Eliminate mdlib/mdrun.h

This file was filled with stuff that works better elsewhere.

Moved the options structs into gmx namespace

Refs #2877

Change-Id: Ib796ef8e9896804c56936f23f67dcd3fc12900fd

diff --git a/src/api/cpp/context_impl.h b/src/api/cpp/context_impl.h
index 0d90d1587c1ec800899f1557b57092be6aaa8d93..f90e323c34f749af03e01466764a7df393095b2d 100644 (file)
--- a/src/api/cpp/context_impl.h
+++ b/src/api/cpp/context_impl.h
@@ -45,6 +45,7 @@
 #include <string>
 
 #include "gromacs/mdrun/legacymdrunoptions.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 
 #include "gmxapi/context.h"
 #include "gmxapi/session.h"

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 3a7a230a66a97179c5cf7271e92a06b1aa9d1b76..2090b4697ea4dd8358a460b5073a9eeec343c1e7 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -66,11 +66,11 @@
 #include "gromacs/mdlib/calc_verletbuf.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/constraintrange.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/updategroups.h"
 #include "gromacs/mdlib/vsite.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
@@ -1934,7 +1934,7 @@ static DlbState forceDlbOffOrBail(DlbState             cmdlineDlbState,
  */
 static DlbState determineInitialDlbState(const gmx::MDLogger &mdlog,
                                          DlbOption dlbOption, gmx_bool bRecordLoad,
-                                         const MdrunOptions &mdrunOptions,
+                                         const gmx::MdrunOptions &mdrunOptions,
                                          const t_inputrec *ir)
 {
     DlbState dlbState = DlbState::offCanTurnOn;
@@ -2137,7 +2137,7 @@ static void setupUpdateGroups(const gmx::MDLogger &mdlog,
 static void set_dd_limits_and_grid(const gmx::MDLogger &mdlog,
                                    t_commrec *cr, gmx_domdec_t *dd,
                                    const DomdecOptions &options,
-                                   const MdrunOptions &mdrunOptions,
+                                   const gmx::MdrunOptions &mdrunOptions,
                                    const gmx_mtop_t *mtop,
                                    const t_inputrec *ir,
                                    const matrix box,
@@ -2953,7 +2953,7 @@ static void set_dd_envvar_options(const gmx::MDLogger &mdlog,
 gmx_domdec_t *init_domain_decomposition(const gmx::MDLogger           &mdlog,
                                         t_commrec                     *cr,
                                         const DomdecOptions           &options,
-                                        const MdrunOptions            &mdrunOptions,
+                                        const gmx::MdrunOptions       &mdrunOptions,
                                         const gmx_mtop_t              *mtop,
                                         const t_inputrec              *ir,
                                         const matrix                   box,

diff --git a/src/gromacs/domdec/domdec.h b/src/gromacs/domdec/domdec.h
index 56208a19308fc65ce607a112c4053d0711066a08..5ea2ef1f8ee594338c2007438559e0131fa260b7 100644 (file)
--- a/src/gromacs/domdec/domdec.h
+++ b/src/gromacs/domdec/domdec.h
@@ -73,7 +73,6 @@ struct gmx_domdec_zones_t;
 struct gmx_localtop_t;
 struct gmx_mtop_t;
 struct gmx_vsite_t;
-struct MdrunOptions;
 struct t_block;
 struct t_blocka;
 struct t_commrec;
@@ -87,6 +86,7 @@ class t_state;
 namespace gmx
 {
 class MDLogger;
+struct MdrunOptions;
 class LocalAtomSetManager;
 } // namespace
 
@@ -203,7 +203,7 @@ gmx_domdec_t *
 init_domain_decomposition(const gmx::MDLogger            &mdlog,
                           t_commrec                      *cr,
                           const DomdecOptions            &options,
-                          const MdrunOptions             &mdrunOptions,
+                          const gmx::MdrunOptions        &mdrunOptions,
                           const gmx_mtop_t               *mtop,
                           const t_inputrec               *ir,
                           const matrix                    box,

diff --git a/src/gromacs/essentialdynamics/edsam.cpp b/src/gromacs/essentialdynamics/edsam.cpp
index 8ba72b64dca4462e1270c0a1eb50e8e56306fcc0..4ae03b76b86409d7c7646ab797a781d3edeeee93 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.cpp
+++ b/src/gromacs/essentialdynamics/edsam.cpp
@@ -59,7 +59,6 @@
 #include "gromacs/mdlib/broadcaststructs.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/groupcoord.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/update.h"
 #include "gromacs/mdtypes/commrec.h"

diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp
index 389188933c833e3e34f185ea1e8b9888eaac1416..d4d2941a239f04642636e327e2d63249f32c525c 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.cpp
+++ b/src/gromacs/gmxana/gmx_disre.cpp
@@ -59,7 +59,6 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdtypes/fcdata.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"

diff --git a/src/gromacs/gmxpreprocess/genion.cpp b/src/gromacs/gmxpreprocess/genion.cpp
index 297b2190e9606cb57a3db683f44d4b4e0b3f6c53..feea7e573c1656eb17d7a3cbbabe334580b28021 100644 (file)
--- a/src/gromacs/gmxpreprocess/genion.cpp
+++ b/src/gromacs/gmxpreprocess/genion.cpp
@@ -49,7 +49,6 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/threefry.h"
 #include "gromacs/random/uniformintdistribution.h"

diff --git a/src/gromacs/gmxpreprocess/readpull.cpp b/src/gromacs/gmxpreprocess/readpull.cpp
index 16f00271e791882196cf1426218ab7de66758227..d39aecc8534cfbd34dddf8ff60abd5286c372393 100644 (file)
--- a/src/gromacs/gmxpreprocess/readpull.cpp
+++ b/src/gromacs/gmxpreprocess/readpull.cpp
@@ -46,7 +46,6 @@
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/mdtypes/pull_params.h"

diff --git a/src/gromacs/imd/imd.cpp b/src/gromacs/imd/imd.cpp
index ce4e7bc0cc6d2fa71a50d1f5e6cc69cb677bf6ea..3f59bcdc5223c2615d2155c972a452a33e9dee8f 100644 (file)
--- a/src/gromacs/imd/imd.cpp
+++ b/src/gromacs/imd/imd.cpp
@@ -72,12 +72,12 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/broadcaststructs.h"
 #include "gromacs/mdlib/groupcoord.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sighandler.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdtypes/enerdata.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"
@@ -979,11 +979,11 @@ static void imd_readcommand(t_gmx_IMD_setup *IMDsetup)
  *
  * Call on master only.
  */
-static FILE *open_imd_out(const char                *fn,
-                          t_gmx_IMD_setup           *IMDsetup,
-                          int                        nat_total,
-                          const gmx_output_env_t    *oenv,
-                          const ContinuationOptions &continuationOptions)
+static FILE *open_imd_out(const char                     *fn,
+                          t_gmx_IMD_setup                *IMDsetup,
+                          int                             nat_total,
+                          const gmx_output_env_t         *oenv,
+                          const gmx::ContinuationOptions &continuationOptions)
 {
     FILE       *fp;
 
@@ -1283,17 +1283,17 @@ static void imd_check_integrator_parallel(t_inputrec *ir, const t_commrec *cr)
     }
 }
 
-void init_IMD(t_inputrec             *ir,
-              const t_commrec        *cr,
-              const gmx_multisim_t   *ms,
-              const gmx_mtop_t       *top_global,
-              FILE                   *fplog,
-              int                     defnstimd,
-              const rvec              x[],
-              int                     nfile,
-              const t_filenm          fnm[],
-              const gmx_output_env_t *oenv,
-              const MdrunOptions     &mdrunOptions)
+void init_IMD(t_inputrec              *ir,
+              const t_commrec         *cr,
+              const gmx_multisim_t    *ms,
+              const gmx_mtop_t        *top_global,
+              FILE                    *fplog,
+              int                      defnstimd,
+              const rvec               x[],
+              int                      nfile,
+              const t_filenm           fnm[],
+              const gmx_output_env_t  *oenv,
+              const gmx::MdrunOptions &mdrunOptions)
 {
     int              i;
     int              nat_total;
@@ -1311,7 +1311,7 @@ void init_IMD(t_inputrec             *ir,
     // user asked for should be handled with a fatal error, not just a
     // warning.
 
-    const ImdOptions &options = mdrunOptions.imdOptions;
+    const auto &options = mdrunOptions.imdOptions;
 
     /* It seems we have a .tpr file that defines an IMD group and thus allows IMD sessions.
      * Check whether we can actually provide the IMD functionality for this setting: */

diff --git a/src/gromacs/imd/imd.h b/src/gromacs/imd/imd.h
index 70fc97f1a299eae827147c997cdf1f8d453f5d29..e1543453713f4a4b3c27117fa88ba0f825ee1a72 100644 (file)
--- a/src/gromacs/imd/imd.h
+++ b/src/gromacs/imd/imd.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
@@ -79,7 +79,6 @@ struct gmx_mtop_t;
 struct gmx_multisim_t;
 struct gmx_output_env_t;
 struct gmx_wallcycle;
-struct MdrunOptions;
 struct t_commrec;
 struct t_filenm;
 struct t_gmx_IMD;
@@ -87,6 +86,11 @@ struct t_IMD;
 struct t_inputrec;
 class t_state;
 
+namespace gmx
+{
+struct MdrunOptions;
+}
+
 static const char IMDstr[] = "IMD:";  /**< Tag output from the IMD module with this string. */
 
 /*! \brief Writes out the group of atoms selected for interactive manipulation.
@@ -144,7 +148,7 @@ void init_IMD(t_inputrec *ir, const t_commrec *cr,
               const gmx_mtop_t *top_global,
               FILE *fplog, int defnstimd, const rvec x[],
               int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv,
-              const MdrunOptions &mdrunOptions);
+              const gmx::MdrunOptions &mdrunOptions);
 
 
 /*! \brief IMD required in this time step?

diff --git a/src/gromacs/mdlib/broadcaststructs.cpp b/src/gromacs/mdlib/broadcaststructs.cpp
index 51fd02767e9d8253d18aacde08fa2da2a4bb3cbf..4feac1f229c9578e9f92e89ad6ca98e165cbc1f5 100644 (file)
--- a/src/gromacs/mdlib/broadcaststructs.cpp
+++ b/src/gromacs/mdlib/broadcaststructs.cpp
@@ -45,7 +45,6 @@
 
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/tgroup.h"
 #include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"

diff --git a/src/gromacs/mdlib/broadcaststructs.h b/src/gromacs/mdlib/broadcaststructs.h
index d89d636d51d6bd456756768d7e8cccb998f17308..e4273078ba9fb85a04025084c8b8aaec5f65298e 100644 (file)
--- a/src/gromacs/mdlib/broadcaststructs.h
+++ b/src/gromacs/mdlib/broadcaststructs.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019, 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.
@@ -52,6 +52,11 @@
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/smalloc.h"
 
+struct gmx_mtop_t;
+struct t_commrec;
+struct t_inputrec;
+class t_state;
+
 //! Convenience wrapper for gmx_bcast of a single value.
 template <typename T>
 void block_bc(const t_commrec *cr, T &data)
@@ -97,4 +102,14 @@ void nblock_abc(const t_commrec *cr, int numElements, std::vector<T> *v)
     gmx_bcast(numElements*sizeof(T), v->data(), cr);
 }
 
+//! \brief Broadcasts the, non-dynamic, state from the master to all ranks in cr->mpi_comm_mygroup
+//
+// This is intended to be used with MPI parallelization without
+// domain decompostion (currently with NM and TPI).
+void broadcastStateWithoutDynamics(const t_commrec *cr, t_state *state);
+
+//! \brief Broadcast inputrec and mtop and allocate node-specific settings
+void init_parallel(t_commrec *cr, t_inputrec *inputrec,
+                   gmx_mtop_t *mtop);
+
 #endif

diff --git a/src/gromacs/mdlib/checkpointhandler.h b/src/gromacs/mdlib/checkpointhandler.h
index c9f9cfe5acb3d6a270f72ff8edb1945f99c97183..bfd98a5c578fb84ef310a9e8928e9a8047751bbe 100644 (file)
--- a/src/gromacs/mdlib/checkpointhandler.h
+++ b/src/gromacs/mdlib/checkpointhandler.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, 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.
@@ -58,7 +58,6 @@
 #include <memory>
 
 #include "gromacs/compat/pointers.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/simulationsignal.h"
 
 struct gmx_walltime_accounting;

diff --git a/src/gromacs/mdlib/constr.cpp b/src/gromacs/mdlib/constr.cpp
index e75f429e782970b325c02bd160075f5c89dcc2a7..a888364b74c1cacb82071ca0923b72f65635c278 100644 (file)
--- a/src/gromacs/mdlib/constr.cpp
+++ b/src/gromacs/mdlib/constr.cpp
@@ -62,7 +62,6 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/lincs.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/settle.h"
 #include "gromacs/mdlib/shake.h"
 #include "gromacs/mdtypes/commrec.h"
@@ -72,6 +71,7 @@
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
+#include "gromacs/timing/wallcycle.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/mtop_lookup.h"

diff --git a/src/gromacs/mdlib/energyoutput.cpp b/src/gromacs/mdlib/energyoutput.cpp
index b2f55c715855f168ebe02618f92ba24044ebc497..f90aabe1630fa82f45f46e729ae8187605d39da2 100644 (file)
--- a/src/gromacs/mdlib/energyoutput.cpp
+++ b/src/gromacs/mdlib/energyoutput.cpp
@@ -57,7 +57,6 @@
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/ebin.h"
 #include "gromacs/mdlib/mdebin_bar.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdtypes/energyhistory.h"
 #include "gromacs/mdtypes/fcdata.h"
 #include "gromacs/mdtypes/group.h"

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index ef7b727ce0916fe057b02f0cb02bc1912d4de6bc..3ca8b6de2925eee675f4824decc4a34bd1084543 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -58,7 +58,6 @@
 #include "gromacs/math/vecdump.h"
 #include "gromacs/mdlib/force_flags.h"
 #include "gromacs/mdlib/forcerec_threading.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/mdlib/rf_util.h"

diff --git a/src/gromacs/mdlib/lincs.cpp b/src/gromacs/mdlib/lincs.cpp
index ac37a7b54ecd837eb2295caf351e3712fb7914e9..185d968f57da4926708bcb1716ec6f8a2ad1e6b4 100644 (file)
--- a/src/gromacs/mdlib/lincs.cpp
+++ b/src/gromacs/mdlib/lincs.cpp
@@ -63,7 +63,6 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"

diff --git a/src/gromacs/mdlib/md_support.cpp b/src/gromacs/mdlib/md_support.cpp
index b843bf32c186b41eb9c1d7aa438f22e056157a1e..a7154d9afddf3e8d516781504d86696433160a22 100644 (file)
--- a/src/gromacs/mdlib/md_support.cpp
+++ b/src/gromacs/mdlib/md_support.cpp
@@ -49,7 +49,6 @@
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/dispersioncorrection.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/simulationsignal.h"
 #include "gromacs/mdlib/tgroup.h"

diff --git a/src/gromacs/mdlib/md_support.h b/src/gromacs/mdlib/md_support.h
index eb6c45d615ceeef5f7d98b885a33a65458b6a4fe..e218d383c0162f526e8c60f36940c99e385e6c12 100644 (file)
--- a/src/gromacs/mdlib/md_support.h
+++ b/src/gromacs/mdlib/md_support.h
@@ -48,6 +48,7 @@ struct gmx_signalling_t;
 struct t_extmass;
 struct t_forcerec;
 struct t_grpopts;
+struct t_inputrec;
 struct t_lambda;
 struct t_nrnb;
 class t_state;
@@ -107,6 +108,9 @@ bool multisim_int_all_are_equal(const gmx_multisim_t *ms,
 void rerun_parallel_comm(t_commrec *cr, t_trxframe *fr,
                          gmx_bool *bLastStep);
 
+//! \brief Allocate and initialize node-local state entries
+void set_state_entries(t_state *state, const t_inputrec *ir);
+
 /* Set the lambda values in the global state from a frame read with rerun */
 void setCurrentLambdasRerun(int64_t step, const t_lambda *fepvals,
                             const t_trxframe *rerun_fr, const double *lam0,

diff --git a/src/gromacs/mdlib/mdoutf.cpp b/src/gromacs/mdlib/mdoutf.cpp
index 225dbc1ed818be2db2d6551471d6602a38763e1b..93967223fae2d9557b411723811669af0ce9958d 100644 (file)
--- a/src/gromacs/mdlib/mdoutf.cpp
+++ b/src/gromacs/mdlib/mdoutf.cpp
@@ -46,12 +46,12 @@
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/trajectory_writing.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/imdoutputprovider.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/topology/topology.h"
@@ -83,7 +83,7 @@ struct gmx_mdoutf {
 
 
 gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
-                         const MdrunOptions &mdrunOptions,
+                         const gmx::MdrunOptions &mdrunOptions,
                          const t_commrec *cr,
                          gmx::IMDOutputProvider *outputProvider,
                          const t_inputrec *ir, gmx_mtop_t *top_global,

diff --git a/src/gromacs/mdlib/mdoutf.h b/src/gromacs/mdlib/mdoutf.h
index 115fa0bb33a6c47b6f601a6103776912bb6e36ff..f8c7a7754dddf10794965886bba4b13dd106b47d 100644 (file)
--- a/src/gromacs/mdlib/mdoutf.h
+++ b/src/gromacs/mdlib/mdoutf.h
@@ -46,7 +46,6 @@
 class energyhistory_t;
 struct gmx_mtop_t;
 struct gmx_output_env_t;
-struct MdrunOptions;
 struct ObservablesHistory;
 struct t_commrec;
 struct t_filenm;
@@ -55,6 +54,7 @@ struct t_inputrec;
 namespace gmx
 {
 class IMDOutputProvider;
+struct MdrunOptions;
 }
 
 typedef struct gmx_mdoutf *gmx_mdoutf_t;
@@ -64,16 +64,16 @@ typedef struct gmx_mdoutf *gmx_mdoutf_t;
  * Returns a pointer to a data structure with all output file pointers
  * and names required by mdrun.
  */
-gmx_mdoutf_t init_mdoutf(FILE                   *fplog,
-                         int                     nfile,
-                         const t_filenm          fnm[],
-                         const MdrunOptions     &mdrunOptions,
-                         const t_commrec        *cr,
-                         gmx::IMDOutputProvider *outputProvider,
-                         const t_inputrec       *ir,
-                         gmx_mtop_t             *mtop,
-                         const gmx_output_env_t *oenv,
-                         gmx_wallcycle_t         wcycle);
+gmx_mdoutf_t init_mdoutf(FILE                    *fplog,
+                         int                      nfile,
+                         const t_filenm           fnm[],
+                         const gmx::MdrunOptions &mdrunOptions,
+                         const t_commrec         *cr,
+                         gmx::IMDOutputProvider  *outputProvider,
+                         const t_inputrec        *ir,
+                         gmx_mtop_t              *mtop,
+                         const gmx_output_env_t  *oenv,
+                         gmx_wallcycle_t          wcycle);
 
 /*! \brief Getter for file pointer */
 ener_file_t mdoutf_get_fp_ene(gmx_mdoutf_t of);

diff --git a/src/gromacs/mdlib/shellfc.cpp b/src/gromacs/mdlib/shellfc.cpp
index ff3aa7a123b3862d6fb7c88012bf4b5aa34f3369..deee367081ceab38b59317da934239717592589f 100644 (file)
--- a/src/gromacs/mdlib/shellfc.cpp
+++ b/src/gromacs/mdlib/shellfc.cpp
@@ -58,7 +58,6 @@
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/force_flags.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/vsite.h"
 #include "gromacs/mdtypes/commrec.h"

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index 055b5a8d91ff3fe0e8789edf8e8087c0767197ae..0457c20f0c89f7105765d9c3aafb329b7d6254ef 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -78,7 +78,6 @@
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/ppforceworkload.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/mdlib/update.h"

diff --git a/src/gromacs/mdlib/sim_util.h b/src/gromacs/mdlib/sim_util.h
index 5d256b3ad9f078637429907fc19255c1565eb8e7..c44b967fe1745437edd2ac27d9687377a69c5dba 100644 (file)
--- a/src/gromacs/mdlib/sim_util.h
+++ b/src/gromacs/mdlib/sim_util.h
@@ -47,7 +47,6 @@ struct gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct gmx_output_env_t;
 struct gmx_pme_t;
-struct MdrunOptions;
 struct nonbonded_verlet_t;
 struct t_forcerec;
 struct t_mdatoms;

diff --git a/src/gromacs/mdlib/stat.cpp b/src/gromacs/mdlib/stat.cpp
index b45431c9f04c78fa1e0f3f741a01ab0f1fdad6cc..fdaa251c482a15baad56664f13e2d5f4559ef45d 100644 (file)
--- a/src/gromacs/mdlib/stat.cpp
+++ b/src/gromacs/mdlib/stat.cpp
@@ -48,7 +48,6 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/md_support.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/rbin.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/tgroup.h"

diff --git a/src/gromacs/mdlib/trajectory_writing.cpp b/src/gromacs/mdlib/trajectory_writing.cpp
index 75c9806d5e1e305ab6614ab54d85904263cc1548..6e075020b358114464bb04d0712b2a9dc8b8ac2b 100644 (file)
--- a/src/gromacs/mdlib/trajectory_writing.cpp
+++ b/src/gromacs/mdlib/trajectory_writing.cpp
@@ -41,7 +41,6 @@
 #include "gromacs/fileio/tngio.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/mdoutf.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/update.h"
 #include "gromacs/mdtypes/commrec.h"

diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp
index c1f2c983a595be181b14069f3573bc68be2b4c85..2cce59af024da1ab362dbbb45bf667dc30a739d4 100644 (file)
--- a/src/gromacs/mdlib/update.cpp
+++ b/src/gromacs/mdlib/update.cpp
@@ -59,7 +59,6 @@
 #include "gromacs/mdlib/boxdeformation.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/tgroup.h"
 #include "gromacs/mdtypes/commrec.h"

diff --git a/src/gromacs/mdrun/integrator.h b/src/gromacs/mdrun/integrator.h
index 26b10d08d173640c53513cea917af4406b3a7cf7..ba3e4fac985a0e5710288ecb16a069cc62f26168 100644 (file)
--- a/src/gromacs/mdrun/integrator.h
+++ b/src/gromacs/mdrun/integrator.h
@@ -58,7 +58,6 @@ struct gmx_output_env_t;
 struct gmx_vsite_t;
 struct gmx_wallcycle;
 struct gmx_walltime_accounting;
-struct MdrunOptions;
 struct ObservablesHistory;
 struct ReplicaExchangeParameters;
 struct t_commrec;
@@ -79,6 +78,7 @@ class IMDOutputProvider;
 class MDLogger;
 class MDAtoms;
 class StopHandlerBuilder;
+struct MdrunOptions;
 
 //! Function type for integrator code.
 using IntegratorFunctionType = void();

diff --git a/src/gromacs/mdrun/legacymdrunoptions.h b/src/gromacs/mdrun/legacymdrunoptions.h
index d65b417c48be3c866f962a3fbc67fe755184f974..69602710e85733e56145047f4556a07e2bf8de53 100644 (file)
--- a/src/gromacs/mdrun/legacymdrunoptions.h
+++ b/src/gromacs/mdrun/legacymdrunoptions.h
@@ -53,8 +53,8 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/hardware/hw_info.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdrun/logging.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 
 #include "replicaexchange.h"
 

diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index d853a25d75bc5cc5ae310d64c41c9b5aa3aff97a..a1d389b70d6213428b44e14c81f9b65758556c21 100644 (file)
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -84,7 +84,6 @@
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdoutf.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/mdsetup.h"
 #include "gromacs/mdlib/membed.h"
 #include "gromacs/mdlib/ns.h"
@@ -112,6 +111,7 @@
 #include "gromacs/mdtypes/interaction_const.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/observableshistory.h"
 #include "gromacs/mdtypes/pullhistory.h"
 #include "gromacs/mdtypes/state.h"

diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp
index eaefb86f225ff49dc5595bbd46fa26e63e1772d4..c12962ab130f4482fd55c433ced290e80ef3d4fd 100644 (file)
--- a/src/gromacs/mdrun/mimic.cpp
+++ b/src/gromacs/mdrun/mimic.cpp
@@ -83,7 +83,6 @@
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdoutf.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/mdsetup.h"
 #include "gromacs/mdlib/membed.h"
 #include "gromacs/mdlib/ns.h"
@@ -112,6 +111,7 @@
 #include "gromacs/mdtypes/interaction_const.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/observableshistory.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/mimic/MimicCommunicator.h"

diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp
index 2f013cc59b072cac7798c910ab3c77082640a1b5..81e5971781a5e21da04d562672e057d8d3433eab 100644 (file)
--- a/src/gromacs/mdrun/minimize.cpp
+++ b/src/gromacs/mdrun/minimize.cpp
@@ -78,7 +78,6 @@
 #include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/mdsetup.h"
 #include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/shellfc.h"
@@ -91,6 +90,7 @@
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
@@ -354,7 +354,7 @@ static void init_em(FILE *fplog,
                     const t_commrec *cr,
                     const gmx_multisim_t *ms,
                     t_inputrec *ir,
-                    const MdrunOptions &mdrunOptions,
+                    const gmx::MdrunOptions &mdrunOptions,
                     t_state *state_global, gmx_mtop_t *top_global,
                     em_state_t *ems, gmx_localtop_t *top,
                     t_nrnb *nrnb,

diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp
index 4340831023ec53e7972b4cced7f224b5fd22a94e..fa2ad1253866cb600c0ddcf7bfb3cc4ce53dfeed 100644 (file)
--- a/src/gromacs/mdrun/rerun.cpp
+++ b/src/gromacs/mdrun/rerun.cpp
@@ -84,7 +84,6 @@
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdoutf.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/mdsetup.h"
 #include "gromacs/mdlib/membed.h"
 #include "gromacs/mdlib/ns.h"
@@ -112,6 +111,7 @@
 #include "gromacs/mdtypes/interaction_const.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/observableshistory.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/mimic/MimicUtils.h"

diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index df8da62702851906590509c380fb0a288c0e24ee..d5f6614e6332e346bfce5679eef846a1c6451bd2 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -82,20 +82,19 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/boxdeformation.h"
+#include "gromacs/mdlib/broadcaststructs.h"
 #include "gromacs/mdlib/calc_verletbuf.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/makeconstraints.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/membed.h"
 #include "gromacs/mdlib/ppforceworkload.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/mdlib/sighandler.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/stophandler.h"
-#include "gromacs/mdrun/legacymdrunoptions.h"
 #include "gromacs/mdrun/logging.h"
 #include "gromacs/mdrun/multisim.h"
 #include "gromacs/mdrun/simulationcontext.h"
@@ -106,6 +105,7 @@
 #include "gromacs/mdtypes/fcdata.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/observableshistory.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/nbnxm/gpu_data_mgmt.h"

diff --git a/src/gromacs/mdrun/runner.h b/src/gromacs/mdrun/runner.h
index 465fdd27f159bed229f161b9222d320f8e300eb5..deb2fb1ca0e3aba811c96fa8e1fc17618328a3b9 100644 (file)
--- a/src/gromacs/mdrun/runner.h
+++ b/src/gromacs/mdrun/runner.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018,2019, 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.
@@ -52,7 +52,7 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/hardware/hw_info.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 

diff --git a/src/gromacs/mdrun/tpi.cpp b/src/gromacs/mdrun/tpi.cpp
index e6b77668abb9fcd4a72b9b2f238ae947fe624cbe..227ce96fd7529f925874c7074f6bf5ba48d550c7 100644 (file)
--- a/src/gromacs/mdrun/tpi.cpp
+++ b/src/gromacs/mdrun/tpi.cpp
@@ -71,7 +71,6 @@
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/force_flags.h"
 #include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/tgroup.h"
@@ -83,6 +82,7 @@
 #include "gromacs/mdtypes/group.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/threefry.h"

diff --git a/src/gromacs/mdlib/mdrun.h b/src/gromacs/mdtypes/mdrunoptions.h
similarity index 82%
rename from src/gromacs/mdlib/mdrun.h
rename to src/gromacs/mdtypes/mdrunoptions.h
index b4f85cfeac94ac3b2125b470facbad48fac53512..8e7f626310950117209bafa8cdfbbdb7760091fe 100644 (file)
--- a/src/gromacs/mdlib/mdrun.h
+++ b/src/gromacs/mdtypes/mdrunoptions.h
@@ -1,9 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2019, 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.
@@ -34,25 +32,28 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
 /*! \libinternal \file
  *
- * \brief This file declares types and functions for initializing an MD run
+ * \brief This file declares helper functionality for legacy option handling for mdrun
+ *
+ * It is likely that much of this content will move closer to the
+ * functionality that supports the respective features. For example,
+ * modules that change behaviour according to whether it is a rerun
+ * could register themselves with the rerun module and get notified at
+ * setup time to set their own boolean, rather than rely on a central
+ * glob of mdrun options being passed around.
  *
- * \author Berk Hess <hess@kth.se>
+ * \ingroup module_mdtypes
  * \inlibraryapi
  */
+#ifndef GMX_MDTYPES_MDRUNOPTIONS_H
+#define GMX_MDTYPES_MDRUNOPTIONS_H
 
-#ifndef GMX_MDLIB_MDRUN_H
-#define GMX_MDLIB_MDRUN_H
-
-#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
-struct gmx_mtop_t;
-struct t_commrec;
-struct t_inputrec;
-class t_state;
+namespace gmx
+{
 
 //! \internal \brief Options and settings for continuing from checkpoint
 struct ContinuationOptions
@@ -133,17 +134,6 @@ struct MdrunOptions
     int                 verboseStepPrintInterval = 100;
 };
 
-//! \brief Allocate and initialize node-local state entries
-void set_state_entries(t_state *state, const t_inputrec *ir);
-
-//! \brief Broadcast inputrec and mtop and allocate node-specific settings
-void init_parallel(t_commrec *cr, t_inputrec *inputrec,
-                   gmx_mtop_t *mtop);
-
-//! \brief Broadcasts the, non-dynamic, state from the master to all ranks in cr->mpi_comm_mygroup
-//
-// This is intended to be used with MPI parallelization without
-// domain decompostion (currently with NM and TPI).
-void broadcastStateWithoutDynamics(const t_commrec *cr, t_state *state);
+} // end namespace gmx
 
 #endif

diff --git a/src/gromacs/pulling/output.cpp b/src/gromacs/pulling/output.cpp
index 4f5c58ec9d8f516e5db0323f1e054ea0120009ed..55a140c4f6844058df566ae10aac05fb0af4f4e9 100644 (file)
--- a/src/gromacs/pulling/output.cpp
+++ b/src/gromacs/pulling/output.cpp
@@ -46,6 +46,7 @@
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/observableshistory.h"
 #include "gromacs/mdtypes/pullhistory.h"
 #include "gromacs/pulling/pull.h"
@@ -385,7 +386,7 @@ static void set_legend_for_coord_components(const pull_coord_work_t *pcrd, int c
 static FILE *open_pull_out(const char *fn, struct pull_t *pull,
                            const gmx_output_env_t *oenv,
                            gmx_bool bCoord,
-                           const ContinuationOptions &continuationOptions)
+                           const gmx::ContinuationOptions &continuationOptions)
 {
     FILE  *fp;
     int    nsets, m;
@@ -498,11 +499,11 @@ static FILE *open_pull_out(const char *fn, struct pull_t *pull,
     return fp;
 }
 
-void init_pull_output_files(pull_t                    *pull,
-                            int                        nfile,
-                            const t_filenm             fnm[],
-                            const gmx_output_env_t    *oenv,
-                            const ContinuationOptions &continuationOptions)
+void init_pull_output_files(pull_t                         *pull,
+                            int                             nfile,
+                            const t_filenm                  fnm[],
+                            const gmx_output_env_t         *oenv,
+                            const gmx::ContinuationOptions &continuationOptions)
 {
     /* Check for px and pf filename collision, if we are writing
        both files */

diff --git a/src/gromacs/pulling/output.h b/src/gromacs/pulling/output.h
index 3da5993b9fc77524a09608a46de89c7d5ab86b2b..fccbb10eb27b3df8f08e7210c5006d9f01fb29f6 100644 (file)
--- a/src/gromacs/pulling/output.h
+++ b/src/gromacs/pulling/output.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -51,11 +51,15 @@
 #include "gromacs/utility/basedefinitions.h"
 
 struct pull_t;
-struct ContinuationOptions;
 struct gmx_output_env_t;
 struct ObservablesHistory;
 struct t_filenm;
 
+namespace gmx
+{
+struct ContinuationOptions;
+}
+
 /*! \brief Set up and open the pull output files, when requested.
  *
  * NOTE: This should only be called on the master rank and only when
@@ -67,11 +71,11 @@ struct t_filenm;
  * \param oenv        Output options.
  * \param continuationOptions  Options for continuing from checkpoint file
  */
-void init_pull_output_files(pull_t                    *pull,
-                            int                        nfile,
-                            const t_filenm             fnm[],
-                            const gmx_output_env_t    *oenv,
-                            const ContinuationOptions &continuationOptions);
+void init_pull_output_files(pull_t                         *pull,
+                            int                             nfile,
+                            const t_filenm                  fnm[],
+                            const gmx_output_env_t         *oenv,
+                            const gmx::ContinuationOptions &continuationOptions);
 
 /*! \brief Print the pull output (x and/or f)
  *

diff --git a/src/gromacs/pulling/pull.cpp b/src/gromacs/pulling/pull.cpp
index 89eac4578ed5bc5e282179ad5da144ef9b29b100..54ba106a6296e8d250900af33a58dfcadd4daaa3 100644 (file)
--- a/src/gromacs/pulling/pull.cpp
+++ b/src/gromacs/pulling/pull.cpp
@@ -59,7 +59,6 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/forceoutput.h"
 #include "gromacs/mdtypes/inputrec.h"

diff --git a/src/gromacs/pulling/pull.h b/src/gromacs/pulling/pull.h
index 9ae87394d065c828f7f4e28f3fd651926b1828e7..46e47767d19f4f9cd5a94d6c91d7eedb896c98be 100644 (file)
--- a/src/gromacs/pulling/pull.h
+++ b/src/gromacs/pulling/pull.h
@@ -53,13 +53,11 @@
 #include <cstdio>
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
-struct ContinuationOptions;
 struct gmx_mtop_t;
 struct gmx_output_env_t;
 struct pull_coord_work_t;

diff --git a/src/gromacs/pulling/pull_rotation.cpp b/src/gromacs/pulling/pull_rotation.cpp
index a2c3210fb55cd36338379dce9faa77bdaa1e82a4..81a41009a0661b67ca5ffe1062f4515f2c162ddd 100644 (file)
--- a/src/gromacs/pulling/pull_rotation.cpp
+++ b/src/gromacs/pulling/pull_rotation.cpp
@@ -61,11 +61,11 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/groupcoord.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/cyclecounter.h"
@@ -3594,7 +3594,7 @@ static int calc_mpi_bufsize(const gmx_enfrot *er)
 std::unique_ptr<gmx::EnforcedRotation>
 init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
          const t_commrec *cr, gmx::LocalAtomSetManager * atomSets, const t_state *globalState, gmx_mtop_t *mtop, const gmx_output_env_t *oenv,
-         const MdrunOptions &mdrunOptions)
+         const gmx::MdrunOptions &mdrunOptions)
 {
     int             nat_max = 0;       /* Size of biggest rotation group */
     rvec           *x_pbc   = nullptr; /* Space for the pbc-correct atom positions */

diff --git a/src/gromacs/pulling/pull_rotation.h b/src/gromacs/pulling/pull_rotation.h
index fe313c39068b3cd95625618eeeb49a42a37a8c25..2b2c4dc04e0967589422914213c76060e2005622 100644 (file)
--- a/src/gromacs/pulling/pull_rotation.h
+++ b/src/gromacs/pulling/pull_rotation.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -60,7 +60,6 @@ struct gmx_domdec_t;
 struct gmx_enfrot;
 struct gmx_mtop_t;
 struct gmx_output_env_t;
-struct MdrunOptions;
 struct t_commrec;
 struct t_filenm;
 struct t_inputrec;
@@ -70,6 +69,8 @@ class t_state;
 namespace gmx
 {
 class LocalAtomSetManager;
+struct MdrunOptions;
+
 class EnforcedRotation
 {
     public:
@@ -111,7 +112,7 @@ class EnforcedRotation
 std::unique_ptr<gmx::EnforcedRotation>
 init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
          const t_commrec *cr, gmx::LocalAtomSetManager * atomSets, const t_state *globalState, gmx_mtop_t *mtop, const gmx_output_env_t *oenv,
-         const MdrunOptions &mdrunOptions);
+         const gmx::MdrunOptions &mdrunOptions);
 
 /*! \brief Calculates the enforced rotation potential(s).
  *

diff --git a/src/gromacs/swap/swapcoords.cpp b/src/gromacs/swap/swapcoords.cpp
index 212ddd300ad8fab0a55c5c568e72cfa9d0a2e7ed..7673365bc8fa284335d4147052ab6d05445e2305 100644 (file)
--- a/src/gromacs/swap/swapcoords.cpp
+++ b/src/gromacs/swap/swapcoords.cpp
@@ -60,11 +60,11 @@
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/groupcoord.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
 #include "gromacs/mdtypes/observableshistory.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/mdtypes/swaphistory.h"
@@ -1462,7 +1462,7 @@ void init_swapcoords(
         t_commrec                *cr,
         gmx::LocalAtomSetManager *atomSets,
         const gmx_output_env_t   *oenv,
-        const MdrunOptions       &mdrunOptions)
+        const gmx::MdrunOptions  &mdrunOptions)
 {
     t_swapcoords          *sc;
     t_swap                *s;

diff --git a/src/gromacs/swap/swapcoords.h b/src/gromacs/swap/swapcoords.h
index 736b5f193f167ce38c7a930b45623bb9c0190b40..df3a9c614552c0baa8b2dc3210e2a1b707eece14 100644 (file)
--- a/src/gromacs/swap/swapcoords.h
+++ b/src/gromacs/swap/swapcoords.h
@@ -2,7 +2,7 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * Copyright (c) 2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -61,7 +61,6 @@ struct gmx_domdec_t;
 struct gmx_mtop_t;
 struct gmx_output_env_t;
 struct gmx_wallcycle;
-struct MdrunOptions;
 struct swaphistory_t;
 struct t_commrec;
 struct t_inputrec;
@@ -72,6 +71,7 @@ struct ObservablesHistory;
 namespace gmx
 {
 class LocalAtomSetManager;
+struct MdrunOptions;
 }
 
 /*! \brief Initialize ion / water position swapping ("Computational Electrophysiology").
@@ -101,7 +101,7 @@ void init_swapcoords(
         t_commrec                *cr,
         gmx::LocalAtomSetManager *atomSets,
         const gmx_output_env_t   *oenv,
-        const MdrunOptions       &mdrunOptions);
+        const gmx::MdrunOptions  &mdrunOptions);
 
 
 /*! \brief Finalizes ion / water position swapping.

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index 5f06e0ad3cf2e447adb7b3a37d6b6064d26368c1..32be1b5ef95d3d8bf438eadde377b20dd457cae3 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -59,7 +59,6 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/gmxlib/network.h"
-#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdrun/legacymdrunoptions.h"
 #include "gromacs/mdrun/logging.h"
 #include "gromacs/mdrun/runner.h"