From 81fdb5e4188e6a3ee4dbaac3f22f2c872167c236 Mon Sep 17 00:00:00 2001
From: Teemu Murtola <teemu.murtola@cbr.su.se>
Date: Wed, 11 Nov 2009 19:44:22 +0100
Subject: [PATCH] Fixed segfaults with empty selections.

Selections like 'com of none' used to segfault or cause other problems,
but now they should cleanly return an empty selection.
---
 include/position.h              |  7 +++++++
 src/gmxlib/selection/compiler.c |  1 +
 src/gmxlib/selection/params.c   |  1 +
 src/gmxlib/trajana/indexutil.c  |  5 ++++-
 src/gmxlib/trajana/poscalc.c    |  1 +
 src/gmxlib/trajana/position.c   | 15 +++++++++++++--
 6 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/include/position.h b/include/position.h
index af98e55aff..a169e821b2 100644
--- a/include/position.h
+++ b/include/position.h
@@ -66,6 +66,10 @@ typedef struct gmx_ana_pos_t
      * Pointer to the current evaluation group.
      */
     gmx_ana_index_t    *g;
+    /*! \brief
+     * Number of elements allocated for \c x.
+     */
+    int                 nalloc_x;
 } gmx_ana_pos_t;
 
 /** Initializes an empty position structure. */
@@ -87,6 +91,9 @@ gmx_ana_pos_free(gmx_ana_pos_t *pos);
 extern void
 gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst);
 
+/** Sets the number of positions in a position structure. */
+extern void
+gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int n);
 /** Sets the evaluation group of a position data structure. */
 extern void
 gmx_ana_pos_set_evalgrp(gmx_ana_pos_t *pos, gmx_ana_index_t *g);
diff --git a/src/gmxlib/selection/compiler.c b/src/gmxlib/selection/compiler.c
index 4c7209f666..90615af25c 100644
--- a/src/gmxlib/selection/compiler.c
+++ b/src/gmxlib/selection/compiler.c
@@ -1640,6 +1640,7 @@ analyze_static(gmx_sel_evaluate_t *data, t_selelem *sel, gmx_ana_index_t *g)
             if (sel->v.type == POS_VALUE && !(sel->flags & SEL_OUTINIT))
             {
                 gmx_ana_indexmap_copy(&sel->v.u.p->m, &sel->child->child->v.u.p->m, TRUE);
+                gmx_ana_pos_set_nr(sel->v.u.p, sel->child->child->v.u.p->nr);
                 sel->flags |= SEL_OUTINIT;
             }
             rc = sel->cdata->evaluate(data, sel, g);
diff --git a/src/gmxlib/selection/params.c b/src/gmxlib/selection/params.c
index 6276bc4f5e..9c40f0434e 100644
--- a/src/gmxlib/selection/params.c
+++ b/src/gmxlib/selection/params.c
@@ -457,6 +457,7 @@ parse_values_varnum(int nval, t_selexpr_value *values, gmx_ana_selparam_t *param
     if (param->val.type == POS_VALUE)
     {
         gmx_ana_pos_reserve(param->val.u.p, nval, 0);
+        gmx_ana_pos_set_nr(param->val.u.p, nval);
         gmx_ana_indexmap_init(&param->val.u.p->m, NULL, NULL, INDEX_UNKNOWN);
     }
     else
diff --git a/src/gmxlib/trajana/indexutil.c b/src/gmxlib/trajana/indexutil.c
index 95351f4fb6..5b43d6616d 100644
--- a/src/gmxlib/trajana/indexutil.c
+++ b/src/gmxlib/trajana/indexutil.c
@@ -1293,7 +1293,10 @@ gmx_ana_indexmap_update(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
     }
     if (m->type == INDEX_ALL)
     {
-        m->mapb.index[1] = g->isize;
+        if (m->b.nr > 0)
+        {
+            m->mapb.index[1] = g->isize;
+        }
         return;
     }
     /* Reset the reference IDs and mapping if necessary */
diff --git a/src/gmxlib/trajana/poscalc.c b/src/gmxlib/trajana/poscalc.c
index 02aa7f289b..02788b68a0 100644
--- a/src/gmxlib/trajana/poscalc.c
+++ b/src/gmxlib/trajana/poscalc.c
@@ -1094,6 +1094,7 @@ gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p)
 {
     gmx_ana_indexmap_init(&p->m, &pc->gmax, pc->coll->top, pc->itype);
     gmx_ana_pos_reserve(p, p->m.nr, 0);
+    gmx_ana_pos_set_nr(p, p->m.nr);
     p->g = &pc->gmax;
 }
 
diff --git a/src/gmxlib/trajana/position.c b/src/gmxlib/trajana/position.c
index a17b476766..e407e712e0 100644
--- a/src/gmxlib/trajana/position.c
+++ b/src/gmxlib/trajana/position.c
@@ -56,6 +56,7 @@ gmx_ana_pos_clear(gmx_ana_pos_t *pos)
     pos->x  = NULL;
     gmx_ana_indexmap_clear(&pos->m);
     pos->g  = NULL;
+    pos->nalloc_x = 0;
 }
 
 /*!
@@ -69,9 +70,9 @@ gmx_ana_pos_clear(gmx_ana_pos_t *pos)
 void
 gmx_ana_pos_reserve(gmx_ana_pos_t *pos, int n, int isize)
 {
-    if (pos->nr < n)
+    if (pos->nalloc_x < n)
     {
-        pos->nr = n;
+        pos->nalloc_x = n;
         srenew(pos->x, n);
     }
     if (isize > 0)
@@ -149,6 +150,16 @@ gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst)
 
 /*!
  * \param[in,out] pos  Position data structure.
+ * \param[in]     nr   Number of positions.
+ */
+void
+gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int nr)
+{
+    pos->nr = nr;
+}
+
+/*!
+ * \param[in,out] pos  Position data structure.
  * \param         g    Evaluation group.
  *
  * The old group, if any, is discarded.
-- 
2.11.4.GIT