Author: bugman
Date: Sat Jun 2 19:30:35 2012
New Revision: 16601
URL: http://svn.gna.org/viewcvs/relax?rev=16601&view=rev
Log:
The Monte Carlo description now uses an itemised list for the listing of the
steps involved.
Modified:
branches/uf_redesign/user_functions/monte_carlo.py
Modified: branches/uf_redesign/user_functions/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/user_functions/monte_carlo.py?rev=16601&r1=16600&r2=16601&view=diff
==============================================================================
--- branches/uf_redesign/user_functions/monte_carlo.py (original)
+++ branches/uf_redesign/user_functions/monte_carlo.py Sat Jun 2 19:30:35
2012
@@ -33,14 +33,14 @@
# Generic description document, used in all user functions.
monte_carlo_desc = Desc_container("Monte Carlo Simulation Overview")
monte_carlo_desc.add_paragraph("For proper error analysis using Monte Carlo
simulations, a sequence of function calls is required for running the various
simulation components. The steps necessary for implementing Monte Carlo
simulations are:")
-monte_carlo_desc.add_list_element("1. The measured data set together with
the corresponding error set should be loaded into relax.")
-monte_carlo_desc.add_list_element("2. Either minimisation is used to
optimise the parameters of the chosen model, or a calculation is run.")
-monte_carlo_desc.add_list_element("3. To initialise and turn on Monte Carlo
simulations, the number of simulations, n, needs to be set.")
-monte_carlo_desc.add_list_element("4. The simulation data needs to be
created either by back calculation from the fully minimised model parameters
from step 2 or by direct calculation when values are calculated rather than
minimised. The error set is used to randomise each simulation data set by
assuming Gaussian errors. This creates a synthetic data set for each Monte
Carlo simulation.")
-monte_carlo_desc.add_list_element("5. Prior to minimisation of the
parameters of each simulation, initial parameter estimates are required.
These are taken as the optimised model parameters. An alternative is to use
a grid search for each simulation to generate initial estimates, however this
is extremely computationally expensive. For the case where values are
calculated rather than minimised, this step should be skipped (although the
results will be unaffected if this is accidentally run).")
-monte_carlo_desc.add_list_element("6. Each simulation requires minimisation
or calculation. The same techniques as used in step 2, excluding the grid
search when minimising, should be used for the simulations.")
-monte_carlo_desc.add_list_element("7. Failed simulations are removed using
the techniques of model elimination.")
-monte_carlo_desc.add_list_element("8. The model parameter errors are
calculated from the distribution of simulation parameters.")
+monte_carlo_desc.add_item_list_element("1", "The measured data set together
with the corresponding error set should be loaded into relax.")
+monte_carlo_desc.add_item_list_element("2", "Either minimisation is used to
optimise the parameters of the chosen model, or a calculation is run.")
+monte_carlo_desc.add_item_list_element("3", "To initialise and turn on Monte
Carlo simulations, the number of simulations, n, needs to be set.")
+monte_carlo_desc.add_item_list_element("4", "The simulation data needs to be
created either by back calculation from the fully minimised model parameters
from step 2 or by direct calculation when values are calculated rather than
minimised. The error set is used to randomise each simulation data set by
assuming Gaussian errors. This creates a synthetic data set for each Monte
Carlo simulation.")
+monte_carlo_desc.add_item_list_element("5", "Prior to minimisation of the
parameters of each simulation, initial parameter estimates are required.
These are taken as the optimised model parameters. An alternative is to use
a grid search for each simulation to generate initial estimates, however this
is extremely computationally expensive. For the case where values are
calculated rather than minimised, this step should be skipped (although the
results will be unaffected if this is accidentally run).")
+monte_carlo_desc.add_item_list_element("6", "Each simulation requires
minimisation or calculation. The same techniques as used in step 2,
excluding the grid search when minimising, should be used for the
simulations.")
+monte_carlo_desc.add_item_list_element("7", "Failed simulations are removed
using the techniques of model elimination.")
+monte_carlo_desc.add_item_list_element("8", "The model parameter errors are
calculated from the distribution of simulation parameters.")
monte_carlo_desc.add_paragraph("Monte Carlo simulations can be turned on or
off using functions within this class. Once the function for setting up
simulations has been called, simulations will be turned on. The effect of
having simulations turned on is that the functions used for minimisation
(grid search, minimise, etc) or calculation will only affect the simulation
parameters and not the model parameters. By subsequently turning simulations
off using the appropriate function, the functions used in minimisation will
affect the model parameters and not the simulation parameters.")
monte_carlo_desc.add_paragraph("An example for model-free analysis using the
prompt UI mode which includes only the functions required for implementing
the above steps is:")
monte_carlo_desc.add_prompt("relax> grid_search(inc=11)
# Step 2.")
r16601 - /branches/uf_redesign/user_functions/monte_carlo.py