5 |
6 | **SpinW** (*spin-double-u*) is a Matlab library that can optimize magnetic structures using mean field theory and calculate spin wave dispersion and spin-spin correlation function for complex crystal and magnetic structures. For details check http://www.psi.ch/spinw.
7 |
8 | Keep up to date on announcements and more by following [@spinw4](https://twitter.com/intent/user?screen_name=spinw4) on Twitter.
9 |
10 | # Documentation
11 | * experimental and under construction, the address can change in the future
12 | * documentation of the master branch
13 | * use `swdoc`/`swhelp` instead of the Matlab built-in `doc`/`help` functions to get help on SpinW
14 | * can be also accessed from the browser: https://tsdev.github.io/spinwdoc/
15 |
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/dat_files/icons.mat:
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https://raw.githubusercontent.com/tsdev/spinw/03e6d885c1d992404572c6fe22f930bd3330a7e5/dat_files/icons.mat
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/dev/doctest2.m:
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1 | function doctest2()
2 | % Summary line.
3 | %
4 | % :code:`[b1, b2] = doctest2(a,b)`
5 | %
6 | % Extended description of function.
7 | %
8 | % Parameters
9 | % ----------
10 | % a1:
11 | % Description of arg1.
12 | % a2:
13 | % Description of arg2.
14 | %
15 | % Returns
16 | % -------
17 | % b1:
18 | % Description of return value.
19 | % b2:
20 | % Other output.
21 | %
22 | % Examples
23 | % --------
24 | % This will calculate the spectrum::
25 | %
26 | % doctest(1,2);
27 | %
28 |
29 | 1+1;
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/dev/sw_counter.m:
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1 | function sw_counter(reset, text)
2 | % prints the number of function calls
3 | %
4 | % ### Syntax
5 | %
6 | % `sw_counter`
7 | %
8 | % `sw_counter(reset, text)`
9 | %
10 | % ### Description
11 | %
12 | % `sw_counter(reset, text)` prints the number of calls to this function.
13 | %
14 | % ### Input Arguments
15 | %
16 | % `reset`
17 | % : If `true` the counter is reset to zero.
18 | %
19 | % `text`
20 | % : Sets the text to print before the number, default value is `'The number
21 | % of function calls:'`.
22 | %
23 |
24 | persistent cnt
25 |
26 | if nargin == 0
27 | reset = 0;
28 | end
29 |
30 | if reset
31 | cnt = 0;
32 | else
33 | if isempty(cnt)
34 | cnt = 0;
35 | end
36 | cnt = cnt + 1;
37 | end
38 |
39 | if nargin < 2
40 | text = 'The number of function calls:';
41 | end
42 |
43 | nT = numel(text);
44 | bb = repmat('\b',[1 nT+7]);
45 |
46 | if cnt == 0
47 | fprintf(['\n' text '%6d\n'],cnt);
48 | else
49 | fprintf([bb text '%6d\n'],cnt);
50 | end
51 |
52 | end
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/dev/sw_initialize.m:
--------------------------------------------------------------------------------
1 | function sw_initialize()
2 | % initializes spinw by removing user entries from the symmetry.dat file
3 | %
4 | % SW_INITIALIZE()
5 | %
6 | % See also SPINW.
7 | %
8 |
9 | %cd(sw_rootdir);
10 | %m2html('mfiles','swfiles','htmldir','doc')
11 | %builddocsearchdb([sw_rootdir 'doc']);
12 |
13 | % clear symmetry.dat file
14 | symPath = [sw_rootdir 'dat_files' filesep 'symmetry.dat'];
15 | % Count the number of lines
16 | fid = fopen(symPath);
17 | fidNew = fopen([symPath '0'],'w');
18 |
19 |
20 | if fid == -1
21 | error('spinw:sw_gensym:FileNotFound',['Symmetry definition file not found: '...
22 | regexprep(symPath,'\' , '\\\') '!']);
23 | end
24 |
25 | nLines = 1;
26 | % number of space group operators in symmetry.dat
27 | nOp = 231;
28 |
29 | while (~feof(fid)) && (nLines <= nOp)
30 | line = fgetl(fid);
31 | if nLines < nOp
32 | fprintf(fidNew,[line '\n']);
33 | else
34 | fprintf(fidNew,line);
35 | end
36 | nLines = nLines + 1;
37 | end
38 | fclose(fid);
39 | fclose(fidNew);
40 |
41 | % copy file
42 | delete(symPath);
43 | copyfile([symPath '0'],symPath);
44 | delete([symPath '0']);
45 |
46 | end
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/dev/sw_notify.m:
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1 | function sw_notify(varargin)
2 | % sends notification in OSX
3 | %
4 | % SW_NOTIFY(message)
5 | %
6 | % SW_NOTIFY('option1',value1, ...)
7 | %
8 | %
9 | % The function can be used to show a notification when a calculation is
10 | % finished. Note that the notification only shows up if Matlab is not
11 | % the active window.
12 | %
13 | % Install terminal-notifier:
14 | % Using Ruby, you can install it through RubyGems:
15 | % $ [sudo] gem install terminal-notifier
16 | % You can also install it via Homebrew:
17 | % $ brew install terminal-notifier
18 | %
19 | % Options:
20 | %
21 |
22 |
23 | if ~ismac
24 | warning('sw_notify:WrongOS','The function only works in OSX!')
25 | return
26 | end
27 |
28 | path0 = '';
29 |
30 | if nargin == 1
31 | param.message = varargin{1};
32 | param.path = path0;
33 | param.group = 'spinw';
34 | param.subtitle = 'SpinW';
35 | param.sound = 'ping';
36 | else
37 | inpForm.fname = {'message' 'path' 'group' 'subtitle' 'sound'};
38 | inpForm.defval = {'Done!' path0 'spinw' 'SpinW' 'ping' };
39 | inpForm.size = {[1 -1] [1 -2] [1 -3] [1 -4] [1 -5] };
40 | inpForm.soft = {false true false false false };
41 |
42 | param = sw_readparam(inpForm, varargin{:});
43 | end
44 |
45 | cmd = [param.path 'terminal-notifier -message "' param.message '" -group "' param.group...
46 | '" -title "MATLAB" -sender com.mathworks.matlab -subtitle ' param.subtitle...
47 | ' -sound ' param.sound];
48 |
49 | % execute bash_profile
50 | [~,~] = system(['source ~/.bash_profile && ' cmd]);
51 |
52 | end
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/dev/sw_plotcell.m:
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1 | function varargout = sw_plotcell(dat,xLab,yLab,tLab,aRange,sc,depth)
2 | % plots cell structure with circles
3 | %
4 | % SW_PLOTCELL(dat,xLab,yLab,tLab,aRange,sc,depth)
5 | %
6 |
7 | if nargin<7
8 | depth = 0;
9 | end
10 |
11 | nDat = numel(dat.x);
12 | zMax = -inf;
13 |
14 | % find maximum data value
15 | for ii = 1:nDat
16 | zMax = max([abs(real(dat.z{ii}(:))); zMax]);
17 | end
18 |
19 | if nargin>4
20 | xMin = aRange(1);
21 | xMax = aRange(2);
22 | yMin = aRange(3);
23 | yMax = aRange(4);
24 | else
25 | xMin = min(dat.x)-max(diff(dat.x));
26 | xMax = max(dat.x)+max(diff(dat.x));
27 | yMin = inf;
28 | yMax = -inf;
29 |
30 | % find x and y range
31 | for ii = 1:nDat
32 | yMin = min([abs(real(dat.y{ii}(:))); yMin]);
33 | yMax = max([abs(real(dat.y{ii}(:))); yMax]);
34 | end
35 | end
36 |
37 | % radius of circles
38 | C = sw_circle([0 0 0]',[0 0 1]',1,300);
39 |
40 | if nargin<6
41 | sc = 0.02;
42 | rx = (xMax-xMin)*sc;
43 | ry = (yMax-yMin)*sc;
44 |
45 | Cx = C(1,:)*rx/zMax;
46 | Cy = C(2,:)*ry/zMax;
47 | elseif numel(sc)==1
48 | rx = (xMax-xMin)*sc;
49 | ry = (yMax-yMin)*sc;
50 |
51 | Cx = C(1,:)*rx/zMax;
52 | Cy = C(2,:)*ry/zMax;
53 |
54 | else
55 | Cx = C(1,:)*sc(1);
56 | Cy = C(2,:)*sc(2);
57 |
58 | end
59 |
60 | % draw circles
61 | for ii = 1:nDat
62 | for jj = 1:numel(dat.y{ii})
63 | r = dat.z{ii}(jj);
64 | p(ii,jj) = patch(dat.x(ii)+Cx*r,dat.y{ii}(jj)+Cy*r,Cx*0+depth,'k');
65 | hold on
66 | end
67 | end
68 |
69 | dy = (yMax-yMin)/20;
70 | axis([xMin xMax yMin-dy yMax+dy]);
71 |
72 | if nargin>1
73 | xlabel(xLab)
74 | end
75 | if nargin>2
76 | ylabel(yLab)
77 | end
78 | if nargin>3
79 | title(tLab)
80 | end
81 |
82 | if nargout > 0
83 | varargout{1} = p;
84 | end
85 |
86 | end
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/docs/docgenerator/docgen.m:
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1 | %% setup help generator options
2 |
3 | swPath = {'swfiles/@spinw' 'swfiles' 'swfiles/+swplot' 'swfiles/@swpref' 'swfiles/+swsym' 'swfiles/+swfunc' 'swfiles/+ndbase'};
4 | swr = sw_rootdir;
5 | swPath = cellfun(@(C)[swr C],swPath,'UniformOutput',false);
6 | swver = sw_version;
7 | outPath = '~/spinwdoc_git';
8 | docPath = '~/spinw_git/docs';
9 | upload = true;
10 | recalc = true;
11 |
12 | %% generate help
13 |
14 | %fun0 = {'swfiles' 'spinw' 'gm_planard' 'sw_version'};
15 | %fun0 = {'swfiles' 'sw_egrid'};
16 | fun0 = cell(1,0);
17 |
18 | clc
19 | doctree = sw_genhelp('sourcepath',swPath,'outpath',outPath,'docpath',docPath,'fun',fun0,'verstr',swver,'recalc',recalc,'upload',upload);
20 |
21 |
22 | %% get all help
23 |
24 | content = [doctree.content];
25 | allhelp = {content.text};
26 | isCont = [content.isContents];
27 |
28 | for ii = 1:numel(allhelp)
29 | allhelp{ii} = cellfun(@(C)[C newline],allhelp{ii},'UniformOutput',false);
30 | allhelp{ii} = [allhelp{ii}{:}];
31 | end
32 |
33 | %% generate all links
34 |
35 | pLink = cellfun(@(C)C.permalink,{content.frontmatter},'UniformOutput',false);
36 | fun = {content.fun};
37 |
38 | %% replace function names with links
39 |
40 | for ii = 1:numel(pLink)
41 | allhelp = regexprep(allhelp,fun{ii},['[' fun{ii} '](' pLink{ii} ')']);
42 | end
43 |
44 |
45 |
46 |
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/docs/docgenerator/sw_convdef.m:
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1 | function text0 = sw_convdef(text0,idx,foredit)
2 | % convert list into MD definitions
3 |
4 | if nargin<2
5 | idx = 2;
6 | end
7 |
8 | if nargin<3
9 | foredit = true;
10 | end
11 |
12 | % convert arguments and options into definitions
13 | %text0 = sec([sec.idx] == ii).text;
14 | % lines of definition
15 | defIdx = cellfun(@(C)~isempty(C) && C(1)~=' ' ,text0);
16 | %spaceIdx = cellfun(@(C)find(C==' ',1),text0(defIdx));
17 | [spaceIdx, spaceEnd] = regexp(text0(defIdx),'\s+','once');
18 | spaceEnd = round(mean(cell2mat(spaceEnd)));
19 | text0 = [text0;cell(1,numel(text0))];
20 | fdefIdx = find(defIdx);
21 | for jj = 1:numel(fdefIdx)
22 | text0{2,fdefIdx(jj)} = [':' text0{1,fdefIdx(jj)}(spaceEnd:end)];
23 | if idx == 3
24 | textTemp = [ '`''' text0{1,fdefIdx(jj)}(1:(spaceIdx{jj}-1)) '''`'];
25 | else
26 | textTemp = [ '`' text0{1,fdefIdx(jj)}(1:(spaceIdx{jj}-1)) '`'];
27 | end
28 |
29 | if foredit
30 | text0{1,fdefIdx(jj)} = [newline '% ' textTemp];
31 | else
32 | text0{1,fdefIdx(jj)} = [newline textTemp];
33 | end
34 | end
35 | text0(1,~defIdx) = cellfun(@(C)[' ' C(spaceEnd:end)],text0(1,~defIdx),'UniformOutput',false);
36 | text0 = text0(cellfun(@(C)~isempty(C),text0(:)));
37 |
38 | end
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/docs/docgenerator/sw_rmspace.m:
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1 | function str = sw_rmspace(str)
2 | % remove leading spaces from a cell of strings
3 |
4 | % remove empty lines
5 | str(cellfun(@(C)isempty(C),str)) = [];
6 | % lines that begin with space
7 |
8 | if all(cellfun(@(C)isempty(C),regexp(str,'^\S','once')))
9 | sIdx = cellfun(@(C)C(1)==' ' && any(C~=' '),str);
10 | % minimum space
11 | nSpace = min(cellfun(@(C)find(diff(C==' '),1,'first'),str(sIdx)));
12 | % remove leading spaces
13 | str(sIdx) = cellfun(@(C)C(nSpace+1:end),str(sIdx),'UniformOutput',false);
14 | end
15 |
16 | end
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/docs/resources/file.pdf:
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https://raw.githubusercontent.com/tsdev/spinw/03e6d885c1d992404572c6fe22f930bd3330a7e5/docs/resources/file.pdf
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/docs/resources/spinw_cheatsheet.png:
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/docs/source/04_magstr.md:
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1 | ---
2 | title: Magnetic structure
3 | keywords: docs
4 | sidebar: sw_sidebar
5 | permalink: magstr.html
6 | summary: Representation of magnetic structures and optimization
7 | folder: documentation
8 | mathjax: true
9 | ---
10 |
11 | ## Complex magnetic representation
12 |
13 | If the expectation value of the spin operator is non-zero ($\langle \mathbf{S}\rangle\neq 0$) the spin vectors will make a pattern that can be mathematically best described by its Fourier transform. A concise description of this topic can be found in the article [A. Wills: Magnetic structures and their determination using group theory](https://doi.org/10.1051/jp4:2001906).
14 |
15 | To define a magnetic structure first we need to find the correct magnetic unit cell. Although in symmetry analysis of magnetic structures the magnetic and the crystallographic unit cells are identical, in SpinW no symmetry analysis of magnetic structures is not possible. SpinW will analyze magnetic structures based on the classical energy of a given spin Hamiltonian. It is also possible in SpinW to define a magnetic supercell, that is the multiples of the crystallographic unit cell. This can help sometimes to optimize the spin wave calculation and gives more flexibility to test new models without changing the crystal structure. The magnetic structure is stored in the [spinw.mag_str] property of the SpinW class with the `nExt` subfield (`int32` type) storing the size of the magnetic supercell in units of the crystallographic unit cell. By default the magnetic supercell is identical to the crystallographic one which is given by `nExt=[1 1 1]`.
16 |
17 | Once we defined the magnetic unit cell, the magnetic structure is given by a complex spin vector on each magnetic site and a propagation vector. The real spin vector at a given site $i$ in the $l$th unit cell is given by
18 |
19 |
20 |
21 |
22 | ## Magnetic lattice
23 |
24 | ## Single-k representation
25 |
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/docs/source/05_hamiltonian.md:
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1 | ---
2 | title: Spin Hamiltonian
3 | keywords: docs
4 | sidebar: sw_sidebar
5 | permalink: hamiltonian.html
6 | summary: Definition of the complete spin Hamiltonian
7 | folder: documentation
8 | mathjax: true
9 | ---
10 |
11 | ## General spin Hamiltonian
12 | ## Bonds
13 | ## General matrices
14 | ## Single ion properties
15 | ## Tensors
16 | ## Classical ground state
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/docs/source/06_symmetry.md:
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1 | ---
2 | title: Symmetry and tensors
3 | keywords: docs
4 | sidebar: sw_sidebar
5 | permalink: symmetry.html
6 | summary: Representation of space groups and coordinate systems
7 | folder: documentation
8 | mathjax: true
9 | ---
10 |
11 |
12 | ## Symmetry operators
13 | ## Space groups
14 |
15 |
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/docs/source/07_spinwave.md:
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1 | ---
2 | title: Solvers
3 | keywords: docs
4 | sidebar: sw_sidebar
5 | permalink: spinwave.html
6 | summary: Solvers to calculate spin-spin correlation function
7 | folder: documentation
8 | mathjax: true
9 | ---
10 |
11 | * linear spin wave solver
12 | * spin-spin correlation function
13 | * powder spectrum
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/docs/source/08_spec.md:
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1 | ---
2 | title: Correlation function post processing and fitting
3 | keywords: docs
4 | sidebar: sw_sidebar
5 | permalink: spec.html
6 | summary: Post processing the spin-spin correlation function
7 | folder: documentation
8 | mathjax: true
9 | ---
10 |
11 |
12 | * cross section calculation
13 | * resolution convolution
14 | * fitting spin wave spectrum
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/docs/source/09_symbolic.md:
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1 | ---
2 | title: Symbolic calculation
3 | keywords: docs
4 | sidebar: sw_sidebar
5 | permalink: symbolic.html
6 | summary: Symbolic spin wave calculation mode
7 | folder: documentation
8 | mathjax: true
9 | ---
10 |
11 | * defining a symbolic model
12 | * analytical solution to the ground state
13 | * solving and analysing spin wave spectrum
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/docs/source/10_onemorething.md:
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1 | ---
2 | title: Usefull functions in neutron/x-ray scattering
3 | keywords: docs
4 | sidebar: sw_sidebar
5 | permalink: onemorething.html
6 | summary: List of usefull functions that are not directly connected to SpinW
7 | folder: documentation
8 | mathjax: true
9 | ---
10 |
11 | * converters
12 | * etc.
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/docs/source/11_contribute.md:
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1 | ---
2 | title: How to contribute and discuss
3 | keywords: docs
4 | sidebar: sw_sidebar
5 | permalink: contribute.html
6 | summary:
7 | folder: documentation
8 | mathjax: true
9 | ---
10 |
11 | ## Help
12 | ## Online help
13 | ## How to contribute
14 |
15 |
16 | {% include links.html %}
17 |
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/docs/source/index.md:
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1 | ---
2 | title: Documentation for SpinW
3 | keywords: homepage
4 | sidebar: sw_sidebar
5 | permalink: index.html
6 | summary:
7 | mathjax: true
8 | ---
9 |
10 | This is the **official documentation** of SpinW. The documentation contains the general description of the code (under the "Documentation" menu) and the function reference for all SpinW classes, packages and function.
11 |
12 | SpinW is a Matlab library that can define spin Hamiltonians including general quadratic exchange interactions, single ion anistropy and external magnetic field, applying space group symmetries and solve the resulting equation of motion.
13 |
14 | SpinW constist of a [spinw](spinw) class, that stores all parameters of the spin Hamiltonian as a set of properties and has several methods to prepare the Hamiltonian and calculate the spin-spin correlation function.
15 |
16 | The [swfiles](swfiles) folder contains additional function that can be used to post-process the calculated spin-spin correlation function, e.g. calculating cross section or convoluting instrumental resolution.
17 |
18 | The [swplot](swplot) package contains functions that can visualize the spin Hamiltonian as 3D plot including bonds, magnetic moments and exchange interactions.
19 |
20 | The [swpref](swpref) package stores persistent preferences, [swsym](swsym) package manipulates space group operators and [swfunc](swfunc) package contains spectral peak shape functions.
21 |
22 | **Feel free to ask questions & requests!**
23 |
24 |
25 | {% include links.html %}
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/external/bsxfunsym.m:
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1 | function C = bsxfunsym(op,A,B)
2 | % C = BSXFUNSYM(@op,A,B) extends the bsxfun to sym class variables, for any
3 | % other input type it calls the standrd bsxfun function.
4 | %
5 | % See also sym, syms.
6 | %
7 |
8 | if ~isa(A,'sym') && ~isa(B,'sym')
9 | C = bsxfun(op,A,B);
10 | return
11 | elseif ~isa(B,'sym')
12 | B = sym(B);
13 | elseif ~isa(A,'sym')
14 | A = sym(A);
15 | end
16 |
17 | nA = ndims(A);
18 | nB = ndims(B);
19 |
20 | nD = max(nA,nB);
21 |
22 | sA = ones(1,nD);
23 | sB = ones(1,nD);
24 |
25 | sA(1:nA) = size(A);
26 | sB(1:nB) = size(B);
27 |
28 | if ~all(sA) || ~all(sB)
29 | C = A;
30 | else
31 | % repeat dimensions of A where B is non-one, A is one
32 | rA = (sA==1) & (sB~=1);
33 | rB = (sB==1) & (sA~=1);
34 |
35 | sA(~rB) = 1;
36 | sB(~rA) = 1;
37 |
38 | C = op(repmat(A,sB),repmat(B,sA));
39 | end
40 |
41 | end
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/external/changem.m:
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1 | function A = changem(A,newval,oldval)
2 | % vectorized version of changem
3 | %
4 | % B = CHANGEM(A,newval,oldval)
5 | %
6 | % The function changes the old values in A to the new values pair wise.
7 | %
8 |
9 | [idx1, idx2] = ismember(A,oldval);
10 | A(idx1) = newval(idx2(idx1));
11 |
12 | end
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/external/chol_omp/chol_omp.m:
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1 | % calculates the Cholesky factorisation of a stack of matrices
2 | %
3 | % R = CHOL_OMP(M); - Errors if M not positive definite.
4 | % [R,P] = CHOL_OMP(M); - No error, R is PxP.
5 | % L = CHOL_OMP(M,'lower');
6 | % [L,P] = CHOL_OMP(M,'lower');
7 | %
8 | % The code uses Lapack calls and OpenMP to speed up the calculation. Unlike
9 | % the matlab built-in this mex does not handle sparse matrices.
10 | %
11 | % Input:
12 | %
13 | % M Matrix with dimensions of [N N L], M=R'*R=L*L'
14 | %
15 | % Options:
16 | %
17 | % tol Tolerance, if the input is not positive definite, the tol value
18 | % will be added to each NxN matrix diagonal.
19 | % Colpa The output is redefined:
20 | % [K2,invK] = CHOL_OMP(M,'Colpa');
21 | % where K2 = (R*gComm*R') Hermitian matrix with
22 | % gComm = [1...1,-1...1] is the commutator and invK = inv(R).
23 | %
24 | %
25 | % Note this function does not check for symmetry. Also note that we do not
26 | % truncate the output matrix if the input is not positive definite, unlike
27 | % the built-in. i.e. R or L is always of size (N x N) not (P x P).
28 | %
29 | % This is a MEX-file for MATLAB.
30 | %
31 | % Original Author: M. D. Le [duc.le@stfc.ac.uk]
32 |
33 |
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/external/chol_omp/chol_omp.mexa64:
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/external/chol_omp/chol_omp.mexmaci64:
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/external/chol_omp/chol_omp.mexw64:
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/external/clipboardimage.m:
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1 | function rgbData = clipboardimage()
2 | % returns the RGB image from clipboard
3 | %
4 | % rgbData = CLIPBOARDIMAGE()
5 | %
6 | % The function at the moment works with print screen images on OXS and
7 | % Windows.
8 | %
9 | % Output:
10 | %
11 | % rgbData Matrix with dimensions W x H x 3, containing the RGB values
12 | % from the clipboard. Empty matrix if the clipboard doesn't
13 | % contain image data.
14 | %
15 | % Example:
16 | %
17 | % figure
18 | % imshow(clipboardimage)
19 | %
20 |
21 | % Based on code from Saurabh Kumar, saurabhkumar_@rediffmailcom
22 | %
23 |
24 | tKit = java.awt.Toolkit.getDefaultToolkit();
25 | % get clipboard handle
26 | cbrd = tKit.getSystemClipboard();
27 | reqObj = java.lang.Object;
28 | img = cbrd.getContents(reqObj);
29 | Dflavor = img.getTransferDataFlavors();
30 | imgDfvr = java.awt.datatransfer.DataFlavor.imageFlavor;
31 |
32 | % only import if the clipboard stores image data
33 | if Dflavor(1).equals(imgDfvr)
34 | % got image
35 | jImage = img.getTransferData(java.awt.datatransfer.DataFlavor.imageFlavor);
36 | % dimensions of the image
37 | imSize = [jImage.getHeight jImage.getWidth];
38 | % convert the javs image to Matlab matrix
39 | cmykDat = double(permute(reshape(typecast(jImage.getData.getDataStorage, 'uint8'), 4, imSize(2), imSize(1)),[3 2 1]))/255;
40 | % convert CMYK to RGB the transposed image
41 | rgbData = bsxfun(@times,cmykDat(:,:,[3 2 1]),cmykDat(:,:,4));
42 | else
43 | % return empty matrix if there is no image
44 | rgbData = [];
45 | end
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/external/colormap/license.txt:
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1 | Copyright (c) 2016, Ander Biguri
2 | All rights reserved.
3 |
4 | Redistribution and use in source and binary forms, with or without
5 | modification, are permitted provided that the following conditions are
6 | met:
7 |
8 | * Redistributions of source code must retain the above copyright
9 | notice, this list of conditions and the following disclaimer.
10 | * Redistributions in binary form must reproduce the above copyright
11 | notice, this list of conditions and the following disclaimer in
12 | the documentation and/or other materials provided with the distribution
13 |
14 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
15 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
16 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
17 | ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
18 | LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
19 | CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
20 | SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
21 | INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
22 | CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
23 | ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
24 | POSSIBILITY OF SUCH DAMAGE.
25 |
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/external/eig_omp/eig_omp.m:
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1 | % Diagonalises a stack of matrices
2 | %
3 | % [V, D] = EIG_OMP(H,'orth','sort')
4 | %
5 | % The code uses Lapack calls and OpenMP to speed up the calculation.
6 | %
7 | % Input:
8 | %
9 | % H Matrix with dimensions [N N L].
10 | %
11 | % Options:
12 | %
13 | % orth Orthogonalize the eigenvectors in case of degenerate eigenvalues
14 | % for non-Hermitian matrices (for Hermitian matrices the eigenvectors
15 | % are always orthogonal).
16 | % sort Sort the eigenvalues in increasing order (and sort the
17 | % corresponding eigenvectors as well).
18 | %
19 | % Output:
20 | %
21 | % V Matrix with dimesions [N N L], contains the eigenvectors for each
22 | % NxN matrix in columns.
23 | % D Matrix with dimensions [N L], each column contain the corresponding
24 | % eigenvalues.
25 | %
26 | % This is a MEX-file for MATLAB.
27 | %
28 | % In addition the the mexFunction, the following subsidiary functions are
29 | % defined:
30 | %
31 | % void fliplr() - Flips matrix by columns
32 | % void quicksort() - Quicksort algorithm, returns indices
33 | % void sort() - Sort and permutes eigenvalue/vectors
34 | % void orth() - Orthogonalises degenerate eigenvecs
35 | %
36 | % Original Author: M. D. Le [duc.le@stfc.ac.uk]
37 |
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/external/eig_omp/eig_omp.mexa64:
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https://raw.githubusercontent.com/tsdev/spinw/03e6d885c1d992404572c6fe22f930bd3330a7e5/external/eig_omp/eig_omp.mexa64
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/external/eig_omp/eig_omp.mexmaci64:
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https://raw.githubusercontent.com/tsdev/spinw/03e6d885c1d992404572c6fe22f930bd3330a7e5/external/eig_omp/eig_omp.mexmaci64
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/external/eig_omp/eig_omp.mexw64:
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https://raw.githubusercontent.com/tsdev/spinw/03e6d885c1d992404572c6fe22f930bd3330a7e5/external/eig_omp/eig_omp.mexw64
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/external/findmax.m:
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1 | function varargout = findmax(X,varargin)
2 | % find the maximum valued element in a vector
3 | %
4 | % I = FINDMAX(X,val)
5 | % I = FINDMAX(X,val,k)
6 | % I = FINDMAX(X,val,k,direction)
7 | %
8 | % [row,col] = FINDMAX(___)
9 | % [row,col,v] = FINDMAX(___)
10 | %
11 | % It has the same parameters and output as find().
12 | %
13 | % See also find.
14 |
15 | switch nargout
16 | case 0
17 | varargout{1} = find(X==max(X),varargin{:});
18 | case 1
19 | varargout{1} = find(X==max(X),varargin{:});
20 | case 2
21 | [varargout{1},varargout{2}] = find(X==max(X),varargin{:});
22 | case 3
23 | [row,col] = find(X==max(X),varargin{:});
24 |
25 | varargout{1} = row;
26 | varargout{2} = col;
27 | varargout{3} = X(sub2ind(size(X),row,col));
28 | end
29 |
30 | end
31 |
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/external/findmin.m:
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1 | function varargout = findmin(X,varargin)
2 | % find the minimum valued element in a vector
3 | %
4 | % I = FINDMIN(X,val)
5 | % I = FINDMIN(X,val,k)
6 | % I = FINDMIN(X,val,k,direction)
7 | %
8 | % [row,col] = FINDMIN(___)
9 | % [row,col,v] = FINDMIN(___)
10 | %
11 | % It has the same parameters and output as find().
12 | %
13 | % See also find.
14 |
15 | switch nargout
16 | case 0
17 | varargout{1} = find(X==min(X),varargin{:});
18 | case 1
19 | varargout{1} = find(X==min(X),varargin{:});
20 | case 2
21 | [varargout{1},varargout{2}] = find(X==min(X),varargin{:});
22 | case 3
23 | [row,col] = find(X==min(X),varargin{:});
24 |
25 | varargout{1} = row;
26 | varargout{2} = col;
27 | varargout{3} = X(sub2ind(size(X),row,col));
28 | end
29 |
30 | end
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/external/findval.m:
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1 | function varargout = findval(X,val,varargin)
2 | % find the an element in a vector that is closest to a given value
3 | %
4 | % I = FINDVAL(X,val)
5 | % I = FINDVAL(X,val,k)
6 | % I = FINDVAL(X,val,k,direction)
7 | %
8 | % [row,col] = FINDVAL(___)
9 | % [row,col,v] = FINDVAL(___)
10 | %
11 | % It has the same parameters and output as find() plus the extra val value.
12 | %
13 | % See also find.
14 |
15 | switch nargout
16 | case 0
17 | varargout{1} = find(abs(X-val)==min(abs(X-val)),varargin{:});
18 | case 1
19 | varargout{1} = find(abs(X-val)==min(abs(X-val)),varargin{:});
20 | case 2
21 | [varargout{1},varargout{2}] = find(abs(X-val)==min(abs(X-val)),varargin{:});
22 | case 3
23 | [row,col] = find(abs(X-val)==min(abs(X-val)),varargin{:});
24 |
25 | varargout{1} = row;
26 | varargout{2} = col;
27 | varargout{3} = X(sub2ind(size(X),row,col));
28 | end
29 |
30 | end
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/external/fprintf0.m:
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1 | function fprintf0(fid,varargin)
2 | % same as fprintf, expect if fid is zero, will not produce output.
3 |
4 | if fid~=0
5 | fprintf(fid,varargin{:});
6 | end
7 |
8 | end
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/external/gcdv.m:
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1 | function g = gcdv(v)
2 | % calculates the greates common divisor of a set of numbers
3 | %
4 | % G = VECGCD(V)
5 | %
6 | % is the greatest common divisor of the elements of the integer vector V. V
7 | % must be a row or a column vector of integers. We define gcd([]) = 1 and
8 | % gcd([0 0 ... 0]) = 0.
9 | %
10 |
11 | [r,c] = size(v);
12 | if (r>1) && (c>1)
13 | error('v must be a row or a column vector');
14 | end
15 |
16 | % vecgcd([]) = 1
17 | if isempty(v)
18 | g = 1;
19 | return
20 | end
21 |
22 | % vecgcd([0 0 ... 0]) = 0
23 | if all(v==0)
24 | g = 0;
25 | return
26 | end
27 |
28 |
29 | % I want a to work with a row vector
30 | if c==1
31 | v = v';
32 | end
33 |
34 | % remove the zeros and sort
35 | v = v(v>0);
36 | v = sort(abs(v),2,'descend');
37 |
38 | i = 1;
39 | j = length(v);
40 | while i < j
41 | x = mod(v(i), v(j));
42 | x = min([x, v(j) - x]);
43 | % x|v(i), x|v(j), g|x
44 | % and x is smaller than min[v]
45 |
46 | i = i + 1; % "remove" v(i)
47 | if x > 0 % if x > 0 append it to v
48 | j = j + 1;
49 | v = [v, x]; %#okAtom.dat
The atom.dat file contains information about different elements/isotopes, where each row defines an element/isotope. The meaning of the columns are the following:
- Name of element, string. These labels can be used in the [[SwpropertiesEN#2][sw.unit_cell]].label field to assign different atoms to crystallographic positions.
- Radius in Angstrom, double. This gives the atomic radius for plotting.
- Color RGB code, 3 integer. This gives the color for plottig the atom.
- Mass, double. The mass of the element/isotope for unit cell mass calculation.
- Long name, string. Long name of the element/isotope.