Author: tlinnet
Date: Fri Jun 20 19:13:14 2014
New Revision: 24217
URL: http://svn.gna.org/viewcvs/relax?rev=24217&view=rev
Log:
Renamed some numerical matrices, to get consistency in naming.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/lib/dispersion/ns_matrices.py
branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
Modified: branches/disp_spin_speed/lib/dispersion/ns_matrices.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_matrices.py?rev=24217&r1=24216&r2=24217&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_matrices.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_matrices.py Fri Jun 20
19:13:14 2014
@@ -700,6 +700,194 @@
+ m_k_AB_tcp + m_k_BA_tcp + m_k_BC_tcp
+ m_k_CB_tcp + m_k_AC_tcp + m_k_CA_tcp)
+ return matrix
+
+
+def rr1rho_3d_2site(matrix=None, R1=None, r1rho_prime=None, pA=None,
pB=None, wA=None, wB=None, w1=None, k_AB=None, k_BA=None):
+ """Definition of the 3D exchange matrix.
+
+ This code originates from the funNumrho.m file from the Skrynikov &
Tollinger code (the sim_all.tar file
https://gna.org/support/download.php?file_id=18404 attached to
https://gna.org/task/?7712#comment5).
+
+
+ @keyword matrix: The matrix to fill.
+ @type matrix: numpy rank-2 6D array
+ @keyword R1: The longitudinal, spin-lattice relaxation rate.
+ @type R1: float
+ @keyword r1rho_prime: The R1rho transverse, spin-spin relaxation rate
in the absence of exchange.
+ @type r1rho_prime: float
+ @keyword pA: The population of state A.
+ @type pA: float
+ @keyword pB: The population of state B.
+ @type pB: float
+ @keyword wA: The chemical shift offset of state A from the
spin-lock.
+ @type wA: float
+ @keyword wB: The chemical shift offset of state A from the
spin-lock.
+ @type wB: float
+ @keyword w1: The spin-lock field strength in rad/s.
+ @type w1: float
+ @keyword k_AB: The forward exchange rate from state A to state
B.
+ @type k_AB: float
+ @keyword k_BA: The reverse exchange rate from state B to state
A.
+ @type k_BA: float
+ """
+
+ # The AB auto-block.
+ matrix[0, 0] = -r1rho_prime - k_AB
+ matrix[0, 1] = -wA
+ matrix[1, 0] = wA
+ matrix[1, 1] = -r1rho_prime - k_AB
+ matrix[1, 2] = -w1
+ matrix[2, 1] = w1
+ matrix[2, 2] = -R1 - k_AB
+
+ # The BA auto-block.
+ matrix[3, 3] = -r1rho_prime - k_BA
+ matrix[3, 4] = -wB
+ matrix[4, 3] = wB
+ matrix[4, 4] = -r1rho_prime - k_BA
+ matrix[4, 5] = -w1
+ matrix[5, 4] = w1
+ matrix[5, 5] = -R1 - k_BA
+
+ # The AB cross-block.
+ matrix[0, 3] = k_BA
+ matrix[1, 4] = k_BA
+ matrix[2, 5] = k_BA
+ matrix[3, 0] = k_AB
+ matrix[4, 1] = k_AB
+ matrix[5, 2] = k_AB
+
+
+def rr1rho_3d_2site_rankN(R1=None, r1rho_prime=None, pA=None, pB=None,
dw=None, omega=None, offset=None, w1=None, k_AB=None, k_BA=None,
relax_time=None):
+ """Definition of the multidimensional 3D exchange matrix, of rank
[NE][NS][NM][NO][ND][6][6].
+
+ This code originates from the funNumrho.m file from the Skrynikov &
Tollinger code (the sim_all.tar file
https://gna.org/support/download.php?file_id=18404 attached to
https://gna.org/task/?7712#comment5).
+
+
+ @keyword R1: The longitudinal, spin-lattice relaxation rate.
+ @type R1: numpy float array of rank [NE][NS][NM][NO][ND]
+ @keyword r1rho_prime: The R1rho transverse, spin-spin relaxation rate
in the absence of exchange.
+ @type r1rho_prime: numpy float array of rank [NE][NS][NM][NO][ND]
+ @keyword pA: The population of state A.
+ @type pA: float
+ @keyword pB: The population of state B.
+ @type pB: float
+ @keyword dw: The chemical exchange difference between states
A and B in rad/s.
+ @type dw: numpy float array of rank [NS][NM][NO][ND]
+ @keyword omega: The chemical shift for the spin in rad/s.
+ @type omega: numpy float array of rank [NS][NM][NO][ND]
+ @keyword offset: The spin-lock offsets for the data.
+ @type offset: numpy float array of rank [NS][NM][NO][ND]
+ @keyword w1: The spin-lock field strength in rad/s.
+ @type w1: numpy float array of rank [NE][NS][NM][NO][ND]
+ @keyword k_AB: The forward exchange rate from state A to state
B.
+ @type k_AB: float
+ @keyword k_BA: The reverse exchange rate from state B to state
A.
+ @type k_BA: float
+ @keyword k_BA: The reverse exchange rate from state B to state
A.
+ @type k_BA: float
+ @keyword relax_time: The total relaxation time period for each
spin-lock field strength (in seconds).
+ @type relax_time: numpy float array of rank [NS][NM][NO][ND]
+ @return: The relaxation matrix.
+ @rtype: numpy float array of rank
[NE][NS][NM][NO][ND][6][6]
+ """
+
+ # Wa: The chemical shift offset of state A from the spin-lock. Larmor
frequency [s^-1].
+ Wa = omega
+ # Wb: The chemical shift offset of state A from the spin-lock. Larmor
frequency [s^-1].
+ Wb = omega + dw
+
+ # Population-averaged Larmor frequency [s^-1].
+ W = pA*Wa + pB*Wb
+
+ # Offset of spin-lock from A.
+ dA = Wa - offset
+
+ # Offset of spin-lock from B.
+ dB = Wb - offset
+
+ # Offset of spin-lock from population-average.
+ d = W - offset
+
+ # Alias to original parameter name.
+ wA=dA
+ wB=dB
+
+ m_r1rho_prime = array([
+ [-1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, -1.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, -1.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]])
+
+ m_wA = array([
+ [0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
+ [1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]])
+
+ m_wB = array([
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, -1.0, 0.0],
+ [0.0, 0.0, 0.0, 1.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]])
+
+ m_w1 = array([
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
+ [0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
+ [0.0, 0.0, 0.0, 0.0, 1.0, 0.0]])
+
+ m_k_AB = array([
+ [-1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
+ [1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 1.0, 0.0, 0.0, 0.0]])
+
+ m_k_BA = array([
+ [0.0, 0.0, 0.0, 1.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 1.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
+ [0.0, 0.0, 0.0, -1.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, -1.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, -1.0]])
+
+ m_R1 = array([
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0, 0.0, 0.0, -1.0]])
+
+ # Multiply and expand.
+ mat_r1rho_prime = multiply.outer( r1rho_prime * relax_time,
m_r1rho_prime )
+
+ mat_wA = multiply.outer( wA * relax_time, m_wA )
+ mat_wB = multiply.outer( wB * relax_time, m_wB )
+
+ mat_w1 = multiply.outer( w1 * relax_time, m_w1 )
+
+ mat_k_AB = multiply.outer( k_AB * relax_time, m_k_AB )
+ mat_k_BA = multiply.outer( k_BA * relax_time, m_k_BA )
+
+ mat_R1 = multiply.outer( R1 * relax_time, m_R1 )
+
+ # Collect matrix.
+ matrix = (mat_r1rho_prime + mat_wA + mat_wB
+ + mat_w1 + mat_k_AB + mat_k_BA
+ + mat_R1)
+
+ # Return the matrix.
return matrix
@@ -789,192 +977,4 @@
matrix[5, 8] = k_CB
matrix[6, 3] = k_BC
matrix[7, 4] = k_BC
- matrix[8, 5] = k_BC
-
-
-def rr1rho_3d(matrix=None, R1=None, r1rho_prime=None, pA=None, pB=None,
wA=None, wB=None, w1=None, k_AB=None, k_BA=None):
- """Definition of the 3D exchange matrix.
-
- This code originates from the funNumrho.m file from the Skrynikov &
Tollinger code (the sim_all.tar file
https://gna.org/support/download.php?file_id=18404 attached to
https://gna.org/task/?7712#comment5).
-
-
- @keyword matrix: The matrix to fill.
- @type matrix: numpy rank-2 6D array
- @keyword R1: The longitudinal, spin-lattice relaxation rate.
- @type R1: float
- @keyword r1rho_prime: The R1rho transverse, spin-spin relaxation rate
in the absence of exchange.
- @type r1rho_prime: float
- @keyword pA: The population of state A.
- @type pA: float
- @keyword pB: The population of state B.
- @type pB: float
- @keyword wA: The chemical shift offset of state A from the
spin-lock.
- @type wA: float
- @keyword wB: The chemical shift offset of state A from the
spin-lock.
- @type wB: float
- @keyword w1: The spin-lock field strength in rad/s.
- @type w1: float
- @keyword k_AB: The forward exchange rate from state A to state
B.
- @type k_AB: float
- @keyword k_BA: The reverse exchange rate from state B to state
A.
- @type k_BA: float
- """
-
- # The AB auto-block.
- matrix[0, 0] = -r1rho_prime - k_AB
- matrix[0, 1] = -wA
- matrix[1, 0] = wA
- matrix[1, 1] = -r1rho_prime - k_AB
- matrix[1, 2] = -w1
- matrix[2, 1] = w1
- matrix[2, 2] = -R1 - k_AB
-
- # The BA auto-block.
- matrix[3, 3] = -r1rho_prime - k_BA
- matrix[3, 4] = -wB
- matrix[4, 3] = wB
- matrix[4, 4] = -r1rho_prime - k_BA
- matrix[4, 5] = -w1
- matrix[5, 4] = w1
- matrix[5, 5] = -R1 - k_BA
-
- # The AB cross-block.
- matrix[0, 3] = k_BA
- matrix[1, 4] = k_BA
- matrix[2, 5] = k_BA
- matrix[3, 0] = k_AB
- matrix[4, 1] = k_AB
- matrix[5, 2] = k_AB
-
-
-def rr1rho_3d_rankN(R1=None, r1rho_prime=None, pA=None, pB=None, dw=None,
omega=None, offset=None, w1=None, k_AB=None, k_BA=None, relax_time=None):
- """Definition of the multidimensional 3D exchange matrix, of rank
[NE][NS][NM][NO][ND][6][6].
-
- This code originates from the funNumrho.m file from the Skrynikov &
Tollinger code (the sim_all.tar file
https://gna.org/support/download.php?file_id=18404 attached to
https://gna.org/task/?7712#comment5).
-
-
- @keyword R1: The longitudinal, spin-lattice relaxation rate.
- @type R1: numpy float array of rank [NE][NS][NM][NO][ND]
- @keyword r1rho_prime: The R1rho transverse, spin-spin relaxation rate
in the absence of exchange.
- @type r1rho_prime: numpy float array of rank [NE][NS][NM][NO][ND]
- @keyword pA: The population of state A.
- @type pA: float
- @keyword pB: The population of state B.
- @type pB: float
- @keyword dw: The chemical exchange difference between states
A and B in rad/s.
- @type dw: numpy float array of rank [NS][NM][NO][ND]
- @keyword omega: The chemical shift for the spin in rad/s.
- @type omega: numpy float array of rank [NS][NM][NO][ND]
- @keyword offset: The spin-lock offsets for the data.
- @type offset: numpy float array of rank [NS][NM][NO][ND]
- @keyword w1: The spin-lock field strength in rad/s.
- @type w1: numpy float array of rank [NE][NS][NM][NO][ND]
- @keyword k_AB: The forward exchange rate from state A to state
B.
- @type k_AB: float
- @keyword k_BA: The reverse exchange rate from state B to state
A.
- @type k_BA: float
- @keyword k_BA: The reverse exchange rate from state B to state
A.
- @type k_BA: float
- @keyword relax_time: The total relaxation time period for each
spin-lock field strength (in seconds).
- @type relax_time: numpy float array of rank [NS][NM][NO][ND]
- @return: The relaxation matrix.
- @rtype: numpy float array of rank
[NE][NS][NM][NO][ND][6][6]
- """
-
- # Wa: The chemical shift offset of state A from the spin-lock. Larmor
frequency [s^-1].
- Wa = omega
- # Wb: The chemical shift offset of state A from the spin-lock. Larmor
frequency [s^-1].
- Wb = omega + dw
-
- # Population-averaged Larmor frequency [s^-1].
- W = pA*Wa + pB*Wb
-
- # Offset of spin-lock from A.
- dA = Wa - offset
-
- # Offset of spin-lock from B.
- dB = Wb - offset
-
- # Offset of spin-lock from population-average.
- d = W - offset
-
- # Alias to original parameter name.
- wA=dA
- wB=dB
-
- m_r1rho_prime = array([
- [-1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, -1.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, -1.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]])
-
- m_wA = array([
- [0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
- [1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]])
-
- m_wB = array([
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, -1.0, 0.0],
- [0.0, 0.0, 0.0, 1.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]])
-
- m_w1 = array([
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
- [0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
- [0.0, 0.0, 0.0, 0.0, 1.0, 0.0]])
-
- m_k_AB = array([
- [-1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
- [1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 1.0, 0.0, 0.0, 0.0]])
-
- m_k_BA = array([
- [0.0, 0.0, 0.0, 1.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 1.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
- [0.0, 0.0, 0.0, -1.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, -1.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, -1.0]])
-
- m_R1 = array([
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- [0.0, 0.0, 0.0, 0.0, 0.0, -1.0]])
-
- # Multiply and expand.
- mat_r1rho_prime = multiply.outer( r1rho_prime * relax_time,
m_r1rho_prime )
-
- mat_wA = multiply.outer( wA * relax_time, m_wA )
- mat_wB = multiply.outer( wB * relax_time, m_wB )
-
- mat_w1 = multiply.outer( w1 * relax_time, m_w1 )
-
- mat_k_AB = multiply.outer( k_AB * relax_time, m_k_AB )
- mat_k_BA = multiply.outer( k_BA * relax_time, m_k_BA )
-
- mat_R1 = multiply.outer( R1 * relax_time, m_R1 )
-
- # Collect matrix.
- matrix = (mat_r1rho_prime + mat_wA + mat_wB
- + mat_w1 + mat_k_AB + mat_k_BA
- + mat_R1)
-
- # Return the matrix.
- return matrix
+ matrix[8, 5] = k_BC
Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24217&r1=24216&r2=24217&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py Fri Jun 20
19:13:14 2014
@@ -54,7 +54,7 @@
from numpy import dot, sum
# relax module imports.
-from lib.dispersion.ns_matrices import rr1rho_3d, rr1rho_3d_rankN
+from lib.dispersion.ns_matrices import rr1rho_3d_2site_rankN
from lib.float import isNaN
from lib.linear_algebra.matrix_exponential import matrix_exponential,
matrix_exponential_rankN
@@ -102,7 +102,7 @@
NE, NS, NM, NO = num_points.shape
# The matrix that contains all the contributions to the evolution, i.e.
relaxation, exchange and chemical shift evolution.
- R_mat = rr1rho_3d_rankN(R1=r1, r1rho_prime=r1rho_prime, pA=pA, pB=pB,
dw=dw, omega=omega, offset=offset, w1=spin_lock_fields, k_AB=k_AB, k_BA=k_BA,
relax_time=relax_time)
+ R_mat = rr1rho_3d_2site_rankN(R1=r1, r1rho_prime=r1rho_prime, pA=pA,
pB=pB, dw=dw, omega=omega, offset=offset, w1=spin_lock_fields, k_AB=k_AB,
k_BA=k_BA, relax_time=relax_time)
# This matrix is a propagator that will evolve the magnetization with
the matrix R.
Rexpo_mat = matrix_exponential_rankN(R_mat)
r24217 - in /branches/disp_spin_speed/lib/dispersion: ns_matrices.py ns_r1rho_2site.py