Re: r3241 - in /branches/multi_processor: maths_fns/mf.py multi/mpi4py_processor.py -- March 27, 2007

Edward d'Auvergne wrote:

Hi,

Gary, why have you changed the 'maths_fns/mf.py' file?

Cheers,

Edward

Hi ed this is a local fix for my own sanity that I checked in by mistake. I am still working out how to revert it ;-) i guess I will have to check out an older revision of the file over it and recommit it?

However it does throw up a couple of questions (if there is iterest I will add these to a new thread)

1. should we have a width limit? It is quite common to have a convention of the maximum width that source code runs to in a program so as to aid legibility(especially for functions such as maths_fns.Mf which has a huge parameter list). is this something we should adopt? 2. not all of the arguments seem to be documented for this function

regards
gary

On 3/27/07, garyt@xxxxxxxxxxxxxxx <garyt@xxxxxxxxxxxxxxx> wrote:
Author: varioustoxins
Date: Tue Mar 27 15:35:16 2007
New Revision: 3241
URL: http://svn.gna.org/viewcvs/relax?rev=3241&view=rev
Log:
installation of simplistic remote minimisation command
Modified:
    branches/multi_processor/maths_fns/mf.py
    branches/multi_processor/multi/mpi4py_processor.py
Modified: branches/multi_processor/maths_fns/mf.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor/maths_fns/mf.py?rev=3241&r1=3240&r2=3241&view=diff

==============================================================================
--- branches/multi_processor/maths_fns/mf.py (original)
+++ branches/multi_processor/maths_fns/mf.py Tue Mar 27 15:35:16 2007
@@ -37,7 +37,11 @@
class Mf: - def __init__(self, init_params=None, param_set=None, diff_type=None, diff_params=None, scaling_matrix=None, num_res=None, equations=None, param_types=None, param_values=None, relax_data=None, errors=None, bond_length=None, csa=None, num_frq=0, frq=None, num_ri=None, remap_table=None, noe_r1_table=None, ri_labels=None, gx=0, gh=0, g_ratio=0, h_bar=0, mu0=0, num_params=None, vectors=None): + def __init__(self, init_params=None, param_set=None, diff_type=None, diff_params=None, + scaling_matrix=None, num_res=None, equations=None, param_types=None, + param_values=None, relax_data=None, errors=None, bond_length=None, + csa=None, num_frq=0, frq=None, num_ri=None, remap_table=None, noe_r1_table=None, + ri_labels=None, gx=0, gh=0, g_ratio=0, h_bar=0, mu0=0, num_params=None, vectors=None): """The model-free minimisation class.
         This class should be initialised before every calculation.
@@ -45,7 +49,8 @@
Arguments ~~~~~~~~~ - + FIXME: widths + FIXME: no arguments equation: The model-free equation string which should be either 'mf_orig' or 'mf_ext'.

param_types: An array of the parameter types used in minimisation. @@ -115,7 +120,7 @@ dthetaj dthetaj

- dNOE() gH 1 / dsigma_noe() dR1() \ + dNOE() gH 1 / dsigma_noe() dR1() \ ------- = -- . ------- . | R1() . ------------ - sigma_noe() . ------- | dthetaj gN R1()**2 \ dthetaj dthetaj /
@@ -141,11 +146,11 @@
         dthetai.dthetaj     dthetai.dthetaj
- d2NOE() gH 1 / / dR1() dR1() d2R1() \ + d2NOE() gH 1 / / dR1() dR1() d2R1() \ --------------- = -- . ------- . | sigma_noe() . | 2 . ------- . ------- - R1() . --------------- | dthetai.dthetaj gN R1()**3 \ \ dthetai dthetaj dthetai.dthetaj /

- / dsigma_noe() dR1() dR1() dsigma_noe() d2sigma_noe() \ \ + / dsigma_noe() dR1() dR1() dsigma_noe() d2sigma_noe() \ \ - R1() . | ------------ . ------- + ------- . ------------ - R1() . --------------- | | \ dthetai dthetaj dthetai dthetaj dthetai.dthetaj / /

@@ -168,7 +173,7 @@ The chi-sqared gradient ~~~~~~~~~~~~~~~~~~~~~~~ _n_ - dChi2 \ / Ri - Ri() dRi() \ + dChi2 \ / Ri - Ri() dRi() \ ------- = -2 > | ---------- . ------- | dthetaj /__ \ sigma_i**2 dthetaj / i=1 @@ -182,7 +187,7 @@ The chi-sqared Hessian ~~~~~~~~~~~~~~~~~~~~~~ _n_ - d2chi2 \ 1 / dRi() dRi() d2Ri() \ + d2chi2 \ 1 / dRi() dRi() d2Ri() \ --------------- = 2 > ---------- | ------- . ------- - (Ri - Ri()) . --------------- | dthetaj.dthetak /__ sigma_i**2 \ dthetaj dthetak dthetaj.dthetak / i=1

Modified: branches/multi_processor/multi/mpi4py_processor.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor/multi/mpi4py_processor.py?rev=3241&r1=3240&r2=3241&view=diff

==============================================================================

--- branches/multi_processor/multi/mpi4py_processor.py (original) +++ branches/multi_processor/multi/mpi4py_processor.py Tue Mar 27 15:35:16 2007 @@ -5,6 +5,9 @@ import os import math
+#FIXME: me move top generic command module
+from maths_fns.mf import Mf
+from minimise.generic import generic_minimise
 # load mpi
 try:
@@ -74,6 +77,7 @@
 NULL_RESULT=Null_result_command()
+ class Slave_command(object): def run(self,processor): pass @@ -92,6 +96,41 @@ msg = processor.get_name() result = Result_string(msg,True) processor.return_object(result) + +class MF_minimise_command(Slave_command): + def __init__(self): + #!! 'a0':1.0,'mu':0.0001,'eta':0.1, + self.minimise_map={'args':(), 'x0':None, 'min_algor':None, 'min_options':None, 'func_tol':1e-25, 'grad_tol':None, + 'maxiter':1e6, 'A':None, 'b':'None', 'l':None, 'u':None, 'c':None, 'dc':None, 'd2c':None, + 'dc':None, 'd2c':None, 'full_output':0, 'print_flag':0, + 'print_prefix':""} + + + + self.mf_map={'init_params':None, 'param_set':None, 'diff_type':None, 'diff_params':None, + 'scaling_matrix':None, 'num_res':None, 'equations':None, 'param_types':None, + 'param_values':None, 'relax_data':None, 'errors':None, 'bond_length':None, + 'csa':None, 'num_frq':0, 'frq':None, 'num_ri':None, 'remap_table':None, 'noe_r1_table':None, + 'ri_labels':None, 'gx':0, 'gh':0, 'g_ratio':0, 'h_bar':0, 'mu0':0, 'num_params':None, 'vectors':None} + + + #FIXME: bad names + def set_mf(self, **kwargs): + self.mf_map.update(**kwargs) + + + def set_minimise(self,**kwargs): + self.minimise_map.update(**kwargs) + + def build_mf(self): + return Mf(**self.mf_map) + + def do_minimise(self): + return generic_minimise(func=self.mf.func, dfunc=self.mf.dfunc, d2func=self.mf.d2func, **self.minimise_map) + + def run(self,processor): + self.mf = self.build_mf() + self.results = generic_minimise(func=self.mf.func, dfunc=self.mf.dfunc, d2func=self.mf.d2func, **self.minimise_map)
 #FIXME do some inheritance
 class Mpi4py_processor:
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--
-------------------------------------------------------------------
Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK             Tel. +44-113-3433024
email: garyt@xxxxxxxxxxxxxxx                   Fax  +44-113-2331407
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Re: r3241 - in /branches/multi_processor: maths_fns/mf.py multi/mpi4py_processor.py

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