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Implementing the rlu transformation
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- minor bug fixes
- newcell() and spinwave() are now compatible with the rlu
transformation
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@tsdev
tsdev committed Apr 12, 2017
1 parent c3d48a7 commit 2434933
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178 changes: 93 additions & 85 deletions swfiles/+swplot/plotmag.m
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
% 'circle' Plot only the rotation plane of incommensurate
% magnetic structures.
% 'arrow' Plots only the moment directions.
% 'none' Don't plot anything.
% figure Handle of the swplot figure. Default is the selected figure.
% legend Whether to add the plot to the legend, default is true.
% label Whether to plot labels for atoms, default is true.
Expand Down Expand Up @@ -207,98 +208,105 @@
% do nothing
case 'circle'
case 'arrow'
case 'none'
otherwise
error('plotmag:WrongInput','The given mode string is invalid!');
end

% number of unit cells
nCell = prod(nExtPlot);

% keep track of types of atoms
aIdx = repmat(mAtom.idx,[nCell 1])';
a2Idx = repmat(1:numel(mAtom.idx),[nCell 1])';
pos = reshape(pos,3,[]);

% cut out the atoms that are out of range
switch param.unit
case 'lu'
% L>= lower range, L<= upper range
pIdx = all(bsxfun(@ge,pos,range(:,1)-10*eps) & bsxfun(@le,pos,range(:,2)+10*eps),1);
case 'xyz'
% convert to xyz
posxyz = BV*pos;
pIdx = all(bsxfun(@ge,posxyz,range(:,1)-10*eps) & bsxfun(@le,posxyz,range(:,2)+10*eps),1);
end

if ~any(pIdx)
warning('plotatom:EmptyPlot','There are no magnetic moments in the plotting range!')
return
end

M = M(:,pIdx);
pos = pos(:,pIdx);
aIdx = aIdx(pIdx);
a2Idx = a2Idx(pIdx);

% normalization
if param.normalize
% normalize moments
M = bsxfun(@rdivide,M,sqrt(sum(M.^2,1)));
end

% save magnetic moment vector values into data before rescaling
MDat = mat2cell([M;pos;a2Idx],7,ones(1,size(M,2)));

% scale moments
% get the length of the shortest bond
if ~isempty(obj.coupling.atom2)
apos1 = obj.matom.r(:,obj.coupling.atom1(1));
apos2 = obj.matom.r(:,obj.coupling.atom2(1))+double(obj.coupling.dl(:,1));
lBond = norm(BV*(apos2-apos1));
else
lBond = 3;
end

% normalize the longest moment vector to scale*(shortest bond length)
M = M/sqrt(max(sum(M.^2,1)))*param.scale*lBond;

if param.centered
% double the length for centered moments
M = 2*M;
end

% convert to lu units
Mlu = BV\M;

if param.centered
% center on atoms
vpos = cat(3,pos-Mlu/2,pos+Mlu/2);
else
vpos = cat(3,pos,pos+Mlu);
end

% color
if strcmp(param.color,'auto')
color = double(obj.unit_cell.color(:,aIdx));
if ~strcmp(param.mode,'none')

% number of unit cells
nCell = prod(nExtPlot);

% keep track of types of atoms
aIdx = repmat(mAtom.idx,[nCell 1])';
a2Idx = repmat(1:numel(mAtom.idx),[nCell 1])';
pos = reshape(pos,3,[]);

% cut out the atoms that are out of range
switch param.unit
case 'lu'
% L>= lower range, L<= upper range
pIdx = all(bsxfun(@ge,pos,range(:,1)-10*eps) & bsxfun(@le,pos,range(:,2)+10*eps),1);
case 'xyz'
% convert to xyz
posxyz = BV*pos;
pIdx = all(bsxfun(@ge,posxyz,range(:,1)-10*eps) & bsxfun(@le,posxyz,range(:,2)+10*eps),1);
end

if ~any(pIdx)
warning('plotatom:EmptyPlot','There are no magnetic moments in the plotting range!')
return
end

M = M(:,pIdx);
pos = pos(:,pIdx);
aIdx = aIdx(pIdx);
a2Idx = a2Idx(pIdx);

% normalization
if param.normalize
% normalize moments
M = bsxfun(@rdivide,M,sqrt(sum(M.^2,1)));
end

% save magnetic moment vector values into data before rescaling
MDat = mat2cell([M;pos;a2Idx],7,ones(1,size(M,2)));

% scale moments
% get the length of the shortest bond
if ~isempty(obj.coupling.atom2)
apos1 = obj.matom.r(:,obj.coupling.atom1(1));
apos2 = obj.matom.r(:,obj.coupling.atom2(1))+double(obj.coupling.dl(:,1));
lBond = norm(BV*(apos2-apos1));
else
lBond = 3;
end

% normalize the longest moment vector to scale*(shortest bond length)
M = M/sqrt(max(sum(M.^2,1)))*param.scale*lBond;

if param.centered
% double the length for centered moments
M = 2*M;
end

% convert to lu units
Mlu = BV\M;

if param.centered
% center on atoms
vpos = cat(3,pos-Mlu/2,pos+Mlu/2);
else
vpos = cat(3,pos,pos+Mlu);
end

% color
if strcmp(param.color,'auto')
color = double(obj.unit_cell.color(:,aIdx));
else
color = swplot.color(param.color);
end

% shift positions
vpos = bsxfun(@plus,vpos,BV\param.shift);

% prepare legend labels
mAtom.name = obj.unit_cell.label(mAtom.idx);
lLabel = repmat(mAtom.name,[nCell 1]);
lLabel = lLabel(pIdx);

% plot moment vectors
swplot.plot('type','arrow','name','mag','position',vpos,'text','',...
'figure',hFigure,'legend',false,'color',color,'R',param.radius0,...
'fontsize',param.fontsize,'tooltip',false,'replace',param.replace,...
'data',MDat,'label',lLabel,'nmesh',param.nmesh,'ang',param.ang,...
'lHead',param.lHead,'translate',param.translate,'zoom',param.zoom);

else
color = swplot.color(param.color);
% don't plot anything just remove previous plot
end

% shift positions
vpos = bsxfun(@plus,vpos,BV\param.shift);

% prepare legend labels
mAtom.name = obj.unit_cell.label(mAtom.idx);
lLabel = repmat(mAtom.name,[nCell 1]);
lLabel = lLabel(pIdx);


% plot moment vectors
swplot.plot('type','arrow','name','mag','position',vpos,'text','',...
'figure',hFigure,'legend',false,'color',color,'R',param.radius0,...
'fontsize',param.fontsize,'tooltip',false,'replace',param.replace,...
'data',MDat,'label',lLabel,'nmesh',param.nmesh,'ang',param.ang,...
'lHead',param.lHead,'translate',param.translate,'zoom',param.zoom);

% save range
setappdata(hFigure,'range',struct('range',range,'unit',param.unit));
Expand Down
3 changes: 2 additions & 1 deletion swfiles/@spinw/energy.m
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Expand Up @@ -113,7 +113,8 @@
dRIdx = find(any(dR));
for ii = 1:numel(dRIdx)
%M2(:,dRIdx(ii)) = sw_rot(n, kExt*dR(:,dRIdx(ii))*2*pi, M2(:,dRIdx(ii)));
M2(:,dRIdx(ii)) = real(bsxfunsym(@times,M2cmplx(:,dRIdx(ii)),exp(1i*kExt*dR(:,dRIdx(ii))*2*pi)));
% TODO check - sign in front of phase
M2(:,dRIdx(ii)) = real(bsxfunsym(@times,M2cmplx(:,dRIdx(ii)),exp(-1i*kExt*dR(:,dRIdx(ii))*2*pi)));
end
end

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94 changes: 62 additions & 32 deletions swfiles/@spinw/newcell.m
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Original file line number Diff line number Diff line change
@@ -1,22 +1,35 @@
function varargout = newcell(obj,bvect, bshift)
function varargout = newcell(obj,varargin)
% changes lattice vectors while keeping atoms
%
% {T} = NEWCELL(obj, bvect, {bshift})
% {T} = NEWCELL(obj, 'option1', value1, ...)
%
% The function defines new unit cell using the 3 vectors contained in
% bvect. The three vectors in lattice units define a parallelepiped. This
% will be the new unit cell. The atoms from the original unit cell will
% fill the new unit cell. Also the magnetic structure and bond and single
% ion property definitions will be erased from the structure.
% ion property definitions will be erased from the structure. The new cell
% will naturally have different reciprocal lattice, however the original
% reciprocal lattice units can be retained using the 'keepq' option. In
% this case the spinw.spinwave() function will calculate spin wave
% dispersion at reciprocal lattice points of the original lattice. The
% transformation between the two lattices is stored in spinw.unit.qmat.
%
% Input:
%
% obj spinw class object.
%
% Options:
%
% bvect Defines the new lattice vectors in the original lattice
% coordinate system. Cell with the following elements
% {v1 v2 v3}.
% bshift Vector defines a shift of the position of the unit cell.
% {v1 v2 v3} or a 3x3 matrix with v1, v2 and v3 as column
% vectors: [v1 v2 v3].
% bshift Row vector defines a shift of the position of the unit cell.
% Optional.
% keepq If true, the reciprocal lattice units of the new model will be
% the same as in the old model. This is achieved by storing the
% transformation matrix between the new and the old coordinate
% system in spinw.unit.qmat.
%
% Output:
%
Expand All @@ -28,14 +41,31 @@
%
% Example:
%
% tri = spinw;
% tri.genlattice('lat_const',[3 3 5],'angled',[90 90 120])
% tri.addatom('r',[0 0 0])
% tri.newcell({[1 0 0] [1 2 0] [0 0 1]})
% plot(tri)
% In this example we generate the triangular lattice antiferromagnet and
% convert the hexagonal cell to orthorhombic. This doubles the number of
% magnetic atoms in the cell and changes the reciprocal lattice. However we
% use 'keepq' to able to index the reciprocal lattice of the orthorhombic
% cell with the reciprocal lattice of the original hexagonal cell. To show
% that the two models are equivalent, we calculate the spin wave spectrum
% on both model using the same rlu. On the orthorhombic cell, the q value
% will be converted automatically and the calculated spectrum will be the
% same for both cases.
%
% tri = sw_model('triAF',1);
% tri_orth = copy(tri);
% tri_orth.newcell('bvect',{[1 0 0] [1 2 0] [0 0 1]},'keepq',true);
% tri_orth.gencoupling
% tri_orth.addcoupling('bond',1,'mat','J1')
% newk = ((tri_orth.unit.qmat)*tri.magstr.k')';
% tri_orth.genmagstr('mode','helical','k',newk,'S',[1 0 0]')
% plot(tri_orth)
%
% figure
% subplot(2,1,1)
% sw_plotspec(sw_egrid(tri.spinwave({[0 0 0] [1 1 0] 501})),'mode','color','dE',0.2)
% subplot(2,1,2)
% sw_plotspec(sw_egrid(tri_orth.spinwave({[0 0 0] [1 1 0] 501})),'mode','color','dE',0.2)
%
% The example show how to convert a triangular lattice into orthorhombic
% lattice vectors and plots the new unit cell.
%
% See also SPINW.GENLATTICE, SPINW.GENCOUPLING, SPINW.NOSYM.
%
Expand All @@ -45,18 +75,18 @@
return
end

%warning('spinw:newcell:PossibleBug','There might be an error, if there are atoms at the faces of the original cell!')
inpForm.fname = {'bvect' 'bshift' 'keepq'};
inpForm.defval = {eye(3) [0 0 0] true };
inpForm.size = {[-1 3] [1 3] [1 1] };

param = sw_readparam(inpForm, varargin{:});

if ~iscell(bvect) || numel(bvect)~=3
error('spinw:newcell:WrongInput','Input has to be cell type with 3 vectors inside!');
if ~iscell(param.bvect) && size(param.bvect,1)~=3
error('spinw:newcell:WrongInput','Input has to be 1x3 cell or 3x3 matrix!');
end

% shift
if nargin == 2
bshift = [0;0;0];
else
bshift = bshift(:);
end
bshift = param.bshift(:);

% here 3 coordinate systems are used:
% - xyz real space, Cartesian
Expand All @@ -66,8 +96,11 @@

% transformation matrix from the new lattice units into the original
% lattice
% v_orig = Tn_o*v_new
Tn_o = [bvect{1}(:) bvect{2}(:) bvect{3}(:)];
if iscell(param.bvect)
Tn_o = [param.bvect{1}(:) param.bvect{2}(:) param.bvect{3}(:)];
else
Tn_o = param.bvect;
end

% transformation from the original lattice into xyz real space
% xyz = To_xyz * v_orig
Expand All @@ -87,8 +120,6 @@

% number of cells needed for the extension
nExt = ceil(max(pp,[],2) - min(pp,[],2))'+2;
%obj.mag_str.N_ext = int32(nExt);


% generated atoms
atomList = obj.atom;
Expand All @@ -100,7 +131,6 @@
idxExt = atomList.idxext;



rExt = bsxfun(@plus,rExt,bshift);
% atomic positions in the new unit cell
rNew = inv(Tn_o)*rExt; %#ok<MINV>
Expand All @@ -111,7 +141,7 @@
idxCut = any((rNew<-epsilon) | (rNew>(1-epsilon)),1);
rNew(:,idxCut) = [];
idxExt(idxCut) = [];
atomList.Sext(idxCut) = [];
atomList.Sext(idxCut) = [];

% atoms are close to the face or origin --> put them exactly
rNew(rNew<epsilon) = 0;
Expand All @@ -135,11 +165,6 @@
obj.unit_cell.(fNames{ii}) = obj.unit_cell.(fNames{ii})(:,idxExt);
end

% reset the magnetic structure
% obj.mag_str.F = zeros(3,0,0);
% obj.mag_str.k = zeros(3,0);
% obj.mag_str.N_ext = int32([1 1 1]);

% reset the magnetic structure and the bonds
obj.initfield({'coupling' 'mag_str'});

Expand All @@ -149,7 +174,12 @@
% transformation from the original reciprocal lattice into the new
% reciprocal lattice
if nargout>0
varargout{1} = Tn_o;
varargout{1} = Tn_o';
end

if param.keepq
% keep the new coordinate system
obj.unit.qmat = Tn_o';
end

end
2 changes: 1 addition & 1 deletion swfiles/@spinw/optmagsteep.m
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Original file line number Diff line number Diff line change
Expand Up @@ -280,7 +280,7 @@
end

if fid == 1
sw_status(0,1);
sw_status(0,1,'Magnetic structure optimization');
end

if nargout == 1
Expand Down
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