- Update to 0.89

PR:		ports/105035
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Sponsored by:   FreeBSD Bug-a-thon #2

9 files changed, 376 insertions, 37 deletions

diff --git a/science/gdis/Makefile b/science/gdis/Makefile
index 50e404c34688..3087a8e81d9a 100644
--- a/science/gdis/Makefile
+++ b/science/gdis/Makefile
@@ -7,8 +7,7 @@
 #
 
 PORTNAME=	gdis
-PORTVERSION=	0.86
-PORTREVISION=	3
+PORTVERSION=	0.89
 CATEGORIES=	science
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	${PORTNAME}
@@ -21,36 +20,27 @@ LIB_DEPENDS=	gtkglext-x11-1.0.0:${PORTSDIR}/x11-toolkits/gtkglext
 
 USE_GL=		yes
 USE_GNOME=	gtk20
+USE_GMAKE=	yes
+MAKEFILE=	makefile
+MAKE_ARGS=	CC="${CC}" CFLAGS="${CFLAGS}"
+ALL_TARGET=	${PORTNAME}
 
 CFLAGS+=	-DINSTALL=\"\\\"${DATADIR}\\\"\"
 
-PORTDOCS=	CHANGELOG README TODO gdis_manual.txt
-PLIST_FILES=	bin/gdis %%DATADIR%%/gdis.elements
+PORTDOCS=	CHANGELOG README TODO
+PLIST_FILES=	bin/gdis %%DATADIR%%/gdis.elements %%DATADIR%%/gdis.library \
+		%%DATADIR%%/gdis.manual
 PLIST_DIRS=	%%DATADIR%%
 
-post-patch:
-	@${FIND} ${WRKSRC} -name "*.c" | ${XARGS} ${REINPLACE_CMD} -e \
-		's|<sys/dir.h>|<dirent.h>|g ; \
-		 s|struct direct|struct dirent|g'
-
-do-configure:
-	@${SED} 's|SRC.*=|SRCS=|g' < ${WRKSRC}/makefile.src > ${WRKSRC}/Makefile
-	@${ECHO_CMD} 'PROG=gdis' >> ${WRKSRC}/Makefile
-	@${ECHO_CMD} 'CFLAGS+=`pkg-config --cflags gtk+-2.0 gthread-2.0 gtkglext-1.0`' >> ${WRKSRC}/Makefile
-	@${ECHO_CMD} 'LDADD=`pkg-config --libs gtk+-2.0 gthread-2.0 gtkglext-1.0`' >> ${WRKSRC}/Makefile
-	@${ECHO_CMD} 'PREFIX?=/usr/local' >> ${WRKSRC}/Makefile
-	@${ECHO_CMD} 'DESTDIR=$${PREFIX}' >> ${WRKSRC}/Makefile
-	@${ECHO_CMD} 'BINDIR=/bin' >> ${WRKSRC}/Makefile
-	@${ECHO_CMD} 'NOMAN=true' >> ${WRKSRC}/Makefile
-	@${ECHO_CMD} '.include <bsd.prog.mk>' >> ${WRKSRC}/Makefile
-
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/gdis ${PREFIX}/bin
 	@${MKDIR} ${DATADIR}
-	${INSTALL_DATA} ${WRKSRC}/gdis.elements ${DATADIR}
+.for file in gdis.elements gdis.library gdis.manual
+	${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR}
+.endfor
 .if !defined(NOPORTDOCS)
 	@${MKDIR} ${DOCSDIR}
-.for file in CHANGELOG README TODO gdis_manual.txt
+.for file in CHANGELOG README TODO
 	${INSTALL_DATA} ${WRKSRC}/${file} ${DOCSDIR}
 .endfor
 .endif
diff --git a/science/gdis/distinfo b/science/gdis/distinfo
index 0f73cb7227b9..cbdb39d96e77 100644
--- a/science/gdis/distinfo
+++ b/science/gdis/distinfo
@@ -1,3 +1,3 @@
-MD5 (gdis-0.86-source.tgz) = 55d3db8b382001300abe1795b1320a4b
-SHA256 (gdis-0.86-source.tgz) = 1348b6f151e532852743ce4d0fc528efacbc500bef1f5d27c0b0fc6f1e290840
-SIZE (gdis-0.86-source.tgz) = 649570
+MD5 (gdis-0.89-source.tgz) = 81da7f83b5eb8b7fc6c6a66416221373
+SHA256 (gdis-0.89-source.tgz) = 594e9c199d1911e2b3d4da0a704e8cf14e7813c099e1bfdde294abb4895dfcec
+SIZE (gdis-0.89-source.tgz) = 829113
diff --git a/science/gdis/files/patch-crystal_graph.c b/science/gdis/files/patch-crystal_graph.c
new file mode 100644
index 000000000000..d1f76909f64e
--- /dev/null
+++ b/science/gdis/files/patch-crystal_graph.c
@@ -0,0 +1,71 @@
+--- crystal_graph.c.orig	Thu Nov 24 15:07:31 2005
++++ crystal_graph.c	Thu Nov  2 00:00:23 2006
+@@ -110,6 +110,9 @@
+ gdouble run_gulp(GSList *cores, gchar *species)
+ {
+   struct model_pak *new_model, *result_model;  
++  gchar *cmd;
++  gdouble result;
++
+   new_model = g_malloc(sizeof(struct model_pak));
+   result_model = g_malloc(sizeof(struct model_pak));
+     
+@@ -128,13 +131,13 @@
+   new_model->periodic = 0;
+   
+   write_gulp(new_model->gulp.temp_file, new_model);
+-  gchar * cmd = g_strdup_printf("%s < %s > %s", sysenv.gulp_path, 
++  cmd = g_strdup_printf("%s < %s > %s", sysenv.gulp_path, 
+                                 new_model->gulp.temp_file, new_model->gulp.out_file);
+   system(cmd);
+   g_free(cmd);
+   
+   read_gulp_output(new_model->gulp.out_file, result_model);
+-  gdouble result = result_model->gulp.energy;
++  result = result_model->gulp.energy;
+   model_free(new_model);
+   model_free(result_model);
+ 
+@@ -156,6 +159,9 @@
+   gint b_images =(gint) model->monty.image_y + 0.5;
+   gint c_images =(gint) model->monty.image_z + 0.5;
+   
++  gint nr_molecules;
++  gdouble * single_energies;
++
+   /* checks */ 
+   g_return_val_if_fail(sysenv.gulp_path != NULL, 4);
+   g_return_val_if_fail(model != NULL, 1);
+@@ -165,7 +171,7 @@
+     gui_text_show(ERROR, "Can not calculate a crystal graph for non crystalline models");
+     return 3;
+   }
+-  gint nr_molecules = g_slist_length(model->moles);
++  nr_molecules = g_slist_length(model->moles);
+   /* initialize the key chunk to hold the maximum number of  */
+   key_chunk = g_mem_chunk_create(gint, 
+                                  nr_molecules * nr_molecules *(2*a_images+1)*(2*b_images+1)*(2*c_images+1),
+@@ -180,7 +186,7 @@
+   type_dreiding_gasteiger(model, DREIDING);
+   
+   /* calculate the single energies */
+-  gdouble * single_energies = g_new0(gdouble, nr_molecules);
++  single_energies = g_new0(gdouble, nr_molecules);
+   
+   for (mol_iter = model->moles; mol_iter; mol_iter = mol_iter->next)
+   {
+@@ -218,12 +224,13 @@
+             if (pair != NULL)
+             {              
+               gdouble *key_ptr;
++              gchar * combination;
+               key_ptr = g_chunk_new(gdouble, key_chunk);
+               *key_ptr = run_gulp(pair, model->gulp.species);
+               *key_ptr *= 96.48474; //eV --> kJ / mol
+               *key_ptr -= single_energies[m1];
+               *key_ptr -= single_energies[m2];
+-              gchar * combination = g_strdup_printf(" %i - %i [ %i %i %i ]", m1+1, m2+1, x,y,z);
++              combination = g_strdup_printf(" %i - %i [ %i %i %i ]", m1+1, m2+1, x,y,z);
+               g_tree_insert(tree, key_ptr, combination);
+             }
+           }
diff --git a/science/gdis/files/patch-file_bgf.c b/science/gdis/files/patch-file_bgf.c
new file mode 100644
index 000000000000..634868ed7248
--- /dev/null
+++ b/science/gdis/files/patch-file_bgf.c
@@ -0,0 +1,20 @@
+--- file_bgf.c.orig	Thu Nov 24 13:58:48 2005
++++ file_bgf.c	Thu Nov  2 00:04:15 2006
+@@ -140,7 +140,7 @@
+ gint read_bgf(gchar *filename, struct model_pak *data)
+ {
+   gint n=0, w, i, num_tokens;
+-  gchar **buff, **buff2, line[LINELEN];
++  gchar **buff, **buff2, line[LINELEN], *species_string;
+   struct core_pak *core, *core_bond_to;
+   
+   GHashTable * atom_types_and_labels = g_hash_table_new_full(g_str_hash, g_str_equal, g_free, g_free);
+@@ -278,7 +278,7 @@
+   }
+   
+   /* allocate 25 characters for each species line, that should be enough */
+-  gchar * species_string = g_new(gchar, g_hash_table_size(atom_types_and_labels) * 25 );
++  species_string = g_new(gchar, g_hash_table_size(atom_types_and_labels) * 25 );
+   /* get all species from the hash table */
+   g_hash_table_foreach(atom_types_and_labels, species_line_from_hash_table, &species_string);
+   
diff --git a/science/gdis/files/patch-file_cgf.c b/science/gdis/files/patch-file_cgf.c
new file mode 100644
index 000000000000..3ba1b617f06f
--- /dev/null
+++ b/science/gdis/files/patch-file_cgf.c
@@ -0,0 +1,69 @@
+--- file_cgf.c.orig	Thu Nov 24 13:58:48 2005
++++ file_cgf.c	Thu Nov  2 00:10:25 2006
+@@ -188,7 +188,7 @@
+   GSList *core_iter, *bond_iter;//,
+   GSList *primary_cores = NULL;
+   FILE *fp;
+-  gint nr_primary_cores = 0, max_bonds = 0, bond_counter = 0, num_tokens = 0, offset_counter = 0;
++  gint nr_primary_cores = 0, max_bonds = 0, bond_counter = 0, num_tokens = 0, offset_counter = 0, total_bonds = 0;
+    
+   gint *nr_bonds = g_new(gint, g_slist_length(data->cores));
+   
+@@ -197,6 +197,9 @@
+   
+   gchar **buff;
+   
++  gdouble *bond_strengths;
++  gint *bond_to_values, *bond_offsets;
++
+   /* checks and open file */
+   g_return_val_if_fail(data != NULL, 1);
+   fp = fopen(filename, "wt");
+@@ -208,8 +211,6 @@
+   fprintf(fp, "alpha= %3.5f beta= %3.5f gamma= %3.5f\n", data->pbc[3] * R2D, data->pbc[4] * R2D, data->pbc[5] * R2D);
+   fprintf(fp, "Spacegroup information:      SPGR = %-24s OPT = %i\n", data->sginfo.spacename, data->sginfo.cellchoice);
+   
+-  gint total_bonds = 0;
+-  
+   for (core_iter = data->cores; core_iter; core_iter = core_iter->next)
+   {
+     core = (struct core_pak *)core_iter->data;
+@@ -229,9 +230,9 @@
+     }
+   }
+   
+-  gdouble * bond_strengths = g_new0(gdouble, total_bonds);
+-  gint * bond_to_values =  g_new0(gint, total_bonds);
+-  gint * bond_offsets = g_new0(gint, total_bonds * 3);
++  bond_strengths = g_new0(gdouble, total_bonds);
++  bond_to_values =  g_new0(gint, total_bonds);
++  bond_offsets = g_new0(gint, total_bonds * 3);
+   
+   fprintf(fp, "Nr of centres of mass: %i\n", nr_primary_cores);
+   fprintf(fp, "Maximum connectivity: %i\n", max_bonds);
+@@ -280,6 +281,8 @@
+   gint *bondto; 
+   gdouble *bond_offsets;
+   gdouble *bond_strengths;
++
++  gint bondto_counter = 0, bond_offsets_counter = 0, total_bonds = 0;
+   
+   /* checks */
+   g_return_val_if_fail(data != NULL, 1);
+@@ -366,8 +369,6 @@
+   bond_offsets = g_new(gdouble, nr_bond_lines * num_gu * 15);
+   //bond_strengths = g_new(gdouble, nr_bond_lines * num_gu * 5);
+   
+-  gint bondto_counter = 0, bond_offsets_counter = 0;
+-  
+   /* create GUs a priori  */
+   for (n = 0; n < num_gu; ++n)
+   {
+@@ -442,7 +443,6 @@
+     fgetline(fp, line);
+   }
+ 
+-  gint total_bonds = 0;
+   /* now we create new cores for each bond */
+   w = 0;
+   for (n = 0; n < num_gu; ++n)
diff --git a/science/gdis/files/patch-gui_monty.c b/science/gdis/files/patch-gui_monty.c
new file mode 100644
index 000000000000..84c29b055ce5
--- /dev/null
+++ b/science/gdis/files/patch-gui_monty.c
@@ -0,0 +1,37 @@
+--- gui_monty.c.orig	Thu Nov 24 13:58:48 2005
++++ gui_monty.c	Thu Nov  2 00:13:29 2006
+@@ -492,6 +492,7 @@
+   FILE *fp;
+   struct model_pak *model = data;
+   gchar *last_dirsep, *yes, *no;
++  gchar **hkls, **supersats, **out_dirs;
+   gint i;
+   
+   yes = g_strdup("yes");
+@@ -513,7 +514,7 @@
+   g_strstrip(model->monty.hkls);
+   
+   /* split the string by endline characters */
+-  gchar **hkls = g_strsplit(model->monty.hkls, "\n", INT_MAX);  
++  hkls = g_strsplit(model->monty.hkls, "\n", INT_MAX);  
+   
+   /* print all hkl values to the file */
+   for (i = 0; *(hkls+i); ++i)
+@@ -523,7 +524,7 @@
+   
+   /* remove any whitespace, this also includes trailing \n characters */
+   g_strstrip(model->monty.supersaturations);
+-  gchar **supersats = g_strsplit(model->monty.supersaturations, "\n", INT_MAX);
++  supersats = g_strsplit(model->monty.supersaturations, "\n", INT_MAX);
+   for (i = 0; *(supersats+i); ++i)
+   {
+     fprintf(fp, " -supersat %s\n", *(supersats +i));
+@@ -551,7 +552,7 @@
+   
+   /* remove any whitespace, this also includes trailing \n characters */
+   g_strstrip(model->monty.output_dirs);
+-  gchar **out_dirs = g_strsplit(model->monty.output_dirs, "\n", INT_MAX);
++  out_dirs = g_strsplit(model->monty.output_dirs, "\n", INT_MAX);
+   for (i = 0; *(out_dirs + i); ++i)
+   {
+     fprintf(fp, " -directory %s %s\n", *(hkls + i), *(out_dirs + i));
diff --git a/science/gdis/files/patch-gui_siesta.c b/science/gdis/files/patch-gui_siesta.c
new file mode 100644
index 000000000000..39450b620bf8
--- /dev/null
+++ b/science/gdis/files/patch-gui_siesta.c
@@ -0,0 +1,113 @@
+--- gui_siesta.c.orig	Mon Oct 16 10:59:37 2006
++++ gui_siesta.c	Thu Nov  2 00:30:56 2006
+@@ -58,10 +58,10 @@
+ /*************************/
+ void gui_siesta_dialog(void)
+ {
+-    siestafileWRITE = FALSE;
+     GtkWidget *window;
+     gpointer dialog;
+     struct model_pak *model;
++    siestafileWRITE = FALSE;
+ 
+     model = sysenv.active_model;
+ 
+@@ -797,6 +797,8 @@
+ struct model_pak * model;
+ struct core_pak *core_i;
+ struct core_pak *core_j;
++GtkWidget *hbox, *vbox, *vbox2, *window;
++GtkWidget *dialog, *frame;
+ 
+ 
+     model = sysenv.active_model;
+@@ -826,8 +828,6 @@
+ 
+     num_lines = 3*2*num_atoms*num_atoms;
+ 
+-    GtkWidget *hbox, *vbox, *vbox2, *window;
+-    GtkWidget *dialog, *frame;
+     /* Create the widgets */
+ 
+     /* request a dialog */
+@@ -844,6 +844,10 @@
+         FILE *fp, *matout;
+ 
+         gchar * modelFCname, *modelFCnameCSV;
++        gdouble correction;
++        gint temp_int;
++        gdouble freq_i, freq_ii;
++        gint sizeofeig;
+ 
+         modelFCname = g_strdup_printf("%s/%s.FC", sysenv.cwd, model->basename);
+         modelFCnameCSV = g_strdup_printf("%s.csv", modelFCname);
+@@ -1102,7 +1106,6 @@
+     //         enddo
+     //       enddo
+ 
+-        gdouble correction;
+         for (i=0; i<num_atoms; i++)
+         {
+             for (j=0; j<num_atoms; j++)
+@@ -1219,13 +1222,11 @@
+             model->siesta.sorted_eig_values[i] = i;
+         }
+ 
+-        gint temp_int;
+-        gdouble freq_i, freq_ii;
+ 
+ /*
+         gint sizeofeig = model->siesta.eigen_values->dim;
+ */
+-        gint sizeofeig = mesch_dim_get(model->siesta.eigen_values);
++        sizeofeig = mesch_dim_get(model->siesta.eigen_values);
+ 
+ 
+         for (j=sizeofeig-1; j>1; j--)
+@@ -1350,10 +1351,10 @@
+ {
+     //evil active model call - evil evil evil
+     struct model_pak *model;
+-    model = sysenv.active_model;
+-
+     gchar *buff;
+ 
++    model = sysenv.active_model;
++
+     buff = g_strdup(gtk_entry_get_text(GTK_ENTRY(GTK_COMBO(data)->entry)));
+     if (g_ascii_strncasecmp("Verlet", buff, 6) == 0)
+         model->siesta.md_type_of_run = VERLET_MDRUN;
+@@ -1747,6 +1748,9 @@
+ 
+     for (i=0; i<total_files; i++)
+     {
++        //grab current grid_config_pak
++        struct grid_config_pak * grid_pak;
++
+         //set the range for md_fc_first, and md_fc_last
+         model->siesta.md_fc_first = i* model->siesta.atoms_per_job + 1;
+         model->siesta.md_fc_last = i * model->siesta.atoms_per_job + model->siesta.atoms_per_job;
+@@ -1763,9 +1767,6 @@
+         // call the fdf save bit....
+         file_save_as(filename, model);
+ 
+-        //grab current grid_config_pak
+-        struct grid_config_pak * grid_pak;
+-
+         //get job directory
+         siesta_make_runscript(model->basename, sysenv.cwd, grid_pak);
+ 
+@@ -1851,12 +1852,11 @@
+     int i, jobID;
+     int total_files;
+     gchar * filename, * orig_basename, *queuepath, *jobID_string;
++    struct grid_config_pak * grid_pak;
+ 
+     total_files = model->num_atoms / model->siesta.atoms_per_job +1;
+ 
+     orig_basename = g_strdup(model->basename);
+-
+-    struct grid_config_pak * grid_pak;
+ 
+     //default jobstorage dir??
+     //"$homedir/.gdis_jobs/  ?
diff --git a/science/gdis/files/patch-main.c b/science/gdis/files/patch-main.c
index 6270599e5ea9..221909b316a3 100644
--- a/science/gdis/files/patch-main.c
+++ b/science/gdis/files/patch-main.c
@@ -1,15 +1,32 @@
---- main.c.orig	Tue Nov  4 15:08:29 2003
-+++ main.c	Wed Dec 31 02:11:54 2003
-@@ -433,6 +433,12 @@
-     }
-   }
+--- main.c.orig	Wed Jul 26 15:15:28 2006
++++ main.c	Wed Nov  1 23:53:11 2006
+@@ -364,7 +364,7 @@
+ void sys_init(gint argc, gchar *argv[])
+ {
+ gchar *temp;
+-const gchar *ctemp;
++const gchar *envdir, *ctemp;
+ struct light_pak *light;
+ FILE *fp;
  
+@@ -500,7 +500,7 @@
+ 
+ /* setup directory and file pointers */
+ sysenv.cwd = g_get_current_dir();
+-const gchar *envdir = g_getenv("GDIS_START_DIR");
++envdir = g_getenv("GDIS_START_DIR");
+ if (envdir)
+   sysenv.cwd = (gchar *) envdir;
+ 
+@@ -510,7 +510,11 @@
+ 
+ /* generate element file full pathname */
+ /* sometimes this returns the program name, and sometimes it doesn't */
 +#ifdef INSTALL
-+strcpy(sysenv.elem_file, INSTALL);
-+strcat(sysenv.elem_file, DIR_SEP);
-+strcat(sysenv.elem_file, ELEM_FILE);
++temp = g_strdup(INSTALL);
++#else
+ temp = g_find_program_in_path(argv[0]);
 +#endif
-+
- /* defaults */
- sysenv.povray_exe = g_strdup("povray");
- sysenv.convert_exe = g_strdup("convert");
+ /* remove program name (if attached) */
+ if (g_file_test(temp, G_FILE_TEST_IS_DIR))
+   sysenv.gdis_path = temp;
diff --git a/science/gdis/files/patch-molsurf.c b/science/gdis/files/patch-molsurf.c
new file mode 100644
index 000000000000..3f9b741f653b
--- /dev/null
+++ b/science/gdis/files/patch-molsurf.c
@@ -0,0 +1,22 @@
+--- molsurf.c.orig	Mon Jun 19 17:42:29 2006
++++ molsurf.c	Wed Nov  1 23:55:43 2006
+@@ -745,7 +745,7 @@
+ gdouble Dx, Dy, Dz; 			/* gradient */
+ gdouble temp[3]; 			/* the dreaded temporary variable */
+ gdouble theta, sinTheta, cosTheta;
+-gfloat hue, red, green, blue;
++gfloat hue, red, green, blue, colourRange, hueStep;
+ time_t jobStartTime;
+ 
+ #if DEBUG_SHAPE 
+@@ -761,9 +761,7 @@
+ #endif
+ 	
+ 	/* setup for colours */
+-    gfloat colourRange= 256;
+-    gfloat hueStep;
+-    
++    colourRange= 256;
+     hueStep = 240/colourRange;
+ 	
+