/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* calculated.
* Currently, no other processing is done.
*/
-#include "compiler.h"
+#include "gmxpre.h"
-#include <algorithm>
+#include "compiler.h"
#include <math.h>
#include <stdarg.h>
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/string2.h"
-#include "gromacs/legacyheaders/vec.h"
+#include <algorithm>
+#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "evaluate.h"
#include "keywords.h"
#include "mempool.h"
+#include "poscalc.h"
#include "selectioncollection-impl.h"
#include "selelem.h"
+#include "selmethod.h"
using std::min;
using gmx::SelectionTreeElement;
/** Whether memory has been allocated for \p gmin and \p gmax. */
SEL_CDATA_MINMAXALLOC = 16,
/** Whether to update \p gmin and \p gmax in static analysis. */
- SEL_CDATA_DOMINMAX = 128,
+ SEL_CDATA_DOMINMAX = 256,
/** Whether the subexpression uses simple pass evaluation functions. */
SEL_CDATA_SIMPLESUBEXPR = 32,
+ /*! \brief
+ * Whether a static subexpression needs to support multiple evaluations.
+ *
+ * This flag may only be set on \ref SEL_SUBEXPR elements that also have
+ * SEL_CDATA_SIMPLESUBEXPR.
+ */
+ SEL_CDATA_STATICMULTIEVALSUBEXPR = 64,
/** Whether this expression is a part of a common subexpression. */
- SEL_CDATA_COMMONSUBEXPR = 64
+ SEL_CDATA_COMMONSUBEXPR = 128
};
/*! \internal \brief
{
fprintf(fp, "Ss");
}
+ if (sel.cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR)
+ {
+ fprintf(fp, "Sm");
+ }
if (sel.cdata->flags & SEL_CDATA_COMMONSUBEXPR)
{
fprintf(fp, "Sc");
evaluate = cdata->evaluate;
if (cdata->flags & SEL_CDATA_MINMAXALLOC)
{
- cdata->gmin->name = NULL;
- cdata->gmax->name = NULL;
gmx_ana_index_deinit(cdata->gmin);
gmx_ana_index_deinit(cdata->gmax);
sfree(cdata->gmin);
GMX_RELEASE_ASSERT(child,
"Subexpression elements should always have a child element");
}
- nalloc = child->v.u.p->nr;
+ nalloc = child->v.u.p->count();
isize = child->v.u.p->m.b.nra;
/* For positions, we want to allocate just a single structure
{
std::string name(gmx::formatString("SubExpr %d", i));
sel->setName(name);
- sel->u.cgrp.name = strdup(name.c_str());
}
/*! \brief
break;
case SEL_SUBEXPR:
- sel->evaluate = ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
- ? &_gmx_sel_evaluate_subexpr_simple
- : &_gmx_sel_evaluate_subexpr);
+ if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
+ && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
+ {
+ sel->evaluate = &_gmx_sel_evaluate_subexpr_simple;
+ }
+ else
+ {
+ sel->evaluate = &_gmx_sel_evaluate_subexpr;
+ }
break;
case SEL_SUBEXPRREF:
}
if (sel->type == SEL_SUBEXPR
- && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
+ && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
+ && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
{
sel->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
init_item_staticeval(child);
}
}
+ /* If an expression is evaluated for a dynamic group, then also
+ * atom-valued parameters need to be evaluated every time. */
+ if ((sel->flags & SEL_DYNAMIC)
+ && (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER)
+ && (child->flags & SEL_ATOMVAL))
+ {
+ child->flags |= SEL_DYNAMIC;
+ child->cdata->flags &= ~SEL_CDATA_STATIC;
+ }
child = child->next;
}
}
else if (sel->type == SEL_SUBEXPRREF
&& (sel->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
{
- sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
+ /* See similar condition in init_item_staticeval(). */
+ if ((sel->flags & SEL_ATOMVAL)
+ && (sel->flags & SEL_DYNAMIC)
+ && !(sel->child->flags & SEL_DYNAMIC))
+ {
+ sel->child->cdata->flags |= SEL_CDATA_STATICMULTIEVALSUBEXPR;
+ }
+ else
+ {
+ sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
+ }
}
/* Process children, but only follow subexpression references if the
* \param[in,out] sc Selection collection data.
*
* The evaluation group of each \ref SEL_ROOT element corresponding to a
- * selection in \p sc is set to NULL. The evaluation grop for \ref SEL_ROOT
+ * selection in \p sc is set to NULL. The evaluation group for \ref SEL_ROOT
* elements corresponding to subexpressions that need full evaluation is set
* to \c sc->gall.
*/
if (root->child->type != SEL_SUBEXPR
|| (root->child->v.type != GROUP_VALUE && !(root->flags & SEL_ATOMVAL)))
{
- gmx_ana_index_set(&root->u.cgrp, -1, 0, root->u.cgrp.name, 0);
+ gmx_ana_index_set(&root->u.cgrp, -1, 0, 0);
}
else if (root->child->cdata->flags & SEL_CDATA_FULLEVAL)
{
- gmx_ana_index_set(&root->u.cgrp, sc->gall.isize, sc->gall.index,
- root->u.cgrp.name, 0);
+ gmx_ana_index_set(&root->u.cgrp, sc->gall.isize, sc->gall.index, 0);
}
root = root->next;
}
* */
if (sel->v.type == GROUP_VALUE)
{
- gmx_ana_index_set(&sel->u.cgrp, sel->v.u.g->isize, sel->v.u.g->index, NULL, 0);
+ gmx_ana_index_set(&sel->u.cgrp, sel->v.u.g->isize, sel->v.u.g->index, 0);
}
}
{
child->cdata->evaluate = &_gmx_sel_evaluate_static;
/* The cgrp has only been allocated if it originated from an
- * external index group. In that case, we need special handling
- * to preserve the name of the group and to not leak memory.
+ * external index group.
* If cgrp has been set in make_static(), it is not allocated,
* and hence we can overwrite it safely. */
if (child->u.cgrp.nalloc_index > 0)
{
- char *name = child->u.cgrp.name;
gmx_ana_index_copy(&child->u.cgrp, child->v.u.g, false);
gmx_ana_index_squeeze(&child->u.cgrp);
- child->u.cgrp.name = name;
}
else
{
gmx_ana_index_copy(sel->child->v.u.g, gmin, false);
if (sel->child->u.cgrp.nalloc_index > 0)
{
- /* Keep the name as in evaluate_boolean_static_part(). */
- char *name = sel->child->u.cgrp.name;
gmx_ana_index_reserve(&sel->child->u.cgrp, gmin->isize);
gmx_ana_index_copy(&sel->child->u.cgrp, gmin, false);
- sel->child->u.cgrp.name = name;
}
else
{
break;
case SEL_SUBEXPR:
- if (sel->cdata->flags & (SEL_CDATA_SIMPLESUBEXPR | SEL_CDATA_FULLEVAL))
+ if (((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR) &&
+ !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
+ || (sel->cdata->flags & SEL_CDATA_FULLEVAL))
{
sel->cdata->evaluate(data, sel, g);
_gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
{
gmx_ana_index_squeeze(sel->cdata->gmin);
gmx_ana_index_squeeze(sel->cdata->gmax);
- sfree(sel->cdata->gmin->name);
- sfree(sel->cdata->gmax->name);
- sel->cdata->gmin->name = NULL;
- sel->cdata->gmax->name = NULL;
}
/* Replace the result of the evaluation */
}
/* Set the evaluation group */
- char *name = root->u.cgrp.name;
if (root->evaluate)
{
/* Non-atom-valued non-group expressions don't care about the group, so
if ((expr->flags & SEL_VARNUMVAL)
|| ((expr->flags & SEL_SINGLEVAL) && expr->v.type != GROUP_VALUE))
{
- gmx_ana_index_set(&root->u.cgrp, -1, NULL, NULL, 0);
+ gmx_ana_index_set(&root->u.cgrp, -1, NULL, 0);
}
else if (expr->cdata->gmax->isize == gall->isize)
{
/* Save some memory by only referring to the global group. */
- gmx_ana_index_set(&root->u.cgrp, gall->isize, gall->index, NULL, 0);
+ gmx_ana_index_set(&root->u.cgrp, gall->isize, gall->index, 0);
}
else
{
/* For selections, store the maximum group for
* gmx_ana_selcollection_evaluate_fin() as the value of the root
* element (unused otherwise). */
- if (expr->type != SEL_SUBEXPR && expr->v.u.p->g)
+ if (expr->type != SEL_SUBEXPR && expr->v.u.p->m.mapb.a != NULL)
{
SelectionTreeElementPointer child = expr;
}
if (child->child->flags & SEL_DYNAMIC)
{
+ gmx_ana_index_t g;
+ gmx_ana_index_set(&g, expr->v.u.p->m.mapb.nra, expr->v.u.p->m.mapb.a, 0);
_gmx_selelem_set_vtype(root, GROUP_VALUE);
root->flags |= (SEL_ALLOCVAL | SEL_ALLOCDATA);
_gmx_selvalue_reserve(&root->v, 1);
- gmx_ana_index_copy(root->v.u.g, expr->v.u.p->g, true);
+ gmx_ana_index_copy(root->v.u.g, &g, true);
}
}
}
{
gmx_ana_index_clear(&root->u.cgrp);
}
- root->u.cgrp.name = name;
+}
+
+
+/********************************************************************
+ * REQUIRED ATOMS ANALYSIS
+ ********************************************************************/
+
+/*! \brief
+ * Finds the highest atom index required to evaluate a selection subtree.
+ *
+ * \param[in] sel Root of the selection subtree to process.
+ * \param[in,out] maxAtomIndex The highest atom index required to evaluate the
+ * subtree. The existing value is never decreased, so multiple calls with
+ * the same parameter will compute the maximum over several subtrees.
+ *
+ * For evaluation that starts from a \ref SEL_ROOT element with a fixed group,
+ * children will never extend the evaluation group except for method parameter
+ * evaluation (which have their own root element), so it is sufficient to check
+ * the root. However, children of \ref SEL_EXPRESSION elements (i.e., the
+ * method parameters) may have been independently evaluated to a static group
+ * that no longer has a separate root, so those need to be checked as well.
+ *
+ * Position calculations are not considered here, but are analyzed through the
+ * position calculation collection in the main compilation method.
+ */
+static void
+init_required_atoms(const SelectionTreeElementPointer &sel, int *maxAtomIndex)
+{
+ // Process children.
+ if (sel->type != SEL_SUBEXPRREF)
+ {
+ SelectionTreeElementPointer child = sel->child;
+ while (child)
+ {
+ init_required_atoms(child, maxAtomIndex);
+ child = child->next;
+ }
+ }
+
+ if (sel->type == SEL_ROOT
+ || (sel->type == SEL_CONST && sel->v.type == GROUP_VALUE))
+ {
+ if (sel->u.cgrp.isize > 0)
+ {
+ *maxAtomIndex =
+ std::max(*maxAtomIndex, gmx_ana_index_get_max_index(&sel->u.cgrp));
+ }
+ }
}
&& (sel->cdata->flags & SEL_CDATA_STATICEVAL)
&& !(sel->cdata->flags & SEL_CDATA_FULLEVAL))
{
- char *name;
-
/* We need to free memory allocated for the group, because it is no
* longer needed (and would be lost on next call to the evaluation
- * function). But we need to preserve the name. */
- name = sel->u.cgrp.name;
+ * function). */
gmx_ana_index_deinit(&sel->u.cgrp);
- sel->u.cgrp.name = name;
sel->evaluate = &_gmx_sel_evaluate_subexpr_staticeval;
sel->cdata->evaluate = sel->evaluate;
sel->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
sel->child->v.nalloc = -1;
}
+
+ /* For static subexpressions with a dynamic evaluation group, there is
+ * no need to evaluate them again, as the SEL_SUBEXPRREF takes care of
+ * everything during evaluation. */
+ if (sel->type == SEL_SUBEXPR
+ && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
+ && (sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
+ {
+ sel->evaluate = NULL;
+ sel->cdata->evaluate = NULL;
+ }
}
gmx_ana_poscalc_set_flags(sel->u.expr.pc, cflags);
}
gmx_ana_poscalc_set_maxindex(sel->u.expr.pc, sel->cdata->gmax);
- snew(sel->u.expr.pos, 1);
+ sel->u.expr.pos = new gmx_ana_pos_t();
gmx_ana_poscalc_init_pos(sel->u.expr.pc, sel->u.expr.pos);
}
}
/* Initialize the evaluation callbacks and process the tree structure
* to conform to the expectations of the callback functions. */
/* Also, initialize and allocate the compiler data structure */
+ // TODO: Processing the tree in reverse root order would be better,
+ // as it would make dependency handling easier (all subexpression
+ // references would be processed before the actual subexpression) and
+ // could remove the need for most of these extra loops.
item = sc->root;
while (item)
{
optimize_arithmetic_expressions(item);
/* Initialize the compiler data */
init_item_compilerdata(item);
+ item = item->next;
+ }
+ // Initialize the static evaluation compiler flags.
+ // Requires the FULLEVAL compiler flag for the whole tree.
+ item = sc->root;
+ while (item)
+ {
init_item_staticeval(item);
init_item_subexpr_refcount(item);
item = item->next;
coll->printTree(stderr, false);
}
- /* Initialize evaluation groups, position calculations for methods, perform
- * some final optimization, and free the memory allocated for the
- * compilation. */
+ // Initialize evaluation groups, maximum atom index needed for evaluation,
+ // position calculations for methods, perform some final optimization, and
+ // free the memory allocated for the compilation.
+ coll->impl_->maxAtomIndex_ = 0;
/* By default, use whole residues/molecules. */
flags = POS_COMPLWHOLE;
PositionCalculationCollection::typeFromEnum(coll->impl_->rpost_.c_str(),
{
init_root_item(item, &sc->gall);
postprocess_item_subexpressions(item);
+ init_required_atoms(item, &coll->impl_->maxAtomIndex_);
init_item_comg(item, &sc->pcc, post, flags);
free_item_compilerdata(item);
item = item->next;
}
+ coll->impl_->maxAtomIndex_ =
+ std::max(coll->impl_->maxAtomIndex_,
+ sc->pcc.getHighestRequiredAtomIndex());
/* Allocate memory for the evaluation memory pool. */
_gmx_sel_mempool_reserve(sc->mempool, 0);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff