Master dev

.github/workflows/ci_test.yaml

@@ -47,7 +47,7 @@ jobs:
               if: ${{matrix.os == 'macos-latest'}}
               shell: bash
               working-directory: ${{runner.workspace}}/Stellarator-Tools/build
-              run: cmake -DCMAKE_BUILD_TYPE=${{matrix.mode}} -DCMAKE_Fortran_COMPILER=gfortran-14 -DBUILD_BOOZ_XFORM=ON -DBUILD_V3FIT=ON -DBUILD_V3RFUN=ON -DBUILD_SIESTA=ON -DBUILD_LGRID=ON -DBUILD_SURFACE=ON -DBUILD_BMW=ON -DBUILD_PARVMEC=ON -DBUILD_DESCUR=ON -DBUILD_TAG_BOOZ_XFORM=master_dev -DBUILD_TAG_V3FIT=${{github.ref_name}} -DBUILD_TAG_V3RFUN=master_dev -DBUILD_TAG_SIESTA=master_dev -DBUILD_TAG_LGRID=master_dev -DBUILD_TAG_SURFACE=master_dev -DBUILD_TAG_BMW=master_dev -DBUILD_TAG_LIBSTELL=master_dev -DBUILD_TAG_MAKEGRID=master_dev -DBUILD_TAG_PARVMEC=master_dev -DBUILD_TAG_DESCUR=master_dev -DUSE_FAST_COPY=ON -DUSE_PROFILER=ON ${{runner.workspace}}/Stellarator-Tools/
+              run: cmake -DCMAKE_BUILD_TYPE=${{matrix.mode}} -DCMAKE_Fortran_COMPILER=gfortran-15 -DBUILD_BOOZ_XFORM=ON -DBUILD_V3FIT=ON -DBUILD_V3RFUN=ON -DBUILD_SIESTA=ON -DBUILD_LGRID=ON -DBUILD_SURFACE=ON -DBUILD_BMW=ON -DBUILD_PARVMEC=ON -DBUILD_DESCUR=ON -DBUILD_TAG_BOOZ_XFORM=master_dev -DBUILD_TAG_V3FIT=${{github.ref_name}} -DBUILD_TAG_V3RFUN=master_dev -DBUILD_TAG_SIESTA=master_dev -DBUILD_TAG_LGRID=master_dev -DBUILD_TAG_SURFACE=master_dev -DBUILD_TAG_BMW=master_dev -DBUILD_TAG_LIBSTELL=master_dev -DBUILD_TAG_MAKEGRID=master_dev -DBUILD_TAG_PARVMEC=master_dev -DBUILD_TAG_DESCUR=master_dev -DUSE_FAST_COPY=ON -DUSE_PROFILER=ON ${{runner.workspace}}/Stellarator-Tools/
             - name: Configure CMake Linux
               if: ${{matrix.os == 'ubuntu-latest'}}
               shell: bash

.github/workflows/ci_test_master.yaml

@@ -47,7 +47,7 @@ jobs:
               if: ${{matrix.os == 'macos-latest'}}
               shell: bash
               working-directory: ${{runner.workspace}}/Stellarator-Tools/build
-              run: cmake -DCMAKE_BUILD_TYPE=${{matrix.mode}} -DCMAKE_Fortran_COMPILER=gfortran-14 -DBUILD_BOOZ_XFORM=ON -DBUILD_V3FIT=ON -DBUILD_V3RFUN=ON -DBUILD_SIESTA=ON -DBUILD_LGRID=ON -DBUILD_SURFACE=ON -DBUILD_BMW=ON -DBUILD_PARVMEC=ON -DBUILD_DESCUR=ON -DBUILD_TAG_V3FIT=${{github.ref_name}} -DUSE_FAST_COPY=ON -DUSE_PROFILER=ON ${{runner.workspace}}/Stellarator-Tools/
+              run: cmake -DCMAKE_BUILD_TYPE=${{matrix.mode}} -DCMAKE_Fortran_COMPILER=gfortran-15 -DBUILD_BOOZ_XFORM=ON -DBUILD_V3FIT=ON -DBUILD_V3RFUN=ON -DBUILD_SIESTA=ON -DBUILD_LGRID=ON -DBUILD_SURFACE=ON -DBUILD_BMW=ON -DBUILD_PARVMEC=ON -DBUILD_DESCUR=ON -DBUILD_TAG_V3FIT=${{github.ref_name}} -DUSE_FAST_COPY=ON -DUSE_PROFILER=ON ${{runner.workspace}}/Stellarator-Tools/
             - name: Configure CMake Linux
               if: ${{matrix.os == 'ubuntu-latest'}}
               shell: bash

Sources/siesta_equilibrium.f

@@ -318,6 +318,11 @@ FUNCTION siesta_construct(file_name, restart_file_name,                  &
          state_flags = IBSET(state_flags, model_state_siesta_flag)
       END IF
 
+      IF (recon_rank .gt. 0) THEN
+         CALL siesta_construct%run_context%clear_state(                        &
+     &           siesta_run_write_profiles)
+      END IF
+
       CALL profiler_set_stop_time('siesta_construct', start_time)
 
 1000  FORMAT('siesta_',a,'.nc')

Testing/tests/CMakeLists.txt

@@ -18,3 +18,4 @@ add_subdirectory (lasym_boundary)
 add_subdirectory (preconditioner_test)
 add_subdirectory (limiter_test)
 add_subdirectory (siesta_recon_test)
+add_subdirectory (siesta_recon_asym_test)

Testing/tests/siesta_recon_asym_test/CMakeLists.txt

@@ -0,0 +1,54 @@
+#  Run the reconstruction task. This just tests if the reconstruction executes correctly. 
+#  Subsequent tests will examine the results of the reconstruction for correct 
+#  results.
+
+#  Copy input file from source to the build directory.
+configure_file (${CMAKE_CURRENT_SOURCE_DIR}/thomson.dot
+                ${CMAKE_CURRENT_BINARY_DIR}/thomson.dot
+                COPYONLY)
+configure_file (${CMAKE_CURRENT_SOURCE_DIR}/input.test.vmec
+                ${CMAKE_CURRENT_BINARY_DIR}/input.test.vmec
+                COPYONLY)
+configure_file (${CMAKE_CURRENT_SOURCE_DIR}/siesta.jcf
+                ${CMAKE_CURRENT_BINARY_DIR}/siesta.jcf
+                COPYONLY)
+SET (VMEC_FILE_NAME input.test.vmec)
+SET (SIESTA_FILE_NAME siesta.jcf)
+configure_file (${CMAKE_CURRENT_SOURCE_DIR}/input.test.v3fit
+                ${CMAKE_CURRENT_BINARY_DIR}/input.test.v3fit)
+
+add_test (NAME    siesta_recon_asym_task_test
+          COMMAND $<TARGET_PROPERTY:stell,MPIEXEC_EXECUTABLE> $<TARGET_PROPERTY:stell,MPIEXEC_NUMPROC_FLAG> $<TARGET_PROPERTY:stell,MPIEXEC_MAX_NUMPROCS> $<TARGET_PROPERTY:xv3fit,BINARY_DIR>/xv3fit input.test.v3fit -para=-1)
+set_tests_properties (siesta_recon_asym_task_test
+                      PROPERTIES
+                      PROCESSORS $<TARGET_PROPERTY:stell,MPIEXEC_MAX_NUMPROCS>)
+
+#  Since the reconstruction task test was run, Check the output files for correct values.
+
+#  Check that the reconstruction parameter reconstructed to the correct values.
+add_test (NAME    siesta_recon_asym_task_test_helpert
+          COMMAND ${Python3_EXECUTABLE} ${TEST_SCRIPT_DIR}/check_param_value.py --file=recout.input.test.v3fit --p_type=helpert --value=5.0E-4 --range=1.0E-4 --index1=1)
+set_tests_properties (siesta_recon_asym_task_test_helpert
+                      PROPERTIES
+                      DEPENDS siesta_recon_asym_task_test)
+
+#  Check that the reconstruction parameter reconstructed to the correct values.
+add_test (NAME    siesta_recon_asym_task_test_helphase
+          COMMAND ${Python3_EXECUTABLE} ${TEST_SCRIPT_DIR}/check_param_value.py --file=recout.input.test.v3fit --p_type=helphase --value=25.0 --range=2.0 --index1=1)
+set_tests_properties (siesta_recon_asym_task_test_helphase
+                      PROPERTIES
+                      DEPENDS siesta_recon_asym_task_test)
+
+#  Check that the signal effectiveness total.
+add_test (NAME    siesta_recon_asym_task_test_sem_totals
+          COMMAND ${Python3_EXECUTABLE} ${TEST_SCRIPT_DIR}/check_sem_total.py --file=recout.input.test.v3fit)
+set_tests_properties (siesta_recon_asym_task_test_sem_totals
+                      PROPERTIES
+                      DEPENDS siesta_recon_asym_task_test)
+
+#  Check correlation matrix values.
+add_test (NAME siesta_recon_asym_task_test_check_reconstruction_correlation_matrix
+          COMMAND ${Python3_EXECUTABLE} ${TEST_SCRIPT_DIR}/check_correlation_matrix.py --file=recout.input.test.v3fit --param=Reconstruction)
+set_tests_properties (siesta_recon_asym_task_test_check_reconstruction_correlation_matrix
+                      PROPERTIES
+                      DEPENDS siesta_recon_asym_task_test)

Testing/tests/siesta_recon_asym_test/input.test.v3fit

@@ -0,0 +1,125 @@
+&v3fit_main_nli
+my_task = 'reconstruct',
+vmec_nli_filename = '${VMEC_FILE_NAME}'
+siesta_nli_filename = '${SIESTA_FILE_NAME}'
+
+model_eq_type = 'siesta'
+
+thscte_dot_filename = 'thomson.dot',
+
+model_te_type = 'pp_te'
+pp_te_ptype = 'two_power_r'
+pp_te_b = 0.0, 5.0, 1.0, 0.5,
+
+nrstep = 20,
+dg2_stop = 0.1,
+cut_svd = 2.0E-5,
+cut_eff = 1.0E-8,
+cut_marg_eff = 0.0,
+cut_delta_a = 0.0,
+cut_dg2 = 0.0,
+astep_max = 100.0,
+step_type = 'lm',
+
+n_rp = 2,
+
+rp_type(1) = 'helpert',
+rp_vrnc(1) = 1.0E-5,
+rp_index(1) = 1,
+rp_range_type(1,1) = 'value',
+rp_range_value(1,1) = 0,
+
+rp_type(2) = 'helphase',
+rp_vrnc(2) = 1.0,
+rp_index(2) = 1,
+rp_range_type(2,1) = 'value',
+rp_range_value(2,1) = 0,
+rp_range_type(2,2) = 'value',
+rp_range_value(2,2) = 360.0,
+
+sdo_data_a(1) = 0.00000E+00
+sdo_data_a(2) = 1.18088E+00
+sdo_data_a(3) = 2.55109E+00
+sdo_data_a(4) = 3.55848E+00
+sdo_data_a(5) = 4.00024E+00
+sdo_data_a(6) = 4.25356E+00
+sdo_data_a(7) = 4.45003E+00
+sdo_data_a(8) = 4.60264E+00
+sdo_data_a(9) = 4.71822E+00
+sdo_data_a(10) = 4.80434E+00
+sdo_data_a(11) = 4.86823E+00
+sdo_data_a(12) = 0.00000E+00
+sdo_data_a(13) = 1.17942E+00
+sdo_data_a(14) = 2.56126E+00
+sdo_data_a(15) = 3.62447E+00
+sdo_data_a(16) = 4.06574E+00
+sdo_data_a(17) = 4.30416E+00
+sdo_data_a(18) = 4.48670E+00
+sdo_data_a(19) = 4.62837E+00
+sdo_data_a(20) = 4.73565E+00
+sdo_data_a(21) = 4.81571E+00
+sdo_data_a(22) = 4.87539E+00
+sdo_data_a(23) = 0.00000E+00
+sdo_data_a(24) = 1.18253E+00
+sdo_data_a(25) = 2.53952E+00
+sdo_data_a(26) = 3.48220E+00
+sdo_data_a(27) = 3.92470E+00
+sdo_data_a(28) = 4.19548E+00
+sdo_data_a(29) = 4.40811E+00
+sdo_data_a(30) = 4.57332E+00
+sdo_data_a(31) = 4.69840E+00
+sdo_data_a(32) = 4.79142E+00
+sdo_data_a(33) = 4.86010E+00
+sdo_data_a(34) = 0.00000E+00
+sdo_data_a(35) = 1.18935E+00
+sdo_data_a(36) = 2.49102E+00
+sdo_data_a(37) = 3.14651E+00
+sdo_data_a(38) = 3.59486E+00
+sdo_data_a(39) = 3.94576E+00
+sdo_data_a(40) = 4.23001E+00
+sdo_data_a(41) = 4.44977E+00
+sdo_data_a(42) = 4.61535E+00
+sdo_data_a(43) = 4.73752E+00
+sdo_data_a(44) = 4.82630E+00
+sdo_data_a(45) = 0.00000E+00
+sdo_data_a(46) = 1.19800E+00
+sdo_data_a(47) = 2.42763E+00
+sdo_data_a(48) = 2.65658E+00
+sdo_data_a(49) = 3.12315E+00
+sdo_data_a(50) = 3.60158E+00
+sdo_data_a(51) = 3.99090E+00
+sdo_data_a(52) = 4.28673E+00
+sdo_data_a(53) = 4.50702E+00
+sdo_data_a(54) = 4.66775E+00
+sdo_data_a(55) = 4.78276E+00
+sdo_data_a(56) = 0.00000E+00
+sdo_data_a(57) = 1.20615E+00
+sdo_data_a(58) = 2.36588E+00
+sdo_data_a(59) = 2.08763E+00
+sdo_data_a(60) = 2.59720E+00
+sdo_data_a(61) = 3.24119E+00
+sdo_data_a(62) = 3.74981E+00
+sdo_data_a(63) = 4.12599E+00
+sdo_data_a(64) = 4.40170E+00
+sdo_data_a(65) = 4.60053E+00
+sdo_data_a(66) = 4.74105E+00
+sdo_data_a(67) = 0.00000E+00
+sdo_data_a(68) = 1.21165E+00
+sdo_data_a(69) = 2.32303E+00
+sdo_data_a(70) = 1.58940E+00
+sdo_data_a(71) = 2.16874E+00
+sdo_data_a(72) = 2.97178E+00
+sdo_data_a(73) = 3.57694E+00
+sdo_data_a(74) = 4.01323E+00
+sdo_data_a(75) = 4.32876E+00
+sdo_data_a(76) = 4.55434E+00
+sdo_data_a(77) = 4.71254E+00
+
+sdo_s_spec_imin(1) = 1,
+sdo_s_spec_imax(1) = 77,
+sdo_s_spec_floor(1) = 0.001,
+sdo_s_spec_fraction(1) = 0.01,
+
+n_sdata_o = 77,
+
+&END

Testing/tests/siesta_recon_asym_test/input.test.vmec

@@ -0,0 +1,44 @@
+&INDATA
+
+! VMEC execution parameters.
+LFORBAL = F,
+LFREEB = F,
+DELT = 1.0,
+TCON0 = 2.0,
+NFP = 2,
+NS_ARRAY = 100,
+FTOL_ARRAY = 1.0E-20,
+NITER = 25000,
+NSTEP = 200,
+NTOR = 0,
+MPOL = 2,
+NVACSKIP = 9,
+LASYM = F,
+LNYQUIST = T,
+
+! Fitting parameters.
+GAMMA = 0.0,
+PHIEDGE = -0.05,
+BLOAT = 1.0,
+
+! Initial Position.
+RAXIS(0) = 0.75,
+ZAXIS(0) = 0.0,
+RBC(0,0) = 0.70,
+RBC(0,1) = 0.2,
+ZBS(0,0) = 0.0,
+ZBS(0,1) = 0.2,
+
+! Plasma current parameters.
+NCURR = 1,
+CURTOR = 40000.0,
+AC = 1.0, 5.0, 10.0
+PCURR_TYPE = 'two_power',
+
+! Plasma pressure parameters.
+SPRES_PED = 1.0,
+PRES_SCALE = 400.0,
+am = 1.0, 2.0, 2.0
+pmass_type = 'two_power',
+/
+&END

Testing/tests/siesta_recon_asym_test/siesta.jcf

@@ -0,0 +1,24 @@
+&SIESTA_INFO
+ LADD_PERT=T,
+ LRESISTIVE=F,
+ LRESTART=F,
+ LCOLSCALE=T,
+ LASYM=T,
+ LRECON=T,
+ NITER=1000
+ FTOL=  1.0E-20
+ LEVMARQ_PARAM=  0.1
+ MRES = 2
+ HELPERT = 1.0E-4
+ HELPHASE = 0.0
+ NSIN = 100
+ NTOR_TYPE = "sparse"
+ MPOLIN = 2
+ NTORIN = 1
+ NFPIN = 1
+ NTOR_MODES(0) = 0,
+ NTOR_MODES(-1) = -1
+ NTOR_MODES(1) = 1
+ WOUT_FILE="wout_test.vmec.nc"
+ RESTART_EXT="restart_w7x"
+ /