Author: bugman
Date: Tue Mar 26 11:43:52 2013
New Revision: 19155
URL: http://svn.gna.org/viewcvs/relax?rev=19155&view=rev
Log:
Shifted calc_chi_tensor() and kappa() from pipe_control.align_tensor to
lib.alignment.alignment_tensor.
Modified:
trunk/lib/alignment/alignment_tensor.py
trunk/pipe_control/align_tensor.py
Modified: trunk/lib/alignment/alignment_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/alignment/alignment_tensor.py?rev=19155&r1=19154&r2=19155&view=diff
==============================================================================
--- trunk/lib/alignment/alignment_tensor.py (original)
+++ trunk/lib/alignment/alignment_tensor.py Tue Mar 26 11:43:52 2013
@@ -25,6 +25,35 @@
# Python imports.
from numpy.linalg import eigvals
+# relax module imports.
+from lib.physical_constants import g1H, h_bar, kB, mu0,
return_gyromagnetic_ratio
+
+
+def calc_chi_tensor(A, B0, T):
+ """Convert the alignment tensor into the magnetic susceptibility (chi)
tensor.
+
+ A can be either the full tensor (3D or 5D), a component Aij of the
tensor, Aa, or Ar, anything that can be multiplied by the constants to
convert from one to the other.
+
+
+ @param A: The alignment tensor or alignment tensor component.
+ @type A: numpy array or float
+ @param B0: The magnetic field strength in Hz.
+ @type B0: float
+ @param T: The temperature in Kalvin.
+ @type T: float
+ @return: A multiplied by the PCS constant.
+ @rtype: numpy array or float
+ """
+
+ # B0 in Tesla.
+ B0 = 2.0 * pi * B0 / g1H
+
+ # The conversion factor.
+ conv = 15.0 * mu0 * kB * T / B0**2
+
+ # Return the converted value.
+ return conv * A
+
def dAi_dAxx(A):
"""The dAi/dAxx gradient.
@@ -124,6 +153,32 @@
A[0, 0] = 0.0; A[0, 1] = 0.0; A[0, 2] = 0.0
A[1, 0] = 0.0; A[1, 1] = 0.0; A[1, 2] = 1.0
A[2, 0] = 0.0; A[2, 1] = 1.0; A[2, 2] = 0.0
+
+
+def kappa(nuc1='15N', nuc2='1H'):
+ """Function for calculating the kappa constant.
+
+ The kappa constant is::
+
+ kappa = -3/(8pi^2).gI.gS.mu0.h_bar,
+
+ where gI and gS are the gyromagnetic ratios of the I and S spins, mu0 is
the permeability of
+ free space, and h_bar is Planck's constant divided by 2pi.
+
+ @param nuc1: The first nucleus type.
+ @type nuc1: str
+ @param nuc2: The first nucleus type.
+ @type nuc2: str
+ @return: The kappa constant value.
+ @rtype: float
+ """
+
+ # Gyromagnetic ratios.
+ gI = return_gyromagnetic_ratio(nuc1)
+ gS = return_gyromagnetic_ratio(nuc2)
+
+ # Kappa.
+ return -3.0/(8.0*pi**2) * gI * gS * mu0 * h_bar
def maxA(tensor):
Modified: trunk/pipe_control/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/align_tensor.py?rev=19155&r1=19154&r2=19155&view=diff
==============================================================================
--- trunk/pipe_control/align_tensor.py (original)
+++ trunk/pipe_control/align_tensor.py Tue Mar 26 11:43:52 2013
@@ -35,7 +35,7 @@
from data_store.align_tensor import AlignTensorList
from pipe_control.angles import wrap_angles
from pipe_control import pipes
-from lib.physical_constants import g1H, h_bar, kB, mu0,
return_gyromagnetic_ratio
+from lib.alignment.alignment_tensor import calc_chi_tensor, kappa
from lib.errors import RelaxError, RelaxNoTensorError, RelaxStrError,
RelaxTensorError, RelaxUnknownParamCombError, RelaxUnknownParamError
from lib.io import write_data
from lib.warnings import RelaxWarning
@@ -83,32 +83,6 @@
# All tensors are fixed.
return True
-
-
-def calc_chi_tensor(A, B0, T):
- """Convert the alignment tensor into the magnetic susceptibility (chi)
tensor.
-
- A can be either the full tensor (3D or 5D), a component Aij of the
tensor, Aa, or Ar, anything that can be multiplied by the constants to
convert from one to the other.
-
-
- @param A: The alignment tensor or alignment tensor component.
- @type A: numpy array or float
- @param B0: The magnetic field strength in Hz.
- @type B0: float
- @param T: The temperature in Kalvin.
- @type T: float
- @return: A multiplied by the PCS constant.
- @rtype: numpy array or float
- """
-
- # B0 in Tesla.
- B0 = 2.0 * pi * B0 / g1H
-
- # The conversion factor.
- conv = 15.0 * mu0 * kB * T / B0**2
-
- # Return the converted value.
- return conv * A
def copy(tensor_from=None, pipe_from=None, tensor_to=None, pipe_to=None):
@@ -988,32 +962,6 @@
return [0, 2*pi]
-def kappa(nuc1='15N', nuc2='1H'):
- """Function for calculating the kappa constant.
-
- The kappa constant is::
-
- kappa = -3/(8pi^2).gI.gS.mu0.h_bar,
-
- where gI and gS are the gyromagnetic ratios of the I and S spins, mu0 is
the permeability of
- free space, and h_bar is Planck's constant divided by 2pi.
-
- @param nuc1: The first nucleus type.
- @type nuc1: str
- @param nuc2: The first nucleus type.
- @type nuc2: str
- @return: The kappa constant value.
- @rtype: float
- """
-
- # Gyromagnetic ratios.
- gI = return_gyromagnetic_ratio(nuc1)
- gS = return_gyromagnetic_ratio(nuc2)
-
- # Kappa.
- return -3.0/(8.0*pi**2) * gI * gS * mu0 * h_bar
-
-
def map_labels(index, params, bounds, swap, inc):
"""Function for creating labels, tick locations, and tick values for an
OpenDX map.
r19155 - in /trunk: lib/alignment/alignment_tensor.py pipe_control/align_tensor.py