Kernel utilities - Revision history

Kuprov: Index the new Spinach 2.12 spin-boson functions and tutorial (PR 195)

2026-08-06T04:42:20Z

Index the new Spinach 2.12 spin-boson functions and tutorial (PR 195)

Kuprov: Add missing Spinach function to function index

2026-06-06T18:38:18Z

Add missing Spinach function to function index

Kuprov: /* Housekeeping functions */

2026-04-25T11:48:53Z

‎Housekeeping functions

Kuprov: /* Housekeeping functions */

2026-04-25T11:48:46Z

‎Housekeeping functions

Kuprov: /* Housekeeping functions */

2026-04-25T11:48:35Z

‎Housekeeping functions

Kuprov: /* Numerical infrastructure */

2026-04-25T11:48:24Z

‎Numerical infrastructure

Kuprov: /* Numerical infrastructure */

2026-04-25T11:48:09Z

‎Numerical infrastructure

Kuprov: /* Data analysis and plotting */

2026-04-25T11:48:00Z

‎Data analysis and plotting

Kuprov: /* SU(2), SO(3), and other groups */

2026-04-25T11:47:48Z

‎SU(2), SO(3), and other groups

Kuprov: /* SU(2), SO(3), and other groups */

2026-04-25T11:46:53Z

‎SU(2), SO(3), and other groups

@@ Line 66: / Line 66: @@
 [[axrh2mat.m]] - axiality and rhombicity into 3x3 matrix.
 [[castep2nqi.m]] – converts CASTEP EFG tensor (it is printed in atomic units) to NQI tensor in Hz that is required by Spinach.
@@ Line 76: / Line 78: @@
 [[dihedral.m]] – calculates the dihedral angle defined by four sets of atomic coordinates supplied.
 [[eeqq2nqi.m]] – converts literature conventions for the quadrupolar interaction specification into a 3x3 matrix in Hz.
@@ Line 94: / Line 98: @@
 [[ias2mat.m]] - Interaction matrix from isotropic-antisymmetric-symmetric decomposition.
 [[mat2axrh.m]] - axiality and rhombicity from a 3x3 matrix.
 [[mat2ias.m]] - Isotropic-antisymmetric-symmetric decomposition of an interaction matrix.
 [[mhz2gauss.m]] - converts hyperfine couplings from MHz into Gauss.
@@ Line 301: / Line 309: @@
 [[ngce.m]] - numerical generalised cumulant expansion.
 [[rlx_scalar.m]] - scalar relaxation superoperator.

← Older revision		Revision as of 18:38, 6 June 2026
Line 495:		Line 495:

	[[swizzle.m]] - nested loop unrolling for parallel processing.		[[swizzle.m]] - nested loop unrolling for parallel processing.
		+
		+	==Miscellaneous utilities==
		+
		+	[[autoexec.m]] - This include is executed at the start of create.m, it overrides all user input.
		+
		+	[[bos_product_table.m]] - Structure coefficient tables for the associative envelopes of truncated Weyl algebras spanned by orthogonalised bosonic mo- nomials.
		+
		+	[[fft_freq_axis.m]] - Frequency axis for FFT with optional zero-filling.
		+
		+	[[fwhm2rlx.m]] - Converts full width at half-maximum (FWHM) of an NMR signal into an approximation of the R2 rate.
		+
		+	[[icm2hz.m]] - Converts cm^-1 units used in spectroscopy into Hz units preferred in magnetic resonance; arrays of any dimensions are supported.
		+
		+	[[ifft_time_axis.m]] - Time axis for IFFT with optional zero-filling.
		+
		+	[[intrep.m]] - Interaction representation transformation with respect to a specified Hamiltonian to specified order in perturbation theory (https://doi.org/10.1063/1.4928978).
		+
		+	[[istraceless.m]] - A floating-point precision consistent check for whether a particular matrix is traceless.
		+
		+	[[kq2lin.m]] - Converts k,q indexing of matrices into their linear serpentine indexing.
		+
		+	[[kronm.m]] - Calculates (Q{1}(x)Q{2}(x)...(x)Q{n})*x without opening Kronecker products.
		+
		+	[[lcurve.m]] - L-curve analysis function.
		+
		+	[[lin2kq.m]] - Converts linear serpentine indexing of matrices into their k,q indexing.
		+
		+	[[min_int_type.m]] - Minimum integer data type sufficient to store the specified value.
		+
		+	[[prune_subgraphs.m]] - Removes subgraphs that are contained entirely within other subgraphs.
		+
		+	[[redfield_integral_async.m]] - Evaluates the Redfield integral through the asynchronous parallel path used inside relaxation.m, following the notation of IK's paper (http://dx.doi.org/10.1016/j.jmr.2010.12.004).
		+
		+	[[redfield_integral_serial.m]] - Evaluates the Redfield integral through the serial path used inside relaxation.m, following the notation of IK's paper (http://dx.doi.org/10.1016/j.jmr.2010.12.004) but replacing.
		+
		+	[[repcols.m]] - Replicates specified columns of a matrix or cell array a specified number of times.
		+
		+	[[reprows.m]] - Replicates specified rows of a matrix or cell array a specified number of times.
		+
		+	[[serpentine.m]] - Serpentine index matrix used in Spinach for single-index numbering of matrix elements.
		+
		+	[[st_product_table.m]] - Structure coefficient tables for single transition operators.
		+
		+	[[tikhol1n.m]] - L1 norm Tikhonov regularised solver for A*x=y where A is an ill-conditioned matrix.
		+
		+	[[unihash.m]] - Hash table based stable duplicate row eliminator, for use with large sparse matrices where Matlab's unique(...,'rows') is too slow.
		+
		+	[[which_subst.m]] - Finds out which substance hosts the specified spins; throws an error if there is more than one.
		+
		+	[[xyz2hfc.m]] - Converts point electron and nuclear coordinates into a hyperfine interaction tensor.

	''Version 2.11, authors: [[Ilya Kuprov]]''		''Version 2.11, authors: [[Ilya Kuprov]]''

← Older revision		Revision as of 11:48, 25 April 2026
Line 455:		Line 455:

	[[iseye.m]] - returns true for unit matrices.		[[iseye.m]] - returns true for unit matrices.
−
−	~~[[pad.m]] - pads character strings with spaces.~~

	[[patrol.m]] - continuous patrol through the example set.		[[patrol.m]] - continuous patrol through the example set.

← Older revision		Revision as of 11:48, 25 April 2026
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	[[forum.m]] - opens the Spinach support forum page.		[[forum.m]] - opens the Spinach support forum page.
−
−	~~[[gpt_pack.m]] - copies all m-files from the Spinach code tree into a specified directory.~~

	[[hebrew.m]] - Hebrew flashcards utility.		[[hebrew.m]] - Hebrew flashcards utility.

← Older revision		Revision as of 11:48, 25 April 2026
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	[[cacheman.m]] - cache management heuristics for the scratch folder.		[[cacheman.m]] - cache management heuristics for the scratch folder.
−
−	~~[[basic_sanity_check.m]] - tests MDCS, Java, and Spinach basics.~~

	[[compile_mex.m]] - MEX compilation utility.		[[compile_mex.m]] - MEX compilation utility.

← Older revision		Revision as of 11:48, 25 April 2026
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	[[mprealloc.m]] - Preallocates an operator in the current formalism and basis.		[[mprealloc.m]] - Preallocates an operator in the current formalism and basis.
−
−	~~[[picks.m]] - All picks of the specified number of elements from the vector provided, without repetitions.~~
−
−	~~[[present.m]] - Returns the non-NaN elements of a numerical array.~~

	[[remncomm.m]] - The part of the matrix that commutes with another matrix.		[[remncomm.m]] - The part of the matrix that commutes with another matrix.

← Older revision		Revision as of 11:48, 25 April 2026
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	[[herm_spline.m]] - Cubic Hermite spline on [0,1] interval from values and derivatives at the interval edges.		[[herm_spline.m]] - Cubic Hermite spline on [0,1] interval from values and derivatives at the interval edges.
−
−	~~[[issquare.m]] - Returns true for square matrices.~~

	[[jacobianest.m]] - Numerical Jacobian estimation.		[[jacobianest.m]] - Numerical Jacobian estimation.

← Older revision		Revision as of 11:48, 25 April 2026
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	[[stack_2d.m]] - stack plotting utility for 2D NMR spectra.		[[stack_2d.m]] - stack plotting utility for 2D NMR spectra.
−
−	~~[[try_to_savefig.m]] - figure save replacement that tolerates write-protected media~~

	[[mri_2d_plot.m]] - 2D MRI plotting utility.		[[mri_2d_plot.m]] - 2D MRI plotting utility.

@@ Line 137: / Line 137: @@
 [[perm_group.m]] – a database of common finite groups.
 [[pauli.m]] - spin operators with user-specified multiplicity.
@@ Line 157: / Line 155: @@
 [[stevens.m]] - Extended Stevens operators.
 [[twospinist.m]] - Two-spin irreducible spherical tensor operators.

@@ Line 117: / Line 117: @@
 ==SU(2), SO(3), and other groups==
 [[add_spins.m]] - Reduces direct products of two su(2) irreps.
 [[cg_fast.m]] - fast but less accurate Clebsch-Gordan coefficient calculation.