Add new capabilities

- module -T: fixed weibull distribution, made minor fixes.
- module -M: changed default value of -order to 2, changed -nset default value
  to faces,edges,vertices in 3D and edges,vertices in 2D, fixed msh4 format,
  fixed meshing of -transform cut(cylinder) tessellations.
- module -V: fixed -datanodecoofact.
- module -S: changed simulation.config onto simulation.cfg.
- documentation: made minor fix.
- general: cleaned tests.

VERSIONS

@@ -1,11 +1,15 @@
-New in 4.7.1-17 (21 Dec 2023):
+New in 4.8.0 (09 Jan 2024):
 - module -T: fixed weibull distribution, made minor fixes.
-- module -M: fixed meshing of -transform cut(cylinder) tessellations,
-  fixed msh4 format.
+- module -M: changed default value of -order to 2, changed -nset default value
+  to faces,edges,vertices in 3D and edges,vertices in 2D, fixed msh4 format,
+  fixed meshing of -transform cut(cylinder) tessellations.
 - module -V: fixed -datanodecoofact.
+- module -S: changed simulation.config onto simulation.cfg.
 - documentation: made minor fix.
 - general: cleaned tests.
 
+* Incompatible changes:  In -M, changed default value of -order to 2.
+
 New in 4.7.0 (17 Nov 2023):
 - module -T: added -ori odf, added -orisampling, improved -domain rodrigues,
   added -statcell scale and voxnb, fixed -morpho cube, fixed -transform rmsat,

doc/conf.py

@@ -11,8 +11,8 @@
 import sphinx_rtd_theme
 
 project = u'Neper'
-version = u'4.7.1-17'
-release = u'4.7.1-17'
+version = u'4.8.0'
+release = u'4.8.0'
 author = u'Romain Quey'
 copyright = u'Romain Quey'
 language = 'en'

doc/fileformat.rst

@@ -718,7 +718,7 @@ Here are details on the :file:`.sim` simulation directory (the :file:`.sim` exte
   simulation.sim
   |-- inputs
   |   |-- job.sh
-  |   |-- simulation.config
+  |   |-- simulation.cfg
   |   |-- simulation.msh
   |   `-- simulation.tess
   `-- results

doc/neper_m.rst

@@ -30,7 +30,7 @@ For mapped meshing, mesh cleaning options enable the removal of isolated element
 
 Mesh partitioning allows for the division the mesh nodes and elements into several sets while minimizing the interfaces between them [#partitioning]_, as needed for parallel simulations with FEPX.  Partitioning can return any number of partitions or be done according to a given parallel computer architecture (options :data:`-part*`).
 
-In the output mesh, the individual entities of the tessellations (the vertices, edges, faces and polyhedra) can be described by element sets (option :option:`-dim`).  Node sets of the vertices, edges and faces located on the boundary of the tessellation are also provided for prescribing the boundary conditions (option :option:`-nset`).  The surface element sets are also provided (option :option:`-faset`).  Element sets other than those corresponding to the tessellation cells can be defined (option :option:`-elset`). The mesh order can be 1 or 2 (option :option:`-order`).  Statistical data can be obtained on the meshes (options :data:`-stat*`).
+In the output mesh, the individual entities of the tessellations (the vertices, edges, faces and polyhedra) can be described by element sets (option :option:`-dim`).  Node sets of the vertices, edges and faces located on the boundary of the tessellation are also provided for prescribing the boundary conditions (option :option:`-nset`).  The surface element sets are also provided (option :option:`-faset`).  Element sets other than those corresponding to the tessellation cells can be defined (option :option:`-elset`). The mesh order can be 1 or 2 (option :option:`-order`, default :data:`2`).  Statistical data can be obtained on the meshes (options :data:`-stat*`).
 
 The methods implemented for meshing are described in [CMAME2011]_.
 
@@ -196,7 +196,7 @@ Meshing Options
 
   - :data:`2`: quadratic-interpolation elements (3-node linear elements, 6-node triangular elements, 8-node or 9-node quadrangular elements, 10-node tetrahedral elements and 20-node hexahedral elements).
 
-  **Default value**: :data:`1`.
+  **Default value**: :data:`2`.
 
 .. option:: -cl{ver,edge,face} or -rcl{ver,edge,face} <characteritic_length> (secondary options
 
@@ -482,7 +482,7 @@ Output Options
 
   - :data:`none`: none.
 
-  **Default value**: :data:`faces` in 3D and :data:`edges` in 2D.
+  **Default value**: :data:`faces,edges,vertices` in 3D and :data:`edges,vertices` in 2D.
 
 .. option:: -faset <faset1>,<faset2>,...
 
@@ -652,11 +652,11 @@ Below are some examples of use of neper -M.
 
     $ neper -M n100-id1.tesr
 
-- Mesh tessellation :file:`n100-id1.tess` with a mesh size of rcl = 0.5 and in 2nd-order elements:
+- Mesh tessellation :file:`n100-id1.tess` with a mesh size of rcl = 0.5 and in 1st-order elements:
 
   .. code-block:: console
 
-    $ neper -M n100-id1.tess -rcl 0.5 -order 2
+    $ neper -M n100-id1.tess -rcl 0.5
 
 - Mesh tessellation :file:`n100-id1.tess` with small elements for the interior cells and bigger elements for the boundary cells:
 

doc/neper_s.rst

@@ -8,13 +8,8 @@ Simulation Module (-S)
 
 Module -S is the module for post-processing simulation results.  It generates and works on a simply-structured and human-friendly :ref:`simulation_directory`.  The :ref:`simulation_directory` is particularly well suited for result management and allows for the computation of new results.
 
-A :ref:`simulation_directory` is typically generated from an FEPX raw result directory, which can be done as simply as follows:
-
-.. code-block:: console
-
-  $ neper -S <fepx_raw_result_directory>
-
-A :ref:`simulation_directory` can also be generated by the :ref:`neper_t` or the :ref:`neper_m` (option :data:`-format sim`), in which case it contains the (raster) tessellation or mesh file but no simulation results --- the various post-processing capabilities of :ref:`neper_s` can then be used on the (raster) tessellation or mesh.   Finally, simulation directories that represent successive parts of a simulation (e.g. resulting from FEPX restarts) can be merged into a single one.
+A :ref:`simulation_directory` is typically generated by FEPX.
+It can also be generated by the :ref:`neper_t` or the :ref:`neper_m` (option :data:`-format sim`), in which case it contains the (raster) tessellation or mesh file but no simulation results --- the various post-processing capabilities of :ref:`neper_s` can then be used on the (raster) tessellation or mesh.   Finally, simulation directories that represent successive parts of a simulation (e.g. resulting from FEPX restarts) can be merged into a single one.
 
 New results can be computed for several *entities* of the (raster) tessellation and mesh, including the (raster) tessellation cells and the mesh nodes, elements and elsets.  The whole (raster) tessellation and mesh can also serve as *entities*.  New *entities* corresponding to sets of elements can also be defined.
 
@@ -26,48 +21,40 @@ Here is what a typical run of module -S looks like:
 
 .. code-block:: console
 
-  $ neper -S fepx-simulation
+  $  neper -S simulation.sim -reselset stress
 
   ========================    N   e   p   e   r    =======================
   Info   : A software package for polycrystal generation and meshing.
-  Info   : Version 4.0.0
+  Info   : Version 4.8.0
   Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
-  Info   : Running on 8 threads.
+  Info   : Running on 20 threads.
   Info   : <https://neper.info>
-  Info   : Copyright (C) 2003-2021, and GNU GPL'd, by Romain Quey.
+  Info   : Copyright (C) 2003-2022, and GNU GPL'd, by Romain Quey.
   Info   : Loading initialization file `/home/rquey/.neperrc'...
   Info   : ---------------------------------------------------------------
   Info   : MODULE  -S loaded with arguments:
   Info   : [ini file] (none)
-  Info   : [com line] fepx-simulation
+  Info   : [com line] simulation.sim -reselset stress
   Info   : ---------------------------------------------------------------
   Info   : Reading input data...
   Info   :   - Reading arguments...
-  Info   : Writing simulation directory from FEPX result directory...
-  Info   :     [o] Writing directory `fepx-simulation.sim'...
-  Info   :   - Parsing FEPX results...
-  Info   :     [i] Parsing file `fepx-simulation/post.report'...
-  Info   :     [i] Parsed file `fepx-simulation/post.report'.
-  Info   :     > Partition number: 8.
-  Info   :     > Step      number: 10.
-  Info   :     > Node      number: 2752.
-  Info   :     > Element   number: 1596.
-  Info   :   - Writing report file...
-  Info   :     [o] Writing file `fepx-simulation.sim/report'...
-  Info   :     [o] Wrote file `fepx-simulation.sim/report'.
-  Info   :   - Writing inputs...
-  Info   :     [o] Writing directory `fepx-simulation.sim/inputs'...
-  Info   :       . simulation.tess...
-  Info   :       . simulation.msh...
-  Info   :       . simulation.config...
-  Info   :     [o] Wrote directory `fepx-simulation.sim/inputs'.
+  Info   :     > Input files: msh config
+  Info   :     > Node number      : 49
+  Info   :     > Element number   : 16
+  Info   :     > Elset number     : 2
+  Info   :     > Partition number : 2
+  Info   :     > Step number      : 2
+  Info   :     > Node results     : coo disp vel
+  Info   :     > Elt results      : ori stress
+  Info   : Running post-processing...
+  Info   :   - Loading inputs...
+  Info   :     > simulation.msh...
+  Info   :     > simulation.cfg...
   Info   :   - Writing results...
-  Info   :     [o] Writing directory `fepx-simulation.sim/results'...
-  Info   :       . coo...       100%
-  Info   :       . ori...       100%
-  Info   :     [o] Wrote directory `fepx-simulation.sim/results'.
-  Info   :     [o] Wrote directory `fepx-simulation.sim'.
-  Info   : Elapsed time: 0.075 secs.
+  Info   :     [o] Writing directory `simulation.sim/results/elsets'...
+  Info   :       . stress ........................................... 100%
+  Info   :     [o] Wrote directory `simulation.sim/results/elsets'.
+  Info   : Elapsed time: 0.010 secs.
   ========================================================================
 
 Arguments
@@ -80,7 +67,6 @@ Input Data
 
   Specify the name of the input directory, which can be:
 
-  - an FEPX raw result directory [#f1]_  (to convert into a :ref:`simulation_directory`);
   - a :ref:`simulation_directory`;
   - a series of simulation directories combined with :data:`,` (to merge).
 

doc/tutorials/orientation_trajectories/n20.sim/.sim

@@ -8,8 +8,8 @@
    simulation.tesr
   *msh
    simulation.msh
-  *config
-   simulation.config
+  *cfg
+   simulation.cfg
  **general
    0 3606 2201 20 2
   *orides

src/CMakeLists.txt

@@ -7,7 +7,7 @@ if(POLICY CMP0077)
   cmake_policy(SET CMP0077 NEW)
 endif()
 
-set(NEPER_VERSION \"4.7.1-17\")
+set(NEPER_VERSION \"4.8.0\")
 project(neper)
 
 if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.8.1)

src/neper_m/nem_input/nem_input3.c

@@ -42,7 +42,7 @@ nem_input_options_default (struct IN_M *pIn)
   strcpy ((*pIn).format, "msh");
 
   /* Options for meshing ------------------------------- */
-  (*pIn).order = 1;
+  (*pIn).order = 2;
   (*pIn).dimstring = ut_alloc_1d_char (9);
   strcpy ((*pIn).dimstring, "inputdim");
 

src/neper_m/nem_writemesh/nem_writemesh1.c

@@ -26,6 +26,14 @@ nem_writemesh (struct IN_M In, struct TESS Tess, struct NODES Nodes,
   strcpy (sizestring[2], "area");
   strcpy (sizestring[3], "volume");
 
+  if (!strcmp (In.nset, "default"))
+  {
+    if (dim == 3)
+      ut_string_string ("faces,edges,vertices", &(In.nset));
+    else if (dim == 2)
+      ut_string_string ("edges,vertices", &(In.nset));
+  }
+
   neut_nset_expand (NSet[0], NSet[1], NSet[2], In.nset, &nsetlist);
   if (!strcmp (Mesh[dim].EltType, "tri"))
     neut_nset_expand (NSet[0], NSet[1], NSet[2], In.faset, &fasetlist);

src/neper_s/nes_convert/nes_convert1.c

@@ -9,6 +9,8 @@ nes_convert (struct IN_S In, struct SIM *pSim)
 {
   struct FEPXSIM FSim;
 
+  ut_print_message (1, 2, "Conversion will be removed in a future version.\n");
+
   neut_fepxsim_set_zero (&FSim);
 
   nes_convert_parse (In, &FSim, pSim);

src/neper_s/nes_convert/nes_convert_write/nes_convert_write2.c

@@ -23,10 +23,10 @@ nes_convert_write_inputs (struct IN_S In, struct FEPXSIM *pFSim)
     ut_string_string ((*pFSim).msh, filename + filenameqty - 1);
   }
 
-  if ((*pFSim).config)
+  if ((*pFSim).cfg)
   {
     filename = ut_realloc_1d_pchar_null (filename, ++filenameqty, 1);
-    ut_string_string ((*pFSim).config, filename + filenameqty - 1);
+    ut_string_string ((*pFSim).cfg, filename + filenameqty - 1);
   }
 
   // *.sh

src/neper_s/nes_pproc/nes_pproc2.c

@@ -23,7 +23,7 @@ nes_pproc_load (struct SIM *pSim, struct TESS *pTess, struct TESR *pTesr,
   if ((*pSim).msh)
     nes_loadmesh (pSim, pNodes, Mesh, 2);
 
-  if ((*pSim).config)
+  if ((*pSim).cfg)
     nes_loadconfig (*pSim, &GroupCrySym, &GroupQty, 2);
 
   neut_sim_testinputs (*pSim, *pTess, Mesh);

src/neper_s/nes_pproc/nes_pproc3.c

@@ -4,7 +4,7 @@
 
 #include "nes_pproc_.h"
 
-// Checking consistency between Tess and Sim crysym, if simulation.config exists
+// Checking consistency between Tess and Sim crysym, if simulation.cfg exists
 void
 nes_pproc_load_crysym (struct TESS *pTess, struct TESR *pTesr,
                        struct NODES *pNodes, struct MESH *Mesh,
@@ -14,7 +14,7 @@ nes_pproc_load_crysym (struct TESS *pTess, struct TESR *pTesr,
 
   if (GroupQty)
   {
-    // Does simulation.config have multiple crystal symmetries?
+    // Does simulation.cfg have multiple crystal symmetries?
     multiple = 0;
     for (i = 1; i < GroupQty; i++)
       if (strcmp (GroupCrySym[0], GroupCrySym[i]))

src/neper_s/nes_utils/nes_utils1.c

@@ -123,14 +123,14 @@ void
 nes_loadconfig (struct SIM Sim, char ***pGroupCrySym, int *pGroupQty, int verbosity)
 {
   int id;
-  char *filename = ut_string_paste3 (Sim.simdir, "/inputs/", Sim.config);
+  char *filename = ut_string_paste3 (Sim.simdir, "/inputs/", Sim.cfg);
   char *string = ut_alloc_1d_char (1000);
   FILE *fp = NULL;
 
-  if (Sim.config && ut_file_exist (filename))
+  if (Sim.cfg && ut_file_exist (filename))
   {
     if (verbosity)
-      ut_print_message (0, verbosity + 1, "%s...\n", Sim.config);
+      ut_print_message (0, verbosity + 1, "%s...\n", Sim.cfg);
 
     fp = ut_file_open (filename, "R");
 

src/neut/neut_fepxsim/neut_fepxsim_fscanf/neut_fepxsim_fscanf1.c

@@ -39,8 +39,11 @@ neut_fepxsim_fscanf (char *dir, struct FEPXSIM *pFSim, char *mode)
     ut_string_string ("simulation.tesr", &(*pFSim).tesr);
   if (ut_file_exist ("%s/simulation.msh", (*pFSim).fepxdir))
     ut_string_string ("simulation.msh", &(*pFSim).msh);
-  if (ut_file_exist ("%s/simulation.config", (*pFSim).fepxdir))
-    ut_string_string ("simulation.config", &(*pFSim).config);
+
+  if (ut_file_exist ("%s/simulation.cfg", (*pFSim).fepxdir))
+    ut_string_string ("simulation.cfg", &(*pFSim).cfg);
+  else if (ut_file_exist ("%s/simulation.config", (*pFSim).fepxdir))
+    ut_string_string ("simulation.config", &(*pFSim).cfg);
 
   file = ut_file_open (filename, mode);
 
@@ -155,7 +158,7 @@ neut_fepxsim_fscanf (char *dir, struct FEPXSIM *pFSim, char *mode)
 
   ut_free_1d_char (&filename);
 
-  filename = ut_string_paste3 (name, "/", (*pFSim).config);
+  filename = ut_string_paste3 (name, "/", (*pFSim).cfg);
 
   file = ut_file_open (filename, "R");
   while (fscanf (file, "%s", tmp) == 1)

src/neut/neut_fepxsim/neut_fepxsim_op/neut_fepxsim_op.c

@@ -29,7 +29,7 @@ neut_fepxsim_set_zero (struct FEPXSIM *pFSim)
   (*pFSim).bcs = NULL;
   (*pFSim).ori = NULL;
   (*pFSim).phase = NULL;
-  (*pFSim).config = NULL;
+  (*pFSim).cfg = NULL;
 
   return;
 }
@@ -47,7 +47,7 @@ neut_fepxsim_free (struct FEPXSIM *pFSim)
   ut_free_1d_char (&(*pFSim).bcs);
   ut_free_1d_char (&(*pFSim).ori);
   ut_free_1d_char (&(*pFSim).phase);
-  ut_free_1d_char (&(*pFSim).config);
+  ut_free_1d_char (&(*pFSim).cfg);
 
   ut_free_1d_int (&(*pFSim).PartNodeQty);
   ut_free_1d_int (&(*pFSim).PartEltQty);

src/neut/neut_fepxsim/neut_fepxsim_sim/neut_fepxsim_sim.c

@@ -58,7 +58,7 @@ neut_fepxsim_sim (struct FEPXSIM FSim, struct SIM *pSim)
   ut_string_string (FSim.bcs, &(*pSim).bcs);
   ut_string_string (FSim.ori, &(*pSim).ori);
   ut_string_string (FSim.phase, &(*pSim).phase);
-  ut_string_string (FSim.config, &(*pSim).config);
+  ut_string_string (FSim.cfg, &(*pSim).cfg);
 
   (*pSim).RestartId = FSim.RestartId;
   (*pSim).RestartFiles = FSim.RestartFiles;

src/neut/neut_nset/neut_nset.c

@@ -19,20 +19,6 @@ neut_nset_expand (struct NSET NSet0D, struct NSET NSet1D, struct NSET NSet2D,
   if (!in || strlen (in) == 0 || !strcmp (in, "none"))
     return;
 
-  if (strstr (in, "default"))
-  {
-    qty = 1;
-    list = ut_alloc_2d_char (qty, 11);
-    if (NSet2D.qty > 0)
-      strcpy (list[0], "faces");
-    else if (NSet1D.qty > 0)
-      strcpy (list[0], "edges");
-    else if (NSet0D.qty > 0)
-      strcpy (list[0], "vertices");
-    else
-      ut_print_neperbug ();
-  }
-
   else if (strstr (in, "all"))
   {
     if (NSet2D.qty > 0)

src/neut/neut_sim/neut_sim_fprintf/neut_sim_fprintf1.c

@@ -31,8 +31,8 @@ neut_sim_fprintf (char *dir, struct SIM Sim, char *mode)
     fprintf (file, "  *ori\n   %s\n", Sim.msh);
   if (Sim.phase)
     fprintf (file, "  *phase\n   %s\n", Sim.msh);
-  if (Sim.config)
-    fprintf (file, "  *config\n   %s\n", Sim.config);
+  if (Sim.cfg)
+    fprintf (file, "  *cfg\n   %s\n", Sim.cfg);
 
   fprintf (file, " **general\n");
   fprintf (file, "   %d %d %d %d %d\n",
@@ -267,8 +267,8 @@ neut_sim_fprintf_asy (char *dir, struct SIM Sim, char *mode)
     fprintf (file, "TreeNode child1%d = makeNode(child1, \"\\tt %s\");\n", ++id, Sim.ori);
   if (Sim.phase)
     fprintf (file, "TreeNode child1%d = makeNode(child1, \"\\tt %s\");\n", ++id, Sim.phase);
-  if (Sim.config)
-    fprintf (file, "TreeNode child1%d = makeNode(child1, \"\\tt %s\");\n", ++id, Sim.config);
+  if (Sim.cfg)
+    fprintf (file, "TreeNode child1%d = makeNode(child1, \"\\tt %s\");\n", ++id, Sim.cfg);
 
   int print_results = 0;
   char *child1 = ut_alloc_1d_char (100);
@@ -343,8 +343,8 @@ neut_sim_verbose (struct SIM Sim)
     printf (" ori");
   if (Sim.phase)
     printf (" phase");
-  if (Sim.config)
-    printf (" config");
+  if (Sim.cfg)
+    printf (" cfg");
   printf ("\n");
 
   if (Sim.RestartId || Sim.RestartFiles)