Added zlib and compression as an option to snapshots
| | |
| | | fi[]dnl |
| | | ])# PKG_CHECK_MODULES |
| | | |
| | | |
| | | # PKG_INSTALLDIR(DIRECTORY) |
| | | # ------------------------- |
| | | # Substitutes the variable pkgconfigdir as the location where a module |
| | | # should install pkg-config .pc files. By default the directory is |
| | | # $libdir/pkgconfig, but the default can be changed by passing |
| | | # DIRECTORY. The user can override through the --with-pkgconfigdir |
| | | # parameter. |
| | | AC_DEFUN([PKG_INSTALLDIR], |
| | | [m4_pushdef([pkg_default], [m4_default([$1], ['${libdir}/pkgconfig'])]) |
| | | m4_pushdef([pkg_description], |
| | | [pkg-config installation directory @<:@]pkg_default[@:>@]) |
| | | AC_ARG_WITH([pkgconfigdir], |
| | | [AS_HELP_STRING([--with-pkgconfigdir], pkg_description)],, |
| | | [with_pkgconfigdir=]pkg_default) |
| | | AC_SUBST([pkgconfigdir], [$with_pkgconfigdir]) |
| | | m4_popdef([pkg_default]) |
| | | m4_popdef([pkg_description]) |
| | | ]) dnl PKG_INSTALLDIR |
| | | |
| | | |
| | | # PKG_NOARCH_INSTALLDIR(DIRECTORY) |
| | | # ------------------------- |
| | | # Substitutes the variable noarch_pkgconfigdir as the location where a |
| | | # module should install arch-independent pkg-config .pc files. By |
| | | # default the directory is $datadir/pkgconfig, but the default can be |
| | | # changed by passing DIRECTORY. The user can override through the |
| | | # --with-noarch-pkgconfigdir parameter. |
| | | AC_DEFUN([PKG_NOARCH_INSTALLDIR], |
| | | [m4_pushdef([pkg_default], [m4_default([$1], ['${datadir}/pkgconfig'])]) |
| | | m4_pushdef([pkg_description], |
| | | [pkg-config arch-independent installation directory @<:@]pkg_default[@:>@]) |
| | | AC_ARG_WITH([noarch-pkgconfigdir], |
| | | [AS_HELP_STRING([--with-noarch-pkgconfigdir], pkg_description)],, |
| | | [with_noarch_pkgconfigdir=]pkg_default) |
| | | AC_SUBST([noarch_pkgconfigdir], [$with_noarch_pkgconfigdir]) |
| | | m4_popdef([pkg_default]) |
| | | m4_popdef([pkg_description]) |
| | | ]) dnl PKG_NOARCH_INSTALLDIR |
| | | |
| | | |
| | | # PKG_CHECK_VAR(VARIABLE, MODULE, CONFIG-VARIABLE, |
| | | # [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND]) |
| | | # ------------------------------------------- |
| | | # Retrieves the value of the pkg-config variable for the given module. |
| | | AC_DEFUN([PKG_CHECK_VAR], |
| | | [AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl |
| | | AC_ARG_VAR([$1], [value of $3 for $2, overriding pkg-config])dnl |
| | | |
| | | _PKG_CONFIG([$1], [variable="][$3]["], [$2]) |
| | | AS_VAR_COPY([$1], [pkg_cv_][$1]) |
| | | |
| | | AS_VAR_IF([$1], [""], [$5], [$4])dnl |
| | | ])# PKG_CHECK_VAR |
| | | |
| | | # Copyright (C) 2002-2013 Free Software Foundation, Inc. |
| | | # |
| | | # This file is free software; the Free Software Foundation |
| | |
| | | # configured tree to be moved without reconfiguration. |
| | | |
| | | AC_DEFUN([AM_AUX_DIR_EXPAND], |
| | | [dnl Rely on autoconf to set up CDPATH properly. |
| | | AC_PREREQ([2.50])dnl |
| | | # expand $ac_aux_dir to an absolute path |
| | | am_aux_dir=`cd $ac_aux_dir && pwd` |
| | | [AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl |
| | | # Expand $ac_aux_dir to an absolute path. |
| | | am_aux_dir=`cd "$ac_aux_dir" && pwd` |
| | | ]) |
| | | |
| | | # AM_CONDITIONAL -*- Autoconf -*- |
| | |
| | | END |
| | | AC_MSG_ERROR([Your 'rm' program is bad, sorry.]) |
| | | fi |
| | | fi]) |
| | | fi |
| | | ]) |
| | | |
| | | dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not |
| | | dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further |
| | |
| | | /* Define to 1 if you have the `m' library (-lm). */ |
| | | #define HAVE_LIBM 1 |
| | | |
| | | /* Define to 1 if you have the `z' library (-lz). */ |
| | | #define HAVE_LIBZ 1 |
| | | |
| | | /* Define to 1 if your system has a GNU libc compatible `malloc' function, and |
| | | to 0 otherwise. */ |
| | | #define HAVE_MALLOC 1 |
| | |
| | | /* Define to 1 if you have the `m' library (-lm). */ |
| | | #undef HAVE_LIBM |
| | | |
| | | /* Define to 1 if you have the `z' library (-lz). */ |
| | | #undef HAVE_LIBZ |
| | | |
| | | /* Define to 1 if your system has a GNU libc compatible `malloc' function, and |
| | | to 0 otherwise. */ |
| | | #undef HAVE_MALLOC |
| | |
| | | AC_CHECK_LIB([gsl],[gsl_blas_dgemm]) |
| | | #AC_CHECK_LIB([xml2],[xmlNodeListGetString]) |
| | | PKG_CHECK_MODULES([libxml2], [libxml-2.0]) |
| | | AC_CHECK_LIB([z],[deflate]) |
| | | |
| | | # Checks for header files. |
| | | AC_CHECK_HEADERS([stdlib.h string.h]) |
| | |
| | | #include<stdio.h> |
| | | #include<general.h> |
| | | #include<snapshot.h> |
| | | #include<stdlib.h> |
| | | #include<stdarg.h> |
| | | #include <zlib.h> |
| | | ts_uint ts_sprintf(ts_string *str, char *fmt, ...){ |
| | | va_list ap; |
| | | va_start(ap,fmt); |
| | | ts_uint n=vsprintf(&(str->string[str->beg]),fmt,ap); |
| | | va_end(ap); |
| | | str->beg+=n; |
| | | return n; |
| | | } |
| | | |
| | | |
| | | ts_bool xml_trisurf_data(FILE *fh, ts_vesicle *vesicle){ |
| | | |
| | | ts_string *data=(ts_string *)malloc(sizeof(ts_sprintf)); |
| | | data->string=(char *)malloc(512000*sizeof(char)); /*TODO: warning, can break if the string is to long */ |
| | | data->beg=0; |
| | | |
| | | xml_trisurf_header(fh, vesicle); |
| | | xml_trisurf_tria(fh,vesicle->tlist); |
| | | xml_trisurf_tria_neigh(fh,vesicle->tlist); |
| | | xml_trisurf_vtx_neigh(fh,vesicle->vlist); |
| | | xml_trisurf_vtx_tristar(fh,vesicle->vlist); |
| | | xml_trisurf_tria(data,vesicle->tlist); |
| | | xml_trisurf_tria_neigh(data,vesicle->tlist); |
| | | xml_trisurf_vtx_neigh(data,vesicle->vlist); |
| | | xml_trisurf_vtx_tristar(data,vesicle->vlist); |
| | | #ifdef COMPRESSION |
| | | z_stream defstream; |
| | | defstream.zalloc = Z_NULL; |
| | | defstream.zfree = Z_NULL; |
| | | defstream.opaque = Z_NULL; |
| | | defstream.avail_in = data->beg+1; |
| | | defstream.next_in = (unsigned char *)data->string; |
| | | char *compr=(char *)malloc((data->beg+1)*sizeof(char *)); |
| | | defstream.avail_out = data->beg+1; |
| | | defstream.next_out = (unsigned char *)compr; |
| | | deflateInit(&defstream, Z_BEST_COMPRESSION); |
| | | deflate(&defstream, Z_FINISH); |
| | | deflateEnd(&defstream); |
| | | fwrite(compr, sizeof(unsigned char), defstream.total_out, fh); |
| | | // fprintf(fh,"%s",compr); |
| | | //printf("Uncompressed size is: %lu\n", defstream.total_out); |
| | | free(compr); |
| | | #else |
| | | fprintf(fh,"%s", data->string); |
| | | #endif |
| | | free(data->string); |
| | | free(data); |
| | | xml_trisurf_footer(fh); |
| | | return TS_SUCCESS; |
| | | } |
| | |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | ts_bool xml_trisurf_tria(FILE *fh, ts_triangle_list *tlist){ |
| | | ts_bool xml_trisurf_tria(ts_string *data, ts_triangle_list *tlist){ |
| | | ts_uint i; |
| | | fprintf(fh,"<tria>\n"); |
| | | ts_sprintf(data,"<tria>\n"); |
| | | for(i=0; i<tlist->n;i++){ |
| | | fprintf(fh,"%u %u %u\n",tlist->tria[i]->vertex[0]->idx, tlist->tria[i]->vertex[1]->idx, tlist->tria[i]->vertex[2]->idx); |
| | | ts_sprintf(data,"%u %u %u\n",tlist->tria[i]->vertex[0]->idx, tlist->tria[i]->vertex[1]->idx, tlist->tria[i]->vertex[2]->idx); |
| | | } |
| | | fprintf(fh,"</tria>\n"); |
| | | ts_sprintf(data,"</tria>\n"); |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | ts_bool xml_trisurf_tria_neigh(FILE *fh, ts_triangle_list *tlist){ |
| | | ts_bool xml_trisurf_tria_neigh(ts_string *data, ts_triangle_list *tlist){ |
| | | ts_uint i; |
| | | fprintf(fh,"<trianeigh>\n"); |
| | | ts_sprintf(data,"<trianeigh>\n"); |
| | | for(i=0; i<tlist->n;i++){ |
| | | fprintf(fh,"%u %u %u\n",tlist->tria[i]->neigh[0]->idx, tlist->tria[i]->neigh[1]->idx, tlist->tria[i]->neigh[2]->idx); |
| | | ts_sprintf(data,"%u %u %u\n",tlist->tria[i]->neigh[0]->idx, tlist->tria[i]->neigh[1]->idx, tlist->tria[i]->neigh[2]->idx); |
| | | } |
| | | fprintf(fh,"</trianeigh>\n"); |
| | | ts_sprintf(data,"</trianeigh>\n"); |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | ts_bool xml_trisurf_vtx_neigh(FILE *fh, ts_vertex_list *vlist){ |
| | | ts_bool xml_trisurf_vtx_neigh(ts_string *data, ts_vertex_list *vlist){ |
| | | ts_uint i,j; |
| | | for(i=0;i<vlist->n;i++){ |
| | | fprintf(fh,"<vtxn idx=\"%u\">",vlist->vtx[i]->idx); |
| | | ts_sprintf(data,"<vtxn idx=\"%u\">",vlist->vtx[i]->idx); |
| | | for(j=0;j<vlist->vtx[i]->neigh_no;j++){ |
| | | fprintf(fh,"%u ",vlist->vtx[i]->neigh[j]->idx); |
| | | ts_sprintf(data,"%u ",vlist->vtx[i]->neigh[j]->idx); |
| | | } |
| | | fprintf(fh, "</vtxn>\n"); |
| | | ts_sprintf(data, "</vtxn>\n"); |
| | | } |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | ts_bool xml_trisurf_vtx_tristar(FILE *fh, ts_vertex_list *vlist){ |
| | | ts_bool xml_trisurf_vtx_tristar(ts_string *data, ts_vertex_list *vlist){ |
| | | ts_uint i,j; |
| | | for(i=0;i<vlist->n;i++){ |
| | | fprintf(fh,"<tristar idx=\"%u\">",vlist->vtx[i]->idx); |
| | | ts_sprintf(data,"<tristar idx=\"%u\">",vlist->vtx[i]->idx); |
| | | for(j=0;j<vlist->vtx[i]->tristar_no;j++){ |
| | | fprintf(fh,"%u ",vlist->vtx[i]->tristar[j]->idx); |
| | | ts_sprintf(data,"%u ",vlist->vtx[i]->tristar[j]->idx); |
| | | } |
| | | fprintf(fh, "</tristar>\n"); |
| | | ts_sprintf(data, "</tristar>\n"); |
| | | } |
| | | return TS_SUCCESS; |
| | | } |
| | |
| | | #ifndef _H_SNAPSHOT |
| | | #define _H_SNAPSHOT |
| | | |
| | | |
| | | |
| | | typedef struct{ |
| | | char *string; |
| | | ts_uint beg; |
| | | } ts_string; |
| | | |
| | | #define COMPRESSION |
| | | |
| | | ts_bool xml_trisurf_data(FILE *fh, ts_vesicle *vesicle); |
| | | ts_bool xml_trisurf_header(FILE *fh, ts_vesicle *vesicle); |
| | | ts_bool xml_trisurf_footer(FILE *fh); |
| | | ts_bool xml_trisurf_tria(FILE *fh, ts_triangle_list *tlist); |
| | | ts_bool xml_trisurf_tria_neigh(FILE *fh, ts_triangle_list *tlist); |
| | | ts_bool xml_trisurf_vtx_neigh(FILE *fh, ts_vertex_list *vlist); |
| | | ts_bool xml_trisurf_vtx_tristar(FILE *fh, ts_vertex_list *vlist); |
| | | ts_bool xml_trisurf_tria(ts_string *data, ts_triangle_list *tlist); |
| | | ts_bool xml_trisurf_tria_neigh(ts_string *data, ts_triangle_list *tlist); |
| | | ts_bool xml_trisurf_vtx_neigh(ts_string *data, ts_vertex_list *vlist); |
| | | ts_bool xml_trisurf_vtx_tristar(ts_string *data, ts_vertex_list *vlist); |
| | | #endif |
| | |
| | | ####### Vesicle definitions ########### |
| | | # nshell is a number of divisions of dipyramid |
| | | nshell=17 |
| | | nshell=19 |
| | | # dmax is the max. bond length (in units l_min) |
| | | dmax=1.7 |
| | | # dmin_interspecies in the min. dist. between different vertex species (in units l_min) |