Move force.h and vsite.h into mdlib/

- Remove a cyclic gmxlib <-> mdlib dependency by removing an unnecessary
  include.
- A tables <-> mdlib cyclic dependency broken by moving flags only used
  in functions in forcetable.h there from force.h.
- Minor cleanup in the moved files.

Change-Id: I544a77927c2ab245437e16b17fe80d32c2badb2c

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 5de9e092900628502ada4b759519bf24d0bdd944..d2160435acb700f6e35360bf60afe03db5d80d85 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -56,7 +56,6 @@
 #include "gromacs/gmxlib/df_history.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
@@ -65,7 +64,6 @@
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/nsgrid.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
@@ -81,12 +79,14 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_grid.h"
 #include "gromacs/mdlib/shellfc.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"

diff --git a/src/gromacs/domdec/domdec.h b/src/gromacs/domdec/domdec.h
index 08b06973359a50d8438e72c33122cc51088f74b2..15a256962a01a07911662c5eaccbd1406a995ca0 100644 (file)
--- a/src/gromacs/domdec/domdec.h
+++ b/src/gromacs/domdec/domdec.h
@@ -60,7 +60,6 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
 #include "gromacs/legacyheaders/types/hw_info.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
@@ -69,6 +68,7 @@
 #include "gromacs/legacyheaders/types/state.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/idef.h"

diff --git a/src/gromacs/domdec/domdec_topology.cpp b/src/gromacs/domdec/domdec_topology.cpp
index 2eedb37b5a4b96df9e098da27963aa76d460ed92..52ce10ea257571d6a168f588f4d1d3634c95f4e4 100644 (file)
--- a/src/gromacs/domdec/domdec_topology.cpp
+++ b/src/gromacs/domdec/domdec_topology.cpp
@@ -54,16 +54,16 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_network.h"
 #include "gromacs/gmxlib/chargegroup.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp
index c75b806564c35cedf0ecdfa10a1b37c8b5fc28de..2bc8028fc18493bbaf2151c4a56ff5cd7647495f 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.cpp
+++ b/src/gromacs/gmxana/gmx_disre.cpp
@@ -54,7 +54,6 @@
 #include "gromacs/gmxana/gstat.h"
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/main.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/typedefs.h"
@@ -62,6 +61,7 @@
 #include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/pbcutil/ishift.h"

diff --git a/src/gromacs/gmxana/gmx_genion.cpp b/src/gromacs/gmxana/gmx_genion.cpp
index 63a1197fc6e56f216a7023899c15e8c05612ad1c..cd5131a8e0d9a1e1b9dcef05bf860a83db1d53e4 100644 (file)
--- a/src/gromacs/gmxana/gmx_genion.cpp
+++ b/src/gromacs/gmxana/gmx_genion.cpp
@@ -44,9 +44,9 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/legacyheaders/force.h"
 #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/random.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.cpp b/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
index 51b9377725fd6d797ab6df5c46ee1d74c550032b..d99e71b7fb6c39c91742654c1a0bc7f112bfc66d 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
@@ -51,7 +51,6 @@
 #include "gromacs/gmxlib/nonbonded/nb_generic_adress.h"
 #include "gromacs/gmxlib/nonbonded/nb_generic_cg.h"
 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"

diff --git a/src/gromacs/listed-forces/listed-forces.cpp b/src/gromacs/listed-forces/listed-forces.cpp
index ad4744489d29b41cc9c8328b3b2d0f5e6963ee20..c5498d6116840c8d67167d6736d35865b5e716a9 100644 (file)
--- a/src/gromacs/listed-forces/listed-forces.cpp
+++ b/src/gromacs/listed-forces/listed-forces.cpp
@@ -53,7 +53,6 @@
 
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/orires.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
@@ -63,6 +62,7 @@
 #include "gromacs/listed-forces/bonded.h"
 #include "gromacs/listed-forces/position-restraints.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/simd/simd.h"

diff --git a/src/gromacs/mdlib/calcvir.cpp b/src/gromacs/mdlib/calcvir.cpp
index 8031a78ac470d2f8c5a2e06958bbb309fce9ea89..79b4e1d52985a5761469291ea2e0bdbe2b109c8d 100644 (file)
--- a/src/gromacs/mdlib/calcvir.cpp
+++ b/src/gromacs/mdlib/calcvir.cpp
@@ -39,8 +39,8 @@
 
 #include <algorithm>
 
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/expanded.cpp b/src/gromacs/mdlib/expanded.cpp
index 2b840ec4e2993a4740544d4e51bbd46991322af5..7da6d05d077756360fef9eaa15133f5618cba457 100644 (file)
--- a/src/gromacs/mdlib/expanded.cpp
+++ b/src/gromacs/mdlib/expanded.cpp
@@ -47,7 +47,6 @@
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/orires.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
@@ -57,6 +56,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/calcmu.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/update.h"
 #include "gromacs/random/random.h"

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index 1e3475c92cadf75aac979c1ae61d6a409981dfb6..aba274c66c0c21af38ee10d025b76c66b397251b 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/force.h"
+#include "force.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/legacyheaders/force.h b/src/gromacs/mdlib/force.h
similarity index 53%
rename from src/gromacs/legacyheaders/force.h
rename to src/gromacs/mdlib/force.h
index 2affdcf3b21645711a6d09cd62e14d11fd7c2a56..b6df17f7845c08fcb3954fe69f03ea7f093afeaf 100644 (file)
--- a/src/gromacs/legacyheaders/force.h
+++ b/src/gromacs/mdlib/force.h
@@ -34,17 +34,18 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
-#ifndef _force_h
-#define _force_h
+#ifndef GMX_MDLIB_FORCE_H
+#define GMX_MDLIB_FORCE_H
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
 #include "gromacs/timing/wallcycle.h"
 
+struct gmx_edsam;
+struct gmx_vsite_t;
+struct nonbonded_verlet_t;
 struct t_commrec;
 struct t_fcdata;
 struct t_graph;
@@ -53,23 +54,18 @@ struct t_lambda;
 struct t_mdatoms;
 struct t_nrnb;
 struct t_pbc;
-struct gmx_edsam;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
 
 void calc_vir(int nxf, rvec x[], rvec f[], tensor vir,
               gmx_bool bScrewPBC, matrix box);
 /* Calculate virial for nxf atoms, and add it to vir */
 
 void f_calc_vir(int i0, int i1, rvec x[], rvec f[], tensor vir,
-                struct t_graph *g, rvec shift_vec[]);
+                t_graph *g, rvec shift_vec[]);
 /* Calculate virial taking periodicity into account */
 
-real RF_excl_correction(const t_forcerec *fr, struct t_graph *g,
-                        const struct t_mdatoms *mdatoms, const t_blocka *excl,
-                        rvec x[], rvec f[], rvec *fshift, const struct t_pbc *pbc,
+real RF_excl_correction(const t_forcerec *fr, t_graph *g,
+                        const t_mdatoms *mdatoms, const t_blocka *excl,
+                        rvec x[], rvec f[], rvec *fshift, const t_pbc *pbc,
                         real lambda, real *dvdlambda);
 /* Calculate the reaction-field energy correction for this node:
  * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
@@ -83,52 +79,49 @@ void calc_rffac(FILE *fplog, int eel, real eps_r, real eps_rf,
 /* Determine the reaction-field constants */
 
 void init_generalized_rf(FILE *fplog,
-                         const gmx_mtop_t *mtop, const struct t_inputrec *ir,
+                         const gmx_mtop_t *mtop, const t_inputrec *ir,
                          t_forcerec *fr);
 /* Initialize the generalized reaction field parameters */
 
 
 /* In wall.c */
 void make_wall_tables(FILE *fplog,
-                      const struct t_inputrec *ir, const char *tabfn,
+                      const t_inputrec *ir, const char *tabfn,
                       const gmx_groups_t *groups,
                       t_forcerec *fr);
 
-real do_walls(struct t_inputrec *ir, t_forcerec *fr, matrix box, struct t_mdatoms *md,
-              rvec x[], rvec f[], real lambda, real Vlj[], struct t_nrnb *nrnb);
-
-#define GMX_MAKETABLES_FORCEUSER  (1<<0)
-#define GMX_MAKETABLES_14ONLY     (1<<1)
+real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
+              rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb);
 
-gmx_bool can_use_allvsall(const struct t_inputrec *ir,
-                          gmx_bool bPrintNote, struct t_commrec *cr, FILE *fp);
+gmx_bool can_use_allvsall(const t_inputrec *ir,
+                          gmx_bool bPrintNote, t_commrec *cr, FILE *fp);
 /* Returns if we can use all-vs-all loops.
  * If bPrintNote==TRUE, prints a note, if necessary, to stderr
  * and fp (if !=NULL) on the master node.
  */
 
 
-gmx_bool nbnxn_gpu_acceleration_supported(FILE                    *fplog,
-                                          const struct t_commrec  *cr,
-                                          const struct t_inputrec *ir,
-                                          gmx_bool                 bRerunMD);
+gmx_bool nbnxn_gpu_acceleration_supported(FILE             *fplog,
+                                          const t_commrec  *cr,
+                                          const t_inputrec *ir,
+                                          gmx_bool          bRerunMD);
 /* Return if GPU acceleration is supported with the given settings.
  *
  * If the return value is FALSE and fplog/cr != NULL, prints a fallback
  * message to fplog/stderr.
  */
 
-gmx_bool nbnxn_simd_supported(FILE                    *fplog,
-                              const struct t_commrec  *cr,
-                              const struct t_inputrec *ir);
+gmx_bool nbnxn_simd_supported(FILE             *fplog,
+                              const t_commrec  *cr,
+                              const t_inputrec *ir);
 /* Return if CPU SIMD support exists for the given inputrec
  * If the return value is FALSE and fplog/cr != NULL, prints a fallback
  * message to fplog/stderr.
  */
 
-gmx_bool uses_simple_tables(int                        cutoff_scheme,
-                            struct nonbonded_verlet_t *nbv,
-                            int                        group);
+gmx_bool uses_simple_tables(int                 cutoff_scheme,
+                            nonbonded_verlet_t *nbv,
+                            int                 group);
 /* Returns whether simple tables (i.e. not for use with GPUs) are used
  * with the type of kernel indicated.
  */
@@ -150,29 +143,29 @@ void reset_enerdata(t_forcerec *fr, gmx_bool bNS,
 void sum_epot(gmx_grppairener_t *grpp, real *epot);
 /* Locally sum the non-bonded potential energy terms */
 
-void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, struct t_lambda *fepvals);
+void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, t_lambda *fepvals);
 /* Sum the free energy contributions */
 
 /* Compute the average C6 and C12 params for LJ corrections */
 void set_avcsixtwelve(FILE *fplog, t_forcerec *fr,
                       const gmx_mtop_t *mtop);
 
-extern void do_force(FILE *log, struct t_commrec *cr,
-                     struct t_inputrec *inputrec,
-                     gmx_int64_t step, struct t_nrnb *nrnb, gmx_wallcycle_t wcycle,
-                     gmx_localtop_t *top,
-                     gmx_groups_t *groups,
-                     matrix box, rvec x[], history_t *hist,
-                     rvec f[],
-                     tensor vir_force,
-                     struct t_mdatoms *mdatoms,
-                     gmx_enerdata_t *enerd, struct t_fcdata *fcd,
-                     real *lambda, struct t_graph *graph,
-                     t_forcerec *fr,
-                     gmx_vsite_t *vsite, rvec mu_tot,
-                     double t, FILE *field, struct gmx_edsam *ed,
-                     gmx_bool bBornRadii,
-                     int flags);
+void do_force(FILE *log, t_commrec *cr,
+              t_inputrec *inputrec,
+              gmx_int64_t step, struct t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+              gmx_localtop_t *top,
+              gmx_groups_t *groups,
+              matrix box, rvec x[], history_t *hist,
+              rvec f[],
+              tensor vir_force,
+              t_mdatoms *mdatoms,
+              gmx_enerdata_t *enerd, t_fcdata *fcd,
+              real *lambda, struct t_graph *graph,
+              t_forcerec *fr,
+              gmx_vsite_t *vsite, rvec mu_tot,
+              double t, FILE *field, struct gmx_edsam *ed,
+              gmx_bool bBornRadii,
+              int flags);
 
 /* Communicate coordinates (if parallel).
  * Do neighbor searching (if necessary).
@@ -183,51 +176,47 @@ extern void do_force(FILE *log, struct t_commrec *cr,
  * f is always required.
  */
 
-void ns(FILE                     *fplog,
-        t_forcerec               *fr,
-        matrix                    box,
-        gmx_groups_t             *groups,
-        gmx_localtop_t           *top,
-        struct t_mdatoms         *md,
-        struct t_commrec         *cr,
-        struct t_nrnb            *nrnb,
-        gmx_bool                  bFillGrid,
-        gmx_bool                  bDoLongRangeNS);
+void ns(FILE              *fplog,
+        t_forcerec        *fr,
+        matrix             box,
+        gmx_groups_t      *groups,
+        gmx_localtop_t    *top,
+        t_mdatoms         *md,
+        t_commrec         *cr,
+        t_nrnb            *nrnb,
+        gmx_bool           bFillGrid,
+        gmx_bool           bDoLongRangeNS);
 /* Call the neighborsearcher */
 
-extern void do_force_lowlevel(t_forcerec   *fr,
-                              struct t_inputrec   *ir,
-                              t_idef       *idef,
-                              struct t_commrec    *cr,
-                              struct t_nrnb       *nrnb,
-                              gmx_wallcycle_t wcycle,
-                              struct t_mdatoms    *md,
-                              rvec         x[],
-                              history_t    *hist,
-                              rvec         f_shortrange[],
-                              rvec         f_longrange[],
-                              gmx_enerdata_t *enerd,
-                              struct t_fcdata     *fcd,
-                              gmx_localtop_t *top,
-                              gmx_genborn_t *born,
-                              gmx_bool         bBornRadii,
-                              matrix       box,
-                              struct t_lambda     *fepvals,
-                              real         *lambda,
-                              struct t_graph      *graph,
-                              t_blocka     *excl,
-                              rvec         mu_tot[2],
-                              int          flags,
-                              float        *cycles_pme);
+void do_force_lowlevel(t_forcerec   *fr,
+                       t_inputrec   *ir,
+                       t_idef       *idef,
+                       t_commrec    *cr,
+                       t_nrnb       *nrnb,
+                       gmx_wallcycle_t wcycle,
+                       t_mdatoms    *md,
+                       rvec         x[],
+                       history_t    *hist,
+                       rvec         f_shortrange[],
+                       rvec         f_longrange[],
+                       gmx_enerdata_t *enerd,
+                       t_fcdata     *fcd,
+                       gmx_localtop_t *top,
+                       gmx_genborn_t *born,
+                       gmx_bool         bBornRadii,
+                       matrix       box,
+                       t_lambda     *fepvals,
+                       real         *lambda,
+                       t_graph      *graph,
+                       t_blocka     *excl,
+                       rvec         mu_tot[2],
+                       int          flags,
+                       float        *cycles_pme);
 /* Call all the force routines */
 
-void free_gpu_resources(const t_forcerec                   *fr,
-                        const struct t_commrec             *cr,
-                        const struct gmx_gpu_info_t        *gpu_info,
-                        const gmx_gpu_opt_t                *gpu_opt);
+void free_gpu_resources(const t_forcerec            *fr,
+                        const t_commrec             *cr,
+                        const gmx_gpu_info_t        *gpu_info,
+                        const gmx_gpu_opt_t         *gpu_opt);
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _force_h */

diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp
index 297c96de1427a2817b094598a1fd12062750fb48..647be0f8fc9255248b50fe7323a72043c3875c8e 100644 (file)
--- a/src/gromacs/mdlib/forcerec.cpp
+++ b/src/gromacs/mdlib/forcerec.cpp
@@ -54,7 +54,6 @@
 #include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_detect_hardware.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/inputrec.h"
@@ -72,6 +71,7 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec-threading.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/nb_verlet.h"

diff --git a/src/gromacs/mdlib/forcerec.h b/src/gromacs/mdlib/forcerec.h
index 2bea6b346753f5f835eeb3c712a97b7ac023dd5f..2739ed861f1b646cf9f52f67ee5292c35a0fda2d 100644 (file)
--- a/src/gromacs/mdlib/forcerec.h
+++ b/src/gromacs/mdlib/forcerec.h
@@ -40,10 +40,10 @@
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
 #include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/timing/wallcycle.h"
 
 struct t_fcdata;

diff --git a/src/gromacs/mdlib/integrator.h b/src/gromacs/mdlib/integrator.h
index 5e741eb4a0f7325094021f3f1dd9729459411640..4bfdb40696ec6f49e5792c77fd6aae31905e1ec0 100644 (file)
--- a/src/gromacs/mdlib/integrator.h
+++ b/src/gromacs/mdlib/integrator.h
@@ -43,7 +43,6 @@
 #include <cstdio>
 
 #include "gromacs/fileio/filenm.h"
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
@@ -51,6 +50,7 @@
 #include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/legacyheaders/types/state.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
 #include "gromacs/utility/basedefinitions.h"

diff --git a/src/gromacs/mdlib/minimize.cpp b/src/gromacs/mdlib/minimize.cpp
index 2e547355657a24a8d5a42b45d2cc9e650f778c51..165272d39cd4a896a059023e728b1c0f6c3c48eb 100644 (file)
--- a/src/gromacs/mdlib/minimize.cpp
+++ b/src/gromacs/mdlib/minimize.cpp
@@ -60,7 +60,6 @@
 #include "gromacs/fileio/mtxio.h"
 #include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
@@ -68,13 +67,13 @@
 #include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
 #include "gromacs/listed-forces/manage-threading.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
@@ -84,6 +83,7 @@
 #include "gromacs/mdlib/tgroup.h"
 #include "gromacs/mdlib/trajectory_writing.h"
 #include "gromacs/mdlib/update.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp
index 362977f06fab9963235974cd514081848a0eecf3..3156b0f22aa8d697e6e1b0ae73f6983c70d82751 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp
@@ -40,9 +40,9 @@
 
 #include <cmath>
 
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
index 98af04f0e3ca9caccc460d7cb2697285e9db1a64..1df14268fdf892554f8369f6d55a9cdf009d74c6 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
@@ -42,9 +42,9 @@
 
 #include <cmath>
 
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"

diff --git a/src/gromacs/mdlib/ns.cpp b/src/gromacs/mdlib/ns.cpp
index 0e215a4f64b2cd19a4c44c0e2f6c00d7f688c4e8..5409fa3892e32e5f02dc265de38c457154cfc0b7 100644 (file)
--- a/src/gromacs/mdlib/ns.cpp
+++ b/src/gromacs/mdlib/ns.cpp
@@ -47,7 +47,6 @@
 #include <algorithm>
 
 #include "gromacs/domdec/domdec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
@@ -59,6 +58,7 @@
 #include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/mdlib/qm_gamess.cpp b/src/gromacs/mdlib/qm_gamess.cpp
index d185161d9fca01006d779fef98516cb40da8c403..e3f9b6d26550d5d703eaf642c8c09b6626701f6f 100644 (file)
--- a/src/gromacs/mdlib/qm_gamess.cpp
+++ b/src/gromacs/mdlib/qm_gamess.cpp
@@ -46,7 +46,6 @@
 #include <string.h>
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
@@ -56,6 +55,7 @@
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/qm_gaussian.cpp b/src/gromacs/mdlib/qm_gaussian.cpp
index e7b7b26092ccc492475e5d88bfac82501aa23533..069bb3d6c88f2383e4b735c25d3161552c6f2618 100644 (file)
--- a/src/gromacs/mdlib/qm_gaussian.cpp
+++ b/src/gromacs/mdlib/qm_gaussian.cpp
@@ -46,7 +46,6 @@
 #include <string.h>
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
@@ -55,6 +54,7 @@
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/qm_mopac.cpp b/src/gromacs/mdlib/qm_mopac.cpp
index 28d9a6bd55c35657321d95926eb0918b66cc7225..0277d4b2ab3e7e708d1b28781a37ad5ac509f5c3 100644 (file)
--- a/src/gromacs/mdlib/qm_mopac.cpp
+++ b/src/gromacs/mdlib/qm_mopac.cpp
@@ -46,7 +46,6 @@
 #include <string.h>
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
@@ -55,6 +54,7 @@
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/qm_orca.cpp b/src/gromacs/mdlib/qm_orca.cpp
index 47a892bf2ff14e80c8146ea9f7b594466c1b08a6..4347120bf2ab4b4108ecfc9a101775b0664e072c 100644 (file)
--- a/src/gromacs/mdlib/qm_orca.cpp
+++ b/src/gromacs/mdlib/qm_orca.cpp
@@ -42,7 +42,6 @@
 #include <string.h>
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
@@ -51,6 +50,7 @@
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/qmmm.cpp b/src/gromacs/mdlib/qmmm.cpp
index 0194429b06b884e9c1fc63239e17879dd7f9cf78..af1311145d4b7cd0926877513bc4db3117234c0d 100644 (file)
--- a/src/gromacs/mdlib/qmmm.cpp
+++ b/src/gromacs/mdlib/qmmm.cpp
@@ -50,7 +50,6 @@
 #include <algorithm>
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
@@ -61,6 +60,7 @@
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/mdlib/rf_util.cpp b/src/gromacs/mdlib/rf_util.cpp
index 4b080ff851ac8970bf8f0a62857efa713dfd83a7..0855c224cb6b88c793d72656edb9234ad8d7c54c 100644 (file)
--- a/src/gromacs/mdlib/rf_util.cpp
+++ b/src/gromacs/mdlib/rf_util.cpp
@@ -39,12 +39,12 @@
 #include <cmath>
 
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/shellfc.cpp b/src/gromacs/mdlib/shellfc.cpp
index 05822bfa8fcd673e83b836bf5c02283667c71fe8..f61bfef4e07ad1ded72a3a0ea7dd5c6d76e58a42 100644 (file)
--- a/src/gromacs/mdlib/shellfc.cpp
+++ b/src/gromacs/mdlib/shellfc.cpp
@@ -45,17 +45,17 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/gmxlib/chargegroup.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/mdlib/shellfc.h b/src/gromacs/mdlib/shellfc.h
index 28d65d0a7ee0603733958571129fc18dec1a3476..5fa342055c9368896c08f8b466a02d411d1e92ae 100644 (file)
--- a/src/gromacs/mdlib/shellfc.h
+++ b/src/gromacs/mdlib/shellfc.h
@@ -38,7 +38,7 @@
 #define GMX_MDLIB_SHELLFC_H
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/timing/wallcycle.h"
 
 struct gmx_constr;

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index f01a839d99b0a322f0b4e383ce87a2bcc0db2827..03af2b6297c01af86e682b286049e67cadc4d6b2 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -57,7 +57,6 @@
 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/names.h"
@@ -72,6 +71,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/calcmu.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/nb_verlet.h"

diff --git a/src/gromacs/mdlib/stat.cpp b/src/gromacs/mdlib/stat.cpp
index 806e744b00b247fed390830bdf315af24d528245..39c3648564fcf4278b5bea1bc7cdc3782b9dd1d8 100644 (file)
--- a/src/gromacs/mdlib/stat.cpp
+++ b/src/gromacs/mdlib/stat.cpp
@@ -42,7 +42,6 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/txtdump.h"
@@ -52,6 +51,7 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/rbin.h"

diff --git a/src/gromacs/mdlib/tpi.cpp b/src/gromacs/mdlib/tpi.cpp
index c317c321d3ffd00412a117bddc558bb2c28d7c15..0cce08ad7762f963db241da8eb83eb7688127508 100644 (file)
--- a/src/gromacs/mdlib/tpi.cpp
+++ b/src/gromacs/mdlib/tpi.cpp
@@ -60,25 +60,25 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdebin.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/tgroup.h"
 #include "gromacs/mdlib/update.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/random/random.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"

diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp
index 76ae56d714c34cdef17e60bf20eefa728be3209c..10254f08c1d93e701c03aeae73ba22473b0cb4ce 100644 (file)
--- a/src/gromacs/mdlib/update.cpp
+++ b/src/gromacs/mdlib/update.cpp
@@ -46,7 +46,6 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/orires.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
@@ -57,6 +56,7 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/tgroup.h"

diff --git a/src/gromacs/mdlib/vsite.cpp b/src/gromacs/mdlib/vsite.cpp
index 4cb0dc8816f7526749f2f6e82ce64e14d8b67578..a6b29b0fd7601e1befff7689e80304bf2e85403f 100644 (file)
--- a/src/gromacs/mdlib/vsite.cpp
+++ b/src/gromacs/mdlib/vsite.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/vsite.h"
+#include "vsite.h"
 
 #include <stdio.h>
 

diff --git a/src/gromacs/legacyheaders/vsite.h b/src/gromacs/mdlib/vsite.h
similarity index 85%
rename from src/gromacs/legacyheaders/vsite.h
rename to src/gromacs/mdlib/vsite.h
index 736a241c4897346f60a94256d978eafd36e9b908..71253dbf18cb769404750a1ac4f6b072dd3df1ab 100644 (file)
--- a/src/gromacs/legacyheaders/vsite.h
+++ b/src/gromacs/mdlib/vsite.h
@@ -34,30 +34,24 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
-#ifndef _vsite_h
-#define _vsite_h
-
-#include <stdio.h>
+#ifndef GMX_MDLIB_VSITE_H
+#define GMX_MDLIB_VSITE_H
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/pbcutil/ishift.h"
 
 struct t_commrec;
+struct t_graph;
 struct t_mdatoms;
 struct t_nrnb;
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-typedef struct {
+typedef struct gmx_vsite_thread_t {
     t_ilist ilist[F_NRE];     /* vsite ilists for this thread            */
     rvec    fshift[SHIFTS];   /* fshift accumulation buffer              */
     matrix  dxdf;             /* virial dx*df accumulation buffer        */
 } gmx_vsite_thread_t;
 
-typedef struct {
+typedef struct gmx_vsite_t {
     gmx_bool            bHaveChargeGroups;    /* Do we have charge groups?               */
     int                 n_intercg_vsite;      /* The number of inter charge group vsites */
     int                 nvsite_pbc_molt;      /* The array size of vsite_pbc_molt        */
@@ -70,14 +64,12 @@ typedef struct {
     int                 th_ind_nalloc;        /* Size of th_ind                          */
 } gmx_vsite_t;
 
-struct t_graph;
-
 void construct_vsites(const gmx_vsite_t *vsite,
                       rvec x[],
                       real dt, rvec v[],
                       const t_iparams ip[], const t_ilist ilist[],
                       int ePBC, gmx_bool bMolPBC,
-                      struct t_commrec *cr, matrix box);
+                      t_commrec *cr, matrix box);
 /* Create positions of vsite atoms based on surrounding atoms
  * for the local system.
  * If v is passed, the velocities of the vsites will be calculated
@@ -98,9 +90,9 @@ void construct_vsites_mtop(gmx_vsite_t *vsite,
 void spread_vsite_f(gmx_vsite_t *vsite,
                     rvec x[], rvec f[], rvec *fshift,
                     gmx_bool VirCorr, matrix vir,
-                    struct t_nrnb *nrnb, t_idef *idef,
-                    int ePBC, gmx_bool bMolPBC, struct t_graph *g, matrix box,
-                    struct t_commrec *cr);
+                    t_nrnb *nrnb, t_idef *idef,
+                    int ePBC, gmx_bool bMolPBC, t_graph *g, matrix box,
+                    t_commrec *cr);
 /* Spread the force operating on the vsite atoms on the surrounding atoms.
  * If fshift!=NULL also update the shift forces.
  * If VirCorr=TRUE add the virial correction for non-linear vsite constructs
@@ -109,7 +101,7 @@ void spread_vsite_f(gmx_vsite_t *vsite,
  * as for instance for the PME mesh contribution.
  */
 
-gmx_vsite_t *init_vsite(const gmx_mtop_t *mtop, struct t_commrec *cr,
+gmx_vsite_t *init_vsite(const gmx_mtop_t *mtop, t_commrec *cr,
                         gmx_bool bSerial_NoPBC);
 /* Initialize the virtual site struct,
  * returns NULL when there are no virtual sites.
@@ -118,23 +110,19 @@ gmx_vsite_t *init_vsite(const gmx_mtop_t *mtop, struct t_commrec *cr,
  * this is useful for correction vsites of the initial configuration.
  */
 
-void split_vsites_over_threads(const t_ilist          *ilist,
-                               const t_iparams        *ip,
-                               const struct t_mdatoms *mdatoms,
-                               gmx_bool                bLimitRange,
-                               gmx_vsite_t            *vsite);
+void split_vsites_over_threads(const t_ilist   *ilist,
+                               const t_iparams *ip,
+                               const t_mdatoms *mdatoms,
+                               gmx_bool         bLimitRange,
+                               gmx_vsite_t     *vsite);
 /* Divide the vsite work-load over the threads.
  * Should be called at the end of the domain decomposition.
  */
 
-void set_vsite_top(gmx_vsite_t *vsite, gmx_localtop_t *top, struct t_mdatoms *md,
-                   struct t_commrec *cr);
+void set_vsite_top(gmx_vsite_t *vsite, gmx_localtop_t *top, t_mdatoms *md,
+                   t_commrec *cr);
 /* Set some vsite data for runs without domain decomposition.
  * Should be called once after init_vsite, before calling other routines.
  */
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif

diff --git a/src/gromacs/mdlib/wall.cpp b/src/gromacs/mdlib/wall.cpp
index 4258765f86d0e9cc771cdccf04a7fecb2932bca4..d2d85e1bd72cf1448d934d03d5d05d314fafa4b5 100644 (file)
--- a/src/gromacs/mdlib/wall.cpp
+++ b/src/gromacs/mdlib/wall.cpp
@@ -42,13 +42,13 @@
 #include <algorithm>
 
 #include "gromacs/fileio/filenm.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/tables/forcetable.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/wnblist.cpp b/src/gromacs/mdlib/wnblist.cpp
index c9a86b0ba4625eadb199c179c7849b1dddec6453..76b4bd9a40a8d53215e51d5cb0f274fb9e31bc46 100644 (file)
--- a/src/gromacs/mdlib/wnblist.cpp
+++ b/src/gromacs/mdlib/wnblist.cpp
@@ -44,11 +44,11 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/tables/forcetable.cpp b/src/gromacs/tables/forcetable.cpp
index 1b18e4a2084508b32a1f9f764bae90c9a2cb1e7c..c1ec70b995405bff1bba5066f4e6b11930f088aa 100644 (file)
--- a/src/gromacs/tables/forcetable.cpp
+++ b/src/gromacs/tables/forcetable.cpp
@@ -43,7 +43,6 @@
 #include <algorithm>
 
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"

diff --git a/src/gromacs/tables/forcetable.h b/src/gromacs/tables/forcetable.h
index 20c385b434e182a5e0a5dd0f016c9b9205361cac..0b8553d7e40c56cb83598dfcb67d2964279d6ba3 100644 (file)
--- a/src/gromacs/tables/forcetable.h
+++ b/src/gromacs/tables/forcetable.h
@@ -40,6 +40,9 @@
 #include "gromacs/legacyheaders/types/interaction_const.h"
 #include "gromacs/utility/real.h"
 
+#define GMX_MAKETABLES_FORCEUSER  (1<<0)
+#define GMX_MAKETABLES_14ONLY     (1<<1)
+
 /* Index in the tables that says which function to use */
 enum {
     etiCOUL, etiLJ6, etiLJ12, etiNR

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index 4b96aec3400898a1292fb1a4455785c7066504f6..ee0ce8775b623091ab7a2d5f18197767096f3d5f 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -58,12 +58,10 @@
 #include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
@@ -82,6 +80,7 @@
 #include "gromacs/mdlib/compute_io.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
@@ -97,6 +96,7 @@
 #include "gromacs/mdlib/trajectory_writing.h"
 #include "gromacs/mdlib/update.h"
 #include "gromacs/mdlib/vcm.h"
+#include "gromacs/mdlib/vsite.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"

diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index 829432470268c6bdb3054eac8228131dc2b90f68..73eb3e55857b07a0dbcb4e7fe8915cf6cc80372d 100644 (file)
--- a/src/programs/mdrun/runner.cpp
+++ b/src/programs/mdrun/runner.cpp
@@ -68,7 +68,6 @@
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_detect_hardware.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/gmx_thread_affinity.h"
@@ -81,6 +80,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/calc_verletbuf.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/integrator.h"
 #include "gromacs/mdlib/md_support.h"