Removed types/mdatom.h from typedefs.h

Change-Id: Icc0b0201523ebc0098e13f789b7e70b7e41c6541

diff --git a/src/gromacs/gmxlib/orires.cpp b/src/gromacs/gmxlib/orires.cpp
index 4be17d711574600b467b03ca80b9f89bb9565901..df1fb6594214be36099ca41f2a6f8f28e35e5343 100644 (file)
--- a/src/gromacs/gmxlib/orires.cpp
+++ b/src/gromacs/gmxlib/orires.cpp
@@ -47,6 +47,7 @@
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/linearalgebra/nrjac.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/legacyheaders/force.h b/src/gromacs/legacyheaders/force.h
index 2a5ca67465bd7781c0cbc2787e593ab4c7814ff5..c205aa8a623d9ad1d977c239218126f4979e05ba 100644 (file)
--- a/src/gromacs/legacyheaders/force.h
+++ b/src/gromacs/legacyheaders/force.h
@@ -50,6 +50,7 @@ struct t_fcdata;
 struct t_graph;
 struct t_grpopts;
 struct t_lambda;
+struct t_mdatoms;
 struct t_pbc;
 struct gmx_edsam;
 
@@ -66,7 +67,7 @@ void f_calc_vir(int i0, int i1, rvec x[], rvec f[], tensor vir,
 /* Calculate virial taking periodicity into account */
 
 real RF_excl_correction(const t_forcerec *fr, struct t_graph *g,
-                        const t_mdatoms *mdatoms, const t_blocka *excl,
+                        const struct t_mdatoms *mdatoms, const t_blocka *excl,
                         rvec x[], rvec f[], rvec *fshift, const struct t_pbc *pbc,
                         real lambda, real *dvdlambda);
 /* Calculate the reaction-field energy correction for this node:
@@ -92,7 +93,7 @@ void make_wall_tables(FILE *fplog,
                       const gmx_groups_t *groups,
                       t_forcerec *fr);
 
-real do_walls(struct t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
+real do_walls(struct t_inputrec *ir, t_forcerec *fr, matrix box, struct t_mdatoms *md,
               rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb);
 
 #define GMX_MAKETABLES_FORCEUSER  (1<<0)
@@ -155,7 +156,7 @@ extern void do_force(FILE *log, struct t_commrec *cr,
                      matrix box, rvec x[], history_t *hist,
                      rvec f[],
                      tensor vir_force,
-                     t_mdatoms *mdatoms,
+                     struct t_mdatoms *mdatoms,
                      gmx_enerdata_t *enerd, struct t_fcdata *fcd,
                      real *lambda, struct t_graph *graph,
                      t_forcerec *fr,
@@ -178,7 +179,7 @@ void ns(FILE                     *fplog,
         matrix                    box,
         gmx_groups_t             *groups,
         gmx_localtop_t           *top,
-        t_mdatoms                *md,
+        struct t_mdatoms         *md,
         struct t_commrec         *cr,
         t_nrnb                   *nrnb,
         gmx_bool                  bFillGrid,
@@ -191,7 +192,7 @@ extern void do_force_lowlevel(t_forcerec   *fr,
                               struct t_commrec    *cr,
                               t_nrnb       *nrnb,
                               gmx_wallcycle_t wcycle,
-                              t_mdatoms    *md,
+                              struct t_mdatoms    *md,
                               rvec         x[],
                               history_t    *hist,
                               rvec         f_shortrange[],

diff --git a/src/gromacs/legacyheaders/genborn.h b/src/gromacs/legacyheaders/genborn.h
index 6ad0797ec46ef11ec0a11fe2c95695b61aaa9aa2..61286b4293166cfbfefd1da16170722a27febad0 100644 (file)
--- a/src/gromacs/legacyheaders/genborn.h
+++ b/src/gromacs/legacyheaders/genborn.h
@@ -47,6 +47,7 @@ struct t_commrec;
 struct t_forcerec;
 struct t_graph;
 struct t_inputrec;
+struct t_mdatoms;
 struct t_pbc;
 
 #ifdef __cplusplus

diff --git a/src/gromacs/legacyheaders/mdrun.h b/src/gromacs/legacyheaders/mdrun.h
index 06f5f0b71041e66b6e01cd19409d9ef811281e48..1d00e9827cbdaa02f6f05e85aac868b6ca1ef772 100644 (file)
--- a/src/gromacs/legacyheaders/mdrun.h
+++ b/src/gromacs/legacyheaders/mdrun.h
@@ -50,6 +50,7 @@ struct gmx_edsam;
 struct gmx_enerdata_t;
 struct t_expanded;
 struct t_lambda;
+struct t_mdatoms;
 struct t_simtemp;
 
 #ifdef __cplusplus

diff --git a/src/gromacs/legacyheaders/ns.h b/src/gromacs/legacyheaders/ns.h
index 8d7832418ea7429a115606ec1a1ffaa4a2cfed50..92fff91d8aad658020dae14339c8fcd36e9c8fe2 100644 (file)
--- a/src/gromacs/legacyheaders/ns.h
+++ b/src/gromacs/legacyheaders/ns.h
@@ -45,6 +45,7 @@
 struct gmx_ns_t;
 struct t_commrec;
 struct t_forcerec;
+struct t_mdatoms;
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/sim_util.h b/src/gromacs/legacyheaders/sim_util.h
index 58ee48b964dc0cb5cedd7bf2a8ef42b0a46c3f44..913904957beb4e91a1fa5b68128dadf6887d47aa 100644 (file)
--- a/src/gromacs/legacyheaders/sim_util.h
+++ b/src/gromacs/legacyheaders/sim_util.h
@@ -48,6 +48,7 @@
 #include "gromacs/timing/walltime_accounting.h"
 
 struct gmx_constr;
+struct t_mdatoms;
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/tgroup.h b/src/gromacs/legacyheaders/tgroup.h
index e83e2b7e8bae52fb23015b9bc7f66f4e8b0da7ed..7194bde173976b339a4846eebcefc54e53c3f127 100644 (file)
--- a/src/gromacs/legacyheaders/tgroup.h
+++ b/src/gromacs/legacyheaders/tgroup.h
@@ -43,6 +43,7 @@
 struct gmx_ekindata_t;
 struct t_commrec;
 struct t_grpopts;
+struct t_mdatoms;
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/typedefs.h b/src/gromacs/legacyheaders/typedefs.h
index ede429c85a09988ff444520f7fd05d7786959cb9..e69e25cf18ee0a3912bcf890f46da5819b368227 100644 (file)
--- a/src/gromacs/legacyheaders/typedefs.h
+++ b/src/gromacs/legacyheaders/typedefs.h
@@ -42,7 +42,6 @@
 /* DEPRECATED! value for signaling unitialized variables */
 #define NOTSET -12345
 
-#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/legacyheaders/types/nblist.h"
 #include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/legacyheaders/types/nsgrid.h"

diff --git a/src/gromacs/legacyheaders/update.h b/src/gromacs/legacyheaders/update.h
index fc18b8a8e899cb37dd6bc95ec414f8d39e981231..5bff507152b8e5658bb71adecbc7a9858074a0eb 100644 (file)
--- a/src/gromacs/legacyheaders/update.h
+++ b/src/gromacs/legacyheaders/update.h
@@ -47,6 +47,7 @@ struct gmx_enerdata_t;
 struct t_fcdata;
 struct t_graph;
 struct t_grpopts;
+struct t_mdatoms;
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/vsite.h b/src/gromacs/legacyheaders/vsite.h
index 3ae5e2c6e09baa4e0081bec4d50d5907fe87c18a..7c3f35491e3b1967c5dae340931b580cb07bbe99 100644 (file)
--- a/src/gromacs/legacyheaders/vsite.h
+++ b/src/gromacs/legacyheaders/vsite.h
@@ -44,6 +44,7 @@
 #include "gromacs/pbcutil/ishift.h"
 
 struct t_commrec;
+struct t_mdatoms;
 
 #ifdef __cplusplus
 extern "C" {
@@ -116,16 +117,16 @@ 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 t_mdatoms *mdatoms,
-                               gmx_bool         bLimitRange,
-                               gmx_vsite_t     *vsite);
+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);
 /* 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, t_mdatoms *md,
+void set_vsite_top(gmx_vsite_t *vsite, gmx_localtop_t *top, struct t_mdatoms *md,
                    struct t_commrec *cr);
 /* Set some vsite data for runs without domain decomposition.
  * Should be called once after init_vsite, before calling other routines.

diff --git a/src/gromacs/listed-forces/listed-forces.h b/src/gromacs/listed-forces/listed-forces.h
index f5603db8b2aa7d3ecd17c5e616c8943b365b42c3..1ecad3c1516dc386618c306e2723b347e03d62bf 100644 (file)
--- a/src/gromacs/listed-forces/listed-forces.h
+++ b/src/gromacs/listed-forces/listed-forces.h
@@ -75,6 +75,7 @@ struct t_fcdata;
 struct t_forcerec;
 struct t_inputrec;
 struct t_lambda;
+struct t_mdatoms;
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/mdlib/adress.cpp b/src/gromacs/mdlib/adress.cpp
index bb8a5ad3aae966e89a51fd0b7046975724af2d35..4699589fc5cc9d0edeb83a9a669d31a21b346aa9 100644 (file)
--- a/src/gromacs/mdlib/adress.cpp
+++ b/src/gromacs/mdlib/adress.cpp
@@ -42,6 +42,7 @@
 
 #include "gromacs/legacyheaders/types/forcerec.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/adress.h b/src/gromacs/mdlib/adress.h
index 51e8b7ee038e0ac07a354a9678cec7ad4d40899e..bbb4f9f644a26c576e787a642d51e484668fc88d 100644 (file)
--- a/src/gromacs/mdlib/adress.h
+++ b/src/gromacs/mdlib/adress.h
@@ -48,6 +48,7 @@ extern "C"
 #endif
 
 struct t_forcerec;
+struct t_mdatoms;
 struct t_pbc;
 
 /** \brief calculates the AdResS weight of a particle

diff --git a/src/gromacs/mdlib/genborn_allvsall.cpp b/src/gromacs/mdlib/genborn_allvsall.cpp
index 42e07f73419972fd02266af0643c409031ea6dcf..b3ee3ee9663533a6c76887f2377b0f8f98c40f36 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall.cpp
+++ b/src/gromacs/mdlib/genborn_allvsall.cpp
@@ -45,6 +45,7 @@
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/genborn_allvsall.h b/src/gromacs/mdlib/genborn_allvsall.h
index ddc9c78dee6f6a847c08082acc41468157630db3..f06126cf9009da1835101e33f0294552153ed5d8 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall.h
+++ b/src/gromacs/mdlib/genborn_allvsall.h
@@ -42,6 +42,7 @@
 
 struct gmx_genborn_t;
 struct t_forcerec;
+struct t_mdatoms;
 
 int
 genborn_allvsall_calc_still_radii(struct t_forcerec *           fr,

diff --git a/src/gromacs/mdlib/nbnxn_atomdata.h b/src/gromacs/mdlib/nbnxn_atomdata.h
index 1b4e4040294bec0be52bfbf2bfcbebea8c007724..f9e9c44f794fee604e2e34f649f7928d87702986 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_atomdata.h
+++ b/src/gromacs/mdlib/nbnxn_atomdata.h
@@ -39,6 +39,7 @@
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/mdlib/nbnxn_pairlist.h"
 
+struct t_mdatoms;
 
 /* Default nbnxn allocation routine, allocates 32 byte aligned,
  * which works for plain C and aligned SSE and AVX loads/stores.

diff --git a/src/gromacs/mdlib/qmmm.cpp b/src/gromacs/mdlib/qmmm.cpp
index e0e1cd388a7113945c4698b0db25895ecb34ccff..0194429b06b884e9c1fc63239e17879dd7f9cf78 100644 (file)
--- a/src/gromacs/mdlib/qmmm.cpp
+++ b/src/gromacs/mdlib/qmmm.cpp
@@ -58,6 +58,7 @@
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"

diff --git a/src/gromacs/mdlib/rf_util.cpp b/src/gromacs/mdlib/rf_util.cpp
index 0c11d72a479733bb5ada28259b2473d14d696e74..4b080ff851ac8970bf8f0a62857efa713dfd83a7 100644 (file)
--- a/src/gromacs/mdlib/rf_util.cpp
+++ b/src/gromacs/mdlib/rf_util.cpp
@@ -42,6 +42,7 @@
 #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/pbcutil/ishift.h"

diff --git a/src/gromacs/mdlib/tgroup.cpp b/src/gromacs/mdlib/tgroup.cpp
index 473a6b5b39a66910e1e0dc6d3d42e49f77d0f028..659db9a13c17c7bfa9df58ed2bcc3eba2f501324 100644 (file)
--- a/src/gromacs/mdlib/tgroup.cpp
+++ b/src/gromacs/mdlib/tgroup.cpp
@@ -45,6 +45,7 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/types/group.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/rbin.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/mdlib/wall.cpp b/src/gromacs/mdlib/wall.cpp
index 119510088cfc4bcdabc775c47a91b74af51dfb16..57f8909665d54100600ae1e62a21cd548b9e1ed5 100644 (file)
--- a/src/gromacs/mdlib/wall.cpp
+++ b/src/gromacs/mdlib/wall.cpp
@@ -45,6 +45,7 @@
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/tables/forcetable.h"

diff --git a/src/gromacs/pulling/pull.cpp b/src/gromacs/pulling/pull.cpp
index 4d6756b7717228c6de40c31eb999593a745db264..13c2b54f5dc4bb2fcc21de4dd90875bcbd90a36a 100644 (file)
--- a/src/gromacs/pulling/pull.cpp
+++ b/src/gromacs/pulling/pull.cpp
@@ -58,6 +58,7 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull_internal.h"

diff --git a/src/gromacs/pulling/pull.h b/src/gromacs/pulling/pull.h
index 2e96d72c68a179bab6be59862c1acd7b3025d93a..8976dfaf4877e590a5d485852e6ce26a08613aae 100644 (file)
--- a/src/gromacs/pulling/pull.h
+++ b/src/gromacs/pulling/pull.h
@@ -58,6 +58,7 @@ extern "C" {
 #endif
 
 struct pull_params_t;
+struct t_mdatoms;
 struct t_pbc;
 
 

diff --git a/src/gromacs/pulling/pullutil.cpp b/src/gromacs/pulling/pullutil.cpp
index a7ff940683cf5434cf5632f551c93f1bd7e2ebf7..00190c615e0445fc09cd9815a90a0126f7dd03e4 100644 (file)
--- a/src/gromacs/pulling/pullutil.cpp
+++ b/src/gromacs/pulling/pullutil.cpp
@@ -47,6 +47,7 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"