Minor Bugfixes

+sw_tests/+system_tests/systemtest_spinwave_pcsmo.m

@@ -95,7 +95,7 @@ function test_pcsmo(testCase, usehorace)
                 spec = testCase.swobj.spinwave(qln, 'formfact', true, 'saveV', true, 'saveH', true, 'optmem', 2);
                 spec = sw_egrid(spec, 'Evect', linspace(0, 100, 200));
                 spec = sw_neutron(spec);
-                testCase.generate_or_verify(spec, {}, struct('V', spec.V, 'H', spec.H), 'approxSab', 0.1);
+                testCase.generate_or_verify(spec, {}, struct('V', spec.V, 'H', spec.H), 'approxSab', 0.11);
             end
         end
     end

+sw_tests/+unit_tests/unittest_spinw_fitspec.m

@@ -0,0 +1,57 @@
+classdef unittest_spinw_fitspec < sw_tests.unit_tests.unittest_super
+    % Tests for fitspec - not strictly a unit test, but make sure it runs
+
+    properties
+        datafile = '';
+        swobj = [];
+        fitpar = struct();
+    end
+
+    methods (TestClassSetup)
+        function setup_model_and_fitpars(testCase)
+            % Writes out the mode data
+            testCase.datafile = fullfile(tempdir, 'triAF_modes.txt');
+            fid = fopen(testCase.datafile, 'w');
+            fprintf(fid, '  QH   QK   QL Elim1 Elim2    I1   EN1   sig1    I2   EN2   sig2\n');
+            fprintf(fid, '   1  0.2    1   0.5   5.0  22.6  2.94  0.056     0     0      0\n');
+            fprintf(fid, '   1  0.4    1   0.5   5.0  65.2  2.48  0.053  13.8  3.23  0.061\n');
+            fprintf(fid, '   1  0.6    1   0.5   5.0  69.5  2.52  0.058  16.3  3.15  0.054\n');
+            fprintf(fid, '   1  0.8    1   0.5   5.0  22.6  2.83  0.057     0     0      0\n');
+            fclose(fid);
+            testCase.swobj = sw_model('triAF', 0.7);
+            testCase.fitpar = struct('datapath', testCase.datafile, ...
+                                     'Evect', linspace(0, 5, 51), ...
+                                     'func', @(obj,p)matparser(obj,'param',p,'mat',{'J_1'},'init',1),...
+                                     'xmin', 0, 'xmax', 2, 'x0', 0.7, ...
+                                     'plot', false, 'hermit', true, ...
+                                     'optimizer', 'simplex', ...
+                                     'maxiter', 1, 'maxfunevals', 1, 'nMax', 1, 'nrun', 1);
+        end
+    end
+
+    methods (TestClassTeardown)
+        function del_mode_file(testCase)
+            try
+                delete(testCase.datafile); % Ignores errors if file already deleted
+            end
+        end
+    end
+
+    methods (Test)
+        function test_fitspec(testCase)
+            fitout = testCase.swobj.fitspec(testCase.fitpar);
+            testCase.verify_val(fitout.x, 1.0, 'abs_tol', 0.25);
+            testCase.verify_val(fitout.redX2, 0.0, 'abs_tol', 10);
+        end
+        function test_fitspec_twin(testCase)
+            % Checks that twins are handled correctly
+            swobj = copy(testCase.swobj);
+            % Adds a twin with very small volume so it doesn't affect original fit
+            % If twins not handled correctly, the fit will be bad.
+            swobj.addtwin('axis', [1 1 1], 'phid', 54, 'vol', 0.01);
+            fitout = swobj.fitspec(testCase.fitpar);
+            testCase.verify_val(fitout.x, 1.0, 'abs_tol', 0.25);
+            testCase.verify_val(fitout.redX2, 0.0, 'abs_tol', 10);
+        end
+    end
+end

+sw_tests/+unit_tests/unittest_spinw_spinwave.m

@@ -332,6 +332,9 @@ function test_sw_qh5_fitmode(testCase, mex)
             % fitmode automatically turns off sortMode
             expected_sw = testCase.swobj.spinwave(qpts, 'sortMode', false);
             expected_sw = rmfield(expected_sw, {'obj', 'datestart', 'dateend'});
+            obj = testCase.swobj;
+            expected_sw.obj = struct('single_ion', obj.single_ion, 'twin', obj.twin, ...
+                'unit', obj.unit, 'basisvector', obj.basisvector, 'nmagext', obj.nmagext);
             testCase.verify_spinwave(sw_out, expected_sw);
         end
         function test_incommensurate(testCase, mex)

.github/workflows/build_pyspinw.yml

@@ -21,11 +21,13 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out SpinW
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
+      - name: Install Dependencies
+        run: ${{ matrix.INSTALL_DEPS }}
       - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v1 # v1.1.0 required for Windows/MacOS support
+        uses: matlab-actions/setup-matlab@v2
         with:
           release: ${{ matrix.matlab_version }}
 
@@ -41,13 +43,13 @@ jobs:
           rm external/mtimesx/sw_mtimesx.mexmaci64
           rm external/mtimesx/sw_mtimesx.mexw64
       - name: Run MEXing
-        uses: matlab-actions/run-command@v1
+        uses: matlab-actions/run-command@v2
         with:
           command: "addpath(genpath('swfiles')); addpath(genpath('external')); sw_mex('compile', true, 'test', false, 'swtest', false);"
       - name: Upload MEX results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: MEX
+          name: mex-${{ matrix.os }}
           path: ${{ github.workspace }}/external/**/*.mex*
 
   build_ctfs:
@@ -58,22 +60,22 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out SpinW
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Download MEX artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: MEX
+          pattern: mex-*
           path: ${{ github.workspace }}/external
       - name: Build ctf
         run: |
           cd python
           /Applications/MATLAB_${{ matrix.matlab_version }}.app/bin/matlab -nodisplay -r "build_ctf; exit"
       - name: Upload CTF results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: CTF
+          name: ctf-${{ matrix.matlab_version }}
           path: ${{ github.workspace }}/python/ctf/*.ctf
 
   build_wheel:
@@ -83,11 +85,11 @@ jobs:
       contents: write
     steps:
       - name: Checkout SpinW
-        uses: actions/checkout@v3    
+        uses: actions/checkout@v4
       - name: Download CTF artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: CTF
+          pattern: ctf-*
           path: python/ctf
       - name: Set up Python environment
         uses: actions/setup-python@v4
@@ -98,15 +100,16 @@ jobs:
           cd python
           echo "PYSPINW_VERSION=$( cat pyproject.toml | grep "version = \"" | awk -F'"' '$0=$2' | sed 's/ //g' )" >> $GITHUB_ENV
           mkdir pyspinw/ctfs
-          mv ctf/*.ctf pyspinw/ctfs
+          find ctf/ -name "*.ctf" -exec mv '{}'  pyspinw/ctfs \;
       - name: Build Wheel
         run: |
           cd ${{ github.workspace }}/python
           python -m pip wheel --no-deps --wheel-dir build .
       - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v1 # v1.1.0 required for Windows/MacOS support
+        uses: matlab-actions/setup-matlab@v2
         with:
           release: R2023a
+          products: MATLAB_Compiler_SDK
       - name: Run python test
         run: |
           pip install scipy
@@ -115,7 +118,7 @@ jobs:
           cd tests
           python -m unittest
       - name: Create wheel artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pySpinW Wheel
           path: ${{ github.workspace }}/python/build/*.whl        
@@ -124,3 +127,6 @@ jobs:
         run: |
           pip3 install requests
           python3 release.py --notest --github --token=${{ secrets.GH_TOKEN }}
+      - name: Setup tmate
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3

.github/workflows/publish_pypi.yml

@@ -10,7 +10,7 @@ jobs:
       # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Download wheels

.github/workflows/release.yml

@@ -10,7 +10,7 @@ jobs:
     name: Creates a SpinW release
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - if: |

.github/workflows/run_tests.yml

@@ -16,40 +16,45 @@ jobs:
         matlab_version: [latest]
         include:
           - os: ubuntu-latest
-            matlab_version: R2020a
+            matlab_version: R2021a
           - os: macos-latest
             INSTALL_DEPS: brew install llvm libomp
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out SpinW
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+      - name: Install Dependencies
+        run: ${{ matrix.INSTALL_DEPS }}
       - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v1 # v1.1.0 required for Windows/MacOS support
+        uses: matlab-actions/setup-matlab@v2
         with:
           release: ${{ matrix.matlab_version }}
       - name: Run tests
-        uses: matlab-actions/run-command@v1
+        uses: matlab-actions/run-command@v2
         with:
           command: "run run_tests.m"
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         if: ${{ always() && matrix.os == 'ubuntu-latest' && matrix.matlab_version == 'latest' }}
         with:
             files: coverage*.xml
             token: ${{ secrets.CODECOV_TOKEN }}
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: Unit test results ${{ matrix.os }}
+          name: Unit test results ${{ matrix.os }}-${{ matrix.matlab_version }}
           path: junit_report*.xml
+      #- name: Setup tmate
+      #  if: ${{ failure() }}
+      #  uses: mxschmitt/action-tmate@v3
   publish-test-results:
     needs: test
     runs-on: ubuntu-latest
     if: success() || failure()
     steps:
       - name: Download Artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           path: artifacts
       - name: Publish test results

swfiles/@spinw/fitspec.m

@@ -264,13 +264,13 @@
             [x(idx,:),~, output(idx)] = ndbase.pso(dat,@(x,p)spec_fitfun(obj, data, param.func, p, param0),x0,'lb',param.xmin,'ub',param.xmax,...
                 'TolX',param.tolx,'TolFun',param.tolfun,'MaxIter',param.maxiter);
 
-            redX2(idx) = output.redX2;
+            redX2(idx) = output(idx).redX2;
 
         case 'simplex'
             [x(idx,:),~, output(idx)] = ndbase.simplex(dat,@(x,p)spec_fitfun(obj, data, param.func, p, param0),x0,'lb',param.xmin,'ub',param.xmax,...
                 'TolX',param.tolx,'TolFun',param.tolfun,'MaxIter',param.maxiter);
 
-            redX2(idx) = output.redX2;
+            redX2(idx) = output(idx).redX2;
 
         case 'lm'
             % does not work due to the binning of the spectrum
@@ -448,7 +448,7 @@
 if param.plot
     text(0.05,0.9,['x = [' sprintf('%6.4f ',x) sprintf(']\nRw = %6.4f',sqrt(R))],'Units','normalized','fontsize',12);
     axis([0.5 Qc+0.5 param.Evect(1) param.Evect(end)]);
-    legend(pHandle(1:2),'simulation','data')
+    legend(pHandle([1, length(simE)+2]),'simulation','data')
     xlabel('Scan index')
     ylabel('Energy transfer (meV)')
     title('Spin wave dispersion fit')

swfiles/@spinw/spinwave.m

@@ -399,6 +399,11 @@
             'structure is commensurate so this will have no effect.']);
 end
 
+% If only one hkl value, convert to column vector
+if numel(hkl) == 3
+    hkl = hkl(:);
+end
+
 % Transform the momentum values to the new lattice coordinate system
 hkl = obj.unit.qmat*hkl;
 
@@ -1265,7 +1270,11 @@
 spectra.title           = param.title;
 spectra.gtensor         = param.gtensor;
 
-if ~param.fitmode
+if param.fitmode
+    % Copies only fields needed by downstream functions (sw_egrid, sw_neutron, sw_plotspec)
+    spectra.obj = struct('single_ion', obj.single_ion, 'twin', obj.twin, ...
+        'unit', obj.unit, 'basisvector', obj.basisvector, 'nmagext', obj.nmagext);
+else
     spectra.dateend = datestr(now);
     spectra.obj = copy(obj);
 end

swfiles/sw_egrid.m

@@ -499,7 +499,8 @@
     if param.T==0
         nBose = double(ebin_cens>=0);
     else
-        nBose = 1./(exp(abs(ebin_cens)./(spectra.obj.unit.kB*param.T))-1)+double(ebin_cens>=0);
+        kB = 0.086173324;
+        nBose = 1./(exp(abs(ebin_cens)./(kB*param.T))-1)+double(ebin_cens>=0);
     end
 
     % Sums up the intensities in DSF into swConv.
@@ -555,7 +556,7 @@
     if isfield(spectra,'obj')
         vol = spectra.obj.twin.vol/sum(spectra.obj.twin.vol);
     else
-        vol = 1;
+        vol = ones(1,nTwin);
     end
     swConvT = cell(nConv,1);
     DSFT    = cell(nConv,1);

swfiles/sw_mex.m

@@ -72,18 +72,30 @@ function sw_mex(varargin)
         mex('-R2018a',['COMPFLAGS= /I eigen-' eigen_ver],'swloop.cpp')
     elseif ismac
         % add =libiomp5 after -fopenmp?
+        if strcmp(mexext, 'mexmaca64')
+           mwlinklib = '-L$MATLABROOT/bin/maca64';
+        else
+           mwlinklib = '-L$MATLABROOT/sys/os/maci64'; 
+        end
+        if exist('/opt/homebrew/opt/libomp/include') == 7
+            omp_inc = '-I/opt/homebrew/opt/libomp/include';
+            omp_lib = '-lomp';
+        else
+            omp_inc = '-I/usr/local/opt/libomp/include';
+            omp_lib = '-liomp5';
+        end
         cd(eig_omp_dir);
         mex('-v','-largeArrayDims','eig_omp.cpp', 'CXX_FLAGS="-Xclang -fopenmp -pthread"', ...
-            'LDFLAGS="$LDFLAGS -L$MATLABROOT/sys/os/maci64 -liomp5 -lmwblas -lmwlapack"', ...
-            'CXXOPTIMFLAGS="$CXXOPTIMFLAGS -Xclang -fopenmp"', "-I/usr/local/opt/libomp/include");
+            ['LDFLAGS="$LDFLAGS ' mwlinklib ' ' omp_lib ' -lmwblas -lmwlapack"'], ...
+            'CXXOPTIMFLAGS="$CXXOPTIMFLAGS -Xclang -fopenmp"', omp_inc);
         cd(chol_omp_dir);
         mex('-v','-largeArrayDims','chol_omp.cpp', 'CXX_FLAGS="-Xclang -fopenmp -pthread"', ...
-            'LDFLAGS="$LDFLAGS -L$MATLABROOT/sys/os/maci64 -liomp5 -lmwblas -lmwlapack"', ...
-            'CXXOPTIMFLAGS="$CXXOPTIMFLAGS -Xclang -fopenmp"', "-I/usr/local/opt/libomp/include");
+            ['LDFLAGS="$LDFLAGS ' mwlinklib ' ' omp_lib ' -lmwblas -lmwlapack"'], ...
+            'CXXOPTIMFLAGS="$CXXOPTIMFLAGS -Xclang -fopenmp"', omp_inc);
         cd(mtimesx_dir);
         mex('-v','-largeArrayDims','sw_mtimesx.c', 'CXX_FLAGS="-Xclang -fopenmp -pthread"', ...
-            'LDFLAGS="$LDFLAGS -L$MATLABROOT/sys/os/maci64 -liomp5 -lmwblas"', ...
-            'CXXOPTIMFLAGS="$CXXOPTIMFLAGS -Xclang -fopenmp"', "-I/usr/local/opt/libomp/include");
+            ['LDFLAGS="$LDFLAGS ' mwlinklib ' ' omp_lib ' -lmwblas"'], ...
+            'CXXOPTIMFLAGS="$CXXOPTIMFLAGS -Xclang -fopenmp"', omp_inc);
         cd(swloop_dir);
         mex('-v','-R2018a',['-Ieigen-' eigen_ver],'swloop.cpp')
     else