Merge branch 'ImperialCollegeLondon:main' into dev_pip2

Dockerfile

@@ -32,11 +32,11 @@ RUN mamba init bash
 RUN mamba config --set always_yes yes --set changeps1 no
 RUN mamba update -q conda
 RUN mamba config --set auto_activate_base false
-RUN mamba env create -f /sharpy_dir/utils/environment.yml && mamba clean -afy && \
-
-    find /mamba/ -follow -type f -name '*.a' -delete && \
-    find /mamba/ -follow -type f -name '*.pyc' -delete && \
-    find /mamba/ -follow -type f -name '*.js.map' -delete
+RUN mamba env create -f /sharpy_dir/utils/environment.yml
+#RUN mamba clean -afy
+RUN find /mamba/ -follow -type f -name '*.a' -delete
+RUN find /mamba/ -follow -type f -name '*.pyc' -delete
+RUN find /mamba/ -follow -type f -name '*.js.map' -delete
 
 #COPY /utils/docker/* /root/
 RUN ln -s /sharpy_dir/utils/docker/* /root/

docs/source/content/example_notebooks/UDP_control/tutorial_udp_control.ipynb

@@ -2368,9 +2368,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Run SHARPy Simulation"
-   "execution_count": 22,
-   ]
+    "### Run SHARPy Simulation"]
   },
   {
    "cell_type": "code",

sharpy/postproc/aeroforcescalculator.py

@@ -132,11 +132,8 @@ def calculate_forces(self, ts):
             self.data.aero.timestep_info[ts].body_unsteady_forces[i_surf, 0:3]
             ) = self.calculate_forces_for_isurf_in_g_frame(force[i_surf], unsteady_force=unsteady_force[i_surf])
 
-        print(self.settings["nonlifting_body"])
         if self.settings["nonlifting_body"]:
-            print(self.data.nonlifting_body.n_surf)
             for i_surf in range(self.data.nonlifting_body.n_surf):
-                print(i_surf)
                 (
                 self.data.nonlifting_body.timestep_info[ts].inertial_steady_forces[i_surf, 0:3], 
                 self.data.nonlifting_body.timestep_info[ts].body_steady_forces[i_surf, 0:3],
@@ -236,8 +233,8 @@ def screen_output(self, ts):
     def file_output(self, filename):
         # assemble forces/moments matrix
         # (1 timestep) + (3+3 inertial steady+unsteady) + (3+3 body steady+unsteady)
-        force_matrix = np.zeros((self.ts_max, 1 + 3 + 3 + 3 + 3 + 3 + 3))
-        moment_matrix = np.zeros((self.ts_max, 1 + 3 + 3 + 3 + 3 + 3 + 3))
+        force_matrix = np.zeros((self.ts_max, 1 + 3 + 3 + 3 + 3 ))
+        moment_matrix = np.zeros((self.ts_max, 1 + 3 + 3 + 3 + 3))
         for ts in range(self.ts_max):
             aero_tstep = self.data.aero.timestep_info[ts]
             i = 0
@@ -271,12 +268,10 @@ def file_output(self, filename):
         header += 'fx_unsteady_G, fy_unsteady_G, fz_unsteady_G, '
         header += 'fx_steady_a, fy_steady_a, fz_steady_a, '
         header += 'fx_unsteady_a, fy_unsteady_a, fz_unsteady_a'
-        header += 'mx_total_G, my_total_G, mz_total_G'
-        header += 'mx_total_a, my_total_a, mz_total_a'
 
         np.savetxt(self.folder + 'forces_' + filename,
                    force_matrix,
-                   fmt='%i' + ', %10e'*18,
+                   fmt='%i' + ', %10e' * (np.shape(force_matrix)[1] - 1),
                    delimiter=',',
                    header=header,
                    comments='#')
@@ -290,7 +285,7 @@ def file_output(self, filename):
 
         np.savetxt(self.folder + 'moments_' + filename,
                    moment_matrix,
-                   fmt='%i' + ', %10e'*18,
+                   fmt='%i' + ', %10e' * (np.shape(moment_matrix)[1] - 1),
                    delimiter=',',
                    header=header,
                    comments='#')

sharpy/postproc/savedata.py

@@ -155,9 +155,7 @@ def initialise(self, data, custom_settings=None, caller=None, restart=False):
         self.filename_linear = self.folder + self.data.settings['SHARPy']['case'] + '.linss.h5'
 
         # remove old file if it exists
-        for file_path in [self.filename, self.filename_linear]:
-            if os.path.isfile(file_path):
-                os.remove(file_path)
+        self.remove_file_if_exist(self.filename)
 
         # check that there is a linear system - else return setting to false
         if self.settings['save_linear'] or self.settings['save_linear_uvlm']:
@@ -204,6 +202,10 @@ def initialise(self, data, custom_settings=None, caller=None, restart=False):
                 self.ClassesToSave += (sharpy.solvers.linearassembler.Linear, sharpy.linear.src.libss.ss_block)
         self.caller = caller
 
+    def remove_file_if_exist(self, filepath):
+        if os.path.isfile(filepath):
+            os.remove(filepath)
+
     def run(self, **kwargs):
 
         online = settings_utils.set_value_or_default(kwargs, 'online', False)
@@ -247,33 +249,37 @@ def run(self, **kwargs):
 
                     hdfile.close()
 
-                    if self.settings['save_linear_uvlm']:
-                        linhdffile = h5py.File(self.filename.replace('.data.h5', '.uvlmss.h5'), 'a')
-                        h5utils.add_as_grp(self.data.linear.linear_system.uvlm.ss, linhdffile, grpname='ss',
+                if self.settings['save_linear_uvlm']:
+                    linhdffile = h5py.File(self.filename.replace('.data.h5', '.uvlmss.h5'), 'a')
+                    self.remove_file_if_exist(linhdffile)
+                    h5utils.add_as_grp(self.data.linear.linear_system.uvlm.ss, linhdffile, grpname='ss',
+                                    ClassesToSave=self.ClassesToSave, SkipAttr=self.settings['skip_attr'],
+                                    compress_float=self.settings['compress_float'])
+                    h5utils.add_as_grp(self.data.linear.linear_system.linearisation_vectors, linhdffile,
+                                    grpname='linearisation_vectors',
+                                    ClassesToSave=self.ClassesToSave, SkipAttr=self.settings['skip_attr'],
+                                    compress_float=self.settings['compress_float'])
+                    linhdffile.close()
+
+                if self.settings['save_linear']:
+                    self.remove_file_if_exist(self.filename_linear)
+                    with h5py.File(self.filename_linear, 'a') as linfile:
+                        h5utils.add_as_grp(self.data.linear.linear_system.linearisation_vectors, linfile,
+                                        grpname='linearisation_vectors',
                                         ClassesToSave=self.ClassesToSave, SkipAttr=self.settings['skip_attr'],
                                         compress_float=self.settings['compress_float'])
-                        h5utils.add_as_grp(self.data.linear.linear_system.linearisation_vectors, linhdffile,
-                                        grpname='linearisation_vectors',
+                        h5utils.add_as_grp(self.data.linear.ss, linfile, grpname='ss',
                                         ClassesToSave=self.ClassesToSave, SkipAttr=self.settings['skip_attr'],
                                         compress_float=self.settings['compress_float'])
-                        linhdffile.close()
-
-                    if self.settings['save_linear']:
-                        with h5py.File(self.filename_linear, 'a') as linfile:
-                            h5utils.add_as_grp(self.data.linear.linear_system.linearisation_vectors, linfile,
-                                            grpname='linearisation_vectors',
-                                            ClassesToSave=self.ClassesToSave, SkipAttr=self.settings['skip_attr'],
-                                            compress_float=self.settings['compress_float'])
-                            h5utils.add_as_grp(self.data.linear.ss, linfile, grpname='ss',
-                                            ClassesToSave=self.ClassesToSave, SkipAttr=self.settings['skip_attr'],
-                                            compress_float=self.settings['compress_float'])
-
-                    if self.settings['save_rom']:
-                        try:
-                            for k, rom in self.data.linear.linear_system.uvlm.rom.items():
-                                rom.save(self.filename.replace('.data.h5', '_{:s}.rom.h5'.format(k.lower())))
-                        except AttributeError:
-                            cout.cout_wrap('Could not locate a reduced order model to save')
+
+                if self.settings['save_rom']:
+                    try:
+                        for k, rom in self.data.linear.linear_system.uvlm.rom.items():
+                            romhdffile = self.filename.replace('.data.h5', '_{:s}.rom.h5'.format(k.lower()))
+                            self.remove_file_if_exist(romhdffile)
+                            rom.save(romhdffile)
+                    except AttributeError:
+                        cout.cout_wrap('Could not locate a reduced order model to save')
 
             elif self.settings['format'] == 'mat':
                 from scipy.io import savemat

sharpy/solvers/noaero.py

@@ -78,7 +78,7 @@ def update_grid(self, beam):
                                          -1,
                                          beam_ts=-1)
 
-    def update_custom_grid(self, structure_tstep, aero_tstep):
+    def update_custom_grid(self, structure_tstep, aero_tstep, nl_body_tstep = None):
         # called by DynamicCoupled
         if self.settings['update_grid']:
             self.data.aero.generate_zeta_timestep_info(structure_tstep,

sharpy/structure/utils/modalutils.py

@@ -283,7 +283,7 @@ def write_modes_vtk(data, eigenvectors, NumLambda, filename_root,
     else:
         num_rigid_body = 0
 
-    for mode in range(num_rigid_body, NumLambda - num_rigid_body):
+    for mode in range(num_rigid_body, NumLambda):
         # scale eigenvector
         eigvec = eigenvectors[:num_dof, mode]
         fact = scale_mode(data, eigvec, rot_max_deg, perc_max)