Make minor improvements and fix bugs

- general: fixed compatibility with Gmsh (version 4.12.2).
- module -S: added -resmesh orifield,orifieldn.

Author: rquey

VERSIONS

@@ -1,6 +1,6 @@
-New in 4.8.1-2 (24 Jan 2024):
-
+New in 4.8.1 (02 Feb 2024):
 - general: fixed compatibility with Gmsh (version 4.12.2).
+- module -S: added -resmesh orifield,orifieldn.
 
 New in 4.8.0 (09 Jan 2024):
 - module -T: fixed weibull distribution, made minor fixes.
@@ -10,7 +10,7 @@ New in 4.8.0 (09 Jan 2024):
 - module -V: fixed -datanodecoofact.
 - module -S: changed simulation.config onto simulation.cfg.
 - documentation: made minor fix.
-- general: fixed compatibility with Gmsh (version 4.12.2).
+- general: cleaned tests.
 
 * Incompatible changes:  In -M, changed default value of -order to 2.
 

doc/conf.py

@@ -11,8 +11,8 @@
 import sphinx_rtd_theme
 
 project = u'Neper'
-version = u'4.8.1-2'
-release = u'4.8.1-2'
+version = u'4.8.1'
+release = u'4.8.1'
 author = u'Romain Quey'
 copyright = u'Romain Quey'
 language = 'en'

doc/exprskeys.rst

@@ -582,17 +582,19 @@ Available results / keys for nodes are the following:
 
 Available results / keys for elements sets are the following:
 
-========================================== ================================================================ ==================================
-**Key**                                    **Descriptor**                                                   **Apply to**
-:data:`ori`                                average orientation                                              elset, mesh
-:data:`gos`                                grain orientation spread [#gos]_                                 elset
-:data:`anisogos`                           grain orientation spread computed from :data:`oridisanisoangles` elset
-:data:`oridisanisoangles`                  orientation distribution principal angles                        elset, mesh
-:data:`oridisanisoaxes`                    orientation distribution principal axes                          elset, mesh
-:data:`oridisanisofact`                    orientation distribution factor                                  elset, mesh
-:data:`odf(<var>=<value>,...)`             ODF defined at elements of orientation space (see also below)    tess, tesr, mesh, cell, elt, elset
-:data:`odfn(<var>=<value>,...)`            ODF defined at nodes of orientation space (see also below)       tess, tesr, mesh
-========================================== ================================================================ ==================================
+========================================== ========================================================================== ===================================
+**Key**                                    **Descriptor**                                                             **Apply to**
+:data:`ori`                                average orientation                                                        elset, mesh
+:data:`gos`                                grain orientation spread [#gos]_                                           elset
+:data:`anisogos`                           grain orientation spread computed from :data:`oridisanisoangles`           elset
+:data:`oridisanisoangles`                  orientation distribution principal angles                                  elset, mesh
+:data:`oridisanisoaxes`                    orientation distribution principal axes                                    elset, mesh
+:data:`oridisanisofact`                    orientation distribution factor                                            elset, mesh
+:data:`odf(<var>=<value>,...)`             ODF defined at elements of orientation space (see also below)              tess, tesr, mesh, cell, elt, elset
+:data:`odfn(<var>=<value>,...)`            ODF defined at nodes of orientation space (see also below)                 tess, tesr, mesh
+:data:`orifield(var=<var>,...)`            :data:`<var>` field defined at elements of orientation space (see below)   mesh
+:data:`orifieldn(var=<var>,...)`           :data:`<var>` field defined at nodes of orientation space (see below)      mesh
+========================================== ========================================================================== ===================================
 
 The ODF (:data:`odf` or :data:`odfn`) of a tessellation or mesh is computed over orientation space (provided using :option:`-orispace`) from the orientations of the (tessellation) cells or (mesh) elsets.  The (optional) parameters are:
 
@@ -604,6 +606,15 @@ The ODF (:data:`odf` or :data:`odfn`) of a tessellation or mesh is computed over
 
 For a cell, element or elset, :data:`odf` returns the value of the ODF of the tessellation or mesh at the corresponding orientation (and simulation step).
 
+The :data:`orifield` and :data:`orifieldn` of a mesh is computed over orientation space (provided using :option:`-orispace`) from the values of the (mesh) elsets.  The mandatory parameter is:
+
+- :data:`var`: the variable, which must be defined for elsets (i.e., have its files in the simulation directory);
+
+and the optional parameters are:
+
+- :data:`theta`: the standard deviation of the kernel (in degrees);
+- :data:`weight`: the weight of an elset, which can be a real value or an expression based on the :ref:`mesh_keys` (for elsets) --  by default, the volumes of the elsets are used.
+
 .. _rotations_and_orientations:
 
 Rotations and Orientations

src/CMakeLists.txt

@@ -7,7 +7,7 @@ if(POLICY CMP0077)
   cmake_policy(SET CMP0077 NEW)
 endif()
 
-set(NEPER_VERSION \"4.8.1-2\")
+set(NEPER_VERSION \"4.8.1\")
 project(neper)
 
 if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.8.1)

src/neper_s/nes_pproc/nes_pproc_entity/nes_pproc_entity_builtin/nes_pproc_entity_builtin2.c

@@ -64,6 +64,14 @@ nes_pproc_entity_builtin_elsets (struct SIM *pSim, struct TESS *pTess,
                                                &SimRes);
   }
 
+  else if (!strncmp (res, "orifield", 8))
+  {
+    // if mesh, we compute the odf over orientation space
+    if (!strcmp (entity, "mesh"))
+      nes_pproc_entity_builtin_elsets_orifield (pSim, pTess, pNodes, Mesh,
+                                                entity, res, &SimRes);
+  }
+
   else
     nes_pproc_entity_builtin_elsets_gen (pSim, pNodes, Mesh, entity, res,
                                          members, memberqty, &SimRes);

src/neper_s/nes_pproc/nes_pproc_entity/nes_pproc_entity_builtin/nes_pproc_entity_builtin3.cpp

@@ -1143,3 +1143,124 @@ nes_pproc_entity_builtin_elsets_gen (struct SIM *pSim,
 
   return;
 }
+
+void
+nes_pproc_entity_builtin_elsets_orifield (struct SIM *pSim, struct TESS *pTess,
+                                     struct NODES *pNodes, struct MESH *Mesh,
+                                     char *entity, char *res, struct SIMRES *pSimRes)
+{
+  int i, step, size, status;
+  double **elsetdata = ut_alloc_2d (Mesh[(*pTess).Dim].ElsetQty + 1, 4);
+  double *elsetdata1d = ut_alloc_1d (Mesh[(*pTess).Dim].ElsetQty + 1);
+  double ***evect = ut_alloc_3d (Mesh[(*pTess).Dim].ElsetQty + 1, 3, 3);
+  double **eval = ut_alloc_2d (Mesh[(*pTess).Dim].ElsetQty + 1, 3);
+  char *prev = ut_alloc_1d_char (1000);
+  char *filename = NULL;
+  FILE *file = NULL;
+  struct OL_SET OSet;
+  struct ODF Odf;
+  char *fct = NULL, **vars = NULL, **vals = NULL;
+  char *weight = NULL;
+  char *var = NULL;
+  char *thetastring = ut_alloc_1d_char (100);
+  struct SIMRES SimRes2;
+
+  neut_simres_set_zero (&SimRes2);
+
+  ut_string_function (res, &fct, &vars, &vals, &size);
+
+  neut_sim_orispace (*pSim, &Odf, (char*) "R");
+
+  ut_print_progress (stdout, 0, (*pSim).StepQty + 1, (char*) "%3.0f%%", prev);
+
+  for (step = 0; step <= (*pSim).StepQty; step++)
+  {
+    neut_sim_setstep (pSim, step);
+    neut_sim_simres (*pSim, (char*) "elsets", (char*) "ori", &SimRes2);
+
+    neut_simres_setstep (pSimRes, step);
+    neut_simres_setstep (&SimRes2, step);
+
+    status = neut_mesh_elsetori (Mesh[(*pTess).Dim], elsetdata);
+    if (status)
+      ut_print_message (2, 0, (char*) "Failed to read elset oris.\n");
+
+    file = ut_file_open ((*pSimRes).file, (char*) "W");
+
+    neut_mesh_elsets_olset (*pNodes, Mesh[(*pTess).Dim], elsetdata,
+                            NULL, Mesh[(*pTess).Dim].ElsetQty, &OSet);
+    ut_string_string (Mesh[(*pTess).Dim].ElsetCrySym, &(OSet.crysym));
+
+    int user_sigma = 0;
+    ut_string_string ("1", &weight);
+    for (i = 0; i < size; i++)
+    {
+      if (!strcmp (vars[i], "theta"))
+      {
+        Odf.sigma = atof (vals[i]);
+        Odf.sigma *= M_PI / 180;
+        user_sigma = 1;
+      }
+      else if (!strcmp (vars[i], "weight"))
+        ut_string_string (vals[i], &weight);
+      else if (!strcmp (vars[i], "var"))
+        ut_string_string (vals[i], &var);
+    }
+    if (!user_sigma)
+      neut_odf_setsigma (&Odf, (char*) "avthetaeq", OSet.size, OSet.crysym);
+
+    sprintf (thetastring, " (theta = %9.6f°)     ", Odf.sigma * 180 / M_PI);
+    ut_print_clearline (stdout, strlen (thetastring) - 1);
+    printf ("%s", thetastring);
+
+    ut_print_progress (stdout, 0, (*pSim).StepQty + 1, (char*) "%3.0f%%", prev);
+
+    // Setting weights
+    for (i = 0; i < size; i++)
+      if (!strcmp (vars[i], "weight"))
+        neut_mesh_entity_expr_val (*pNodes, Mesh, pTess,
+                                   NULL, NULL, NULL, NULL, (char*) "elset", weight,
+                                   OSet.weight, NULL);
+
+    neut_sim_simres (*pSim, (char*) "elset", var, &SimRes2);
+    ut_array_1d_fnscanf (SimRes2.file, elsetdata1d + 1, Mesh[(*pTess).Dim].ElsetQty, (char *) "R");
+
+    if (!strcmp (fct, "orifield"))
+    {
+      neut_odf_orifield_comp ((char *) "m", !strcmp (weight, "1") ? (char *) "5" : (char *) "all", &OSet, elsetdata1d + 1, &Odf);
+
+      for (i = 0; i < Odf.odfqty; i++)
+        fprintf (file, REAL_PRINT_FORMAT "\n", Odf.odf[i]);
+    }
+    else if (!strcmp (fct, "orifieldn"))
+    {
+      neut_odf_orifield_comp ((char *) "n", !strcmp (weight, "1") ? (char *) "5" : (char *) "all", &OSet, elsetdata1d + 1, &Odf);
+      for (i = 0; i < Odf.odfnqty; i++)
+        fprintf (file, REAL_PRINT_FORMAT "\n", Odf.odfn[i]);
+    }
+
+    ut_file_close (file, (*pSimRes).file, "W");
+
+    ut_print_progress (stdout, step + 1, (*pSim).StepQty + 1,  (char *) "%3.0f%%", prev);
+  }
+
+  neut_sim_setstep (pSim, 0);
+  neut_sim_addres (pSim, entity, res, NULL);
+  neut_sim_fprintf ((*pSim).simdir, *pSim, (char *) "W");
+
+  // neut_odf_free (&Odf);
+  ut_free_1d_char (&filename);
+  ut_free_3d (&evect, Mesh[(*pTess).Dim].ElsetQty + 1, 3);
+  ut_free_2d (&eval, Mesh[(*pTess).Dim].ElsetQty + 1);
+  ut_free_2d (&elsetdata, Mesh[(*pTess).Dim].ElsetQty + 1);
+  ut_free_1d (&elsetdata1d);
+  ut_free_1d_char (&prev);
+  ut_free_1d_char (&weight);
+  ut_free_1d_char (&var);
+  ut_free_1d_char (&thetastring);
+  ut_free_2d_char (&vars, size);
+  ut_free_2d_char (&vals, size);
+  neut_simres_free (&SimRes2);
+
+  return;
+}

src/neper_s/nes_pproc/nes_pproc_entity/nes_pproc_entity_builtin/nes_pproc_entity_builtin_.h

@@ -52,6 +52,10 @@ extern void nes_pproc_entity_builtin_elsets_odf (struct SIM *pSim, struct TESS *
                                   struct NODES *pNodes, struct MESH *Mesh,
                                   char *entity, char *res, struct SIMRES *pSimRes);
 
+extern void nes_pproc_entity_builtin_elsets_orifield (struct SIM *pSim, struct TESS *pTess,
+                                  struct NODES *pNodes, struct MESH *Mesh,
+                                  char *entity, char *res, struct SIMRES *pSimRes);
+
 extern void nes_pproc_entity_builtin_elsets_readodf (struct SIM *pSim, struct TESS Tess,
                                   struct MESH *Mesh, char *entity, char *res,
                                   struct SIMRES *pSimRes);

src/neut/neut_odf/neut_odf.h

@@ -24,6 +24,8 @@ extern void neut_odf_convolve (struct ODF *pOdf, char *kernel);
 extern void neut_odf_deconvolve (struct ODF *pOdf, char *kernel);
 
 extern void neut_odf_elt_ori (struct ODF Odf, int elt, gsl_rng *r, double *q);
+extern void neut_odf_orifield_comp (char *mode, char *neigh, struct OL_SET *pOSet,
+                                    double *oridata, struct ODF *pOdf);
 
 #endif /* NEUT_ODF_H */
 

src/neut/neut_odf/neut_odf1.cpp

@@ -7,6 +7,10 @@
 
 extern double neut_odf_comp_elts (char *neigh, struct OL_SET *pOSet, QCLOUD nanocloud, my_kd_tree_t *nano_index, struct ODF *pOdf, int verbosity);
 extern double neut_odf_comp_nodes (char *neigh, struct OL_SET *pOSet, QCLOUD nano_cloud, my_kd_tree_t *nano_index, struct ODF *pOdf, int verbosity);
+extern double neut_odf_orifield_comp_elts (char *neigh, struct OL_SET *pOSet, QCLOUD nano_cloud,
+                             my_kd_tree_t *nano_index, double *oridata, struct ODF *pOdf);
+extern double neut_odf_orifield_comp_nodes (char *neigh, struct OL_SET *pOSet, QCLOUD nano_cloud,
+                     my_kd_tree_t *nano_index, double *oridata, struct ODF *pOdf);
 
 void
 neut_odf_set_zero (struct ODF *pOdf)
@@ -311,3 +315,24 @@ neut_odf_elt_ori (struct ODF Odf, int elt, gsl_rng *r, double *q)
 
   return;
 }
+
+void
+neut_odf_orifield_comp (char *mode, char *neigh, struct OL_SET *pOSet,
+                        double *oridata, struct ODF *pOdf)
+{
+  my_kd_tree_t *nano_index = nullptr;
+  nanoflann::SearchParams params;
+  QCLOUD nano_cloud;
+
+  neut_oset_kdtree (pOSet, &nano_cloud, &nano_index);
+
+  if (strstr (mode, "m") || strstr (mode, "n"))
+    neut_odf_orifield_comp_elts (neigh, pOSet, nano_cloud, nano_index, oridata, pOdf);
+
+  if (strstr (mode, "n"))
+    neut_odf_orifield_comp_nodes (neigh, pOSet, nano_cloud, nano_index, oridata, pOdf);
+
+  delete nano_index;
+
+  return;
+}