From: Magnus Lundborg <lundborg.magnus@gmail.com>
Date: Tue, 25 Sep 2018 08:38:03 +0000 (+0200)
Subject: Add margin as input to pullGroupObeysPbcRestrictions
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=0d5de9982640d82142dd6b9e18bc5656e7357008;p=alexxy%2Fgromacs.git

Add margin as input to pullGroupObeysPbcRestrictions

Make it possible to specify the margin when checking that a pull
group is not too large (compared to the PBC dimensions).

Change-Id: I1a856ae6078c085693ed7add4cf765b5a49abc2d
---

diff --git a/src/gromacs/gmxpreprocess/readpull.cpp b/src/gromacs/gmxpreprocess/readpull.cpp
index a6de96cb82..db4f6a601c 100644
--- a/src/gromacs/gmxpreprocess/readpull.cpp
+++ b/src/gromacs/gmxpreprocess/readpull.cpp
@@ -522,7 +522,7 @@ pull_t *set_pull_init(t_inputrec *ir, const gmx_mtop_t *mtop,
 
     pull_calc_coms(nullptr, pull_work, md, &pbc, t_start, x, nullptr);
 
-    int groupThatFailsPbc = pullCheckPbcWithinGroups(*pull_work, x, pbc);
+    int groupThatFailsPbc = pullCheckPbcWithinGroups(*pull_work, x, pbc, c_pullGroupPbcMargin);
     if (groupThatFailsPbc >= 0)
     {
         char buf[STRLEN];
diff --git a/src/gromacs/pulling/pull.h b/src/gromacs/pulling/pull.h
index ccb7cb8ab0..9ea3eefe20 100644
--- a/src/gromacs/pulling/pull.h
+++ b/src/gromacs/pulling/pull.h
@@ -288,7 +288,7 @@ void pull_calc_coms(const t_commrec *cr,
                     const rvec       x[],
                     rvec            *xp);
 
-/*! \brief Margin for checking PBC distances compared to half the box size in pullCheckPbcWithinGroups() */
+/*! \brief Margin for checking pull group PBC distances compared to half the box size */
 static constexpr real c_pullGroupPbcMargin = 0.9;
 
 /*! \brief Checks whether all groups that use a reference atom are within PBC restrictions
@@ -297,19 +297,22 @@ static constexpr real c_pullGroupPbcMargin = 0.9;
  * atoms within half the box size from the PBC atom. The box size is used
  * per dimension for rectangular boxes, but can be a combination of
  * dimensions for triclinic boxes, depending on which dimensions are
- * involved in the pull coordinates a group is involved in.
+ * involved in the pull coordinates a group is involved in. A margin is specified
+ * to ensure that atoms are not too close to the maximum distance.
  *
  * Should be called without MPI parallelization and after pull_calc_coms()
  * has been called at least once.
  *
- * \param[in] pull  The pull data structure
- * \param[in] x     The coordinates
- * \param[in] pbc   Information struct about periodicity
+ * \param[in] pull       The pull data structure
+ * \param[in] x          The coordinates
+ * \param[in] pbc        Information struct about periodicity
+ * \param[in] pbcMargin  The minimum margin (as a fraction) to half the box size
  * \returns -1 when all groups obey PBC or the first group index that fails PBC
  */
 int pullCheckPbcWithinGroups(const pull_t &pull,
                              const rvec   *x,
-                             const t_pbc  &pbc);
+                             const t_pbc  &pbc,
+                             real          pbcMargin);
 
 /*! \brief Returns if we have pull coordinates with potential pulling.
  *
diff --git a/src/gromacs/pulling/pullutil.cpp b/src/gromacs/pulling/pullutil.cpp
index 5395ca0595..8280f6d61f 100644
--- a/src/gromacs/pulling/pullutil.cpp
+++ b/src/gromacs/pulling/pullutil.cpp
@@ -808,7 +808,8 @@ static bool pullGroupObeysPbcRestrictions(const pull_group_work_t &group,
                                           const BoolVec           &dimUsed,
                                           const rvec              *x,
                                           const t_pbc             &pbc,
-                                          const gmx::RVec         &x_pbc)
+                                          const gmx::RVec         &x_pbc,
+                                          const real               pbcMargin)
 {
     /* Determine which dimensions are relevant for PBC */
     BoolVec dimUsesPbc       = { false, false, false };
@@ -838,7 +839,7 @@ static bool pullGroupObeysPbcRestrictions(const pull_group_work_t &group,
         /* Use margins for dimensions independently */
         for (int d = 0; d < pbc.ndim_ePBC; d++)
         {
-            marginPerDim[d] = c_pullGroupPbcMargin*pbc.hbox_diag[d];
+            marginPerDim[d] = pbcMargin*pbc.hbox_diag[d];
         }
     }
     else
@@ -848,7 +849,7 @@ static bool pullGroupObeysPbcRestrictions(const pull_group_work_t &group,
         {
             if (dimUsesPbc[d])
             {
-                marginDistance2 += c_pullGroupPbcMargin*gmx::square(0.5)*norm2(pbc.box[d]);
+                marginDistance2 += pbcMargin*gmx::square(0.5)*norm2(pbc.box[d]);
             }
         }
     }
@@ -894,7 +895,8 @@ static bool pullGroupObeysPbcRestrictions(const pull_group_work_t &group,
 
 int pullCheckPbcWithinGroups(const pull_t &pull,
                              const rvec   *x,
-                             const t_pbc  &pbc)
+                             const t_pbc  &pbc,
+                             real          pbcMargin)
 {
     if (pbc.ePBC == epbcNONE)
     {
@@ -924,7 +926,7 @@ int pullCheckPbcWithinGroups(const pull_t &pull,
     {
         const pull_group_work_t &group = pull.group[g];
         if (group.epgrppbc == epgrppbcREFAT &&
-            !pullGroupObeysPbcRestrictions(group, dimUsed[g], x, pbc, pull.comm.pbcAtomBuffer[g]))
+            !pullGroupObeysPbcRestrictions(group, dimUsed[g], x, pbc, pull.comm.pbcAtomBuffer[g], pbcMargin))
         {
             return g;
         }