Merge branch release-2016

Dropped the post-submit change because where we test
with older clang we now always specify a suitable
status for openmp.

Change-Id: I993da20856861c0b8a0888f7fa0deed8853349a8

diff --git a/src/gromacs/gmxlib/nrnb.cpp b/src/gromacs/gmxlib/nrnb.cpp
index c0509feb606207a47365a3caae88975aab46a620..4bc3f67230888a05c9d20651976d2411cd33997d 100644 (file)
--- a/src/gromacs/gmxlib/nrnb.cpp
+++ b/src/gromacs/gmxlib/nrnb.cpp
@@ -189,7 +189,11 @@ static const t_nrnb_data nbdata[eNRNB] = {
     { "Virtual Site 4fd",              110 },
     { "Virtual Site 4fdn",             254 },
     { "Virtual Site N",                 15 },
-    { "Mixed Generalized Born stuff",   10 }
+    { "Mixed Generalized Born stuff",   10 },
+    { "CMAP",                         1700 }, // Estimate!
+    { "Urey-Bradley",                  183 },
+    { "Cross-Bond-Bond",               163 },
+    { "Cross-Bond-Angle",              163 }
 };
 
 static void pr_two(FILE *out, int c, int i)

diff --git a/src/gromacs/gmxlib/nrnb.h b/src/gromacs/gmxlib/nrnb.h
index 49f256eee70ad66621de9ee0b3a5ef4d5b3ce2c7..5cc1d8a7d53e453007f35ed570bf2613e3b25c98 100644 (file)
--- a/src/gromacs/gmxlib/nrnb.h
+++ b/src/gromacs/gmxlib/nrnb.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, 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.
@@ -116,7 +116,8 @@ enum
     eNR_VSITE2,               eNR_VSITE3,               eNR_VSITE3FD,
     eNR_VSITE3FAD,            eNR_VSITE3OUT,            eNR_VSITE4FD,
     eNR_VSITE4FDN,            eNR_VSITEN,               eNR_GB,
-    eNR_CMAP,
+    eNR_CMAP,                 eNR_UREY_BRADLEY,         eNR_CROSS_BOND_BOND,
+    eNR_CROSS_BOND_ANGLE,
     eNRNB
 };
 

diff --git a/src/gromacs/mdlib/trajectory_writing.cpp b/src/gromacs/mdlib/trajectory_writing.cpp
index 1be40ba2b1e242b6abd9783e2c23e2873590653d..af0bc7785de4bd5acc973bec604e5da04ed14497 100644 (file)
--- a/src/gromacs/mdlib/trajectory_writing.cpp
+++ b/src/gromacs/mdlib/trajectory_writing.cpp
@@ -179,7 +179,7 @@ do_md_trajectory_writing(FILE               *fplog,
              * at the last step.
              */
             fprintf(stderr, "\nWriting final coordinates.\n");
-            if (fr->bMolPBC)
+            if (fr->bMolPBC && !ir->bPeriodicMols)
             {
                 /* Make molecules whole only for confout writing */
                 do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, x_for_confout);

diff --git a/src/gromacs/topology/ifunc.cpp b/src/gromacs/topology/ifunc.cpp
index b5de6c87148fd066de32f5dcdd9a434c18c7e105..376e46402c02545bd423779d180bd643dac211ce 100644 (file)
--- a/src/gromacs/topology/ifunc.cpp
+++ b/src/gromacs/topology/ifunc.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, 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.
@@ -99,9 +99,9 @@ const t_interaction_function interaction_function[F_NRE] =
     def_angle   ("G96ANGLES", "G96Angle",        3, 2, 2,  eNR_ANGLES, g96angles     ),
     def_angle   ("RESTRANGLES", "Restricted Angles", 3, 2, 2,  eNR_ANGLES, restrangles),
     def_angle   ("LINEAR_ANGLES", "Lin. Angle", 3, 2, 2,  eNR_LINEAR_ANGLES, linear_angles ),
-    def_bonded  ("CROSS_BOND_BOND", "Bond-Cross", 3, 3, 0, 0,          cross_bond_bond ),
-    def_bonded  ("CROSS_BOND_ANGLE", "BA-Cross",   3, 4, 0, 0,          cross_bond_angle ),
-    def_angle   ("UREY_BRADLEY", "U-B",          3, 4, 4,  0,          urey_bradley ),
+    def_bonded  ("CROSS_BOND_BOND", "Bond-Cross", 3, 3, 0, eNR_CROSS_BOND_BOND, cross_bond_bond ),
+    def_bonded  ("CROSS_BOND_ANGLE", "BA-Cross",   3, 4, 0, eNR_CROSS_BOND_ANGLE, cross_bond_angle ),
+    def_angle   ("UREY_BRADLEY", "U-B",          3, 4, 4,  eNR_UREY_BRADLEY, urey_bradley ),
     def_angle   ("QANGLES", "Quartic Angles",    3, 6, 0,  eNR_QANGLES, quartic_angles ),
     def_bondedt ("TABANGLES", "Tab. Angles",    3, 2, 2,  eNR_TABANGLES, tab_angles ),
     def_bonded  ("PDIHS",    "Proper Dih.",     4, 3, 3,  eNR_PROPER, pdihs         ),
@@ -133,10 +133,10 @@ const t_interaction_function interaction_function[F_NRE] =
     def_nofc    ("COUL_RECIP", "Coul. recip."                                       ),
     def_nofc    ("LJ_RECIP", "LJ recip."                                            ),
     def_nofc    ("DPD",      "DPD"                                                  ),
-    def_bondnb  ("POLARIZATION", "Polarization", 2, 1, 0,  0,          polarize      ),
+    def_bondnb  ("POLARIZATION", "Polarization", 2, 1, 0,  eNR_POLARIZE, polarize      ),
     def_bonded  ("WATERPOL", "Water Pol.",      5, 6, 0,  eNR_WPOL,   water_pol     ),
     def_bonded  ("THOLE",    "Thole Pol.",      4, 3, 0,  eNR_THOLE,  thole_pol     ),
-    def_bondnb  ("ANHARM_POL", "Anharm. Pol.", 2, 3, 0, 0,          anharm_polarize      ),
+    def_bondnb  ("ANHARM_POL", "Anharm. Pol.", 2, 3, 0, eNR_ANHARM_POL, anharm_polarize      ),
     def_bonded  ("POSRES",   "Position Rest.",  1, 3, 3,  eNR_POSRES, unimplemented ),
     def_bonded  ("FBPOSRES", "Flat-bottom posres", 1, 3, 0, eNR_FBPOSRES, unimplemented ),
     def_bonded  ("DISRES",   "Dis. Rest.",      2, 6, 0,  eNR_DISRES, ta_disres     ),