-= operation on lists

Parser/Gmsh.tab.hpp

-
-/* A Bison parser, made by GNU Bison 2.4.1.  */
+/* A Bison parser, made by GNU Bison 2.4.3.  */
 
 /* Skeleton interface for Bison's Yacc-like parsers in C
    
-      Copyright (C) 1984, 1989, 1990, 2000, 2001, 2002, 2003, 2004, 2005, 2006
-   Free Software Foundation, Inc.
+      Copyright (C) 1984, 1989, 1990, 2000, 2001, 2002, 2003, 2004, 2005, 2006,
+   2009, 2010 Free Software Foundation, Inc.
    
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
@@ -185,7 +184,7 @@
 typedef union YYSTYPE
 {
 
-/* Line 1676 of yacc.c  */
+/* Line 1685 of yacc.c  */
 #line 89 "Gmsh.y"
 
   char *c;
@@ -198,8 +197,8 @@ typedef union YYSTYPE
 
 
 
-/* Line 1676 of yacc.c  */
-#line 203 "Gmsh.tab.hpp"
+/* Line 1685 of yacc.c  */
+#line 202 "Gmsh.tab.hpp"
 } YYSTYPE;
 # define YYSTYPE_IS_TRIVIAL 1
 # define yystype YYSTYPE /* obsolescent; will be withdrawn */

Parser/Gmsh.y

@@ -104,7 +104,8 @@ fullMatrix<double> ListOfListOfDouble2Matrix(List_T *list);
 %token tAtan tAtan2 tSinh tCosh tTanh tFabs tFloor tCeil
 %token tFmod tModulo tHypot 
 %token tPrintf tSprintf tStrCat tStrPrefix tStrRelative
-%token tBoundingBox tDraw tToday tSyncModel tCreateTopology tCreateTopologyNoHoles tDistanceFunction
+%token tBoundingBox tDraw tToday tSyncModel tCreateTopology tCreateTopologyNoHoles
+%token tDistanceFunction
 %token tPoint tCircle tEllipse tLine tSphere tPolarSphere tSurface tSpline tVolume
 %token tCharacteristic tLength tParametric tElliptic tRefineMesh
 %token tPlane tRuled tTransfinite tComplex tPhysical tCompound tPeriodic
@@ -120,7 +121,6 @@ fullMatrix<double> ListOfListOfDouble2Matrix(List_T *list);
 %token tGMSH_MAJOR_VERSION tGMSH_MINOR_VERSION tGMSH_PATCH_VERSION
 %token tHomRank tHomGen tHomCut tHomSeq
 
-
 %type <d> FExpr FExpr_Single 
 %type <v> VExpr VExpr_Single CircleOptions TransfiniteType
 %type <i> NumericAffectation NumericIncrement PhysicalId
@@ -699,6 +699,16 @@ Affectation :
       Free($1);
       List_Delete($5);
     }
+  | tSTRING '[' ']' tAFFECTMINUS ListOfDouble tEND
+    {
+      // remove from the list
+      for(int i = 0; i < List_Nbr($5); i++)
+        gmsh_yysymbols[$1].erase(std::find(gmsh_yysymbols[$1].begin(), 
+                                           gmsh_yysymbols[$1].end(), 
+                                           *(double*)List_Pointer($5, i)));
+      Free($1);
+      List_Delete($5);
+    }
   | tSTRING NumericIncrement tEND
     {
       if(!gmsh_yysymbols.count($1))

Parser/Gmsh.yy.cpp

@@ -73,6 +73,7 @@ typedef int flex_int32_t;
 typedef unsigned char flex_uint8_t; 
 typedef unsigned short int flex_uint16_t;
 typedef unsigned int flex_uint32_t;
+#endif /* ! C99 */
 
 /* Limits of integral types. */
 #ifndef INT8_MIN
@@ -103,8 +104,6 @@ typedef unsigned int flex_uint32_t;
 #define UINT32_MAX             (4294967295U)
 #endif
 
-#endif /* ! C99 */
-
 #endif /* ! FLEXINT_H */
 
 #ifdef __cplusplus
@@ -161,15 +160,7 @@ typedef unsigned int flex_uint32_t;
 
 /* Size of default input buffer. */
 #ifndef YY_BUF_SIZE
-#ifdef __ia64__
-/* On IA-64, the buffer size is 16k, not 8k.
- * Moreover, YY_BUF_SIZE is 2*YY_READ_BUF_SIZE in the general case.
- * Ditto for the __ia64__ case accordingly.
- */
-#define YY_BUF_SIZE 32768
-#else
 #define YY_BUF_SIZE 16384
-#endif /* __ia64__ */
 #endif
 
 /* The state buf must be large enough to hold one state per character in the main buffer.
@@ -181,7 +172,12 @@ typedef unsigned int flex_uint32_t;
 typedef struct yy_buffer_state *YY_BUFFER_STATE;
 #endif
 
-extern int gmsh_yyleng;
+#ifndef YY_TYPEDEF_YY_SIZE_T
+#define YY_TYPEDEF_YY_SIZE_T
+typedef size_t yy_size_t;
+#endif
+
+extern yy_size_t gmsh_yyleng;
 
 extern FILE *gmsh_yyin, *gmsh_yyout;
 
@@ -207,11 +203,6 @@ extern FILE *gmsh_yyin, *gmsh_yyout;
 
 #define unput(c) yyunput( c, (yytext_ptr)  )
 
-#ifndef YY_TYPEDEF_YY_SIZE_T
-#define YY_TYPEDEF_YY_SIZE_T
-typedef size_t yy_size_t;
-#endif
-
 #ifndef YY_STRUCT_YY_BUFFER_STATE
 #define YY_STRUCT_YY_BUFFER_STATE
 struct yy_buffer_state
@@ -229,7 +220,7 @@ struct yy_buffer_state
 	/* Number of characters read into yy_ch_buf, not including EOB
 	 * characters.
 	 */
-	int yy_n_chars;
+	yy_size_t yy_n_chars;
 
 	/* Whether we "own" the buffer - i.e., we know we created it,
 	 * and can realloc() it to grow it, and should free() it to
@@ -299,8 +290,8 @@ static YY_BUFFER_STATE * yy_buffer_stack = 0; /**< Stack as an array. */
 
 /* yy_hold_char holds the character lost when gmsh_yytext is formed. */
 static char yy_hold_char;
-static int yy_n_chars;		/* number of characters read into yy_ch_buf */
-int gmsh_yyleng;
+static yy_size_t yy_n_chars;		/* number of characters read into yy_ch_buf */
+yy_size_t gmsh_yyleng;
 
 /* Points to current character in buffer. */
 static char *yy_c_buf_p = (char *) 0;
@@ -328,7 +319,7 @@ static void gmsh_yy_init_buffer (YY_BUFFER_STATE b,FILE *file  );
 
 YY_BUFFER_STATE gmsh_yy_scan_buffer (char *base,yy_size_t size  );
 YY_BUFFER_STATE gmsh_yy_scan_string (yyconst char *yy_str  );
-YY_BUFFER_STATE gmsh_yy_scan_bytes (yyconst char *bytes,int len  );
+YY_BUFFER_STATE gmsh_yy_scan_bytes (yyconst char *bytes,yy_size_t len  );
 
 void *gmsh_yyalloc (yy_size_t  );
 void *gmsh_yyrealloc (void *,yy_size_t  );
@@ -949,7 +940,7 @@ void   skipline(void);
 #define YY_NO_UNISTD_H
 #endif
 
-#line 953 "Gmsh.yy.cpp"
+#line 944 "Gmsh.yy.cpp"
 
 #define INITIAL 0
 
@@ -988,7 +979,7 @@ FILE *gmsh_yyget_out (void );
 
 void gmsh_yyset_out  (FILE * out_str  );
 
-int gmsh_yyget_leng (void );
+yy_size_t gmsh_yyget_leng (void );
 
 char *gmsh_yyget_text (void );
 
@@ -1030,12 +1021,7 @@ static int input (void );
 
 /* Amount of stuff to slurp up with each read. */
 #ifndef YY_READ_BUF_SIZE
-#ifdef __ia64__
-/* On IA-64, the buffer size is 16k, not 8k */
-#define YY_READ_BUF_SIZE 16384
-#else
 #define YY_READ_BUF_SIZE 8192
-#endif /* __ia64__ */
 #endif
 
 /* Copy whatever the last rule matched to the standard output. */
@@ -1043,7 +1029,7 @@ static int input (void );
 /* This used to be an fputs(), but since the string might contain NUL's,
  * we now use fwrite().
  */
-#define ECHO do { if (fwrite( gmsh_yytext, gmsh_yyleng, 1, gmsh_yyout )) {} } while (0)
+#define ECHO fwrite( gmsh_yytext, gmsh_yyleng, 1, gmsh_yyout )
 #endif
 
 /* Gets input and stuffs it into "buf".  number of characters read, or YY_NULL,
@@ -1054,7 +1040,7 @@ static int input (void );
 	if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \
 		{ \
 		int c = '*'; \
-		size_t n; \
+		yy_size_t n; \
 		for ( n = 0; n < max_size && \
 			     (c = getc( gmsh_yyin )) != EOF && c != '\n'; ++n ) \
 			buf[n] = (char) c; \
@@ -1139,7 +1125,7 @@ YY_DECL
 #line 49 "Gmsh.l"
 
 
-#line 1143 "Gmsh.yy.cpp"
+#line 1129 "Gmsh.yy.cpp"
 
 	if ( !(yy_init) )
 		{
@@ -2014,7 +2000,7 @@ YY_RULE_SETUP
 #line 235 "Gmsh.l"
 ECHO;
 	YY_BREAK
-#line 2018 "Gmsh.yy.cpp"
+#line 2004 "Gmsh.yy.cpp"
 case YY_STATE_EOF(INITIAL):
 	yyterminate();
 
@@ -2200,7 +2186,7 @@ static int yy_get_next_buffer (void)
 
 	else
 		{
-			int num_to_read =
+			yy_size_t num_to_read =
 			YY_CURRENT_BUFFER_LVALUE->yy_buf_size - number_to_move - 1;
 
 		while ( num_to_read <= 0 )
@@ -2214,7 +2200,7 @@ static int yy_get_next_buffer (void)
 
 			if ( b->yy_is_our_buffer )
 				{
-				int new_size = b->yy_buf_size * 2;
+				yy_size_t new_size = b->yy_buf_size * 2;
 
 				if ( new_size <= 0 )
 					b->yy_buf_size += b->yy_buf_size / 8;
@@ -2245,7 +2231,7 @@ static int yy_get_next_buffer (void)
 
 		/* Read in more data. */
 		YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]),
-			(yy_n_chars), (size_t) num_to_read );
+			(yy_n_chars), num_to_read );
 
 		YY_CURRENT_BUFFER_LVALUE->yy_n_chars = (yy_n_chars);
 		}
@@ -2355,7 +2341,7 @@ static int yy_get_next_buffer (void)
 	if ( yy_cp < YY_CURRENT_BUFFER_LVALUE->yy_ch_buf + 2 )
 		{ /* need to shift things up to make room */
 		/* +2 for EOB chars. */
-		register int number_to_move = (yy_n_chars) + 2;
+		register yy_size_t number_to_move = (yy_n_chars) + 2;
 		register char *dest = &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[
 					YY_CURRENT_BUFFER_LVALUE->yy_buf_size + 2];
 		register char *source =
@@ -2404,7 +2390,7 @@ static int yy_get_next_buffer (void)
 
 		else
 			{ /* need more input */
-			int offset = (yy_c_buf_p) - (yytext_ptr);
+			yy_size_t offset = (yy_c_buf_p) - (yytext_ptr);
 			++(yy_c_buf_p);
 
 			switch ( yy_get_next_buffer(  ) )
@@ -2428,7 +2414,7 @@ static int yy_get_next_buffer (void)
 				case EOB_ACT_END_OF_FILE:
 					{
 					if ( gmsh_yywrap( ) )
-						return EOF;
+						return 0;
 
 					if ( ! (yy_did_buffer_switch_on_eof) )
 						YY_NEW_FILE;
@@ -2680,7 +2666,7 @@ void gmsh_yypop_buffer_state (void)
  */
 static void gmsh_yyensure_buffer_stack (void)
 {
-	int num_to_alloc;
+	yy_size_t num_to_alloc;
     
 	if (!(yy_buffer_stack)) {
 
@@ -2772,17 +2758,16 @@ YY_BUFFER_STATE gmsh_yy_scan_string (yyconst char * yystr )
 
 /** Setup the input buffer state to scan the given bytes. The next call to gmsh_yylex() will
  * scan from a @e copy of @a bytes.
- * @param yybytes the byte buffer to scan
- * @param _yybytes_len the number of bytes in the buffer pointed to by @a bytes.
+ * @param bytes the byte buffer to scan
+ * @param len the number of bytes in the buffer pointed to by @a bytes.
  * 
  * @return the newly allocated buffer state object.
  */
-YY_BUFFER_STATE gmsh_yy_scan_bytes  (yyconst char * yybytes, int  _yybytes_len )
+YY_BUFFER_STATE gmsh_yy_scan_bytes  (yyconst char * yybytes, yy_size_t  _yybytes_len )
 {
 	YY_BUFFER_STATE b;
 	char *buf;
-	yy_size_t n;
-	int i;
+	yy_size_t n, i;
     
 	/* Get memory for full buffer, including space for trailing EOB's. */
 	n = _yybytes_len + 2;
@@ -2864,7 +2849,7 @@ FILE *gmsh_yyget_out  (void)
 /** Get the length of the current token.
  * 
  */
-int gmsh_yyget_leng  (void)
+yy_size_t gmsh_yyget_leng  (void)
 {
         return gmsh_yyleng;
 }

demos/homology.geo

@@ -133,7 +133,7 @@ Physical Surface(74) = {46, 18, 20, 52, 22, 50, 24, 48, 66, 63, 60, 58, 56, 54};
 // Complement of the domain surface respect to the four terminals
 Physical Surface(75) = {46, 63, 66, 52, 50, 48, 54, 60, 58, 56};
 
-/*
+
 // Create a mesh of the model
 Mesh 3;
 
@@ -157,4 +157,4 @@ HomCut("t10_hom.msh") = {{69}, {70, 71, 72, 73}};
 //  HomGen("t10_hom.msh") = {{}, {}};
 //  HomGen("t10_hom.msh") = {{69}, {74}}; 
 //  HomGen("t10_hom.msh") = {{}, {74}}; 
-*/
+

tutorial/t13.geo

+/********************************************************************* 
+ *
+ *  Gmsh tutorial 13
+ *
+ *  Homology computation
+ *
+ *********************************************************************/
+ 
+// Homology computation in Gmsh finds representative chains of
+// (relative) homology spaces using a mesh of a model. Those
+// representatives generate the (relative) homology spaces of the
+// model. Alternatively, Gmsh can only look for the ranks of the
+// (relative) homology spaces, the Betti numbers of the model.
+
+// The generators chains are stored in a given .msh-file as physical
+// groups, whose mesh elements are oriented such that their
+// coefficients are 1 in the generator chain.
+
+// Create an example geometry
+
+m = 0.5; // mesh characteristic length
+h = 2; // height in the z-direction
+
+Point(1) = {0, 0, 0, m};   Point(2) = {10, 0, 0, m};
+Point(3) = {10, 10, 0, m}; Point(4) = {0, 10, 0, m};
+Point(5) = {4, 4, 0, m};   Point(6) = {6, 4, 0, m};
+Point(7) = {6, 6, 0, m};   Point(8) = {4, 6, 0, m};
+
+Point(9) = {2, 0, 0, m};   Point(10) = {8, 0, 0, m};
+Point(11) = {2, 10, 0, m}; Point(12) = {8, 10, 0, m};
+
+Line(1) = {1, 9};  Line(2) = {9, 10}; Line(3) = {10, 2};
+Line(4) = {2, 3};  Line(5) = {3, 12}; Line(6) = {12, 11};
+Line(7) = {11, 4}; Line(8) = {4, 1};  Line(9) = {5, 6};
+Line(10) = {6, 7}; Line(11) = {7, 8}; Line(12) = {8, 5};
+
+Line Loop(13) = {6, 7, 8, 1, 2, 3, 4, 5};
+Line Loop(14) = {11, 12, 9, 10};
+Plane Surface(15) = {13, 14};
+
+Extrude {0, 0, h}{ Surface{15}; }
+
+// Create physical groups, which are used to define the domain of the
+// homology computation and the subdomain of the relative homology
+// computation.
+
+// Whole domain
+Physical Volume(1) = {1};
+
+// Four "terminals" of the model
+Physical Surface(70) = {36};
+Physical Surface(71) = {44};
+Physical Surface(72) = {52};
+Physical Surface(73) = {60};
+
+// Whole domain surface
+bnd[] = Boundary{ Volume{1}; };
+Physical Surface(80) = bnd[];
+
+// Complement of the domain surface respect to the four terminals
+bnd[] -= {36, 44, 52, 60};
+Physical Surface(75) = bnd[];
+
+// Create a mesh of the model
+Mesh 3;
+
+// Find generators of relative homology spaces of the domain modulo
+// the four terminals.  Save the generator chains to t13_hom.msh.
+HomGen("t13_hom.msh") = {{1}, {70, 71, 72, 73}};
+
+// Find the corresponding thin cuts, generators of relative homology
+// spaces modulo the non-terminal domain surface.  Save the cut chains
+// to t13_hom.msh.
+HomGen("t13_hom.msh") = {{1}, {75}};
+
+// Find the corresponding thick cuts.  Save the cut chains to
+// t13_hom.msh.
+HomCut("t13_hom.msh") = {{1}, {70, 71, 72, 73}};
+
+// More examples:
+//  HomGen("t13_hom.msh") = {{1}, {}}; 
+//  HomGen("t13_hom.msh") = {{}, {}};
+//  HomGen("t13_hom.msh") = {{1}, {80}}; 
+//  HomGen("t13_hom.msh") = {{}, {80}};