Merge pull request #173 from taiga-project/feature-166

Feature 166

Makefile

@@ -7,9 +7,10 @@ LIBS = -lcurand
 
 VERSION = -D'TAIGA_VERSION="$(shell git branch | grep \* | cut -d ' ' -f2)"' -D'GIT_REV="$(shell git show -s --pretty=format:%h)"'
 
-DEFAULT_FLAGS = $(VERSION) -D'RENATE=0' -D'FASTMODE=0' -fcommon
+DEFAULT_FLAGS = $(VERSION) -D'RENATE=0' -D'FASTMODE=0'
 RENATE_FLAGS = $(VERSION) -D'RENATE=1' -D'FASTMODE=0'
 RENATE_FAST_FLAGS = $(VERSION) -D'RENATE=1' -D'FASTMODE=1'
+TEST_FLAGS = $(VERSION) -fcommon
 
 OBJ=build
 BIN=bin
@@ -33,28 +34,28 @@ taiga_renate_fast.exe: src/main.cu | $(BIN)
 t: test
 
 test: $(OBJ)/tests.o  $(OBJ)/test_bspline.o  $(OBJ)/test_solver.o $(OBJ)/test_basic_functions.o $(OBJ)/basic_functions.o | $(BIN)
-	$(GCC) $(DEFAULT_FLAGS) -Isrc -Itests $^ -lm -o $(BIN)/test.exe
+	$(GCC) $(TEST_FLAGS) -Isrc -Itests $^ -lm -o $(BIN)/test.exe
 
 $(OBJ)/%.o: tests/%.c $(OBJ)
-	$(GCC) $(DEFAULT_FLAGS) -w -Isrc -Iinclude -Itests -c $< -lm -o $@
+	$(GCC) $(TEST_FLAGS) -w -Isrc -Iinclude -Itests -c $< -lm -o $@
 
 $(OBJ)/basic_functions.o: src/utils/basic_functions.c $(OBJ)
-	$(GCC) $(DEFAULT_FLAGS) -w -Isrc -Iinclude -Itests -I$utils -c $< -o $@
+	$(GCC) $(TEST_FLAGS) -w -Isrc -Iinclude -Itests -I$utils -c $< -o $@
 
 test_init: tests | $(BIN)
-	$(NVCC) $(CFLAGS) $(DEFAULT_FLAGS) -o $(BIN)/test_init.exe tests/test_taiga_init.cu
+	$(NVCC) $(CFLAGS) $(TEST_FLAGS) -o $(BIN)/test_init.exe tests/test_taiga_init.cu
 
 test_framework: tests  | $(BIN)
-	$(GCC) $(DEFAULT_FLAGS) -o $(BIN)/test_framework.exe tests/taiga_test_example.c
+	$(GCC) $(TEST_FLAGS) -o $(BIN)/test_framework.exe tests/taiga_test_example.c
 
 example_solvers: $(OBJ)/example_solvers.o $(OBJ)/test_solver.o | $(BIN)
-	$(GCC) $(DEFAULT_FLAGS) $^ -lm -o $(BIN)/example_solvers.exe
+	$(GCC) $(TEST_FLAGS) $^ -lm -o $(BIN)/example_solvers.exe
 
 $(OBJ)/example_solvers.o: example/solvers/export_solver.c $(OBJ)
-	$(GCC) $(DEFAULT_FLAGS) -w -Isrc -Iinclude -Itests -c $< -lm -o $@
+	$(GCC) $(TEST_FLAGS) -w -Isrc -Iinclude -Itests -c $< -lm -o $@
 
 field: tests | $(BIN)
-	$(NVCC) $(CFLAGS) $(DEFAULT_FLAGS) -o $(BIN)/test_field.exe tests/test_field.cu
+	$(NVCC) $(CFLAGS) $(TEST_FLAGS) -o $(BIN)/test_field.exe tests/test_field.cu
 
 $(OBJ):
 	mkdir $@

include/utils/prop.h

@@ -15,6 +15,7 @@ typedef struct BeamProp{
 
 typedef struct ShotProp{
     char name[STRING_LENGTH];
+    char long_name[STRING_LENGTH];
     char shotnumber[STRING_LENGTH];
     char time[STRING_LENGTH];
     char detector_mask[STRING_LENGTH];

preproc/renate_od/__init__.py

@@ -1 +1,5 @@
-
+import manager
+from manager import RenateODManager
+from beamlet import set_beamlet
+from efit import EFITManager
+from utils import *

preproc/renate_od/interface.py

@@ -6,31 +6,29 @@
 from utils import *
 
 
-def export_beamlet_profile(export_root=get_home_directory() + '/input/ionProf/',
+def export_beamlet_profile(export_root=os.path.join(get_home_directory(), 'input', 'ionProf'),
                            shot_number='17178', time='1097', species='Li', energy='80'):
     z = 0
     tor = 0
     beamlet_geometry = set_beamlet(z, tor)
     r = RenateODManager(beamlet_geometry, shot_number, time, species, energy)
     radial_coordinate, relative_attenuation = r.get_attenuation_profile()
 
-    export_directory = export_root + '/'+shot_number+'_'+time
+    export_directory = os.path.join(export_root, shot_number + '_' + time, species, energy)
     try:
-        os.mkdir(export_directory)
+        os.makedirs(export_directory)
         print('Create directory and write data to ' + export_directory)
-    except FileExistsError:
-        print('Write data to ' + export_directory)
-    else:
-        pass
+    except OSError as error:
+        print('Cannot create and write to ' + export_directory)
     print('Save RENATE-OD ionisation profile to: ' + export_directory)
-    radial_coordinate.fillna(0).to_csv(export_directory+'/rad.dat', index=False, header=False)
-    relative_attenuation.fillna(0).to_csv(export_directory+'/ionyeald.dat', index=False, header=False)
+    radial_coordinate.fillna(0).to_csv(os.path.join(export_directory, 'rad.dat'), index=False, header=False)
+    relative_attenuation.fillna(0).to_csv(os.path.join(export_directory, 'ionyeald.dat'), index=False, header=False)
     plot_attenuation_profile(shot_number, time, radial_coordinate, relative_attenuation, export_directory)
 
 
 def get_lcfs_radial_coordinate(shot_number, time, efit_reconstruction_id=1, database_directory='input/cdb', efit_subdir='EFITXX'):
-    data_directory = get_home_directory() + '/' + database_directory + '/' + str(shot_number)
-    efit_file = data_directory + '/' + efit_subdir + '/' + 'EFITXX.' + str(efit_reconstruction_id) + '.h5'
+    data_directory = os.path.join(get_home_directory(), database_directory, str(shot_number))
+    efit_file = os.path.join(data_directory, efit_subdir, 'EFITXX.' + str(efit_reconstruction_id) + '.h5')
     efit = EFITManager(efit_file, time)
     return efit.get_time_sliced_data('output/separatrixGeometry/rmidplaneOut')
 
@@ -47,13 +45,14 @@ def plot_attenuation_profile(shot_number, time, radial_coordinate, relative_atte
     R_LCFS = get_lcfs_radial_coordinate(shot_number, time)
     matplotlib.pyplot.axvline(R_LCFS, c='red', ls='--')
     matplotlib.pyplot.text(R_LCFS+0.005, 0.45, 'LCFS', c='red', fontsize=12)
-    matplotlib.pyplot.savefig(export_directory+'/attenuation.pdf')
-    matplotlib.pyplot.savefig(export_directory+'/attenuation.svg')
-    print('Attenuation profile saved as: '+export_directory+'/attenuation.pdf')
+    matplotlib.pyplot.savefig(os.path.join(export_directory, 'attenuation.pdf'))
+    matplotlib.pyplot.savefig(os.path.join(export_directory, 'attenuation.svg'))
+    print('Attenuation profile saved to '+ export_directory)
     matplotlib.pyplot.show()
 
 
 if __name__ == "__main__":
     a_shot_number = '17178'
     a_time = '1097'
-    export_beamlet_profile(shot_number=a_shot_number, time=a_time)
+    a_species = 'Li'
+    export_beamlet_profile(shot_number=a_shot_number, time=a_time, species=a_species)

src/init/structures/beam.cu

@@ -79,7 +79,7 @@ void init_beam_profile(BeamProfile *device_prof, ShotProp shot){
     size_t size_prof = sizeof(BeamProfile);
     host_prof = (BeamProfile*)malloc(size_prof);
     shared_prof = (BeamProfile*)malloc(size_prof);
-    init_ion_profile(shot.name, host_prof);
+    init_ion_profile(shot.long_name, host_prof);
     size_t size_rad_prof = sizeof(double)*host_prof->radial_length;
     size_t size_cross_prof = sizeof(double)*host_prof->cross_length;
 

src/interface/data_import/beam_renate.c

@@ -7,13 +7,11 @@ void load_beam_renate(TaigaGlobals *g, BeamProp *beam, ShotProp *shot, RunProp *
     long i, prof_size[2];
     long radial_length, cross_length;
     double *radial_grid, *radial_profile, *cross_section_grid, *cross_section_profile, speed, ionisation_yeald, xsec_rad, xsec_ang;
-
-    char* shotname = concat(shot->shotnumber, "_", shot->time, NULL);
-
+
     BeamProfile *prof;
     size_t size_prof = sizeof(BeamProfile);
     prof = (BeamProfile*)malloc(size_prof);
-    init_ion_profile(shotname, prof);
+    init_ion_profile(shot->long_name, prof);
 
     speed = calculate_speed(beam->energy, get_mass(beam->species, beam->charge));
 

src/interface/parameter_reader.c

@@ -77,6 +77,8 @@ int parameter_reader(BeamProp *beam, ShotProp *shot, RunProp *run){
     }
     fclose(fp);
     strcpy(shot->name, concat(shot->shotnumber, "_", shot->time, NULL));
+
+    strcpy(shot->long_name, concat(shot->shotnumber, "_", shot->time, "/", beam->species, "/", to_str(beam->energy), NULL));
     strcpy(run->folder_out, concat("results/", shot->shotnumber, "_", shot->time, NULL));
     return 0;
 }