Add new capabilities

- module -T: added -per 1 for -morpho cube, added -ori ks (Kurdjumov-Sachs)
  and ti_beta2alpha (titanium).
- module -S: fixed -res* odfn.
- module -V: added -data{elt2d,elset2d}trs, added -step final, fixed -show*
  <result_component>, added -showmeshsliceelt1d.

VERSIONS

@@ -1,5 +1,9 @@
-New in 4.8.3-6 (15 May 2024):
-- module -V: added -showmeshsliceelt1d.
+New in 4.9.0 (15 May 2024):
+- module -T: added -per 1 for -morpho cube, added -ori ks (Kurdjumov-Sachs)
+  and ti_beta2alpha (titanium).
+- module -S: fixed -res* odfn.
+- module -V: added -data{elt2d,elset2d}trs, added -step final, fixed -show*
+  <result_component>, added -showmeshsliceelt1d.
 
 New in 4.8.2 (27 Mar 2024):
 - module -T: added -transform "cut(cube)", added -morphooptiini ori and id,

doc/conf.py

@@ -11,8 +11,8 @@
 import sphinx_rtd_theme
 
 project = u'Neper'
-version = u'4.8.3-6'
-release = u'4.8.3-6'
+version = u'4.9.0'
+release = u'4.9.0'
 author = u'Romain Quey'
 copyright = u'Romain Quey'
 language = 'en'

doc/neper_t.rst

@@ -282,7 +282,7 @@ These options can be used to set the cell morphology.
 
   - :data:`<ori_definition>` can be:
 
-    - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).
+    - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).  :option:`-ori` :data:`from_morpho` must also be used.
 
   - :data:`<id_definition>` can be:
 
@@ -491,6 +491,10 @@ Crystal Orientation Options
 
   - :data:`parent[:<distribution>]`: orientations inherited from the ones of the parent cells, with an optional continuous distribution about the nominal orientations (see below);
 
+  - :data:`ks[:<distribution>]`: orientations inherited from the ones of the parent cells using the Kurdjumov-Sachs (KS) orientation relationship (austenite--ferrite transformation), with an optional continuous distribution about the nominal orientations (see below);
+
+  - :data:`ti_beta2alpha[:<distribution>]`: orientations inherited from the ones of the parent cells using the :math:`\beta\rightarrow\alpha` transformation orientation relationship in titanium, with an optional continuous distribution about the nominal orientations (see below);
+
   - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).
 
   - :data:`from_morpho`: discrete orientations read from :option:`-morphooptiini`:data:`ori`.

doc/neper_v.rst

@@ -124,7 +124,8 @@ When a simulation directory is loaded as input, it is possible to specify the si
 
   Specify the simulation step(s), which can be:
 
-  - :data:`0`: initial state;
+  - :data:`0`: the initial state;
+  - :data:`final`: the final step;
   - any step number;
   - :data:`all`: all steps;
   - a list of steps combined with :data:`,`; a range of values can also be specified using :data:`-`.  An example is :data:`0-10,20` (for steps 0 to 10, and 20).
@@ -424,6 +425,18 @@ The following options enable the definition of the properties (color, size, etc.
 
   **Default value**: :data:`palette` for integer values, :data:`viridis` for real values, and :data:`rodrigues` for crystal orientations.
 
+.. index::
+   single: -dataelt2dtrs
+   single: -dataelset2dtrs
+
+.. option:: -data{elt2d,elset2d}trs <transparency>
+
+  Specify the transparencies (values from 0 to 1), which can be:
+
+  - a real value;
+  - an expression based on the variables described in :ref:`mesh_keys`, such as :data:`x` or :data:`area`;
+  - :data:`file(<file_name>)`: individual values to load from a :ref:`data_file`.
+
 .. option:: -data{elt,elset,node,elt{0-3}d,elset{0-3}d}scale <scale>
 
   Specify the scale relative to the :data:`-data...col real` data, which can be:

src/CMakeLists.txt

@@ -7,7 +7,7 @@ if(POLICY CMP0077)
   cmake_policy(SET CMP0077 NEW)
 endif()
 
-set(NEPER_VERSION \"4.8.3-6\")
+set(NEPER_VERSION \"4.9.0\")
 project(neper)
 
 if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.8.1)

src/neper_t/CMakeLists.txt

@@ -70,6 +70,7 @@ add_library(neper_t
 ./net_tess/net_tess2.c
 ./net_tess/net_tess_cube/net_tess_cube1.c
 ./net_tess/net_tess_cube/net_tess_cube2.c
+./net_tess/net_tess_cube/net_tess_cube3.c
 ./net_tess/net_tess_onecell/net_tess_onecell1.c
 ./net_tess/net_tess_lam/net_tess_lam1.c
 ./net_tess/net_tess_lam//net_tess_lam_seed/net_tess_lam_seed1.c

src/neper_t/net_flatten/net_flatten1.c

@@ -29,11 +29,10 @@ net_flatten (struct MTESS MTess, struct TESS *Tess, struct TESS *pFTess)
       net_mtess_flatten (MTess, Tess2, id, Tess2 + id);
     }
 
-
   neut_tess_tess (Tess2[1], pFTess);
 
-  if (Tess[1].CellCrySym)
-    ut_string_string (Tess[1].CellCrySym, &(*pFTess).CellCrySym);
+  if (Tess[MTess.TessQty].CellCrySym)
+    ut_string_string (Tess[MTess.TessQty].CellCrySym, &(*pFTess).CellCrySym);
 
   (*pFTess).ScaleQty = MTess.LevelQty;
   (*pFTess).ScaleCellId =

src/neper_t/net_ori/net_ori1.c

@@ -101,6 +101,15 @@ net_ori (struct IN_T In, int level, struct MTESS MTess, struct TESS *Tess,
       else if (!strncmp (parts[i], "odf", 3))
         net_ori_odf ((*pSSet).Random, parts[i], OSets + i);
 
+      else if (!strncmp (parts[i], "parent", 6))
+        net_ori_parent (parts[i], SSet, dtess, dcell, OSets + i);
+
+      else if (!strncmp (parts[i], "ks", 2) || !strncmp (parts[i], "KS", 2))
+        net_ori_ks ((*pSSet).Random, parts[i], SSet, dtess, dcell, OSets + i);
+
+      else if (!strcmp (parts[i], "ti_beta2alpha"))
+        net_ori_ti_beta2alpha ((*pSSet).Random, parts[i], SSet, dtess, dcell, OSets + i);
+
       else
         net_ori_label (parts[i], SSet, dtess, dcell, OSets + i);
 

src/neper_t/net_ori/net_ori2.c

@@ -92,39 +92,194 @@ net_ori_fiber (struct SEEDSET *SSet, int dtess, int dcell, long random,
 }
 
 void
-net_ori_label (char *label, struct SEEDSET *SSet, int dtess, int dcell, struct OL_SET *pOSet)
+net_ori_ks (long random, char *label, struct SEEDSET *SSet, int dtess, int dcell, struct OL_SET *pOSet)
 {
   unsigned int i;
-  int status, partqty;
+  int partqty;
   double *q = ol_q_alloc ();
   char **parts = NULL;
-  char *spread = NULL;
+  int status_parent, status_child;
+  double **X = ol_g_alloc ();
+  int n1;
+  double alpha_over_phi = 1.; // pow (2, 1. / 3);
+  double phi_over_alpha = 1. / alpha_over_phi;
+  double d = sqrt (6) * pow (phi_over_alpha, 3);
+  double *qX = ol_q_alloc ();
+  double *qtmp = ol_q_alloc ();
+  gsl_rng *r = NULL;
 
   ut_list_break (label, NEUT_SEP_DEP, &parts, &partqty);
 
+  // After (Fortes, 1984)
+  if (strcmp (parts[0], "ks") && strcmp (parts[0], "KS"))
+    abort ();
+
+  // Checking crystal symmetries
+  status_parent = 0; // 1: warning, 2: error
+  status_child = 0; // 1: warning, 2: error
+  if (strcmp (SSet[dtess].crysym, "cubic") || strcmp ((*pOSet).crysym, "cubic"))
+  {
+    if (strcmp (SSet[dtess].crysym, "cubic"))
+      status_parent = (!strcmp (SSet[dtess].crysym, "triclinic")) ? 1 : 2;
+
+    if (strcmp ((*pOSet).crysym, "cubic"))
+      status_child = (!strcmp (SSet[dtess].crysym, "triclinic")) ? 1 : 2;
+  }
+
+  if (ut_num_max (status_parent, status_child) == 1)
+    ut_print_message (1, 2, "KS transformation assumes cubic parent and child phases.\n");
+  else if (ut_num_max (status_parent, status_child) == 2)
+    ut_print_message (2, 2, "KS transformation requires cubic parent and child phases.\n");
+
+  ut_array_1d_set_3 (X[0], 2 * d + 1, -1, d - 2);
+  ut_array_1d_set_3 (X[1], 1, 2 * d - 1, -d - 2);
+  ut_array_1d_set_3 (X[2], d - 2, d + 2, 4);
+  ut_array_2d_scale (X, 3, 3, 1. / pow (6 * d, 2. / 3));
+
+  ol_g_q (X, qX);
+
+  r = gsl_rng_alloc (gsl_rng_ranlxd2);
+  gsl_rng_set (r, random - 1);
+
+  ut_print_message (0, 2, "Applying KS...\n");
+
+  for (i = 0; i < (*pOSet).size; i++)
+  {
+    n1 = 1 + gsl_rng_uniform_int (r, 24);
+    ol_q_crysym (SSet[dtess].SeedOri[dcell], "cubic", n1, qtmp);
+    ol_q_q_q_cur (qtmp, qX, (*pOSet).q[i]);
+  }
+
+  ol_q_free (qX);
+  ol_q_free (qtmp);
+  gsl_rng_free (r);
+  ol_g_free (X);
+
   if (partqty == 2)
-    ut_string_string (parts[1], &spread);
+    net_ori_addspread (parts[1], SSet[dtess].Random + dcell, pOSet);
 
-  status = 0;
-  if (!strcmp (parts[0], "parent"))
-    ol_q_memcpy (SSet[dtess].SeedOri[dcell], q);
-  else
-    status = ol_label_q (parts[0], q);
+  ol_q_free (q);
+  ut_free_2d_char (&parts, partqty);
 
-  if (!status)
+  return;
+}
+
+void
+net_ori_ti_beta2alpha (long random, char *label, struct SEEDSET *SSet, int dtess, int dcell, struct OL_SET *pOSet)
+{
+  unsigned int i;
+  int partqty;
+  double *q = ol_q_alloc ();
+  char **parts = NULL;
+  int status_parent, status_child;
+  int n1;
+  double **qX = ut_alloc_2d (13, 4);
+  double *qtmp = ol_q_alloc ();
+  gsl_rng *r = NULL;
+
+  ut_list_break (label, NEUT_SEP_DEP, &parts, &partqty);
+
+  // After (Fortes, 1984)
+  if (strcmp (parts[0], "ti_beta2alpha") && strcmp (parts[0], "Ti_beta2alpha"))
+    abort ();
+
+  // Checking crystal symmetries
+  status_parent = 0; // 1: warning, 2: error
+  status_child = 0; // 1: warning, 2: error
+  if (strcmp (SSet[dtess].crysym, "cubic") || strcmp ((*pOSet).crysym, "hexagonal"))
   {
-    ol_set_misorispread (spread, 3, SSet[dtess].Random + dcell, pOSet);
+    if (strcmp (SSet[dtess].crysym, "cubic"))
+      status_parent = (!strcmp (SSet[dtess].crysym, "triclinic")) ? 1 : 2;
 
-    for (i = 0; i < (*pOSet).size; i++)
-      ol_q_q_q_ref (q, (*pOSet).q[i], (*pOSet).q[i]);
+    if (strcmp ((*pOSet).crysym, "hexagonal"))
+      status_child = (!strcmp (SSet[dtess].crysym, "triclinic")) ? 1 : 2;
+  }
+
+  if (ut_num_max (status_parent, status_child) == 1)
+    ut_print_message (1, 2, "beta2alpha transformation assumes cubic parent and hexagonal child phases.\n");
+  else if (ut_num_max (status_parent, status_child) == 2)
+    ut_print_message (2, 2, "beta2alpha transformation requires cubic parent and hexagonal child phases.\n");
+
+  ol_q_set_this (qX[1], 0.704416,  0.541675, -0.454519, -0.061628);
+  ol_q_set_this (qX[2], 0.901980,  0.082828,  0.373612,  0.199964);
+  ol_q_set_this (qX[3], 0.704416,  0.541675,  0.454519,  0.061628);
+  ol_q_set_this (qX[4], 0.901980,  0.082828, -0.373612, -0.199964);
+  ol_q_set_this (qX[5], 0.923000,  0.382319, -0.016692,  0.040299);
+  ol_q_set_this (qX[6], 0.704416, -0.541675, -0.454519,  0.061628);
+  ol_q_set_this (qX[7], 0.923000, -0.382319, -0.016692, -0.040299);
+  ol_q_set_this (qX[8], 0.704416, -0.541675,  0.454519, -0.061628);
+  ol_q_set_this (qX[9], 0.901980, -0.082828,  0.373612, -0.199964);
+  ol_q_set_this (qX[10], 0.923000,  0.382319,  0.016692, -0.040299);
+  ol_q_set_this (qX[11], 0.901980, -0.082828, -0.373612,  0.199964);
+  ol_q_set_this (qX[12], 0.923000, -0.382319,  0.016692,  0.040299);
+  for (i = 1; i <= 12; i++)
+    ol_q_set_unit (qX[i]);
+
+  r = gsl_rng_alloc (gsl_rng_ranlxd2);
+  gsl_rng_set (r, random - 1);
+
+  ut_print_message (0, 2, "Applying beta->alpha...\n");
+
+  for (i = 0; i < (*pOSet).size; i++)
+  {
+    n1 = 1 + gsl_rng_uniform_int (r, 12);
+    // ol_q_crysym (SSet[dtess].SeedOri[dcell], "cubic", n1, qtmp);
+    ol_q_q_q_cur (SSet[dtess].SeedOri[dcell], qX[n1], (*pOSet).q[i]);
   }
 
+  ut_free_2d (&qX, 13);
+  ol_q_free (qtmp);
+  gsl_rng_free (r);
+
+  if (partqty == 2)
+    net_ori_addspread (parts[1], SSet[dtess].Random + dcell, pOSet);
+
+  ol_q_free (q);
+  ut_free_2d_char (&parts, partqty);
+
+  return;
+}
+
+void
+net_ori_parent (char *string, struct SEEDSET *SSet, int dtess, int dcell, struct OL_SET *pOSet)
+{
+  int i, partqty;
+  char **parts = NULL;
+
+  ut_list_break (string, NEUT_SEP_DEP, &parts, &partqty);
+
+  for (i = 0; i < (int) (*pOSet).size; i++)
+    ol_q_memcpy (SSet[dtess].SeedOri[dcell], (*pOSet).q[i]);
+
+  if (partqty == 2)
+    net_ori_addspread (parts[1], SSet[dtess].Random + dcell, pOSet);
+
+  ut_free_2d_char (&parts, partqty);
+
+  return;
+}
+
+void
+net_ori_label (char *label, struct SEEDSET *SSet, int dtess, int dcell, struct OL_SET *pOSet)
+{
+  int i, status, partqty;
+  double *q = ol_q_alloc ();
+  char **parts = NULL;
+
+  ut_list_break (label, NEUT_SEP_DEP, &parts, &partqty);
+
+  status = ol_label_q (parts[0], q);
   if (status)
     abort ();
 
+  for (i = 0; i < (int) (*pOSet).size; i++)
+    ol_q_memcpy (q, (*pOSet).q[i]);
+
+  if (partqty == 2)
+    net_ori_addspread (parts[1], SSet[dtess].Random + dcell, pOSet);
+
   ol_q_free (q);
   ut_free_2d_char (&parts, partqty);
-  ut_free_1d_char (&spread);
 
   return;
 }

src/neper_t/net_ori/net_ori3.c

@@ -50,3 +50,19 @@ net_ori_odf_pre (char *odf, struct OL_SET *pOSet, struct ODF *pOdf)
 
   return;
 }
+
+void
+net_ori_addspread (char *spread, long random, struct OL_SET *pOSet)
+{
+  int i;
+  struct OL_SET OSet2 = ol_set_alloc ((*pOSet).size, (*pOSet).crysym);
+
+  ol_set_misorispread (spread, 3, random, &OSet2);
+
+  for (i = 0; i < (int) (*pOSet).size; i++)
+    ol_q_q_q_ref ((*pOSet).q[i], OSet2.q[i], (*pOSet).q[i]);
+
+  ol_set_free (&OSet2);
+
+  return;
+}

src/neper_t/net_ori/net_ori_.h

@@ -24,9 +24,6 @@ extern void net_ori_qty (struct SEEDSET *pSSet, char **parts, int partqty, int *
 extern void net_ori_fiber (struct SEEDSET *SSet, int dtess, int dcell, long random,
                            char *distrib, struct OL_SET *pOSet);
 
-extern void net_ori_label (char *label, struct SEEDSET *SSet, int dtess, int dcell,
-                           struct OL_SET *pOSet);
-
 extern void net_ori_odf (long random, char *odf, struct OL_SET *pOSet);
 extern void net_ori_odf_pre (char *odf, struct OL_SET *pOSet, struct ODF *pOdf);
 
@@ -42,3 +39,15 @@ extern int net_ori_mtess_randseed_rand (int *N, int *id, int *poly, int levelqty
 extern void net_ori_orispread (char *orispread, struct SEEDSET *pSSet);
 
 extern void net_orispread_file (char *orispread, struct SEEDSET *pSSet);
+
+extern void net_ori_addspread (char *spread, long random, struct OL_SET *pOSet);
+
+extern void net_ori_ks (long random, char *label, struct SEEDSET *SSet, int dtess, int dcell, struct OL_SET *pOSet);
+
+extern void net_ori_ti_beta2alpha (long random, char *label, struct SEEDSET *SSet, int dtess, int dcell, struct OL_SET *pOSet);
+
+extern void net_ori_parent (char *label, struct SEEDSET *SSet, int dtess, int dcell,
+                           struct OL_SET *pOSet);
+
+extern void net_ori_label (char *label, struct SEEDSET *SSet, int dtess, int dcell,
+                           struct OL_SET *pOSet);

src/neper_t/net_tess/net_tess3d/net_tess3d_periodic/net_tess3d_periodic.h

@@ -8,6 +8,10 @@ extern "C"
 #endif
 
   extern void net_tess3d_periodic (struct TESS *pTess);
+  extern void net_tess3d_periodic_ver_shrinkmaster (struct TESS *);
+  extern void net_tess3d_periodic_edge_shrinkmaster (struct TESS *);
+  extern void net_tess2d_periodic_edge_peredgeori (struct TESS *pTess);
+  extern void net_tess3d_periodic_edge_peredgeori (struct TESS *pTess);
 
 #ifdef __cplusplus
 }

src/neper_t/net_tess/net_tess3d/net_tess3d_periodic/net_tess3d_periodic_.h

@@ -17,10 +17,6 @@ extern void net_tess3d_periodic_face (struct TESS *pTess);
 extern void net_tess3d_periodic_edge (struct TESS *pTess);
 extern void net_tess3d_periodic_ver (struct TESS *pTess);
 
-extern void net_tess3d_periodic_ver_shrinkmaster (struct TESS *);
-extern void net_tess3d_periodic_edge_shrinkmaster (struct TESS *);
-extern void net_tess3d_periodic_edge_peredgeori (struct TESS *pTess);
-
 extern void net_tess3d_periodic_face_rodrigues (struct TESS *pTess);
 extern void net_tess3d_periodic_edge_rodrigues (struct TESS *pTess);
 extern void net_tess3d_periodic_ver_rodrigues (struct TESS *pTess);