mirror of
https://git.FreeBSD.org/ports.git
synced 2024-11-22 00:35:15 +00:00
- Update to 0.90
PR: 176549 Submitted by: Ports Fury
This commit is contained in:
Martin Wilke
parent
bd83f9fcad
commit
3867f31f21
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=313207
@ -1,47 +1,88 @@
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# ex:ts=8
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# Ports collection Makefile for: gdis
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# Date created: Mar 3, 2002
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# Whom: ijliao
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#
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# Created y: ijliao
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# $FreeBSD$
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#
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PORTNAME= gdis
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PORTVERSION= 0.89
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PORTREVISION= 6
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PORTVERSION= 0.90
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CATEGORIES= science
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MASTER_SITES= SF/${PORTNAME}/${PORTNAME}/${PORTNAME}-${PORTVERSION}
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EXTRACT_SUFX= -source.tgz
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MASTER_SITES= SF
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EXTRACT_SUFX= -src.tgz
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MAINTAINER= ports@FreeBSD.org
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COMMENT= Display and manipulation of isolated molecules and periodic systems
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LIB_DEPENDS= gtkglext-x11-1.0.0:${PORTSDIR}/x11-toolkits/gtkglext
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LICENSE= GPLv2 # (or later)
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USE_GL= yes
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LIB_DEPENDS= gtkglext-x11-1.0:${PORTSDIR}/x11-toolkits/gtkglext
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OPTIONS_DEFINE= DOCS
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USE_GL= glu
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USE_GNOME= gtk20
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USE_GMAKE= yes
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MAKEFILE= makefile
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MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}"
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ALL_TARGET= ${PORTNAME}
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CFLAGS+= -DINSTALL=\"\\\"${DATADIR}\\\"\"
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MAKEFILE= GNUmakefile
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PORTDOCS= CHANGELOG README TODO
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PLIST_FILES= bin/gdis %%DATADIR%%/gdis.elements %%DATADIR%%/gdis.library \
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%%DATADIR%%/gdis.manual
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%%DATADIR%%/gdis.manual share/pixmaps/gdis.xpm
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PLIST_DIRS= %%DATADIR%%
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DESKTOP_ENTRIES="GDIS" "Molecular modelling GUI" \
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"${PREFIX}/share/pixmaps/gdis.xpm" "${PORTNAME}" "" true
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.include <bsd.port.options.mk>
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post-patch:
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@${REINPLACE_CMD} -e \
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's|"\(gdis.elements\)|"../share/gdis/\1| ; \
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s|"\(gdis.library\)|"../share/gdis/\1|' ${WRKSRC}/gdis.h
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@${REINPLACE_CMD} -e \
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's|"\(gdis.manual\)|"../share/gdis/\1|' ${WRKSRC}/gui_help.c
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do-configure:
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@${ECHO_CMD} -n \
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> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} 'USE_GUI=YES' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} 'USE_GRISU=NO' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} 'include makefile.src' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} 'CFLAGS:=$$(CFLAGS) -DWITH_GUI' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} 'INCS=`pkg-config --cflags gtkglext-1.0`' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} 'LIBS=`pkg-config --libs gtkglext-1.0`' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} 'OBJ=$$(SRC:.c=.o)' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} 'all: gdis' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} 'gdis: $$(OBJ)' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} ' $$(CC) $$(OBJ) $$(LDFLAGS) -o gdis $$(LIBS)' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} '.c.o:' \
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>> ${WRKSRC}/${MAKEFILE}
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@${ECHO_CMD} ' $$(CC) $$(CFLAGS) -c $$< $$(INCS)' \
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>> ${WRKSRC}/${MAKEFILE}
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@(cd ${WRKSRC} && ${SED} -e 's|logo_right_81|gdis|' \
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< logo_right.xpm > gdis.xpm)
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do-install:
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${INSTALL_PROGRAM} ${WRKSRC}/gdis ${PREFIX}/bin
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(cd ${WRKSRC} && ${INSTALL_PROGRAM} gdis ${PREFIX}/bin)
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(cd ${WRKSRC} && ${INSTALL_DATA} gdis.xpm ${PREFIX}/share/pixmaps)
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@${MKDIR} ${DATADIR}
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.for file in gdis.elements gdis.library gdis.manual
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${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR}
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.for i in gdis.elements gdis.library gdis.manual
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(cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${DATADIR})
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.endfor
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.if !defined(NOPORTDOCS)
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.if ${PORT_OPTIONS:MDOCS}
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@${MKDIR} ${DOCSDIR}
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.for file in CHANGELOG README TODO
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${INSTALL_DATA} ${WRKSRC}/${file} ${DOCSDIR}
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.for i in ${PORTDOCS}
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(cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${DOCSDIR})
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.endfor
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.endif
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@ -1,2 +1,2 @@
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SHA256 (gdis-0.89-source.tgz) = 594e9c199d1911e2b3d4da0a704e8cf14e7813c099e1bfdde294abb4895dfcec
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SIZE (gdis-0.89-source.tgz) = 829113
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SHA256 (gdis-0.90-src.tgz) = bbf9de62dc978199d8e13e10d009b03753cee1172dcb7f9ee54c8f96b652d890
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SIZE (gdis-0.90-src.tgz) = 1895353
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@ -1,71 +0,0 @@
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--- crystal_graph.c.orig Thu Nov 24 15:07:31 2005
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+++ crystal_graph.c Thu Nov 2 00:00:23 2006
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@@ -110,6 +110,9 @@
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gdouble run_gulp(GSList *cores, gchar *species)
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{
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struct model_pak *new_model, *result_model;
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+ gchar *cmd;
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+ gdouble result;
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+
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new_model = g_malloc(sizeof(struct model_pak));
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result_model = g_malloc(sizeof(struct model_pak));
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@@ -128,13 +131,13 @@
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new_model->periodic = 0;
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write_gulp(new_model->gulp.temp_file, new_model);
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- gchar * cmd = g_strdup_printf("%s < %s > %s", sysenv.gulp_path,
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+ cmd = g_strdup_printf("%s < %s > %s", sysenv.gulp_path,
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new_model->gulp.temp_file, new_model->gulp.out_file);
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system(cmd);
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g_free(cmd);
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read_gulp_output(new_model->gulp.out_file, result_model);
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- gdouble result = result_model->gulp.energy;
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+ result = result_model->gulp.energy;
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model_free(new_model);
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model_free(result_model);
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@@ -156,6 +159,9 @@
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gint b_images =(gint) model->monty.image_y + 0.5;
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gint c_images =(gint) model->monty.image_z + 0.5;
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+ gint nr_molecules;
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+ gdouble * single_energies;
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+
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/* checks */
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g_return_val_if_fail(sysenv.gulp_path != NULL, 4);
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g_return_val_if_fail(model != NULL, 1);
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@@ -165,7 +171,7 @@
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gui_text_show(ERROR, "Can not calculate a crystal graph for non crystalline models");
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return 3;
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}
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- gint nr_molecules = g_slist_length(model->moles);
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+ nr_molecules = g_slist_length(model->moles);
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/* initialize the key chunk to hold the maximum number of */
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key_chunk = g_mem_chunk_create(gint,
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nr_molecules * nr_molecules *(2*a_images+1)*(2*b_images+1)*(2*c_images+1),
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@@ -180,7 +186,7 @@
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type_dreiding_gasteiger(model, DREIDING);
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/* calculate the single energies */
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- gdouble * single_energies = g_new0(gdouble, nr_molecules);
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+ single_energies = g_new0(gdouble, nr_molecules);
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for (mol_iter = model->moles; mol_iter; mol_iter = mol_iter->next)
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{
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@@ -218,12 +224,13 @@
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if (pair != NULL)
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{
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gdouble *key_ptr;
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+ gchar * combination;
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key_ptr = g_chunk_new(gdouble, key_chunk);
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*key_ptr = run_gulp(pair, model->gulp.species);
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*key_ptr *= 96.48474; //eV --> kJ / mol
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*key_ptr -= single_energies[m1];
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*key_ptr -= single_energies[m2];
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- gchar * combination = g_strdup_printf(" %i - %i [ %i %i %i ]", m1+1, m2+1, x,y,z);
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+ combination = g_strdup_printf(" %i - %i [ %i %i %i ]", m1+1, m2+1, x,y,z);
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g_tree_insert(tree, key_ptr, combination);
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}
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}
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@ -1,20 +0,0 @@
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--- file_bgf.c.orig Thu Nov 24 13:58:48 2005
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+++ file_bgf.c Thu Nov 2 00:04:15 2006
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@@ -140,7 +140,7 @@
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gint read_bgf(gchar *filename, struct model_pak *data)
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{
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gint n=0, w, i, num_tokens;
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- gchar **buff, **buff2, line[LINELEN];
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+ gchar **buff, **buff2, line[LINELEN], *species_string;
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struct core_pak *core, *core_bond_to;
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GHashTable * atom_types_and_labels = g_hash_table_new_full(g_str_hash, g_str_equal, g_free, g_free);
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@@ -278,7 +278,7 @@
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}
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/* allocate 25 characters for each species line, that should be enough */
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- gchar * species_string = g_new(gchar, g_hash_table_size(atom_types_and_labels) * 25 );
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+ species_string = g_new(gchar, g_hash_table_size(atom_types_and_labels) * 25 );
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/* get all species from the hash table */
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g_hash_table_foreach(atom_types_and_labels, species_line_from_hash_table, &species_string);
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@ -1,69 +0,0 @@
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--- file_cgf.c.orig Thu Nov 24 13:58:48 2005
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+++ file_cgf.c Thu Nov 2 00:10:25 2006
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@@ -188,7 +188,7 @@
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GSList *core_iter, *bond_iter;//,
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GSList *primary_cores = NULL;
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FILE *fp;
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- gint nr_primary_cores = 0, max_bonds = 0, bond_counter = 0, num_tokens = 0, offset_counter = 0;
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+ gint nr_primary_cores = 0, max_bonds = 0, bond_counter = 0, num_tokens = 0, offset_counter = 0, total_bonds = 0;
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gint *nr_bonds = g_new(gint, g_slist_length(data->cores));
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@@ -197,6 +197,9 @@
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gchar **buff;
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+ gdouble *bond_strengths;
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+ gint *bond_to_values, *bond_offsets;
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+
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/* checks and open file */
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g_return_val_if_fail(data != NULL, 1);
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fp = fopen(filename, "wt");
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@@ -208,8 +211,6 @@
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fprintf(fp, "alpha= %3.5f beta= %3.5f gamma= %3.5f\n", data->pbc[3] * R2D, data->pbc[4] * R2D, data->pbc[5] * R2D);
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fprintf(fp, "Spacegroup information: SPGR = %-24s OPT = %i\n", data->sginfo.spacename, data->sginfo.cellchoice);
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- gint total_bonds = 0;
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-
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for (core_iter = data->cores; core_iter; core_iter = core_iter->next)
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{
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core = (struct core_pak *)core_iter->data;
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@@ -229,9 +230,9 @@
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}
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}
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- gdouble * bond_strengths = g_new0(gdouble, total_bonds);
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- gint * bond_to_values = g_new0(gint, total_bonds);
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- gint * bond_offsets = g_new0(gint, total_bonds * 3);
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+ bond_strengths = g_new0(gdouble, total_bonds);
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+ bond_to_values = g_new0(gint, total_bonds);
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+ bond_offsets = g_new0(gint, total_bonds * 3);
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fprintf(fp, "Nr of centres of mass: %i\n", nr_primary_cores);
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fprintf(fp, "Maximum connectivity: %i\n", max_bonds);
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@@ -280,6 +281,8 @@
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gint *bondto;
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gdouble *bond_offsets;
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gdouble *bond_strengths;
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+
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+ gint bondto_counter = 0, bond_offsets_counter = 0, total_bonds = 0;
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/* checks */
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g_return_val_if_fail(data != NULL, 1);
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@@ -366,8 +369,6 @@
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bond_offsets = g_new(gdouble, nr_bond_lines * num_gu * 15);
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//bond_strengths = g_new(gdouble, nr_bond_lines * num_gu * 5);
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- gint bondto_counter = 0, bond_offsets_counter = 0;
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-
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/* create GUs a priori */
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for (n = 0; n < num_gu; ++n)
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{
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@@ -442,7 +443,6 @@
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fgetline(fp, line);
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}
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- gint total_bonds = 0;
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/* now we create new cores for each bond */
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w = 0;
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for (n = 0; n < num_gu; ++n)
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20
science/gdis/files/patch-grid.c
Normal file
20
science/gdis/files/patch-grid.c
Normal file
@ -0,0 +1,20 @@
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--- grid.c.orig
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+++ grid.c
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@@ -58,7 +58,7 @@
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if (grid_table)
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g_hash_table_replace(grid_table, g_strdup(name), g_strdup(value));
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#else
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-return(NULL);
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+return;
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#endif
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}
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@@ -80,7 +80,7 @@
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if (grid_table)
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g_hash_table_remove(grid_table, name);
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#else
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-return(NULL);
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+return;
|
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#endif
|
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}
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|
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@ -1,37 +0,0 @@
|
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--- gui_monty.c.orig Thu Nov 24 13:58:48 2005
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+++ gui_monty.c Thu Nov 2 00:13:29 2006
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@@ -492,6 +492,7 @@
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FILE *fp;
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struct model_pak *model = data;
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gchar *last_dirsep, *yes, *no;
|
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+ gchar **hkls, **supersats, **out_dirs;
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gint i;
|
||||
|
||||
yes = g_strdup("yes");
|
||||
@@ -513,7 +514,7 @@
|
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g_strstrip(model->monty.hkls);
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||||
|
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/* split the string by endline characters */
|
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- 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));
|
||||
@ -1,113 +0,0 @@
|
||||
--- 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/ ?
|
||||
@ -1,32 +0,0 @@
|
||||
--- 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
|
||||
+temp = g_strdup(INSTALL);
|
||||
+#else
|
||||
temp = g_find_program_in_path(argv[0]);
|
||||
+#endif
|
||||
/* remove program name (if attached) */
|
||||
if (g_file_test(temp, G_FILE_TEST_IS_DIR))
|
||||
sysenv.gdis_path = temp;
|
||||
@ -1,10 +0,0 @@
|
||||
--- module.c.orig Tue Jun 15 16:05:21 2004
|
||||
+++ module.c Mon Jul 5 05:01:06 2004
|
||||
@@ -23,6 +23,7 @@
|
||||
#include <stdio.h>
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
+#include <sys/types.h>
|
||||
#include <gmodule.h>
|
||||
|
||||
#include "gdis.h"
|
||||
@ -1,22 +0,0 @@
|
||||
--- 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;
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user