From 22721d3dc98cae61db96021c01ee8dc1cbdf462d Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 15 Feb 2016 18:51:48 +0000
Subject: [PATCH] Added zlib and compression as an option to snapshots
---
configure.ac | 1
src/snapshot.c | 80 ++++++++++++++++++++------
src/tape | 2
config.h.in | 3 +
config.h | 3 +
aclocal.m4 | 65 ++++++++++++++++++++-
src/snapshot.h | 17 ++++-
7 files changed, 141 insertions(+), 30 deletions(-)
diff --git a/aclocal.m4 b/aclocal.m4
index da47901..7657505 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -180,6 +180,61 @@
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
@@ -263,10 +318,9 @@
# 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 -*-
@@ -733,7 +787,8 @@
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
diff --git a/config.h b/config.h
index ac9c24a..81910a1 100644
--- a/config.h
+++ b/config.h
@@ -16,6 +16,9 @@
/* 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
diff --git a/config.h.in b/config.h.in
index f865b7a..b68dfc5 100644
--- a/config.h.in
+++ b/config.h.in
@@ -15,6 +15,9 @@
/* 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
diff --git a/configure.ac b/configure.ac
index 3d3e095..4a01fa5 100644
--- a/configure.ac
+++ b/configure.ac
@@ -19,6 +19,7 @@
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])
diff --git a/src/snapshot.c b/src/snapshot.c
index c845e06..ee735f8 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -1,12 +1,52 @@
#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;
}
@@ -21,46 +61,46 @@
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;
}
diff --git a/src/snapshot.h b/src/snapshot.h
index 0d1511d..4c7b528 100644
--- a/src/snapshot.h
+++ b/src/snapshot.h
@@ -1,11 +1,20 @@
#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
diff --git a/src/tape b/src/tape
index a604c91..3e6290b 100644
--- a/src/tape
+++ b/src/tape
@@ -1,6 +1,6 @@
####### 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)
--
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