Author: bugman
Date: Tue Dec 15 15:19:09 2009
New Revision: 10097
URL: http://svn.gna.org/viewcvs/relax?rev=10097&view=rev
Log:
align_tensor.display() now prints the magnetic susceptibility tensor.
This only occurs if the field strength and temperature are given.
Modified:
1.3/generic_fns/align_tensor.py
Modified: 1.3/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/align_tensor.py?rev=10097&r1=10096&r2=10097&view=diff
==============================================================================
--- 1.3/generic_fns/align_tensor.py (original)
+++ 1.3/generic_fns/align_tensor.py Tue Dec 15 15:19:09 2009
@@ -34,7 +34,7 @@
from angles import wrap_angles
from data.align_tensor import AlignTensorList
from generic_fns import pipes
-from physical_constants import h_bar, mu0, return_gyromagnetic_ratio
+from physical_constants import g1H, h_bar, kB, mu0, return_gyromagnetic_ratio
from relax_errors import RelaxError, RelaxNoTensorError, RelaxStrError,
RelaxTensorError, RelaxUnknownParamCombError, RelaxUnknownParamError
@@ -63,6 +63,32 @@
return True
else:
return False
+
+
+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):
@@ -279,7 +305,7 @@
print(("[%25.12e, %25.12e, %25.12e, %25.12e, %25.12e]\n" %
(data.Pxx, data.Pyy, data.Pxy, data.Pxz, data.Pyz)))
# The parameter set {Pzz, Pxx-yy, Pxy, Pxz, Pyz}.
- print("# 5D, rank-1 notation {Pzz, Pxx-yy, Pxy, Pxz, Pyz} (the Pales
default format).")
+ print("# 5D, rank-1 notation {Pzz, Pxx-yy, Pxy, Pxz, Pyz}.")
print(("[%25.12e, %25.12e, %25.12e, %25.12e, %25.12e]\n" %
(data.Pzz, data.Pxxyy, data.Pxy, data.Pxz, data.Pyz)))
# 3D form.
@@ -287,6 +313,58 @@
print("%s" % data.P)
+ # The magnetic susceptibility tensor.
+ #####################################
+
+ title = "# Magnetic susceptibility tensor."
+ print("\n\n" + title + '\n' + '#'*len(title) + '\n')
+ chi_tensor = True
+
+ # The field strength.
+ print("# The magnetic field strength (MHz):")
+ if hasattr(cdp, 'frq') and tensor in cdp.frq:
+ print(("%s\n" % (cdp.frq[tensor] / 1e6)))
+ else:
+ print(("Not set.\n"))
+ chi_tensor = False
+
+ # The temperature.
+ print("# The temperature (K):")
+ if hasattr(cdp, 'temperature') and tensor in cdp.temperature:
+ print(("%s\n" % cdp.temperature[tensor]))
+ else:
+ print(("Not set.\n"))
+ chi_tensor = False
+
+ # No chi tensor.
+ if not chi_tensor:
+ print("# The chi tensor:\nN/A.\n")
+
+ # Calculate the chi tensor.
+ else:
+ # Conversions.
+ chi_xx = calc_chi_tensor(data.Axx, cdp.frq[tensor],
cdp.temperature[tensor])
+ chi_xy = calc_chi_tensor(data.Axy, cdp.frq[tensor],
cdp.temperature[tensor])
+ chi_xz = calc_chi_tensor(data.Axz, cdp.frq[tensor],
cdp.temperature[tensor])
+ chi_yy = calc_chi_tensor(data.Ayy, cdp.frq[tensor],
cdp.temperature[tensor])
+ chi_yz = calc_chi_tensor(data.Ayz, cdp.frq[tensor],
cdp.temperature[tensor])
+ chi_zz = calc_chi_tensor(data.Azz, cdp.frq[tensor],
cdp.temperature[tensor])
+ chi_xxyy = calc_chi_tensor(data.Axxyy, cdp.frq[tensor],
cdp.temperature[tensor])
+ chi = calc_chi_tensor(data.A, cdp.frq[tensor],
cdp.temperature[tensor])
+
+ # The parameter set {chi_xx, chi_yy, chi_xy, chi_xz, chi_yz}.
+ print("# 5D, rank-1 notation {chi_xx, chi_yy, chi_xy, chi_xz,
chi_yz}:")
+ print(("[%25.12e, %25.12e, %25.12e, %25.12e, %25.12e]\n" %
(chi_xx, chi_yy, chi_xy, chi_xz, chi_yz)))
+
+ # The parameter set {chi_zz, chi_xx-yy, chi_xy, chi_xz, chi_yz}.
+ print("# 5D, rank-1 notation {chi_zz, chi_xx-yy, chi_xy, chi_xz,
chi_yz}.")
+ print(("[%25.12e, %25.12e, %25.12e, %25.12e, %25.12e]\n" %
(chi_zz, chi_xxyy, chi_xy, chi_xz, chi_yz)))
+
+ # 3D form.
+ print("# 3D, rank-2 notation.")
+ print("%s" % chi)
+
+
# The Eigensystem.
##################
@@ -294,10 +372,16 @@
print("\n\n" + title + '\n' + '#'*len(title) + '\n')
# Eigenvalues.
- print("# Eigenvalues {Sxx, Syy, Szz}.")
+ print("# Saupe order matrix eigenvalues {Sxx, Syy, Szz}.")
print(("[%25.12e, %25.12e, %25.12e]\n" % (data.S_diag[0, 0],
data.S_diag[1, 1], data.S_diag[2, 2])))
- print("# Eigenvalues {Axx, Ayy, Azz}.")
+ print("# Alignment tensor eigenvalues {Axx, Ayy, Azz}.")
print(("[%25.12e, %25.12e, %25.12e]\n" % (data.A_diag[0, 0],
data.A_diag[1, 1], data.A_diag[2, 2])))
+ print("# Probability tensor eigenvalues {Pxx, Pyy, Pzz}.")
+ print(("[%25.12e, %25.12e, %25.12e]\n" % (data.P_diag[0, 0],
data.P_diag[1, 1], data.P_diag[2, 2])))
+ if chi_tensor:
+ chi_diag = calc_chi_tensor(data.A_diag, cdp.frq[tensor],
cdp.temperature[tensor])
+ print("# Magnetic susceptibility eigenvalues {chi_xx, chi_yy,
chi_zz}.")
+ print(("[%25.12e, %25.12e, %25.12e]\n" % (chi_diag[0, 0],
chi_diag[1, 1], chi_diag[2, 2])))
# Eigenvectors.
print("# Eigenvector x.")
@@ -323,7 +407,7 @@
print("\n\n" + title + '\n' + '#'*len(title) + '\n')
# Anisotropy.
- print("# Axial component (Aa = 3/2 * Azz, where Aii are the
eigenvalues).")
+ print("# Alignment tensor axial component (Aa = 3/2 * Azz, where Aii
are the eigenvalues).")
print("Aa = %-25.12e\n" % data.Aa)
# Rhombicity.
@@ -333,6 +417,16 @@
print("R = %-25.12f\n" % data.R)
print("# Asymmetry parameter (eta = (Axx - Ayy) / Azz, where Aii are
the eigenvalues).")
print("eta = %-25.12f\n" % data.eta)
+
+ # Magnetic susceptibility tensor.
+ if chi_tensor:
+ # Chi tensor anisotropy.
+ print("# Magnetic susceptibility axial parameter (chi_ax =
chi_zz - (chi_xx + chi_yy)/2, where chi_ii are the eigenvalues).")
+ print("chi_ax = %-25.12e\n" % (chi_diag[2, 2] - (chi_diag[0, 0]
+ chi_diag[1, 1])/2.0))
+
+ # Chi tensor rhombicity.
+ print("# Magnetic susceptibility rhombicity parameter (chi_rh =
chi_xx - chi_yy, where chi_ii are the eigenvalues).")
+ print("chi_rh = %-25.12e\n" % (chi_diag[0, 0] - chi_diag[1, 1]))
# Some white space.
print("\n\n\n")
r10097 - /1.3/generic_fns/align_tensor.py