Author: bugman
Date: Mon Sep 22 11:52:24 2014
New Revision: 25948
URL: http://svn.gna.org/viewcvs/relax?rev=25948&view=rev
Log:
Created the backend framework for the frame_order.simulate user function.
The backend specific_analyses.frame_order.uf.simulate() function performs all
data checks required,
prepares the output file object, assembles the frame order parameter values and
pivot point, and
creates a copy of the structural object object with the ensemble collapsed into
a single model.
All this data is then passed into the new lib.frame_order.simulation.brownian()
function. This
initialises all required data structures and the structural object. The main
loop of the simulation
is also implemented, taking snapshots at every fixed number of steps and
terminating the loop once
the total number of snapshots are reached. The snapshot consists of copying
the original unrotated
structural model and rotating it into the new position. The rotation is
currently the identity
matrix.
The old specific_analyses.frame_order.geometric.create_distribution() stub
function has been
deleted.
Added:
branches/frame_order_cleanup/lib/frame_order/simulation.py
Modified:
branches/frame_order_cleanup/lib/frame_order/__init__.py
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
Modified: branches/frame_order_cleanup/lib/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/__init__.py?rev=25948&r1=25947&r2=25948&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/__init__.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/__init__.py Mon Sep 22
11:52:24 2014
@@ -34,5 +34,6 @@
'pseudo_ellipse_free_rotor',
'pseudo_ellipse',
'pseudo_ellipse_torsionless',
- 'rotor'
+ 'rotor',
+ 'simulation'
]
Added: branches/frame_order_cleanup/lib/frame_order/simulation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/simulation.py?rev=25948&view=auto
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/simulation.py (added)
+++ branches/frame_order_cleanup/lib/frame_order/simulation.py Mon Sep 22
11:52:24 2014
@@ -0,0 +1,101 @@
+###############################################################################
+# #
+# Copyright (C) 2014 Edward d'Auvergne #
+# #
+# This file is part of the program relax (http://www.nmr-relax.com). #
+# #
+# This program is free software: you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License as published by #
+# the Free Software Foundation, either version 3 of the License, or #
+# (at your option) any later version. #
+# #
+# This program is distributed in the hope that it will be useful, #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details. #
+# #
+# You should have received a copy of the GNU General Public License #
+# along with this program. If not, see <http://www.gnu.org/licenses/>. #
+# #
+###############################################################################
+
+# Module docstring.
+"""Module for simulating the frame order motions."""
+
+# Python module imports.
+from numpy import eye, float64
+import sys
+
+# relax module imports.
+from lib.errors import RelaxError
+
+
+def brownian(file=None, model=None, structure=None, parameters={}, pivot=None,
step_size=2.0, snapshot=10, total=1000):
+ """Pseudo-Brownian dynamics simulation of the frame order motions.
+
+ @keyword file: The opened and writable file object to place the
snapshots into.
+ @type file: str
+ @keyword structure: The internal structural object containing the
domain to simulate as a single model.
+ @type structure: lib.structure.internal.object.Internal instance
+ @keyword model: The frame order model to simulate.
+ @type model: str
+ @keyword parameters: The dictionary of model parameter values. The key
is the parameter name and the value is the value.
+ @type parameters: dict of float
+ @keyword pivot: The pivot point of the frame order motions.
+ @type pivot: numpy rank-1, 3D float64 array
+ @keyword step_size: The rotation will be of a random direction but
with this fixed angle. The value is in degrees.
+ @type step_size: float
+ @keyword snapshot: The number of steps in the simulation when
snapshots will be taken.
+ @type snapshot: int
+ @keyword total: The total number of snapshots to take before
stopping the simulation.
+ @type total: int
+ """
+
+ # Check the structural object.
+ if structure.num_models() > 1:
+ raise RelaxError("Only a single model is supported.")
+
+ # Set the model number.
+ structure.set_model(model_orig=None, model_new=1)
+
+ # The initial state.
+ state = eye(3, dtype=float64)
+
+ # Initialise the rotation matrix.
+ R = eye(3, dtype=float64)
+
+ # Printout.
+ print("\nRunning the simulation:")
+
+ # Simulate.
+ current_snapshot = 1
+ step = 1
+ while 1:
+ # End the simulation.
+ if current_snapshot == total:
+ print("\nEnd of simulation.")
+ break
+
+ # Take a snapshot.
+ if step == snapshot:
+ # Progress.
+ sys.stdout.write('.')
+ sys.stdout.flush()
+
+ # Increment the snapshot number.
+ current_snapshot += 1
+
+ # Copy the original structural data.
+ structure.add_model(model=current_snapshot, coords_from=1)
+
+ # Rotate the model.
+ structure.rotate(R=R, origin=pivot, model=current_snapshot,
atom_id=None)
+
+ # Reset the step counter.
+ step = 0
+
+ # Increment.
+ step += 1
+
+ # Save the result.
+ structure.write_pdb(file=file)
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py?rev=25948&r1=25947&r2=25948&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Mon Sep 22 11:52:24 2014
@@ -646,27 +646,6 @@
pdb_file.close()
-def create_distribution(format='PDB', file=None, dir=None, compress_type=0,
model=1, force=False):
- """Create a PDB file of a distribution of positions coving the full
dynamics of the moving domain.
-
- @keyword format: The format for outputting the geometric
representation. Currently only the 'PDB' format is supported.
- @type format: str
- @keyword file: The name of the file which will contain multiple
models spanning the full dynamics distribution of the frame order model.
- @type file: str
- @keyword dir: The name of the directory to place the PDB file
into.
- @type dir: str
- @keyword compress_type: The compression type. The integer values
correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2,
Gzip compression.
- @type compress_type: int
- @keyword model: Only one model from an analysed ensemble can be
used for the PDB representation of the Monte Carlo simulations, as these
consists of one model per simulation.
- @type model: int
- @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
- @type force: bool
- """
-
- # Printout.
- subsection(file=sys.stdout, text="Creating a PDB file of a distribution of
positions coving the full dynamics of the moving domain.")
-
-
def create_geometric_rep(format='PDB', file=None, dir=None, compress_type=0,
size=30.0, inc=36, force=False):
"""Create a PDB file containing a geometric object representing the frame
order dynamics.
Modified: branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py?rev=25948&r1=25947&r2=25948&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Mon Sep
22 11:52:24 2014
@@ -23,6 +23,7 @@
"""Module for all of the frame order specific user functions."""
# Python module imports.
+from copy import deepcopy
from math import pi
from numpy import array, cross, float64, ones, transpose, zeros
from numpy.linalg import norm
@@ -32,14 +33,16 @@
from lib.arg_check import is_float_array
from lib.check_types import is_float
from lib.errors import RelaxError, RelaxFault
+from lib.frame_order.simulation import brownian
from lib.geometry.coord_transform import cartesian_to_spherical,
spherical_to_cartesian
from lib.geometry.rotations import euler_to_R_zyz, R_to_euler_zyz
+from lib.io import open_write_file
from lib.warnings import RelaxWarning
from pipe_control import pipes
-from specific_analyses.frame_order.checks import check_domain
-from specific_analyses.frame_order.geometric import create_ave_pos,
create_distribution, create_geometric_rep
+from specific_analyses.frame_order.checks import check_domain, check_model,
check_parameters, check_pivot
+from specific_analyses.frame_order.geometric import create_ave_pos,
create_geometric_rep
from specific_analyses.frame_order.optimisation import count_sobol_points
-from specific_analyses.frame_order.parameters import update_model
+from specific_analyses.frame_order.parameters import assemble_param_vector,
update_model
from specific_analyses.frame_order.variables import MODEL_ISO_CONE,
MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS, MODEL_LIST,
MODEL_LIST_FREE_ROTORS, MODEL_LIST_ISO_CONE, MODEL_LIST_PSEUDO_ELLIPSE,
MODEL_LIST_RESTRICTED_TORSION, MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID
@@ -382,8 +385,34 @@
@type force: bool
"""
+ # Checks.
+ pipes.test()
+ check_model()
+ check_domain()
+ check_parameters()
+ check_pivot()
+
+ # Open the output file.
+ file = open_write_file(file_name=file, dir=dir, force=force)
+
+ # The parameter values.
+ values = assemble_param_vector()
+ params = {}
+ i = 0
+ for name in cdp.params:
+ params[name] = values[i]
+ i += 1
+
+ # The structure.
+ structure = deepcopy(cdp.structure)
+ if structure.num_models() > 1:
+ structure.collapse_ensemble(model_num=model)
+
+ # The pivot point.
+ pivot = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z], float64)
+
# Create the distribution.
- create_distribution(file=file, dir=dir, model=model, force=force)
+ brownian(file=file, model=cdp.model, structure=structure,
parameters=params, pivot=pivot, step_size=step_size, snapshot=snapshot,
total=total)
def sobol_setup(max_num=200, oversample=100):
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