2, sobol_max_points=1)
OPT_SUBSET.add_min(min_algor='simplex',
                   func_tol=1e-2,
                   max_iter=5,
                   sobol_max_points=1)

# Full data set optimisation setup.
OPT_FULL = Optimisation_settings()
OPT_FULL.add_grid(inc=2, sobol_max_points=1)
OPT_FULL.add_min(min_algor='simplex',

Exemple #7

Fichier : full_analysis.py Projet : pombredanne/relax

    'rigid',
    'free rotor',
    'rotor',
    'iso cone, torsionless',
    'iso cone, free rotor',
    'iso cone',
    'pseudo-ellipse, torsionless',
    'pseudo-ellipse',
    'double rotor'
]

# The number of Monte Carlo simulations to be used for error analysis at the end of the protocol.
MC_NUM = 100

# Rigid model optimisation setup.
OPT_RIGID = Optimisation_settings()
OPT_RIGID.add_grid(inc=11, zoom=0, num_int_pts=50)
OPT_RIGID.add_grid(inc=11, zoom=1, num_int_pts=50)
OPT_RIGID.add_grid(inc=11, zoom=2, num_int_pts=50)
OPT_RIGID.add_min(min_algor='simplex', func_tol=1e-2)

# PCS subset optimisation setup.
OPT_SUBSET = Optimisation_settings()
OPT_SUBSET.add_grid(inc=11, num_int_pts=100)
OPT_SUBSET.add_min(min_algor='simplex', func_tol=1e-2, num_int_pts=100)

# Full data set optimisation setup.
OPT_FULL = Optimisation_settings()
OPT_FULL.add_grid(inc=11, num_int_pts=100)
OPT_FULL.add_min(min_algor='simplex', func_tol=1e-2, num_int_pts=100)
OPT_FULL.add_min(min_algor='simplex', func_tol=1e-3, num_int_pts=1000)

Exemple #8

# The frame order models to use.
MODELS = [
    'rigid',
    'rotor',
    'iso cone',
    'pseudo-ellipse',
    'iso cone, torsionless',
    'pseudo-ellipse, torsionless',
    'double rotor'
]

# The number of Monte Carlo simulations to be used for error analysis at the end of the protocol.
MC_NUM = 10

# Rigid model optimisation setup.
OPT_RIGID = Optimisation_settings()
OPT_RIGID.add_grid(inc=21, zoom=0)
OPT_RIGID.add_grid(inc=21, zoom=1)
OPT_RIGID.add_grid(inc=21, zoom=2)
OPT_RIGID.add_grid(inc=21, zoom=3)
OPT_RIGID.add_min(min_algor='simplex')

# PCS subset optimisation setup.
OPT_SUBSET = Optimisation_settings()
OPT_SUBSET.add_grid(inc=11, zoom=0, sobol_max_points=100)
OPT_SUBSET.add_grid(inc=11, zoom=1, sobol_max_points=100)
OPT_SUBSET.add_grid(inc=11, zoom=2, sobol_max_points=100)
OPT_SUBSET.add_min(min_algor='simplex', func_tol=1e-2, sobol_max_points=100)

# Full data set optimisation setup.
OPT_FULL = Optimisation_settings()