plateform stringclasses 1
value | repo_name stringlengths 13 113 | name stringlengths 3 74 | ext stringclasses 1
value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
|---|---|---|---|---|---|---|---|---|
github | tsajed/nmr-pred-master | plot_1d.m | .m | nmr-pred-master/spinach/kernel/utilities/plot_1d.m | 3,959 | utf_8 | 52d2b971d3a325d0883c9ea48b20d266 | % 1D plotting utility. Uses the same parameters structure as 1D pulse
% sequences. Input syntax:
%
% plot_1d(spin_system,spectrum,parameters)
%
% Input parameters:
%
% parameters.sweep sweep width, Hz
%
% parameters.spins spin species, e.g. {'1H'}
%
% parameter... |
github | tsajed/nmr-pred-master | dirdiff.m | .m | nmr-pred-master/spinach/kernel/utilities/dirdiff.m | 2,174 | utf_8 | 741772511db8416d34d4afeb5f30ff0f | % Directional derivatives of the matrix exponential. Implements Equation 11
% of Najfeld and Havel and our Equations 16 and 17. Syntax:
%
% D=dirdiff(spin_system,A,B,T,N)
%
% if A an B are matrices, computes the N-th derivative of the matrix expo-
% nential exp(A*T) in the direction B. If B... |
github | tsajed/nmr-pred-master | report.m | .m | nmr-pred-master/spinach/kernel/utilities/report.m | 2,275 | utf_8 | b265dc54d5bbfddb257f62b35084a2f8 | % Writes a log message to the console or an ACSII file. Syntax:
%
% report(spin_system,report_string)
%
% where report_string is a character string. A newline symbol at the end
% of the string is not necessary - it is added by the function.
%
% i.kuprov@soton.ac.uk
% luke.edwards@ucl.ac.uk
... |
github | tsajed/nmr-pred-master | sphten2mat.m | .m | nmr-pred-master/spinach/kernel/utilities/sphten2mat.m | 2,907 | utf_8 | 48b9796604056dc8abf5df48b34a271b | % Converts the nine components of the irreducible spherical tensor re-
% presentation of an interaction tensor into the Cartesian representa-
% tion with a 3x3 matrix.
%
% Spherical tensor components should be listed in the following order:
%
% rank 0: (0,0)
% rank 1: (1,1) (1,0) (1,-1)
% rank 2: (2,2) (2,1) (... |
github | tsajed/nmr-pred-master | unit_oper.m | .m | nmr-pred-master/spinach/kernel/utilities/unit_oper.m | 1,437 | utf_8 | eb5264b07ec428049c3b023d8026e19c | % Returns a unit operator in the current formalism and basis. Syntax:
%
% A=unit_oper(spin_system)
%
% i.kuprov@soton.ac.uk
% d.savostyanov@soton.ac.uk
function A=unit_oper(spin_system)
% Decide how to proceed
switch spin_system.bas.formalism
case 'sphten-liouv'
... |
github | tsajed/nmr-pred-master | dfpt.m | .m | nmr-pred-master/spinach/kernel/utilities/dfpt.m | 3,132 | utf_8 | f2537d9e3eba296daa3a9a5fcb3cd245 | % Graph partitioning module. Analyzes the system connectivity graph and
% creates a list of all connected subgraphs of up to the user-specified
% size by crawling the graph in all available directions. Syntax:
%
% subgraphs=dfpt(conmatrix,max_subgraph_size)
%
% Arguments:
%
% conmatri... |
github | tsajed/nmr-pred-master | crop_2d.m | .m | nmr-pred-master/spinach/kernel/utilities/crop_2d.m | 2,008 | utf_8 | dae199e0d941af7f931aa94bc1db2b8f | % Crops 2D spectra to user-specified ranges (in ppm).
%
% i.kuprov@soton.ac.uk
function [spec,parameters]=crop_2d(spin_system,spec,parameters,crop_ranges)
% Accommodate homonuclear 2D sequences
if numel(parameters.spins)==1, parameters.spins=[parameters.spins parameters.spins]; end
if numel(parameters.offset... |
github | tsajed/nmr-pred-master | mt2hz.m | .m | nmr-pred-master/spinach/kernel/utilities/mt2hz.m | 632 | utf_8 | 17ba7e517cbe2183eaf1d8981e8f35f1 | % Converts hyperfine couplings from milliTesla to Hz
% (linear frequency). Syntax:
%
% hfc_hz=mt2hz(hfc_mt)
%
% Arrays of any dimension are supported.
%
% i.kuprov@soton.ac.uk
function hfc_hz=mt2hz(hfc_mt)
if isnumeric(hfc_mt)&&isreal(hfc_mt)
hfc_hz=1e7*2.802495365*hfc_mt;
else
e... |
github | tsajed/nmr-pred-master | negligible.m | .m | nmr-pred-master/spinach/kernel/utilities/negligible.m | 728 | utf_8 | fd27a36e877d8ee08925de3155e28ae2 | % An aux function determining whether a given object deserves attention
% given the tolerance specified. Used in the internal decision making
% performed by Spinach kernel functions. Syntax:
%
% answer=negligible(object,tolerance)
%
% Parameters:
%
% object - the object whose significance... |
github | tsajed/nmr-pred-master | slice_2d.m | .m | nmr-pred-master/spinach/kernel/utilities/slice_2d.m | 3,935 | utf_8 | eb2c5288f45d57eb4b8c17d3cf7c3f1a | % Contour plot slicing utility with non-linear adaptive contour spacing.
% Calls plot_3d() and allows slice extraction. Syntax:
%
% plot_2d(spin_system,spectrum,parameters,ncont,delta,k,ncol,m,signs)
%
% The following functions are used to compute contour levels:
%
% cont_levs_pos=delta(2)*xmax*linspace(0,1,nc... |
github | tsajed/nmr-pred-master | cgsppm2ang.m | .m | nmr-pred-master/spinach/kernel/utilities/cgsppm2ang.m | 873 | utf_8 | 1c7a6d162c1d9ebeedd75e7e374df8b0 | % Converts magnetic susceptibility from the cgs-ppm (aka cm^3/mol) units
% quoted by quantum chemistry packages into Angstrom^3 units required by
% Spinach pseudocontact shift functionality. Syntax:
%
% ang=cgsppm2ang(cgsppm)
%
% Arrays of any dimension are supported.
%
% i.kuprov@soton.a... |
github | tsajed/nmr-pred-master | int_2d.m | .m | nmr-pred-master/spinach/kernel/utilities/int_2d.m | 4,987 | utf_8 | bd928c92987972495dcac0057172802f | % 2D spectral integrator. Calls plot_2d.m and then launches either an
% interactive integration procedure (if no range file name is given)
% and records the range data into a file, or runs an automatic integ-
% ration if the range file name from a previous run is supplied.
% Syntax:
%
% int_2d(spin_system,sp... |
github | tsajed/nmr-pred-master | fftdiff.m | .m | nmr-pred-master/spinach/kernel/utilities/fftdiff.m | 1,136 | utf_8 | f948aeace36c979e735e35f96a5f920e | % Spectral differentiation kernel. To be used for accurate numerical
% differentiation of real signals in the following way:
%
% derivative=real(fft(ifft(signal).*fftdiff(1,length(signal),1)'));
%
% i.kuprov@soton.ac.uk
function kern=fftdiff(order,npoints,dx)
if mod(npoints,2)==1
% Kernel for odd ... |
github | tsajed/nmr-pred-master | symmetrize.m | .m | nmr-pred-master/spinach/kernel/utilities/symmetrize.m | 1,156 | utf_8 | 8b16385f90dce90c58510d177dff6c2e | % Symmetrizes interaction tensors. This is required to avoid numerical
% instabilities associated with small asymmetries during the diagonali-
% zation process. Syntax:
%
% A=symmetrize(spin_system,A)
%
% i.kuprov@soton.ac.uk
function A=symmetrize(spin_system,A)
% Check consistency
gru... |
github | tsajed/nmr-pred-master | hilb2liouv.m | .m | nmr-pred-master/spinach/kernel/utilities/hilb2liouv.m | 1,936 | utf_8 | 556ed19d99d4b703f381e73bfc060b88 | % Converts Hilbert space operators into Liouville space superoperators
% or state vectors. Syntax:
%
% L=hilb2liouv(H,conv_type)
%
% Parameters:
%
% H - a Hilbert space operator
%
% conv_type - the type of Liouville space superoperator to return:
%
% 'left... |
github | tsajed/nmr-pred-master | sniff.m | .m | nmr-pred-master/spinach/kernel/utilities/sniff.m | 291 | utf_8 | 0056719e033bec102876cb4b3c75644a | % Validates the spin_system object and prints an informative error message
% or an informative warning if something is found to be askew.
%
% i.kuprov@soton.ac.uk
function sniff(spin_system) %#ok<INUSD>
% Remains to be written
error('this function is currently empty.');
end
|
github | tsajed/nmr-pred-master | transfermat.m | .m | nmr-pred-master/spinach/kernel/utilities/transfermat.m | 1,129 | utf_8 | af3fc494152b115d76c46c1c624abfea | % Transfer matrix calculation for linear amplifiers. Syntax:
%
% T=transfermat(amp_inps,amp_outs)
%
% Parameters:
%
% amp_inps - a matrix with amplifier input vectors as columns
%
% amp_outs - a matrix with amplifier output vectors as columns
%
% Outputs:
%
% T - the transfer matr... |
github | tsajed/nmr-pred-master | statmerge.m | .m | nmr-pred-master/spinach/kernel/utilities/statmerge.m | 928 | utf_8 | ec47242d42574198a26c155938884750 | % Merges means and standard deviations of the mean for multiple sample sets
% into a total mean and total standard deviation of the mean. Syntax:
%
% [total_mean,total_stdm]=statmerge(means,stdms,npoints)
%
% Parameters:
%
% means - a vector of mean values for each sample set
%
% stdms - a ... |
github | tsajed/nmr-pred-master | summary.m | .m | nmr-pred-master/spinach/kernel/utilities/summary.m | 14,385 | utf_8 | 50a2961889419f70d24feb578417241c | % Prints various summaries on behalf of the spin system setup modules
% of Spinach kernel. Edits to this function are discouraged.
%
% i.kuprov@soton.ac.uk
function summary(spin_system,topic,header)
switch topic
case 'zeeman'
report(spin_system,header);
report(spin_system,'========... |
github | tsajed/nmr-pred-master | stitch.m | .m | nmr-pred-master/spinach/kernel/utilities/stitch.m | 1,833 | utf_8 | 84bb801d963fcb263c39896f7818bab0 | % Stitching function for bidirectionally propagated 3D experiments. Syntax:
%
% fid=stitch(spin_system,L,rho_stack,coil_stack,mtp_oper,mtp_time,t1,t2,t3)
%
% Parameters:
%
% L - spin system Liouvillian
%
% rho_stack - state vector stack from the forward part of
% the simulation... |
github | tsajed/nmr-pred-master | dcm2euler.m | .m | nmr-pred-master/spinach/kernel/utilities/dcm2euler.m | 3,633 | utf_8 | f2bce8038fb9fdf1403774d9accce78a | % Converts DCM into Euler angles (Varshalovich B convention). Syntax:
%
% [alpha,beta,gamma]=dcm2euler(dcm)
%
% OR
%
% angles=dcm2euler(dcm)
%
% In the latter case, anglews is a row vector containing the three Euler
% angles, orde... |
github | tsajed/nmr-pred-master | zfs2mat.m | .m | nmr-pred-master/spinach/kernel/utilities/zfs2mat.m | 675 | utf_8 | bfd8d9fb23298f193e2eff0e0d2a0506 | % Converts D and E zero-field splitting parameters to a diagonal matrix.
%
% i.kuprov@soton.ac.uk
function M=zfs2mat(D,E)
% Compute the matrix
M=[-D/3+E, 0, 0; 0, -D/3-E, 0; 0, 0, 2*D/3];
end
% To watch the courageous Afghan freedom fighters battle modern
% arsenals with simple hand-held weapons is an i... |
github | tsajed/nmr-pred-master | anax2quat.m | .m | nmr-pred-master/spinach/kernel/utilities/anax2quat.m | 1,614 | utf_8 | 83ed77433dd697e4a85418a9f85c4821 | % Converts angle-axis rotation parameters into a quaternion. Syntax:
%
% q=anax2quat(rot_axis,rot_angle)
%
% Arguments:
%
% rot_axis - cartesian direction vector given as a row or column
% with three real elements
%
% rot_angle - rotation angle in radians
%
% Output... |
github | tsajed/nmr-pred-master | eeqq2nqi.m | .m | nmr-pred-master/spinach/kernel/utilities/eeqq2nqi.m | 1,585 | utf_8 | 3005ecba9c3aa49523259107f5c61e94 | % Converts the C_q and eta_q quadrupolar interaction specification con-
% vention into a 3x3 interaction matrix in Hz. Usage:
%
% Q=eeqq2nqi(C_q,eta_q,I,euler_angles)
%
% where C_q is the quadrupolar coupling constant (Hz), eta_q is the quad-
% rupolar tensor asymmetry parameter, I is the spin... |
github | tsajed/nmr-pred-master | fdhess.m | .m | nmr-pred-master/spinach/kernel/utilities/fdhess.m | 2,749 | utf_8 | 09491c4660d70ff587b791bda12c8f13 | % Returns the finite-difference Hessian of a 3D array using a finite
% difference scheme with a user-specified number of stencil points.
% The dimensions of the 3D array are assumed to be ordered as [X Y Z].
% Syntax:
% H=fdhess(A,npoints)
%
% where the second parameter specifies the numbe... |
github | tsajed/nmr-pred-master | lin2lmn.m | .m | nmr-pred-master/spinach/kernel/utilities/lin2lmn.m | 1,576 | utf_8 | 5a211d633afeebf95469bc76ed88602c | % Converts linear indexing specification of a Wigner function to L,M,N
% indexing. In the linear indexing convention, the Wigner functions are
% listed in the order of increasing L rank. Within each L rank, the func-
% tions are listed in the order of decreasing left index, and, for each
% left index, in the order ... |
github | tsajed/nmr-pred-master | plot_2d.m | .m | nmr-pred-master/spinach/kernel/utilities/plot_2d.m | 9,638 | utf_8 | b32c60c0d4222dc37608d9a3c1723425 | % Contour plotting utility with non-linear adaptive contour spacing. The
% function is useful for NMR data where small cross-peaks must be adequa-
% tely contoured next to large diagonal peaks. Syntax:
%
% plot_2d(spin_system,spectrum,parameters,ncont,delta,k,ncol,m,signs)
%
% The following functions are used to... |
github | tsajed/nmr-pred-master | fourlap.m | .m | nmr-pred-master/spinach/kernel/utilities/fourlap.m | 2,800 | utf_8 | 157eedbb5c7cb559daf36c67a408cd8f | % Returns a Fourier spectral representation of the Laplacian acting
% on a 3D data array. Syntax:
%
% L=fourlap(npoints,extents)
%
% The following parameters are needed:
%
% npoints - a three-element vector specifying the number of
% discretization points in each dimensio... |
github | tsajed/nmr-pred-master | isworkernode.m | .m | nmr-pred-master/spinach/kernel/utilities/isworkernode.m | 398 | utf_8 | 10a12b853eccd04cb1a4ece6e3df423f | % Returns true if executed inside a parfor or spmd block.
%
% i.kuprov@soton.ac.uk
function answer=isworkernode()
% Best way I could find
answer=~isempty(getCurrentTask());
end
% In the beginning the Universe was created. This has
% made a lot of people very angry and been widely re-
% gar... |
github | tsajed/nmr-pred-master | dilute.m | .m | nmr-pred-master/spinach/kernel/utilities/dilute.m | 1,806 | utf_8 | e2128851d16aa1146bc8ce719b137191 | % Splits the spin system into several independent subsystems, each
% containing only one instance of a user specified isotope that is
% deemed "dilute". All spin system data is updated accordingly and
% basis set information, if found, is destroyed. Syntax:
%
% spin_systems=dilute(spin_system,isotope)... |
github | tsajed/nmr-pred-master | sweep2ticks.m | .m | nmr-pred-master/spinach/kernel/utilities/sweep2ticks.m | 1,674 | utf_8 | 26786ae57adde778620b9517355c65cd | % Converts offset-sweep-npoints specification to axis ticks in Hz.
% Syntax:
% axis_hz=sweep2ticks(offs,sweep,npoints)
%
% Parameters:
%
% offs - offset from carrier frequency, Hz
%
% sweep - sweep width, Hz
%
% npoints - number of points in the spectrum
%
% The funct... |
github | tsajed/nmr-pred-master | path_trace.m | .m | nmr-pred-master/spinach/kernel/utilities/path_trace.m | 5,082 | utf_8 | f58cecde2958673b551d48b82063f1c5 | % Liouvillian path tracing. Treats the user-supplied Liouvillian
% as the adjacency matrix of a graph, computes the weakly connect-
% ed subgraphs of that graph and returns a cell array of project-
% ors into the corresponding independently evolving subspaces.
% Syntax:
% projectors=reduce(spin_syste... |
github | tsajed/nmr-pred-master | fdvec.m | .m | nmr-pred-master/spinach/kernel/utilities/fdvec.m | 2,655 | utf_8 | 43c02d1e65fc491d88f531cb8ea46d03 | % Performs arbitrary-order finite-difference differentiation of a
% user-supplied row or column vector. Uses central finite-differe-
% nce stencils in the middle and sided stencils of the same order
% of accuracy on the sides. Syntax:
%
% dx=fdvec(x,npoints,order)
%
% Parameters:
%
% x ... |
github | tsajed/nmr-pred-master | conmat.m | .m | nmr-pred-master/spinach/kernel/utilities/conmat.m | 1,396 | utf_8 | 448fc7dec5d507ef1286d3a13522c0d7 | % Fast connectivity matrix.
%
% i.kuprov@outlook.com
function conmatrix=conmat(xyz,r0)
% Sort X coordinates
[x_sorted,x_index]=sort(xyz(:,1));
% Scan X coordinates
A=false(size(xyz,1),size(xyz,1));
for n=1:size(xyz,1)
for k=(n+1):size(xyz,1)
if abs(x_sorted(n)-x_sorted(k))<r0
A(... |
github | tsajed/nmr-pred-master | killdiag.m | .m | nmr-pred-master/spinach/kernel/utilities/killdiag.m | 601 | utf_8 | e4c21bf4f4b57f751a828bc59df5df25 | % Wipes the diagonal using the brush with the specified dimensions.
%
% i.kuprov@soton.ac.uk
function spec=killdiag(spec,brush_dim)
% Loop over the column index
for n=1:size(spec,2)
% Find the row index
k=n*size(spec,1)/size(spec,2);
% Find the row index extents
k=floor(k-brush_... |
github | tsajed/nmr-pred-master | quat2anax.m | .m | nmr-pred-master/spinach/kernel/utilities/quat2anax.m | 1,260 | utf_8 | e39d0de4d157bcc0895346b6c513f0ca | % Converts a quaternion into angle-axis rotation parameters. Syntax:
%
% [rot_axis,rot_angle]=quat2anax(q)
%
% where q is a structure with four fields q.u, q.i, q.j, q.k giving
% the four components of the quaternion.
%
% Output:
%
% rot_axis - cartesian direction vector given as a row or c... |
github | tsajed/nmr-pred-master | hdot.m | .m | nmr-pred-master/spinach/kernel/utilities/hdot.m | 848 | utf_8 | 91a69f208649bda9842cf2a1152a2069 | % Hadamard matrix product. Useful as a replacement for trace(A'*B) because
% trace(A'*B)=hadm(conj(A),B) and the latter only needs O(n^2) multiplica-
% tions as opposed to O(n^3) for trace(A'*B). Syntax:
%
% H=hdot(A,B)
%
% i.kuprov@soton.ac.uk
function H=hdot(A,B)
% Check con... |
github | tsajed/nmr-pred-master | relax_split.m | .m | nmr-pred-master/spinach/kernel/utilities/relax_split.m | 1,049 | utf_8 | e721c09e6d54b2569d5ac94e2bbf4801 | % Splits the relaxation superoperator into longitudinal, transverse and
% mixed components.
%
% i.kuprov@soton.ac.uk
function [R1,R2,Rm]=relax_split(spin_system,R)
% Interpret the basis
[L,M]=lin2lm(spin_system.bas.basis);
% Index single- and multi-spin orders (sso and mso)
sso_mask=(sum(logical(spin_syst... |
github | tsajed/nmr-pred-master | fprint.m | .m | nmr-pred-master/spinach/kernel/utilities/fprint.m | 1,431 | utf_8 | 4c495e8aec3d0db6d5697339d500b97e | % 2D spectrum integral fingerprinting utility. Breaks the spectrum
% down into bins of user-specified size and returns the integrals
% over those bins. Syntax:
%
% fp=fprint(spectrum,nbins)
%
% Parameters:
%
% spectrum - the matrix of a real or complex 2D spectrum
%
% nbins... |
github | tsajed/nmr-pred-master | intrep.m | .m | nmr-pred-master/spinach/kernel/utilities/intrep.m | 2,974 | utf_8 | d203a548676b6be940ecef3033e89b1e | % Interaction representation transformation with respect to
% a specified Hamiltonian to specified order in perturbation
% theory. Syntax:
%
% Hr=intrep(spin_system,H0,H,T,order)
%
% Parameters:
%
% H0 - the Hamiltonian with respect to which the
% interaction representation tran... |
github | tsajed/nmr-pred-master | ang2cgsppm.m | .m | nmr-pred-master/spinach/kernel/utilities/ang2cgsppm.m | 663 | utf_8 | 677828861b5d552c086587d4af7395c8 | % Converts magnetic susceptibility from the Angstrom^3 units
% required by Spinach pseudocontact shift functionality into
% the cgs-ppm (aka cm^3/mol) units quoted by quantum chemist-
% ry packages into. Syntax:
%
% cgsppm=ang2cgsppm(ang)
%
% Arrays of any dimension are supported.
%
% i.ku... |
github | tsajed/nmr-pred-master | phan2fpl.m | .m | nmr-pred-master/spinach/kernel/utilities/phan2fpl.m | 756 | utf_8 | 9cd6a0be10ef4e320036b78f3ae3595a | % Projects a spatial intensity distribution into the Fokker-Planck
% space, using the spin state supplied. Syntax:
%
% rho=phan2fpl(phan,rho)
%
% Parameters:
%
% phan - phantom (the spatial distribution of the
% amplitude of the specified spin state)
%
% rho ... |
github | tsajed/nmr-pred-master | kill_spin.m | .m | nmr-pred-master/spinach/kernel/utilities/kill_spin.m | 4,407 | utf_8 | c773a2aa101681bdfba3f89b224e4277 | % Removes the specified spins from the spin_system structure and updates
% all internal structures accordingly. Syntax:
%
% spin_system=kill_spin(spin_system,hit_list)
%
% where hit_list is a vector of integers or a logical matrix giving the
% numbers of spins to be removed from the system.
%
% i.k... |
github | tsajed/nmr-pred-master | gaussfun.m | .m | nmr-pred-master/spinach/kernel/utilities/gaussfun.m | 532 | utf_8 | db46c4330494c2ef7152d464d52e70dc | % Normalized Gaussian function in magnetic resonance notation. Syntax:
%
% g=gaussfun(x,fwhm)
%
% where fwhm is the full width at half-maximum.
%
% i.kuprov@soton.ac.uk
function y=gaussfun(x,fwhm)
% Compute standard deviation
sigma=fwhm/(2*sqrt(2*log(2)));
% Compute the Gaussian... |
github | tsajed/nmr-pred-master | sphten2oper.m | .m | nmr-pred-master/spinach/kernel/utilities/sphten2oper.m | 1,208 | utf_8 | e7a47c3a8e06b54fbb1ae8db1e051386 | % Generates a operator from its spherical tensor expansion produced
% by zeeman2sphten() function. Syntax:
%
% L=sphten2operator(spin_system,stexp,spin_num)
%
% where stexp is a cell array with the first element of each row giving
% the operator name and the second element being the corresponding sphe-
% r... |
github | tsajed/nmr-pred-master | svd_shrink.m | .m | nmr-pred-master/spinach/kernel/utilities/svd_shrink.m | 1,310 | utf_8 | 22cbd18e5b84400a43996baab71df2ac | % Generates a minimal set of vector-covector pairs for the parallel
% implementation of the time propagation algorithm described in
% http://dx.doi.org/10.1063/1.3679656 (Equation 9). Syntax:
%
% [vec,cov]=svd_shrink(spin_system,rho,tol)
%
% Parameters:
%
% rho - density matrix
%
% ... |
github | tsajed/nmr-pred-master | expmint.m | .m | nmr-pred-master/spinach/kernel/utilities/expmint.m | 1,443 | utf_8 | 73fdd6c9439dcc35b826979f99fbde65 | % Computes matrix exponential integrals of the following general type:
%
% Integrate[expm(-i*A*t)*B*expm(i*C*t),{t,0,T}]
%
% Matrix A must be Hermitian. For further information see the paper by
% Charles van Loan (http://dx.doi.org/10.1109/TAC.1978.1101743). Syntax:
%
% R=expmint(... |
github | tsajed/nmr-pred-master | scomponents.m | .m | nmr-pred-master/spinach/kernel/utilities/scomponents.m | 2,172 | utf_8 | d1d43abd56be4bce359c8ae739a65c99 | % Computes the strongly connected components of a graph. Returns
% an index for the component number of every vertex in the graph
% with the adjacency matrix A. Syntax:
%
% sci=scomponents(A)
%
% where A is square logical matrix and sci is a vector indicating
% which component each node o... |
github | tsajed/nmr-pred-master | mat2sphten.m | .m | nmr-pred-master/spinach/kernel/utilities/mat2sphten.m | 2,779 | utf_8 | dcb96a780e3cb92a69e556b768d5e24c | % Converts a 3x3 interaction matrix into the irreducible spherical tensor
% notation: one rank 0 component, three rank 1 components and five rank 2
% components to the total of nine independent components.
%
% The components are listed in the following order:
%
% rank 0: (0,0)
% rank 1: (1,1) (1,0) (1,-1)
% ran... |
github | tsajed/nmr-pred-master | lorentzfun.m | .m | nmr-pred-master/spinach/kernel/utilities/lorentzfun.m | 543 | utf_8 | 428e2c8ff1a296981915b56f51618ff6 | % Normalized Lorentzian function in magnetic resonance notation. Syntax:
%
% g=lorentzfun(x,fwhm)
%
% where fwhm is the full width at half-maximum.
%
% i.kuprov@soton.ac.uk
function y=lorentzfun(x,fwhm)
% Get the width parameter
gamma=fwhm/2;
% Compute the Lorentzian
y=(1/(pi*g... |
github | tsajed/nmr-pred-master | cce.m | .m | nmr-pred-master/spinach/kernel/utilities/cce.m | 1,979 | utf_8 | 332585b9b8dbb41b670e53869698205c | % Cluster Correlation Expansion function - partitions the spin_system
% object into individual subsystems prescribed by the CCE clusterisa-
% tion model [DOI reference here]. Syntax:
%
% [subsystems,indices]=cce(spin_system,system,bath,order)
%
% Parameters:
%
% system - a row vector giving the numb... |
github | tsajed/nmr-pred-master | anax2dcm.m | .m | nmr-pred-master/spinach/kernel/utilities/anax2dcm.m | 1,431 | utf_8 | 69ddaf3bacea8b6f5c3c7f7b1a9d67a8 | % Converts angle-axis rotation parameters to directional
% cosine matrix. Angle should be in radians, axis is nor-
% malized by the function. Syntax:
%
% dcm=anax2dcm(rot_axis,rot_angle)
%
% Arguments:
%
% rot_axis - cartesian direction vector given as
% a row or column with ... |
github | tsajed/nmr-pred-master | dipolar.m | .m | nmr-pred-master/spinach/kernel/utilities/dipolar.m | 6,606 | utf_8 | 827e01525aee4718f439a76ea78494cd | % Computes dipolar couplings in the presence or absence of periodic
% boundary conditions. This is an auxiliary function of Spinach ker-
% nel, direct calls are discouraged. Use xyz2dd to convert Cartesian
% coordinates to dipolar couplings.
%
% i.kuprov@soton.ac.uk
function spin_system=dipolar(spin_system)
... |
github | tsajed/nmr-pred-master | fdlap.m | .m | nmr-pred-master/spinach/kernel/utilities/fdlap.m | 3,339 | utf_8 | d82df57a50cccf027a969a106be10ac8 | % Returns a finite-difference representation of the Laplacian for a 3D
% array with a user-specified finite difference stencil size. The re-
% sulting operator is a sparse matrix designed to act on the vectori-
% zation of the 3D array. The dimensions of the 3D array are assumed
% to be ordered as [X Y Z]. Syntax:
... |
github | tsajed/nmr-pred-master | pauli.m | .m | nmr-pred-master/spinach/kernel/utilities/pauli.m | 2,086 | utf_8 | 94982ebd7f6c7f8dd68c8cafd23752b3 | % Pauli matrices for a spin of user-specified multiplicity. Syntax:
%
% sigma=pauli(mult)
%
% Where mult is an integer specifying the multiplicity and the following
% fields are returned in the output:
%
% sigma.u - unit operator
%
% sigma.p - raising operator
%
% sigma.m - ... |
github | tsajed/nmr-pred-master | frac2cart.m | .m | nmr-pred-master/spinach/kernel/utilities/frac2cart.m | 1,952 | utf_8 | 0c9b8c549348af909189f3550078b96d | % Converts fractional crystallographic coordinates to Cartesian
% coordinates. Syntax:
%
% [XYZ,va,vb,vc]=frac2cart(a,b,c,alpha,beta,gamma,ABC)
%
% Parameters:
%
% a,b,c - three unit cell dimensions
%
% alp,bet,gam - three unit cell angles, degrees
%
% ABC - fractio... |
github | tsajed/nmr-pred-master | significant.m | .m | nmr-pred-master/spinach/kernel/utilities/significant.m | 1,320 | utf_8 | ef8c331e427f57f0ef381578b27360ea | % An aux function determining whether a given object deserves attention
% given the tolerance specified. Used in the internal decision making
% performed by Spinach kernel functions. Syntax:
%
% answer=significant(object,tolerance)
%
% Parameters:
%
% object - the object whose significanc... |
github | tsajed/nmr-pred-master | perm_group.m | .m | nmr-pred-master/spinach/kernel/utilities/perm_group.m | 19,832 | utf_8 | 71e331975b2c3366baddf4db358c5ed4 | % Permutation group database. Returns basic information about permutation
% groups up to S6. Syntax:
%
% group=perm_group(group_name)
%
% The following group names are available: S2, S3, S4, S5, S6, S4A, the
% latter one being the largest Abelian subgroup of S4.
%
% Output fields:
%
% gro... |
github | tsajed/nmr-pred-master | killcross.m | .m | nmr-pred-master/spinach/kernel/utilities/killcross.m | 255 | utf_8 | f6071b17d58bcea310d1fe40e4f234be | % Wipes the specified rows and columns.
%
% i.kuprov@soton.ac.uk
function spec=killcross(spec,f1idx,f2idx)
% Wipe the indices
spec(f2idx,:)=0;
spec(:,f1idx)=0;
end
% A narcissist is someone better-looking than you are.
%
% Gore Vidal
|
github | tsajed/nmr-pred-master | symmetry.m | .m | nmr-pred-master/spinach/kernel/utilities/symmetry.m | 10,436 | utf_8 | ea35bca6be1eb1968685ab6164d9f981 | % Symmetry treatment. This is a service function of the Spinach
% kernel that should not be called directly.
%
% i.kuprov@soton.ac.uk
% hannah.hogben@chem.ox.ac.uk
function spin_system=symmetry(spin_system,bas)
% Check consistency
grumble(spin_system,bas);
% Check the disable switch
if ismember('symmetry... |
github | tsajed/nmr-pred-master | interpmat.m | .m | nmr-pred-master/spinach/kernel/utilities/interpmat.m | 4,437 | utf_8 | e2e9e5f38bde0747e0fd360e530038c8 | % Returns a matrix that acts on a stretched pseudocontact shift density cube
% and projects out the values of the PCS at the Cartesian coordinates given.
% Tricubic interpolation is used. Syntax:
%
% P=interpmat(cube_dims,ranges,xyz)
%
% Parameters:
%
% cube_dims - PCS cube dimensions, ... |
github | tsajed/nmr-pred-master | centroid.m | .m | nmr-pred-master/spinach/kernel/utilities/centroid.m | 586 | utf_8 | 6afe1d74e9878ea3fbb54563acb46f26 | % Finds the centroid of a 3D probability density in a cube.
%
% i.kuprov@outlook.com
function [x,y,z]=centroid(probden,ranges)
% Get coordinate arrays
[X,Y,Z]=ndgrid(linspace(ranges(1),ranges(2),size(probden,1)),...
linspace(ranges(3),ranges(4),size(probden,2)),...
linspace(rang... |
github | tsajed/nmr-pred-master | plot_3d.m | .m | nmr-pred-master/spinach/kernel/utilities/plot_3d.m | 8,479 | utf_8 | e276bec2f80d02566db61985f8d9a41e | % Volume isosurface plotting utility with non-linear adaptive isosurface
% spacing.The function is useful for NMR data where small cross-peaks
% must be adequately contoured next to large diagonal peaks. Syntax:
%
% plot_3d(spin_system,spectrum,parameters,ncont,delta,k,signs)
%
% The following functions are ... |
github | tsajed/nmr-pred-master | hartree2joule.m | .m | nmr-pred-master/spinach/kernel/utilities/hartree2joule.m | 428 | utf_8 | a624aecda234c26d76174690309a3775 | % Converts Hartree energy units into J/mol. Syntax:
%
% energy=hartree2joule(energy)
%
% Arrays of any dimension are supported.
%
% i.kuprov@soton.ac.uk
function energy=hartree2joule(energy)
% Perform the conversion
energy=2625499.62*energy;
end
% "We only need to be lucky once. You need to... |
github | tsajed/nmr-pred-master | mhz2gauss.m | .m | nmr-pred-master/spinach/kernel/utilities/mhz2gauss.m | 657 | utf_8 | a44c974a7f775f085f28b7374165ec01 | % Converts hyperfine couplings from MHz (linear frequency)
% to Gauss. Syntax:
%
% hfc_gauss=mhz2gauss(hfc_mhz)
%
% Arrays of any dimensions are supported.
%
% i.kuprov@soton.ac.uk
function hfc_gauss=mhz2gauss(hfc_mhz)
if isnumeric(hfc_mhz)&&isreal(hfc_mhz)
hfc_gauss=hfc_mhz/2.802495365;... |
github | tsajed/nmr-pred-master | lm2lin.m | .m | nmr-pred-master/spinach/kernel/utilities/lm2lin.m | 1,263 | utf_8 | e449279327599e7929e96a7ac394df81 | % Converts L,M spin state specification to linear indexing specification.
% In the linear indexing convention, the states are listed in the order of
% inc reasing L rank, and, within ranks, in the order of decreasing M pro-
% jection. Syntax: I=lm2lin(L,M)
%
% WARNING - zero base indexing, that is:
% ... |
github | tsajed/nmr-pred-master | tolerances.m | .m | nmr-pred-master/spinach/kernel/utilities/tolerances.m | 14,822 | utf_8 | 410287a797baec77b067198e427f4f4a | % Tolerances and fundamental constants. Sets the various accuracy cut-offs,
% constants and tolerances used throughout Spinach kernel.
%
% Modifications to this function are discouraged -- the accuracy settings
% should be modified by setting the sub-fields of the sys.tols structure,
% see the input preparation m... |
github | tsajed/nmr-pred-master | equilibrate.m | .m | nmr-pred-master/spinach/kernel/utilities/equilibrate.m | 269 | utf_8 | 7dae323be6de9a16df803636cdd1d17c | % Equilibrates a linear chemical kinetics system for
% a user-specified time. Syntax:
%
% c=equilibrate(K,c0,t)
%
% i.kuprov@soton.ac.uk
function c=equilibrate(K,c0,t)
% Run the chemical kinetics for a specified time
c=expm(K*t)*c0;
end
|
github | tsajed/nmr-pred-master | quat2dcm.m | .m | nmr-pred-master/spinach/kernel/utilities/quat2dcm.m | 1,281 | utf_8 | aa4dad5b1d28a070200c6a5530d4c6df | % Converts a quaternion rotation specification into a corresponding
% direction cosine matrix. Syntax:
%
% dcm=quat2anax(q)
%
% where q is a structure with four fields q.u, q.i, q.j, q.k giving
% the four components of the quaternion.
%
% i.kuprov@soton.ac.uk
function dcm=quat2dcm(q)
% Chec... |
github | tsajed/nmr-pred-master | p_superop.m | .m | nmr-pred-master/spinach/kernel/utilities/p_superop.m | 5,872 | utf_8 | e07bac99ee7832977644582da0679a92 | % Sided product superoperator in the spherical tensor basis set. Returns
% superoperators corresponding to right or left multiplication of a den-
% sity matrix by a user-specified operator. Syntax:
%
% A=p_superop(spin_system,opspec,side)
%
% Arguments:
%
% opspec - Spinach operator specifi... |
github | tsajed/nmr-pred-master | sphten2state.m | .m | nmr-pred-master/spinach/kernel/utilities/sphten2state.m | 1,274 | utf_8 | 3e16a8a8db0d6ddd6983c2fb2c518775 | % Generates a state vector from its spherical tensor expansion produced
% by zeeman2sphten() function. Syntax:
%
% rho=sphten2state(spin_system,stexp,spin_num)
%
% where stexp is a cell array with the first element of each row giving
% the operator name and the second element being the corresponding sphe-
... |
github | tsajed/nmr-pred-master | fpl2phan.m | .m | nmr-pred-master/spinach/kernel/utilities/fpl2phan.m | 853 | utf_8 | 0fc482450c034c53ff8ee4842cc54f08 | % Returns the image encoded within the Fokker-Planck vector by the
% user-specified Liouville space coil state. Syntax:
%
% phan=fpl2phan(rho,coil,dims)
%
% Parameters:
%
% rho - state vector in Fokker-Planck space
%
% coil - observable state vector in Liouville space
%
% d... |
github | tsajed/nmr-pred-master | molplot.m | .m | nmr-pred-master/spinach/kernel/utilities/molplot.m | 1,706 | utf_8 | 749ea08b983966a11f451915891ff201 | % Plots a stick representation of a molecule from Cartesian coordinates
% supplied. Coordinates must be in Angstroms. Syntax:
%
% molplot(xyz,conmatrix)
%
% Parameters:
%
% xyz - Cartesian coordinates, as Nx3 matrix
%
% conmatrix - NxN connectivity matrix indicating c... |
github | tsajed/nmr-pred-master | lin2lm.m | .m | nmr-pred-master/spinach/kernel/utilities/lin2lm.m | 1,219 | utf_8 | ed9a2ae330c0b0d26432688d411caa13 | % Converts linear indexing state specification to L,M indexing. In
% the linear indexing convention, the states are listed in the order
% of increasing L rank, and, within ranks, in the order of decreas-
% ing M projection. Syntax: [L,M]=lin2lm(I)
%
% WARNING - zero base indexing, that is:
%
% ... |
github | tsajed/nmr-pred-master | fdkup.m | .m | nmr-pred-master/spinach/kernel/utilities/fdkup.m | 3,777 | utf_8 | a218d6f10a38f735158e9e236425a9a2 | % Returns a finite difference representation of the Kuprov operator:
%
% K[rho]=-(1/3)*Trace(Hessian[rho]*chi)
%
% with the number of stencil points in the finite difference approxi-
% mation specified by user. Syntax:
%
% K=fdkup(npoints,extents,chi,nstenc)
%
% The following p... |
github | tsajed/nmr-pred-master | mprealloc.m | .m | nmr-pred-master/spinach/kernel/utilities/mprealloc.m | 1,856 | utf_8 | ae769ea3bf403d8398d8da53e9fec5eb | % Preallocates an operator in the current basis. Syntax:
%
% A=mprealloc(spin_system,nnzpc)
%
% Parameters:
%
% nnzpc - expected number of non-zeros per column
%
% i.kuprov@soton.ac.uk
function A=mprealloc(spin_system,nnzpc)
% Check the input
if (~isnumeric(nnzpc))||(~isreal(nnzpc))||(~i... |
github | tsajed/nmr-pred-master | spher_harmon.m | .m | nmr-pred-master/spinach/kernel/utilities/spher_harmon.m | 1,443 | utf_8 | 9490c86690e660a11cac1143c9ffd344 | % Computes spherical harmonics. Syntax:
%
% Y=spher_harmon(l,m,theta,phi)
%
% Parameters:
%
% l - L quantum number
%
% m - M quantum number
%
% theta - a vector of theta angles in radians
%
% phi - a vector of phi angles in radians
%
% i.kuprov@so... |
github | tsajed/nmr-pred-master | fdweights.m | .m | nmr-pred-master/spinach/kernel/utilities/fdweights.m | 2,253 | utf_8 | 55f7411498fb404d38d8919c7e2d8ec4 | % Calculates finite difference weights for numerical derivatives (inclu-
% ding order 0, which amounts to interpolation). Syntax:
%
% w=fdweights(target_point,grid_points,max_order)
%
% Parameters:
%
% target_point - the point at which the derivative is required
%
% grid_points - the points at which... |
github | tsajed/nmr-pred-master | dihedral.m | .m | nmr-pred-master/spinach/kernel/utilities/dihedral.m | 980 | utf_8 | 6f9b86e6e2520287a019750bef8fd3c7 | % Computes the dihedral angle between vectors specified
% by the four sets of atomic coordinates. The angle is
% returned in degrees. The atoms are assumed to be bon-
% ded as A-B-C-D. Syntax:
%
% phi=dihedral(A,B,C,D)
%
% i.kuprov@soton.ac.uk
function phi=dihedral(A,B,C,D)
% Check consiste... |
github | tsajed/nmr-pred-master | volplot.m | .m | nmr-pred-master/spinach/kernel/utilities/volplot.m | 5,448 | utf_8 | 704983c4c1885d881504242dacf3a0c9 | % Volumetric plot function for scalar fields. Syntax:
%
% volplot(data_cube,axis_ranges)
%
% where data_cube is a 3D cube of real data and axis
% ranges is a six-element vector giving axis extents
% as [xmin xmax ymin ymax zmin zmax].
%
% i.kuprov@soton.ac.uk
function volplot(data_cube,axis_ranges... |
github | tsajed/nmr-pred-master | clean_up.m | .m | nmr-pred-master/spinach/kernel/utilities/clean_up.m | 1,649 | utf_8 | 81b37e3e9fa2fdcb77716243bdd4ae83 | % Array clean-up utility. Drops non-zero elements with magnitude below the
% user-specified tolerance and converts between sparse and dense represen-
% tations depending on the density of non-zeros in the array. Syntax:
%
% A=clean_up(spin_system,A,nonzero_tol)
%
% i.kuprov@soton.ac.uk
% alex_nev... |
github | tsajed/nmr-pred-master | corrfun.m | .m | nmr-pred-master/spinach/kernel/utilities/corrfun.m | 3,927 | utf_8 | df440de11c91f97ab68786f09c80cbb1 | % Rotational correlation function, normalized to be the correlation func-
% tion between second rank Wigner functions. Syntax:
%
% [weights,rates]=corrfun(spin_system,k,m,p,q)
%
% where the indices k,m,p,q correspond to the four indices found in the
% ensemble-averaged Wigner function product:
%
% ... |
github | tsajed/nmr-pred-master | krondelta.m | .m | nmr-pred-master/spinach/kernel/utilities/krondelta.m | 279 | utf_8 | f7e344eeb76194157948ab9d6887785a | % Kronecker symbol. Syntax:
%
% d=krondelta(a,b)
%
% i.kuprov@soton.ac.uk
function d=krondelta(a,b)
if a==b, d=1; else, d=0; end
end
% Die ganzen Zahlen hat der liebe Gatt gemacht,
% alles andere ist Menschenwerk.
%
% Leopold Kronecker
|
github | tsajed/nmr-pred-master | apodization.m | .m | nmr-pred-master/spinach/kernel/utilities/apodization.m | 8,057 | utf_8 | 0ad443b71611fb9e133cea297325df2e | % Performs free induction decay apodization. Supports 1D, 2D and 3D FIDs with
% the following syntax:
%
% fid=apodization(fid,window_type,params)
%
% Arguments:
%
% fid - The free induction decay. The function expects a column
% vector in the case of 1D FID, a 2D m... |
github | tsajed/nmr-pred-master | zte.m | .m | nmr-pred-master/spinach/kernel/utilities/zte.m | 5,566 | utf_8 | a7003372b5f1eb62c201b8efe1c47394 | % Zero track elimination function. Inspects the first few steps in the
% system trajectory and drops the states that did not get populated to a
% user-specified tolerance. The default tolerance may be altered by set-
% ting sys.tols.zte_tol variable before calling create(). Syntax:
%
% projector=zte... |
github | tsajed/nmr-pred-master | rotor_stack.m | .m | nmr-pred-master/spinach/kernel/utilities/rotor_stack.m | 3,396 | utf_8 | c4ed13d68bf6c33318dd0b8eb1ea7c81 | % Returns a rotor stack of Liouvillians or Hamiltonians. The stack is
% needed for the traditional style calculation of MAS dynamics. Syntax:
%
% L=rotor_stack(spin_system,parameters,assumptions)
%
% Parameters:
%
% parameters.axis - spinning axis, given as a normalized
% ... |
github | tsajed/nmr-pred-master | xyz2dd.m | .m | nmr-pred-master/spinach/kernel/utilities/xyz2dd.m | 1,548 | utf_8 | bdb467f2a77eb37191d097db18fc34a7 | % Converts coordinate specification of the dipolar interaction
% into the dipolar interaction constant (angular frequency un-
% its), three Euler angles in radians and the dipolar interac-
% tion matrix (angular frequency units). Syntax:
%
% [d,alp,bet,gam,m]=xyz2dd(r1,r2,isotope1,isotope2)
%
% where r1 and... |
github | tsajed/nmr-pred-master | zeeman2sphten.m | .m | nmr-pred-master/spinach/kernel/utilities/zeeman2sphten.m | 1,797 | utf_8 | 0980b33c65b4637f8a563833ff7d9abf | % Generates spherical tensor expansions for single-spin Zeeman
% basis operators in Hilbert space. Syntax:
%
% stexp=zeeman2sphten(matrix,type)
%
% where matrix is a single-spin matrix written in the Zeeman ba-
% sis in Hilbert space, type denote the matrix is a density mat-
% rix or a operator, a... |
github | tsajed/nmr-pred-master | sparse2csr.m | .m | nmr-pred-master/spinach/kernel/utilities/sparse2csr.m | 1,474 | utf_8 | 3c80738f30e8449faf35525f8f7e6aae | % Computes a partial Compressed Row Storage transformation for a given
% Matlab sparse matrix. Only returns the index arrays and ignores the
% values. Syntax:
%
% [row_ptr,col_idx]=sparse2csr(A)
%
% Parameters:
%
% A - sparse matrix to be converted into the CSR
% format
%... |
github | tsajed/nmr-pred-master | dcm2quat.m | .m | nmr-pred-master/spinach/kernel/utilities/dcm2quat.m | 3,822 | utf_8 | ae52e6b446c66c6e0897b87cccf44e10 | % Converts a direction cosine matrix representation of a rotation into
% the unit quaternion representation. Syntax:
%
% q=dcm2quat(dcm)
%
% Output: a structure with four fields q.u, q.i, q.j, q.k giving the
% four components of the quaternion.
%
% i.kuprov@soton.ac.uk
function q=dcm2quat(dc... |
github | tsajed/nmr-pred-master | lcurve.m | .m | nmr-pred-master/spinach/kernel/utilities/lcurve.m | 2,869 | utf_8 | c0b8184b4bc2c5e4eb7d99fed4484c38 | % L-curve analysis function. Syntax:
%
% lambda_opt=lcurve(lambda,err,reg,mode)
%
% Parameters:
%
% lam - row vector of regularisation parameters
%
% err - row vector of least squares errors
%
% reg - row vector of regularisation functional values
%
% The function returns ... |
github | tsajed/nmr-pred-master | castep2nqi.m | .m | nmr-pred-master/spinach/kernel/utilities/castep2nqi.m | 1,531 | utf_8 | 3b543d1c141e38ad6a0bd4b6ea36ca2a | % Converts CASTEP EFG tensor (it is printed in atomic units) to NQI
% 3x3 tensor in Hz that is required by Spinach. Syntax:
%
% nqi=castep2nqi(V,Q,I)
%
% Parameters:
%
% V - EFG tensor from CASTEP output, a.u.
%
% Q - nuclear quadrupole moment, barn
%
% I - nuclear spin ... |
github | tsajed/nmr-pred-master | banner.m | .m | nmr-pred-master/spinach/kernel/utilities/banner.m | 3,083 | utf_8 | 731fa3b6606e57b88cee21d2392c22c1 | % Prints the banners. This is an internal function of the Spinach kernel,
% user edits are discouraged.
%
% i.kuprov@soton.ac.uk
function banner(spin_system,identifier)
switch identifier
case 'version_banner'
report(spin_system,' ');
report(spin_system,'==================================... |
github | tsajed/nmr-pred-master | unit_state.m | .m | nmr-pred-master/spinach/kernel/utilities/unit_state.m | 1,223 | utf_8 | 8c6ea4cecf40c375c05daecb33744f15 | % Returns a unit state in the current formalism and basis. Syntax:
%
% rho=unit_state(spin_system)
%
% There are no adjustable parameters.
%
% i.kuprov@soton.ac.uk
% d.savostyanov@soton.ac.uk
function rho=unit_state(spin_system)
% Decide how to proceed
switch spin_system.bas.formalism
... |
github | tsajed/nmr-pred-master | dcm2wigner.m | .m | nmr-pred-master/spinach/kernel/utilities/dcm2wigner.m | 2,585 | utf_8 | 312f02cab4eb464b048bbb6067a0a525 | % Converts a directional cosine matrix into second-rank Wigner function
% matrix. Rows and columns of the resulting Wigner matrix are sorted by
% descending ranks, that is:
%
% [D( 2,2) ... D( 2,-2)
% ... ... ...
% D(-2,2) ... |
github | tsajed/nmr-pred-master | shift_iso.m | .m | nmr-pred-master/spinach/kernel/utilities/shift_iso.m | 2,064 | utf_8 | c8dc1127a718c64ce58873a334fb5db6 | % Replaces the isotropic parts of interaction tensors with user-supplied values.
% This is useful for correcting DFT calculations, where the anisotropy is usually
% satisfactory, but the isotropic part often is not. Arguments:
%
% tensors - a cell array of interaction tensors as 3x3 matrices
%
% sp... |
github | tsajed/nmr-pred-master | euler2dcm.m | .m | nmr-pred-master/spinach/kernel/utilities/euler2dcm.m | 1,944 | utf_8 | 21c30b60b250c5185033c7d66f347e0e | % Converts Euler angles to a direction cosine matrix. Syntax:
%
% R=euler2dcm(alpha,beta,gamma)
%
% OR
%
% R=euler2dcm([alpha beta gamma])
%
% where alpha, beta and gamma are Euler angles in radians. The resulting
% rotation matrix is to be... |
github | tsajed/nmr-pred-master | xyz2hfc.m | .m | nmr-pred-master/spinach/kernel/utilities/xyz2hfc.m | 1,053 | utf_8 | daec3780923b56e7e4a7b0b517b5f953 | % Converts point electron and nuclear coordinates (Angstroms)
% into a hyperfine interaction tensor in Hz. Syntax:
%
% A=xyz2hfc(e_xyz,n_xyz,isotope)
%
% i.kuprov@soton.ac.uk
function A=xyz2hfc(e_xyz,n_xyz,isotope)
% Fundamental constants
hbar=1.054571800e-34; mu0=4*pi*1e-7;
% Get magneto... |
github | tsajed/nmr-pred-master | md5_hash.m | .m | nmr-pred-master/spinach/kernel/utilities/md5_hash.m | 1,231 | utf_8 | 46fcfac57c36c60c3db6fabf66b5310d | % Computes the MD5 hash of any Matlab object and returns it as a
% hex string. Identical sparse and full matrices return different
% hashes. Syntax:
%
% hashstr=md5_hash(A)
%
% i.kuprov@soton.ac.uk
function hashstr=md5_hash(A)
% Create the engine
engine=java.security.MessageDigest.getInstance... |
github | tsajed/nmr-pred-master | chirp_pulse_af.m | .m | nmr-pred-master/spinach/kernel/pulses/chirp_pulse_af.m | 1,778 | utf_8 | 33d42445d2f2960931dc9e2a4e18de68 | % Chirp pulse waveform with a sine bell amplitude envelope in amplitude-
% frequency coordinates. Syntax:
%
% [ampls,freqs]=chirp_pulse_af(npoints,duration,bandwidth,smfactor)
%
% with the following parameters:
%
% npoints - number of discretization points in
% the waveform
%
% ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.