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github | sanghosuh/lens_nmf-matlab-master | compute_total_doc_cvrg.m | .m | lens_nmf-matlab-master/evaluation/total_document_coverage/compute_total_doc_cvrg.m | 3,754 | utf_8 | 04b200587eeed0ab2478d94ed634045a | % Total Document Coverage
%
% Written by Sangho Suh (sh31659@gmail.com)
% Dept. of Computer Science and Engineering,
% Korea University
%
% Reference:
%
% [1] Sangho Suh, Jaegul Choo, Joonseok Lee and Chandan K. Reddy.
% L-EnsNMF: Boosted Local Topic Discovery via Ensemble of Nonnegative ... |
github | sanghosuh/lens_nmf-matlab-master | weakorthonmf.m | .m | lens_nmf-matlab-master/library/ramkis/weakorthonmf.m | 33,961 | utf_8 | 35a6c05d74c3570a95b513b216f63769 | % Weakly Orthogonal Nonnegative Matrix Factorization
%
% Written by Jaegul Choo (jchoo@korea.ac.kr)
% Dept. of Computer Science and Engineering,
% Korea University
%
% Please send bug reports, comments, or questions to Jingu Kim.
% This code comes with no guarantee or warranty of any kind.
%
% Ref... |
github | sanghosuh/lens_nmf-matlab-master | fcnnls.m | .m | lens_nmf-matlab-master/library/nmf/fcnnls.m | 4,407 | utf_8 | b1a8ecaaeeec231beb8a0a043366505e | % M. H. Van Benthem and M. R. Keenan, J. Chemometrics 2004; 18: 441-450
%
% Given A and C this algorithm solves for the optimal
% K in a least squares sense, using that
% A = C*K
% in the problem
% min ||A-C*K||, s.t. K>=0, for given A and C.
%
function [K, Pset, many_iter] = fcnnls(C, A)
% NNLS using norma... |
github | sanghosuh/lens_nmf-matlab-master | nmfsh_comb_original.m | .m | lens_nmf-matlab-master/library/nmf/nmfsh_comb_original.m | 4,989 | utf_8 | 033ed6a9348041d0caab80dc5834ee2b | %
% SNMF/R
%
% Author: Hyunsoo Kim and Haesun Park, Georgia Insitute of Technology
%
% Reference:
%
% Sparse Non-negative Matrix Factorizations via Alternating
% Non-negativity-constrained Least Squares for Microarray Data Analysis
% Hyunsoo Kim and Haesun Park, Bioinformatics, 2007, to appear.
%
% This software ... |
github | sanghosuh/lens_nmf-matlab-master | nmf.m | .m | lens_nmf-matlab-master/library/nmf/nmf.m | 25,072 | utf_8 | 6ff4cbae3d1bff8b4c05b0a8a3485728 | % Nonnegative Matrix Factorization : Algorithms Toolbox
%
% Written by Jingu Kim (jingu.kim@gmail.com)
% School of Computational Science and Engineering,
% Georgia Institute of Technology
%
% Please send bug reports, comments, or questions to Jingu Kim.
% This code comes with no guarantee or warra... |
github | sanghosuh/lens_nmf-matlab-master | nnlsm_blockpivot.m | .m | lens_nmf-matlab-master/library/nmf/nnlsm_blockpivot.m | 4,547 | utf_8 | f7cbdd610f2388c434a4444f43bdc3f2 | % Nonnegativity Constrained Least Squares with Multiple Righthand Sides
% using Block Principal Pivoting method
%
% This software solves the following problem: given A and B, find X such that
% minimize || AX-B ||_F^2 where X>=0 elementwise.
%
% Reference:
% Jingu Kim and Haesun Park, Toward Fas... |
github | sanghosuh/lens_nmf-matlab-master | nmfsh_comb.m | .m | lens_nmf-matlab-master/library/nmf/nmfsh_comb.m | 4,550 | utf_8 | 256156e36e548ecf054efe5ef6c2a532 | %
% SNMF/R
%
% Author: Hyunsoo Kim and Haesun Park, Georgia Insitute of Technology
%
% Reference:
%
% Sparse Non-negative Matrix Factorizations via Alternating
% Non-negativity-constrained Least Squares for Microarray Data Analysis
% Hyunsoo Kim and Haesun Park, Bioinformatics, 2007, to appear.
%
% This software ... |
github | sanghosuh/lens_nmf-matlab-master | nnlsm_activeset.m | .m | lens_nmf-matlab-master/library/nmf/nnlsm_activeset.m | 5,020 | utf_8 | 5d51124cecf5c37d8ab6c1ec91dbad32 | % Nonnegativity Constrained Least Squares with Multiple Righthand Sides
% using Active Set method
%
% This software solves the following problem: given A and B, find X such that
% minimize || AX-B ||_F^2 where X>=0 elementwise.
%
% Reference:
% Charles L. Lawson and Richard J. Hanson, Solving Leas... |
github | sanghosuh/lens_nmf-matlab-master | lens_nmf.m | .m | lens_nmf-matlab-master/library/lens_nmf/lens_nmf.m | 3,937 | utf_8 | 5cbdf2fafe4b052a4903068efafbcbf4 | % Localizd Ensemble of Nonnegative Matrix Factorization (L-EnsNMF)
%
% Written by Sangho Suh (sh31659@gmail.com)
% Dept. of Computer Science and Engineering,
% Korea University
%
% Reference:
%
% [1] Sangho Suh et al.
% Boosted L-EnsNMF: Local Topic Discovery via Ensemble of Nonnegative Matr... |
github | sanghosuh/lens_nmf-matlab-master | lens_nmf.bak.m | .m | lens_nmf-matlab-master/library/lens_nmf/lens_nmf.bak.m | 4,098 | utf_8 | 2d70f47e31eb3f1cc1db8f894af46665 | % NOTE: This version is NOT in use as it is outdated
% (It is before rank-2 NMF has been applied)
%
% Localizd Ensemble of Nonnegative Matrix Factorization (L-EnsNMF)
%
% Written by Sangho Suh (sh31659@gmail.com)
% Dept. of Computer Science and Engineering,
% Korea University
%
% Reference... |
github | sanghosuh/lens_nmf-matlab-master | tfidf2.m | .m | lens_nmf-matlab-master/library/topictoolbox/tfidf2.m | 794 | utf_8 | 7e53767d9b5be3579b2c33e015e1991e | function [Y w] = tfidf2( X )
% FUNCTION applies TF-IDF weighting to word count vector matrix.
%
% [Y w] = tfidf2( X );
%
% INPUT :
% X - word count vectors (one column = one document)
%
% OUTPUT :
% Y - TF-IDF weighted document-term matrix
% w - IDF weights (useful to process other document... |
github | masa-nudt/KCFDPT-master | run_tracker.m | .m | KCFDPT-master/run_tracker.m | 4,772 | utf_8 | 01f944bd59d3493d2df3bc098150dc22 | % KCFDPT enhances KCFDP with "Background Suppression"
% KCFDP is the visual object tracker presented in:
% "Enable Scale and Aspect Ratio Adaptability in Visual Tracking with Detection Proposals" BMVC, 2015
%
% Dafei Huang, Lei Luo, Mei Wen, Zhaoyun Chen and Chunyuan Zhang
%
% Utilization of EdgeBox... |
github | masa-nudt/KCFDPT-master | run_KCFDPT.m | .m | KCFDPT-master/run_KCFDPT.m | 4,286 | utf_8 | 50eee1de0783f61cec78a3c38ae0e7e7 | % KCFDPT enhances KCFDP with "Background Suppression"
% KCFDP is the visual object tracker presented in:
% "Enable Scale and Aspect Ratio Adaptability in Visual Tracking with Detection Proposals" BMVC, 2015
%
% Dafei Huang, Lei Luo, Mei Wen, Zhaoyun Chen and Chunyuan Zhang
%
% Utilization of EdgeBoxes to e... |
github | masa-nudt/KCFDPT-master | tracker.m | .m | KCFDPT-master/tracker.m | 12,152 | utf_8 | 03823a16cd4562c9c8895d265bfebe8f | % Original code is from Kernelized/Dual Correlation Filter (KCF/DCF)
% by Joao F. Henriques, 2015
% Integrated and modified by Dafei Huang
function [rect_position, fps] = tracker(params, ...
padding, sigma, lambda, output_sigma_factor, interp_factor, ...
cell_size, hog_orientations, ...
mode... |
github | masa-nudt/KCFDPT-master | edgeBoxesTrackParam.m | .m | KCFDPT-master/edgeBoxesTrackParam.m | 4,994 | utf_8 | aae1f43113514db72a60c1023b1543cb | function bbs = edgeBoxesTrackParam( I, model, backSup_size, varargin )
% Generate Edge Boxes object proposals in given image(s).
%
% Compute Edge Boxes object proposals as described in:
% C. Lawrence Zitnick and Piotr Doll?
% "Edge Boxes: Locating Object Proposals from Edges", ECCV 2014.
% The proposal boxes ar... |
github | masa-nudt/KCFDPT-master | find_scale_change_level_seqs.m | .m | KCFDPT-master/anno_tool/find_scale_change_level_seqs.m | 1,502 | utf_8 | ff2265e4bcedb5b56bfa05372b7d4d16 | % Use 2.0, 1.8, 1.6 as parameter to find out sequences with different scale variation levels
function find_scale_change_level_seqs(scale_exam_thres)
pathAnno = './anno/';
attPath = './anno/att/';
addpath('./util/');
seqs = configSeqs;
total_sc_variation = 0;
total_frame = 0;
count_variation_seqs = 0;
f... |
github | masa-nudt/KCFDPT-master | find_aspect_ratio_change_seqs.m | .m | KCFDPT-master/anno_tool/find_aspect_ratio_change_seqs.m | 1,666 | utf_8 | 484a19e57cc10a9eb4bc3da64a0835ff | % Find out and annotate sequences with obvious aspect ratio variation
function find_aspect_ratio_change_seqs()
pathAnno = './anno/';
attPath = './anno/att/';
addpath('./util/');
seqs = configSeqs;
total_ar_variation = 0;
total_frame = 0;
for idxSeq=1:length(seqs)
s = seqs{idxSeq};
s.len =... |
github | masa-nudt/KCFDPT-master | find_aspect_ratio_change_level_seqs.m | .m | KCFDPT-master/anno_tool/find_aspect_ratio_change_level_seqs.m | 1,266 | utf_8 | d7d2537ca8c5744e27546ffddf18a76c | % Use 1.6, 1.5, 1.4 as parameter to find out sequences with different aspect ratio variation levels
function find_aspect_ratio_change_level_seqs(aspect_ratio_exam_thres)
pathAnno = './anno/';
attPath = './anno/att/';
addpath('./util/');
seqs = configSeqs;
total_ar_variation = 0;
total_frame = 0;
for idx... |
github | masa-nudt/KCFDPT-master | find_scale_change_rate_seqs.m | .m | KCFDPT-master/anno_tool/find_scale_change_rate_seqs.m | 1,502 | utf_8 | 8cd0438817329932aab7fd4f6f2dc435 | % Use 10, 20, 30 as parameter to find out sequences with different scale variation rates
function find_scale_change_rate_seqs(scale_exam_window)
pathAnno = './anno/';
attPath = './anno/att/';
addpath('./util/');
seqs = configSeqs;
total_sc_variation = 0;
total_frame = 0;
count_variation_seqs = 0;
for i... |
github | masa-nudt/KCFDPT-master | find_aspect_ratio_change_rate_seqs.m | .m | KCFDPT-master/anno_tool/find_aspect_ratio_change_rate_seqs.m | 1,266 | utf_8 | 2b76b2d3af9ff02bb8bf9677ee8f35ea | % Use 10, 20, 30 as parameter to find out sequences with different aspect ratio variation rates
function find_aspect_ratio_change_rate_seqs(aspect_ratio_exam_window)
pathAnno = './anno/';
attPath = './anno/att/';
addpath('./util/');
seqs = configSeqs;
total_ar_variation = 0;
total_frame = 0;
for idxSeq=... |
github | tsajed/nmr-pred-master | s2spinach.m | .m | nmr-pred-master/spinach/etc/s2spinach.m | 5,215 | utf_8 | 66d7be1c0060b13e05fc7e6e10f05a32 | % Reads SIMPSON spin system specification file and converts the
% information into Spinach data structures. Syntax:
%
% [sys,inter]=s2spinach(filename)
%
% i.kuprov@soton.ac.uk
function [sys,inter]=s2spinach(filename)
% Check consistency
grumble(filename);
% Read the file
fid=fopen(filen... |
github | tsajed/nmr-pred-master | fid2ascii.m | .m | nmr-pred-master/spinach/etc/fid2ascii.m | 2,254 | utf_8 | d290db1a84bcaac9d24a144a520fdb7a | % Writes free induction decays into ASCII files.
%
% <http://spindynamics.org/wiki/index.php?title=Fid2ascii.m>
function fid2ascii(file_name,fid)
% Check consistency
grumble(fid)
% Open the file for writing
file_id=fopen(file_name,'w');
% Decide data dimensions
if isvector(fid)
% Interleave ... |
github | tsajed/nmr-pred-master | destreak.m | .m | nmr-pred-master/spinach/etc/destreak.m | 1,830 | utf_8 | e9cdee5122a200e1b85297391b7ffc4e | % Reduces streak artefacts in 2D and 3D NMR spectra.
%
% <http://spindynamics.org/wiki/index.php?title=Destreak.m>
function spectrum=destreak(spectrum)
% Process structures and cell arrays recursively
if isstruct(spectrum)
% Get the field names
struct_fieldnames=fieldnames(spectrum);
... |
github | tsajed/nmr-pred-master | guess_csa_pro.m | .m | nmr-pred-master/spinach/etc/guess_csa_pro.m | 4,861 | utf_8 | fd23d5a9383a5e93c2cb219ad3f6e9c2 | % Chemical shieft anisotropy estimates for peptide bond heteroatoms.
%
% <http://spindynamics.org/wiki/index.php?title=Guess_csa_pro.m>
function CSAs=guess_csa_pro(aa_nums,pdb_ids,coords)
% Check consistency
grumble(aa_nums,pdb_ids,coords);
% Preallocate CSA array
CSAs=cell(numel(pdb_ids),1);
% Number t... |
github | tsajed/nmr-pred-master | zfs_sampling.m | .m | nmr-pred-master/spinach/etc/zfs_sampling.m | 1,871 | utf_8 | 0641b3e36d23a8312fd27193983e1961 | % Sampling function for ZFS parameter distributions.
%
% <http://spindynamics.org/wiki/index.php?title=Zfs_sampling.m>
function [D,E,W]=zfs_sampling(npoints_d,npoints_e,tol)
% Check consistency
grumble(npoints_d,npoints_e,tol);
% Generate Gauss-Legendre point set for D/D1
[X,WX]=lgwt(npoints_d,-2,2);
% ... |
github | tsajed/nmr-pred-master | strychnine.m | .m | nmr-pred-master/spinach/etc/strychnine.m | 6,944 | utf_8 | 1ca29f49a8c2c448992a9ce45a75be9f | % Spin system of strychnine.
%
% <http://spindynamics.org/wiki/index.php?title=Strychnine.m>
function [sys,inter]=strychnine(spins)
% Check consistency
grumble(spins);
% Shorthands for human-readable coupling designations below
H1=1; H2=2; H3=3; H4=4; H8=5; H11a=6; H11b=7; H12=8; H13=9; H14=10;
H15a=11; H15b=12; H16... |
github | tsajed/nmr-pred-master | read_pdb_nuc.m | .m | nmr-pred-master/spinach/etc/read_pdb_nuc.m | 2,126 | utf_8 | 39429a1bc93649e3031f4b00e94ac39b | % Reads DNA/RNA PDB files.
%
% <http://spindynamics.org/wiki/index.php?title=Read_pdb_nuc.m>
function [res_num,res_typ,pdb_id,coords]=read_pdb_nuc(pdb_file_name)
% Check consistency
grumble(pdb_file_name);
% Open the PDB file
file_id=fopen(pdb_file_name,'r');
% Get the outputs started
res_num=[]; res_t... |
github | tsajed/nmr-pred-master | g2spinach.m | .m | nmr-pred-master/spinach/etc/g2spinach.m | 5,250 | utf_8 | 0a51da6a3f1beb6f44e4a32f5bce5cc5 | % Forms Spinach data structures from Gaussian parsing output returned by gparse.m function.
%
% <http://spindynamics.org/wiki/index.php?title=G2spinach.m>
function [sys,inter]=g2spinach(props,particles,references,options)
% Check consistency
grumble(props,particles,references,options);
% Index the particles... |
github | tsajed/nmr-pred-master | nuclacid.m | .m | nmr-pred-master/spinach/etc/nuclacid.m | 6,159 | utf_8 | 2f294048b43c8779677853ea1a7f6d1e | % Nucleic acid data import function.
%
% <http://spindynamics.org/wiki/index.php?title=Nuclacid.m>
function [sys,inter]=nuclacid(pdb_file,shift_file,options)
% Check consistency
grumble(pdb_file,shift_file,options);
% Parse the PDB file
[pdb_res_num,pdb_res_typ,pdb_atom_id,pdb_coords]=read_pdb_nuc(pdb_file... |
github | tsajed/nmr-pred-master | karplus_fit.m | .m | nmr-pred-master/spinach/etc/karplus_fit.m | 2,163 | utf_8 | 88a96f6fa5b27b83469c881f014c0b4f | % Fits a Karplus curve to a Gaussian dihedral angle scan.
%
% <http://spindynamics.org/wiki/index.php?title=Karplus_fit.m>
function [A,B,C]=karplus_fit(dir_path,atoms)
% Get all log files in the directory
logfiles=dir([dir_path '/*.log']);
% Get the arrays going
phi=[]; J=[]; E=[];
% Extract parameters
... |
github | tsajed/nmr-pred-master | guess_j_nuc.m | .m | nmr-pred-master/spinach/etc/guess_j_nuc.m | 22,317 | utf_8 | f8b937a6d65affdaed2c42d5e0fa4f31 | % Assigns J-couplings from literature values and Karplus curves.
%
% <http://spindynamics.org/wiki/index.php?title=Guess_j_nuc.m>
function jmatrix=guess_j_nuc(nuc_num,nuc_typ,pdb_id,coords)
% Check consistency
grumble(nuc_num,nuc_typ,pdb_id,coords);
% Preallocate the answer
jmatrix=cell(numel(coords),numel... |
github | tsajed/nmr-pred-master | read_bmrb.m | .m | nmr-pred-master/spinach/etc/read_bmrb.m | 1,506 | utf_8 | 9db070c1569393233d092fcb8cb1e771 | % This function reads BMRB files.
%
% <http://spindynamics.org/wiki/index.php?title=Read_bmrb.m>
function [aa_num,aa_typ,pdb_id,chemsh]=read_bmrb(bmrb_file_name)
% Check consistency
grumble(bmrb_file_name);
% Open the BMRB file
file_id=fopen(bmrb_file_name,'r');
% Get the outputs started
aa_num=[]; aa_... |
github | tsajed/nmr-pred-master | gparse.m | .m | nmr-pred-master/spinach/etc/gparse.m | 11,883 | utf_8 | 40b0d3197608f1798482b3597c8a2952 | % A parser for Gaussian03 and Gaussian09 calculation logs.
%
% <http://spindynamics.org/wiki/index.php?title=Gparse.m>
function props=gparse(filename,options)
% Read the file
file_id=fopen(filename,'r');
g03_output=textscan(file_id,'%s','delimiter','\n');
fclose(file_id); g03_output=g03_output{1};
% Debla... |
github | tsajed/nmr-pred-master | read_pdb_pro.m | .m | nmr-pred-master/spinach/etc/read_pdb_pro.m | 2,872 | utf_8 | 525d354869dff389bc59cb97e181f54f | % Reads protein PDB data.
%
% <http://spindynamics.org/wiki/index.php?title=Read_pdb_pro.m>
function [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,instance)
% Check consistency
grumble(pdb_file_name,instance);
% Open the PDB file
file_id=fopen(pdb_file_name,'r');
% Scroll to the selected stru... |
github | tsajed/nmr-pred-master | cst_display.m | .m | nmr-pred-master/spinach/etc/cst_display.m | 4,512 | utf_8 | 511a7e959a0f8ca32ef4b579ddebcafd | % Ellipsoid plots of chemical shielding tensors and their eigensystems.
%
% <http://spindynamics.org/wiki/index.php?title=Cst_display.m>
function cst_display(props,atoms,scaling_factor,conmatrix)
% Check consistency
grumble(props,atoms,scaling_factor,conmatrix);
% Set up graphics
figure(); hold on; colorma... |
github | tsajed/nmr-pred-master | hfc_display.m | .m | nmr-pred-master/spinach/etc/hfc_display.m | 4,543 | utf_8 | a50d0d45bec27c2e55cfe2c48509826f | % Ellipsoid plots of hyperfine coupling tensors.
%
% <http://spindynamics.org/wiki/index.php?title=Hfc_display.m>
function hfc_display(props,atoms,scaling_factor,conmatrix)
% Set up graphics
figure(); clf reset; hold on; colormap hot; opengl software;
light('Position',[-2,2,20]); light('Position',[10,10,10]);... |
github | tsajed/nmr-pred-master | oparse.m | .m | nmr-pred-master/spinach/etc/oparse.m | 3,011 | utf_8 | d644fff672c2bdc2ae87f74af0784137 | % A parser for ORCA logs.
%
% <http://spindynamics.org/wiki/index.php?title=Oparse.m>
function props=oparse(file_name)
% Check consistency
grumble(file_name);
% Read the file
file_id=fopen(file_name,'r');
orca_log=textscan(file_id,'%s','delimiter','\n');
fclose(file_id); orca_log=orca_log{1};
props.file... |
github | tsajed/nmr-pred-master | protein.m | .m | nmr-pred-master/spinach/etc/protein.m | 12,478 | utf_8 | 00ed6a47c240f3078156f9a6da717d42 | % Protein data import function.
%
% <http://spindynamics.org/wiki/index.php?title=Protein.m>
function [sys,inter]=protein(pdb_file,bmrb_file,options)
% Check consistency
grumble(pdb_file,bmrb_file,options);
% Parse the PDB file
[pdb_aa_num,pdb_aa_typ,pdb_atom_id,pdb_coords]=read_pdb_pro(pdb_file,options.pd... |
github | tsajed/nmr-pred-master | guess_j_pro.m | .m | nmr-pred-master/spinach/etc/guess_j_pro.m | 43,552 | utf_8 | 14f3a65cfff1df052e1f7bac2961da02 | % Assigns J-couplings from literature values and Karplus curves.
%
% <http://spindynamics.org/wiki/index.php?title=Guess_j_pro.m>
function jmatrix=guess_j_pro(aa_num,aa_typ,pdb_id,coords)
% Check consistency
grumble(aa_num,aa_typ,pdb_id,coords);
% Preallocate the answer
jmatrix=cell(numel(coords),numel(coo... |
github | tsajed/nmr-pred-master | ocparse.m | .m | nmr-pred-master/spinach/etc/ocparse.m | 1,903 | utf_8 | 4c4c8607b6468e09df40c3b31e69d269 | % ORCA cube file parser. Extracts the normalised probability density and
% the associated metric information from ORCA cube files. Syntax:
%
% [density,ext,dx,dy,dz]=ocparse(filename)
%
% Outputs:
%
% density - probability density cube with dimensions
% ordered as [X Y Z]
%
%... |
github | tsajed/nmr-pred-master | write_movie.m | .m | nmr-pred-master/spinach/interfaces/write_movie.m | 501 | utf_8 | 7cd0058285259cf5914ed341292b8b1f | % Orbits the camera around a 3D plot and writes a movie.
%
% i.kuprov@outlook.com
function write_movie(file_name)
% Open the video writer object
writerObj=VideoWriter(file_name,'MPEG-4');
open(writerObj);
% Orbit the camera
for n=1:360
% Grab the frame
writeVideo(writerObj,getframe(gcf));... |
github | tsajed/nmr-pred-master | assume.m | .m | nmr-pred-master/spinach/kernel/assume.m | 22,636 | utf_8 | 2293a974f8af42896f8756162a65df48 | % Sets case-specific assumptions for various simulation contexts. This
% function determines the behaviour of the Hamiltonian generation func-
% tion and should be called before the Hamiltonian is requested.
%
% The function text is self-explanatory -- interaction strength parame-
% ters are set in each section ac... |
github | tsajed/nmr-pred-master | execute.m | .m | nmr-pred-master/spinach/kernel/execute.m | 2,315 | utf_8 | 707e4338d2a351b55fcbd04cc0d08cca | % Applies an event sequence to a state vector. Not very sophisticated
% or efficient at the moment, further improvements to come. Syntax:
%
% rho=execute(spin_system,operators,durations,rho)
%
% where operators is a cell array of Hamiltonians or Liouvilians and
% durations is a vector of times for which t... |
github | tsajed/nmr-pred-master | step.m | .m | nmr-pred-master/spinach/kernel/step.m | 5,336 | utf_8 | 1af6dd98005186946f9b8d5c0e1bd018 | % Propagation step function. Uses Krylov propagation and sparse exponenti-
% ation where appropriate. Syntax:
%
% rho=step(spin_system,L,rho,time_step)
%
% Arguments:
%
% L - Liouvillian or Hamiltonian to be used for propagation
%
% rho - state vector or density ma... |
github | tsajed/nmr-pred-master | relaxation.m | .m | nmr-pred-master/spinach/kernel/relaxation.m | 29,210 | utf_8 | 1c4a5af71f148ab358fa540c512b7035 | % The relaxation superoperator. All options are set during the call to
% create.m function. Syntax:
%
% R=relaxation(spin_system,euler_angles)
%
% where euler_angles should be used for solid state systems in which
% the thermal equilibrium state is orientation-dependent.
%
% Further information ... |
github | tsajed/nmr-pred-master | state.m | .m | nmr-pred-master/spinach/kernel/state.m | 5,293 | utf_8 | 65400ecadbbdef5c48ef7758937b9103 | % State operators (Hilbert space) and state vectors (Liouville space).
%
% <http://spindynamics.org/wiki/index.php?title=State.m>
function rho=state(spin_system,states,spins,method)
% Validate the input
grumble(spin_system,states,spins);
% Default is to use consistent state norms
if ~exist('method','var'),... |
github | tsajed/nmr-pred-master | krylov.m | .m | nmr-pred-master/spinach/kernel/krylov.m | 9,035 | utf_8 | 39d4c50f6ad537a593fcb4dd160b1260 | % Krylov propagation function. Avoids matrix exponentiation, but can be
% slow. Should be used when the Liouvillian exponential does not fit in-
% to the system memory, but the Liouvillian itself does. Syntax:
%
% answer=krylov(spin_system,L,coil,rho,time_step,nsteps,output)
%
% Arguments for Liouville space... |
github | tsajed/nmr-pred-master | stateinfo.m | .m | nmr-pred-master/spinach/kernel/stateinfo.m | 2,008 | utf_8 | d0fad609ddeb1759df04280a957482fb | % Prints the state vector norm and the list of the most populated basis
% states in the order of decreasing population. Syntax:
%
% stateinfo(spin_system,rho,npops)
% Parameters:
%
% rho - state vector
%
% npops - number of largest populations to print
%
% No... |
github | tsajed/nmr-pred-master | evolution.m | .m | nmr-pred-master/spinach/kernel/evolution.m | 39,585 | utf_8 | 5015230a6b7861d68eaaaaad05dd6e63 | % Time evolution function. Performs all types of time propagation with
% automatic trajectory level state space restriction. Syntax:
%
% answer=evolution(spin_system,L,coil,rho,timestep,...
% nsteps,output,destination)
%
% Arguments for Liouville space calculations:
%
% L ... |
github | tsajed/nmr-pred-master | hamiltonian.m | .m | nmr-pred-master/spinach/kernel/hamiltonian.m | 33,597 | utf_8 | 45431ad588a9b53651e7adf0d3d0bff5 | % Hamiltonian operator / superoperator and its rotational decomposition.
% Descriptor and operator generation is parallelized. Syntax:
%
% [H,Q]=hamiltonian(spin_system,operator_type)
%
% In Liouville space calculations, operator_type can be set to:
%
% 'left' - p... |
github | tsajed/nmr-pred-master | orientation.m | .m | nmr-pred-master/spinach/kernel/orientation.m | 1,945 | utf_8 | d225044f72eed3cbc2036cc373a68f1b | % Anisotropic part of the Hamiltonian for a specific spin system
% orientation. Syntax:
%
% H=orientation(Q,euler_angles)
%
% Arguments:
%
% Q - rotational basis as returned by hamiltonian
% function.
%
% euler_angles - a 1x3 vector or a vertical stack o... |
github | tsajed/nmr-pred-master | splice.m | .m | nmr-pred-master/spinach/kernel/splice.m | 4,118 | utf_8 | 765f21f9b3ef8b6b23220e95dedbb5bd | % Merges timing tables of pulse sequence channels. Both timing tables
% should be given as row arrays of the following structure:
%
% A={A_1 A_2 ... A_n}; dtA=[dt_1 dt_2 ... dt_n];
%
% where A_k is a spin operator and dt_k is the time for which it acts.
% The sequence is assumed to be executed chronol... |
github | tsajed/nmr-pred-master | rotframe.m | .m | nmr-pred-master/spinach/kernel/rotframe.m | 2,062 | utf_8 | e115fa73c9e879a9753f418c8537ee1a | % Rotating frame transformation with respect to a specified
% group of spins to specified order in perturbation theory.
% Syntax:
%
% H=rotframe(spin_system,H0,H,isotope,order)
%
% Parameters:
%
% H0 - carrier Hamiltonian with respect to which the
% rotating frame transformation is ... |
github | tsajed/nmr-pred-master | average.m | .m | nmr-pred-master/spinach/kernel/average.m | 9,900 | utf_8 | b95fad736487064601cfde341ec9859b | % Average Hamiltonian theories under Zeeman interaction rotating frame
% transformations. Syntax:
%
% H=average(spin_system,Hp,H0,Hm,omega,theory)
%
% Parameters:
%
% Hp - the part of the rotating frame Hamiltonian that has positive
% frequency under the rotating frame transformatio... |
github | tsajed/nmr-pred-master | carrier.m | .m | nmr-pred-master/spinach/kernel/carrier.m | 1,110 | utf_8 | aa5ea9c3a4ec0a4f321d12e31567ceb6 | % Returns the "carrier" Hamiltonian - the part of the Zeeman
% interaction Hamiltonian that corresponds to all particles
% having the Zeeman frequency prescribed by their magnetogy-
% ric ratio and the magnet field specified by the user. This
% Hamiltonian is frequently used in rotating frame transfor-
% mations ... |
github | tsajed/nmr-pred-master | decouple.m | .m | nmr-pred-master/spinach/kernel/decouple.m | 3,030 | utf_8 | 7872a92a90308c8b6b7282e230084a90 | % Obliterates all interactions and populations in the subspace of states
% that involve user-specified spins in any way. The specified spins would
% not contribute to the system dynamics until the Liouvillian is rebuilt
% from scratch. Syntax:
%
% [L,rho]=decouple(spin_system,L,rho,spins)
%
% ... |
github | tsajed/nmr-pred-master | singlet.m | .m | nmr-pred-master/spinach/kernel/singlet.m | 1,357 | utf_8 | c7fd78a536cdee077971bd06c921bfed | % Returns a two-spin singlet state. Syntax:
%
% rho=singlet(spin_system,spin_a,spin_b)
%
% Arguments:
%
% spin_a - the number of the first spin in the singlet state
%
% spin_b - the number of the second spin in the singlet state
%
% i.kuprov@soton.ac.uk
function rho=singlet(spin... |
github | tsajed/nmr-pred-master | create.m | .m | nmr-pred-master/spinach/kernel/create.m | 66,689 | utf_8 | 9d8a27fd29231970b6edabf2bc1145fd | % Spin system and interaction specification.
%
% <http://spindynamics.org/wiki/index.php?title=Spin_system_specification>
function spin_system=create(sys,inter)
% Close all open files
fclose('all');
% Locate the root and run sanity checks
if isempty(which('existentials'))
% Tell the user to RTFM... |
github | tsajed/nmr-pred-master | spin.m | .m | nmr-pred-master/spinach/kernel/spin.m | 33,566 | utf_8 | f7cdee02ee6b72e8e3619a7abc6b0029 | % Database of multiplicities and magnetogyric ratios for sta-
% ble and long-lived isotopes with non-zero spin. Syntax:
%
% [gamma,multiplicity]=spin(name)
%
% where the name of the isotope is given in the standard way,
% e.g. 13C or 195Pt. High-spin electrons may be requested by
% supplying 'E' f... |
github | tsajed/nmr-pred-master | trajan.m | .m | nmr-pred-master/spinach/kernel/trajan.m | 8,616 | utf_8 | cfdb63f08f3d1bcf49595de836bc1b19 | % Trajectory analysis function. Plots the time dependence of the densi-
% ty matrix norm, partitioned into user-specified property classes.
%
% Call syntax:
%
% trajan(spin_system,trajectory,property)
%
% Arguments:
%
% trajectory - a stack of state vectors of any length. The
% number... |
github | tsajed/nmr-pred-master | frqoffset.m | .m | nmr-pred-master/spinach/kernel/frqoffset.m | 3,566 | utf_8 | 98b35ea109750bbae94e2ee05571b05d | % Adds offset frequencies to the Hamiltonian. Syntax:
%
% H=frqoffset(spin_system,H,parameters)
%
% where H is the Hamiltonian and parameters should contain
% the following subfields:
%
% parameters.spins - a cell array giving the
% spins that the pulse sequence works on, in
... |
github | tsajed/nmr-pred-master | homospoil.m | .m | nmr-pred-master/spinach/kernel/homospoil.m | 2,499 | utf_8 | be97284024d04086a9e28d58d38f9c64 | % Emulates a strong homospoil pulse - only zero-frequency states
% survive the process. Syntax:
%
% rho=homospoil(spin_system,rho,zqc_flag)
%
% Parameters:
%
% rho - a state vector or a horizontal stack thereof
%
% zqc_flag - a flag controlling the fate of zero-quantum
% ... |
github | tsajed/nmr-pred-master | basis.m | .m | nmr-pred-master/spinach/kernel/basis.m | 25,413 | utf_8 | e849e7e3736fb8cf2344dbff1b2f1332 | % Basis set control. This is the second mandatory function (after create.m)
% that must be executed in every calculation to get the Spinach kernel go-
% ing. See the Basis Selection section of the Spinach manual for the detail-
% ed description of the various options.
%
% Note: it is very important that you under... |
github | tsajed/nmr-pred-master | spinlock.m | .m | nmr-pred-master/spinach/kernel/spinlock.m | 1,521 | utf_8 | e73d0f4759754be56c7a5fc9c1bd979a | % Analytical approximation to a spin locking process. This function oblite-
% rates all spin-spin correlations and all magnetization components other
% than those along the indicated direction. Parameters:
%
% Lx - X magnetization operator on the spins that
% should be locked
%
% ... |
github | tsajed/nmr-pred-master | lindbladian.m | .m | nmr-pred-master/spinach/kernel/lindbladian.m | 1,460 | utf_8 | dca11201c0d29cbfc36031996ac2f53d | % Generates a Lindblad superoperator from user-specified left-side and
% right-side product superoperators and calibrates it using the experi-
% mental relaxation rate of a user-specified state. Syntax:
%
% R=lindbladian(A_left,A_right,rho,rlx_rate)
%
% where A_left is the left side product superoper... |
github | tsajed/nmr-pred-master | propagator.m | .m | nmr-pred-master/spinach/kernel/propagator.m | 7,103 | utf_8 | 228cd2cfd371fa8680d2b3d433160043 | % Calculates exponential propagators. Syntax:
%
% P=propagator(spin_system,L,timestep)
%
% returns exp(-i*L*t). The following calculation methods are
% supported:
%
% 'cpu' - Taylor series with scaling and squaring
% on CPU, spmd parallel if possible
%
% 'gpu' - Tayl... |
github | tsajed/nmr-pred-master | kinetics.m | .m | nmr-pred-master/spinach/kernel/kinetics.m | 9,090 | utf_8 | ab73d88d3360660aa7174960706cdba9 | % Chemical kinetics superoperator. All adjustable parameters are specified
% in the call to create.m function -- see the Input Preparation section of
% Spinach manual.
%
% i.kuprov@soton.ac.uk
% luke.edwards@ucl.ac.uk
% hannah.hogben@chem.ox.ac.uk
function K=kinetics(spin_system)
% Preallocate the answer
K... |
github | tsajed/nmr-pred-master | operator.m | .m | nmr-pred-master/spinach/kernel/operator.m | 3,563 | utf_8 | 232e3910e3f858f1c9cd5d85ce3e8b6d | % Hilbert space operators and Liouville space superoperators.
%
% <http://spindynamics.org/wiki/index.php?title=Operator.m>
function A=operator(spin_system,operators,spins,operator_type)
% Validate the input
grumble(spin_system,operators,spins);
% The default type is commutation superoperator
if ~exist('op... |
github | tsajed/nmr-pred-master | residual.m | .m | nmr-pred-master/spinach/kernel/residual.m | 2,306 | utf_8 | caf9051ccf62a2197e7a144614af7573 | % Sets up interaction tensors under partial ordering in a liquid
% crystal with the user-supplied order matrix. All adjustable pa-
% rameters are set during the call to create.m function. Syntax:
%
% spin_system=residual(spin_system)
%
% Note: this function is only applicable to high-field NMR.
%
... |
github | tsajed/nmr-pred-master | thermalize.m | .m | nmr-pred-master/spinach/kernel/thermalize.m | 1,058 | utf_8 | 0202b4d5a16beaabe415ea39be31f719 | % Modifies a symmetric relaxation superoperator to relax the system
% towards a user-specified state. Liouville space spherical tensor
% formalism only. Syntax:
%
% R=thermalize(spin_system,R,rho)
%
% i.kuprov@soton.ac.uk
function R=thermalize(spin_system,R,rho)
if strcmp(spin_system.bas.fo... |
github | tsajed/nmr-pred-master | trajsimil.m | .m | nmr-pred-master/spinach/kernel/trajsimil.m | 5,910 | utf_8 | a3776b1fcac41800e2d9e696b6d9c9e2 | % Computes trajectory similarity scores. Returns a function representing
% "similarity" of the two state space trajectories at different points in
% time. Trajectory must be supplied as nstates x nsteps matrix. Syntax:
%
% trajsimil(spin_system,trajectory_1,trajectory_2,method)
%
% Score functions:
%
%... |
github | tsajed/nmr-pred-master | correlation.m | .m | nmr-pred-master/spinach/kernel/correlation.m | 2,846 | utf_8 | 2e85e82540e5c585bc1fc973376c35fa | % Correlation order selection function -- keeps only the specified orders
% of spin correlation in the state vector. Syntax:
%
% rho=correlation(spin_system,rho,correlation_orders,spins)
%
% Arguments:
%
% rho - a state vector or a horizontal stack thereof
%
% correlation_orders - a ... |
github | tsajed/nmr-pred-master | stepsize.m | .m | nmr-pred-master/spinach/kernel/stepsize.m | 1,987 | utf_8 | 95cd54b97d90c922a925508e0b07cd84 | % Optimal step for time propagation under a given Hamiltonian or a given
% Liouvillian superoperator. The function uses the 1-norm (which is the
% cheapest variety and the safest one in terms of matrix scaling).
%
% Syntax: [timestep,nsteps]=stepsize(L,interval)
%
% Parameters:
%
% L - Liouv... |
github | tsajed/nmr-pred-master | coherence.m | .m | nmr-pred-master/spinach/kernel/coherence.m | 2,569 | utf_8 | 0fee30c7e46dc64919bc2cc9f1691f15 | % Coherence selection function.
%
% <http://spindynamics.org/wiki/index.php?title=Coherence.m>
function rho=coherence(spin_system,rho,spec)
% Check consistency
grumble(spin_system,rho,spec);
% Store dimension statistics
spn_dim=size(spin_system.bas.basis,1);
spc_dim=numel(rho)/spn_dim;
problem_dims=size(... |
github | tsajed/nmr-pred-master | repulsion.m | .m | nmr-pred-master/spinach/kernel/grids/repulsion.m | 3,473 | utf_8 | 538e1a0c3c3f3c705c3cb1270630dafc | % Generates repulsion grids on a unit hypersphere. See the paper by
% Bak and Nielsen (http://dx.doi.org/10.1006/jmre.1996.1087) to get
% further information on the algorithm involved. Syntax:
%
% [alphas,betas,gammas,weights]=repulsion(npoints,ndims,niter)
%
% Parameters:
%
% npoints - number of points ... |
github | tsajed/nmr-pred-master | shrewd.m | .m | nmr-pred-master/spinach/kernel/grids/shrewd.m | 2,339 | utf_8 | 099331e118ef28cc811358b6503178f2 | % Computes SHREWD weights for a given two- or three-angle spherical
% grid. See the paper by Eden and Levitt for details on now the al-
% gorithm works: http://dx.doi.org/10.1006/jmre.1998.1427 Syntax:
%
% weights=shrewd(alphas,betas,gammas,max_rank,max_error)
%
% Parameters:
%
% alphas - alpha Euler ... |
github | tsajed/nmr-pred-master | grid_kron.m | .m | nmr-pred-master/spinach/kernel/grids/grid_kron.m | 1,933 | utf_8 | 90a14b2d08b8e62ae823a695b96a3246 | % Spherical grid direct product. Tiles one grid using the rotations of
% the other. Grids should be supplied using Euler angles in three col-
% umns [alphas betas gammas] in radians. Syntax:
%
% [angles,weights]=grid_kron(angles1,weights1,angles2,weights2)
%
% Parameters:
%
% angles1 - angles of the first... |
github | tsajed/nmr-pred-master | gaussleg.m | .m | nmr-pred-master/spinach/kernel/grids/gaussleg.m | 817 | utf_8 | 9a921d02d31d116cc03d0d80493a2c52 | % Computes Gauss-Legendre points and weights in [a,b] interval
% with accuracy order n.
%
% i.kuprov@soton.ac.uk
function [x,w]=gaussleg(a,b,n)
% Initial guess for the nodes in [-1 1]
x=cos((2*(0:n)'+1)*pi/(2*n+2))+(0.27/(n+1))*sin(pi*linspace(-1,1,n+1)'*n/(n+2));
% Newton-Raphson refinement
V=zeros(n+1,n... |
github | tsajed/nmr-pred-master | grid_test.m | .m | nmr-pred-master/spinach/kernel/grids/grid_test.m | 2,042 | utf_8 | f370fb0071661c47b7bcf44d41044696 | % Plots grid integration quality as a function of spherical rank. The
% quality is defined as the norm of the residual of spherical harmon-
% ics or Wigner functions integrated using the grid provided. Syntax:
%
% grid_profile=grid_test(alphas,betas,gammas,weights,max_rank,sfun)
%
% Parameters:
%
% alphas... |
github | tsajed/nmr-pred-master | fpl2rho.m | .m | nmr-pred-master/spinach/kernel/utilities/fpl2rho.m | 626 | utf_8 | acb785abd725b06f1f125556bd9f68c9 | % Integrates over the spatial degrees of freedom and returns the
% average spin state vector across the sample. Syntax:
%
% rho=fpl2rho(rho,dims)
%
% Parameters:
%
% rho - Fokker-Planck state vector
%
% dims - spatial dimensions of the
% Fokker-... |
github | tsajed/nmr-pred-master | binpack.m | .m | nmr-pred-master/spinach/kernel/utilities/binpack.m | 870 | utf_8 | f10cfd77f138e0e0b946e6bb85b6f4c6 | % A simple 1D bin packing algorithm.
%
% i.kuprov@soton.ac.uk
function bins=binpack(box_sizes,bin_size)
% Number the boxes
box_index=(1:numel(box_sizes))';
% Find boxes that are bigger than bins
big_boxes=(box_sizes>bin_size);
bins=num2cell(box_index(big_boxes));
box_sizes(big_boxes)=[];
box_index(big_... |
github | tsajed/nmr-pred-master | irr_sph_ten.m | .m | nmr-pred-master/spinach/kernel/utilities/irr_sph_ten.m | 2,950 | utf_8 | edc07d4ae6e4da2dde5ff2487b9ebb14 | % Returns a cell array of single-spin irreducible spherical tensor opera-
% tors T(k,m). A two-argument call
%
% T=irr_sph_ten(mult,k)
%
% where 'mult' is the multiplicity of the spin in question and 'k' is the
% irreducible spherical tensor rank required, returns a cell array of ten-
% ... |
github | tsajed/nmr-pred-master | human2opspec.m | .m | nmr-pred-master/spinach/kernel/utilities/human2opspec.m | 5,635 | utf_8 | e938a5147583cb1af886ab53f438f170 | % Converts user-friendly descriptions of spin states and operators into the
% formal description (opspec) used by Spinach kernel. The function supports
% two types of calls:
%
% 1. If both inputs are strings, e.g.
%
% [opspecs,coeffs]=human2opspec(spin_system,'Lz','13C')
%
% the function returns a list o... |
github | tsajed/nmr-pred-master | sphten2zeeman.m | .m | nmr-pred-master/spinach/kernel/utilities/sphten2zeeman.m | 1,071 | utf_8 | 4c8a7a1a8a92a3e13a0be77956ee37bf | % Returns a matrix that converts state vectors written in the
% spherical tensor basis set used by Spinach into state vectors
% written in the Zeeman basis set in Liouville space.
%
% Note: the matrix need not be square and may be huge.
%
% i.kuprov@soton.ac.uk
function P=sphten2zeeman(spin_system)
% Preal... |
github | tsajed/nmr-pred-master | axrh2mat.m | .m | nmr-pred-master/spinach/kernel/utilities/axrh2mat.m | 1,601 | utf_8 | b3d6cd0ee8ee8d3fdebe01b359d1fb5c | % Converts axiality and rhombicity representation of the anisotro-
% pic part of a 3x3 interaction tensor into the corresponding mat-
% rix. Euler angles should be specified in radians. Syntax:
%
% M=axrh2mat(iso,ax,rh,alp,bet,gam)
%
% Parameters:
%
% iso - isotropic part of the interact... |
github | tsajed/nmr-pred-master | existentials.m | .m | nmr-pred-master/spinach/kernel/utilities/existentials.m | 12,935 | utf_8 | 08d056cded782d586ea36dc417733567 | % Kernel integrity control. Checks for collisions between Spinach func-
% tions and anything else that the user may have installed or written
% in the current Matlab instance.
%
% Do not switch this off -- collisions of function names and path probl-
% ems are the most frequent support topic at the forum.
%
% i.... |
github | tsajed/nmr-pred-master | wigner.m | .m | nmr-pred-master/spinach/kernel/utilities/wigner.m | 1,432 | utf_8 | 436429ecce79ecc2493a86cb52ec1c6a | % Computes Wigner matrices of user-specified ranks. Syntax:
%
% D=wigner(l,alp,bet,gam)
%
% where alp, bet and gam are Euler angles in radians. Rows and columns
% of the resulting Wigner matrix are sorted by descending ranks, e.g.:
%
% [D( 2,2) ... D( 2,-2)
% ... |
github | tsajed/nmr-pred-master | tensor_analysis.m | .m | nmr-pred-master/spinach/kernel/utilities/tensor_analysis.m | 1,616 | utf_8 | 207b76ff9b5e1527be86f6ea9132189d | % Returns diagnostic information about an interaction tensor. Syntax:
%
% [eigvals,dcm,iso]=tensor_analysis(spin_system,tensor)
%
% Parameters:
%
% tensor - a 3x3 Cartesian interaction tensor matrix
%
% Outputs:
%
% eigvals - eigenvalues of the tensor
%
% dcm - direct... |
github | tsajed/nmr-pred-master | zoom_3d.m | .m | nmr-pred-master/spinach/kernel/utilities/zoom_3d.m | 1,556 | utf_8 | 43f4854fa234f15ada77b68ae5be45ba | % Zooms a 3D data cube to the fractional limits specified
% by the user. Syntax:
%
% [density,ext]=zoom_3d(density,ext,zoom_ranges)
%
% Parameters:
%
% density - probability density cube with dimensions
% ordered as [X Y Z]
%
% ext - grid extents in Angstrom, ordered as
... |
github | tsajed/nmr-pred-master | clebsch_gordan.m | .m | nmr-pred-master/spinach/kernel/utilities/clebsch_gordan.m | 5,110 | utf_8 | 6d77301826ebda2514757e13819586bb | % Calculates Clebsch-Gordan coefficients. Syntax:
%
% cg=clebsch_gordan(L,M,L1,M1,L2,M2)
%
% If physically inadmissible indices are supplied, a zero is returned.
%
% A very considerable amount of thought has been given to the accuracy
% and performance of this fu... |
github | tsajed/nmr-pred-master | euler2wigner.m | .m | nmr-pred-master/spinach/kernel/utilities/euler2wigner.m | 4,265 | utf_8 | d6513655695ef5113c4156054c60001a | % Second-rank Wigner rotation matrix as a function of Euler angles. Two
% possible input styles are:
%
% W=euler2wigner(alpha,beta,gamma)
% W=euler2wigner([alpha beta gamma])
%
% where alpha, beta and gamma are Euler angles in radians. Rows and columns
% of the resulting Wig... |
github | tsajed/nmr-pred-master | probmax.m | .m | nmr-pred-master/spinach/kernel/utilities/probmax.m | 563 | utf_8 | 62b608e4801e9141cdaa24967600dc43 | % Finds the maximum of the probability density.
%
% i.kuprov@outlook.com
function [x,y,z]=probmax(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(ranges(5),ranges(... |
github | tsajed/nmr-pred-master | fdmat.m | .m | nmr-pred-master/spinach/kernel/utilities/fdmat.m | 1,435 | utf_8 | b51a5ff829b47097c12e13a52b875ade | % Returns arbitrary-order central finite-difference differentiation
% matrix (sparse) with unit spacing and periodic boundary conditions.
% Syntax:
%
% D=fdmat(dim,npoints,order)
%
% Parameters:
%
% dim - dimension of the column vector to be
% differentiated
%
... |
github | tsajed/nmr-pred-master | hess_reorder.m | .m | nmr-pred-master/spinach/kernel/utilities/hess_reorder.m | 2,292 | utf_8 | 72c90d46e3eb7617e958eeb4cca8fb88 | % The waveforms on different channels are assumed to be stored in the
% rows of the input array. The Hessian elements correspond to the ele-
% ments of the waveform array ordered as:
%
% [X1 Y1 Z1 X2 Y2 Z2 ... Xn Yn Zn]
%
% where X,Y,Z are different control channels and the index enumerates
% the time... |
github | tsajed/nmr-pred-master | absorb.m | .m | nmr-pred-master/spinach/kernel/utilities/absorb.m | 1,539 | utf_8 | cdff513e969bcc9b1960712d1a5aed1f | % Designates specific states as "dark" -- any population reaching
% them would end up being summed up and stored in them forever in
% a frozen state. Syntax:
%
% L=absorb(spin_system,L,dark_states)
%
% where L is the Liouvillian and dark_states contains the numbers
% of the states that should be s... |
github | tsajed/nmr-pred-master | gauss2mhz.m | .m | nmr-pred-master/spinach/kernel/utilities/gauss2mhz.m | 557 | utf_8 | 866bc949d001ef3589f27a86a0d187de | % Converts hyperfine couplings from Gauss to MHz (linear
% frequency). Syntax:
%
% hfc_mhz=gauss2mhz(hfc_gauss)
%
% Arrays of any dimensions are supported.
%
% i.kuprov@soton.ac.uk
function hfc_mhz=gauss2mhz(hfc_gauss)
if isnumeric(hfc_gauss)&&isreal(hfc_gauss)
hfc_mhz=2.802495365*hfc_ga... |
github | tsajed/nmr-pred-master | xyz2sph.m | .m | nmr-pred-master/spinach/kernel/utilities/xyz2sph.m | 469 | utf_8 | 4dcdd5ed3aa528bf792f9eb009a41d35 | % Converts Cartesian coordinates [x y z] into spherical coordinates
% according to the ISO convention.
%
% e.suturina@soton.ac.uk
function [r, theta, phi] = xyz2sph(x, y, z)
% Radius 0 <= r < Inf
r=sqrt(x.^2+y.^2+z.^2);
% Inclination 0 <= theta <= pi
theta=acos(z./r);
% Azimuth 0 <= phi < 2*pi
phi=at... |
github | tsajed/nmr-pred-master | v2fplanck.m | .m | nmr-pred-master/spinach/kernel/utilities/v2fplanck.m | 788 | utf_8 | 59585d448a9939f4be64a18af42d9c64 | % Translates a stationary 3D velocity field into a Fokker-Planck
% evolution generator.
%
% a.j.allami@soton.ac.uk
% i.kuprov@soton.ac.uk
function F=v2fplanck(U,V,W,parameters)
% Get the translation generators
[Fx,Fy,Fz]=hydrodynamics(parameters);
% Build the Fokker-Planck flow generator
F=spdiags(Fx*U(:... |
github | tsajed/nmr-pred-master | axis_1d.m | .m | nmr-pred-master/spinach/kernel/utilities/axis_1d.m | 2,492 | utf_8 | 72119cf2ebad8b04c7a2d58b49548c3e | % Generates axes for plotting.
%
% i.kuprov@soton.ac.uk
function [ax,ax_label]=axis_1d(spin_system,parameters)
% Build the axis and apply the offset
if numel(parameters.sweep)==1
ax=linspace(-parameters.sweep/2,parameters.sweep/2,parameters.zerofill)+parameters.offset;
else
ax=linspace(parameters.sw... |
github | tsajed/nmr-pred-master | lmn2lin.m | .m | nmr-pred-master/spinach/kernel/utilities/lmn2lin.m | 2,047 | utf_8 | e694562633c062dd42eb54db4d046c2a | % Converts L,M,N Wigner function specification to linear indexing speci-
% fication. 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 orde... |
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