Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / selection / poscalc.cpp

diff --git a/src/gromacs/selection/poscalc.cpp b/src/gromacs/selection/poscalc.cpp
index 402af13c2f6ba33a9f605a5382ce5f1469ffaf94..f193abd42c577b1445fc4d4707a106080528671e 100644 (file)
--- a/src/gromacs/selection/poscalc.cpp
+++ b/src/gromacs/selection/poscalc.cpp
@@ -1,10 +1,10 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013, 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
@@ -59,19 +59,23 @@
  * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_selection
  */
+#include "gmxpre.h"
+
+#include "poscalc.h"
+
 #include <string.h>
 
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
+#include <algorithm>
 
-#include "gromacs/selection/centerofmass.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "centerofmass.h"
 
 namespace gmx
 {
@@ -188,11 +192,11 @@ struct gmx_ana_poscalc_t
      * already been calculated in \p sbase.
      * The structure pointed by \p sbase is always a static calculation.
      */
-    struct gmx_ana_poscalc_t                 *sbase;
+    gmx_ana_poscalc_t                        *sbase;
     /** Next structure in the linked list of calculations. */
-    struct gmx_ana_poscalc_t                 *next;
+    gmx_ana_poscalc_t                        *next;
     /** Previous structure in the linked list of calculations. */
-    struct gmx_ana_poscalc_t                 *prev;
+    gmx_ana_poscalc_t                        *prev;
     /** Number of references to this structure. */
     int                                       refcount;
     /** Collection this calculation belongs to. */
@@ -559,6 +563,25 @@ PositionCalculationCollection::createCalculationFromEnum(const char *post, int f
     return impl_->createCalculation(type, cflags);
 }
 
+int PositionCalculationCollection::getHighestRequiredAtomIndex() const
+{
+    int                result = 0;
+    gmx_ana_poscalc_t *pc     = impl_->first_;
+    while (pc)
+    {
+        // Calculations with a base just copy positions from the base, so
+        // those do not need to be considered in the check.
+        if (!pc->sbase)
+        {
+            gmx_ana_index_t g;
+            gmx_ana_index_set(&g, pc->b.nra, pc->b.a, 0);
+            result = std::max(result, gmx_ana_index_get_max_index(&g));
+        }
+        pc = pc->next;
+    }
+    return result;
+}
+
 void PositionCalculationCollection::initEvaluation()
 {
     if (impl_->bInit_)
@@ -770,7 +793,7 @@ create_simple_base(gmx_ana_poscalc_t *pc)
     base  = pc->coll->createCalculation(pc->type, flags);
     set_poscalc_maxindex(base, &pc->gmax, true);
 
-    snew(base->p, 1);
+    base->p = new gmx_ana_pos_t();
 
     pc->sbase = base;
     pc->coll->removeCalculation(base);
@@ -1043,7 +1066,7 @@ gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p)
     {
         gmx_ana_indexmap_set_static(&p->m, &pc->b);
     }
-    gmx_ana_pos_reserve(p, p->m.nr, 0);
+    gmx_ana_pos_reserve(p, p->m.mapb.nr, 0);
     if (pc->flags & POS_VELOCITIES)
     {
         gmx_ana_pos_reserve_velocities(p);
@@ -1052,8 +1075,6 @@ gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p)
     {
         gmx_ana_pos_reserve_forces(p);
     }
-    gmx_ana_pos_set_nr(p, p->m.nr);
-    gmx_ana_pos_set_evalgrp(p, &pc->gmax);
 }
 
 /*!
@@ -1088,10 +1109,7 @@ gmx_ana_poscalc_free(gmx_ana_poscalc_t *pc)
     {
         gmx_ana_index_deinit(&pc->gmax);
     }
-    if (pc->p)
-    {
-        gmx_ana_pos_free(pc->p);
-    }
+    delete pc->p;
     if (pc->sbase)
     {
         gmx_ana_poscalc_free(pc->sbase);
@@ -1108,7 +1126,8 @@ gmx_ana_poscalc_free(gmx_ana_poscalc_t *pc)
 bool
 gmx_ana_poscalc_requires_top(gmx_ana_poscalc_t *pc)
 {
-    if ((pc->flags & POS_MASS) || pc->type == POS_RES || pc->type == POS_MOL)
+    if ((pc->flags & POS_MASS) || pc->type == POS_RES || pc->type == POS_MOL
+        || ((pc->flags & POS_FORCES) && pc->type != POS_ATOM))
     {
         return true;
     }
@@ -1148,13 +1167,11 @@ gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
     {
         g = &pc->gmax;
     }
-    gmx_ana_pos_set_evalgrp(p, g);
 
     /* Update the index map */
     if (pc->flags & POS_DYNAMIC)
     {
         gmx_ana_indexmap_update(&p->m, g, false);
-        p->nr = p->m.nr;
     }
     else if (pc->flags & POS_MASKONLY)
     {
@@ -1176,14 +1193,14 @@ gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
          * loop instead of in the beginning. */
         if (pc->flags & POS_DYNAMIC)
         {
-            for (bi = 0; bi < p->nr; ++bi)
+            for (bi = 0; bi < p->count(); ++bi)
             {
                 bj = pc->baseid[p->m.refid[bi]];
                 copy_rvec(pc->sbase->p->x[bj], p->x[bi]);
             }
             if (p->v)
             {
-                for (bi = 0; bi < p->nr; ++bi)
+                for (bi = 0; bi < p->count(); ++bi)
                 {
                     bj = pc->baseid[p->m.refid[bi]];
                     copy_rvec(pc->sbase->p->v[bj], p->v[bi]);
@@ -1191,7 +1208,7 @@ gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
             }
             if (p->f)
             {
-                for (bi = 0; bi < p->nr; ++bi)
+                for (bi = 0; bi < p->count(); ++bi)
                 {
                     bj = pc->baseid[p->m.refid[bi]];
                     copy_rvec(pc->sbase->p->f[bj], p->f[bi]);
@@ -1200,14 +1217,14 @@ gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
         }
         else
         {
-            for (bi = 0; bi < p->nr; ++bi)
+            for (bi = 0; bi < p->count(); ++bi)
             {
                 bj = pc->baseid[bi];
                 copy_rvec(pc->sbase->p->x[bj], p->x[bi]);
             }
             if (p->v)
             {
-                for (bi = 0; bi < p->nr; ++bi)
+                for (bi = 0; bi < p->count(); ++bi)
                 {
                     bj = pc->baseid[bi];
                     copy_rvec(pc->sbase->p->v[bj], p->v[bi]);
@@ -1215,7 +1232,7 @@ gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
             }
             if (p->f)
             {
-                for (bi = 0; bi < p->nr; ++bi)
+                for (bi = 0; bi < p->count(); ++bi)
                 {
                     bj = pc->baseid[bi];
                     copy_rvec(pc->sbase->p->f[bj], p->f[bi]);
@@ -1302,7 +1319,7 @@ gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
                 }
                 if (p->f && fr->bF)
                 {
-                    gmx_calc_comg_blocka(top, fr->f, &pc->b, bMass, p->f);
+                    gmx_calc_comg_f_blocka(top, fr->f, &pc->b, bMass, p->f);
                 }
                 break;
         }