From 12afc3df9e307378a03b7fc30dfc28a2b97b3d16 Mon Sep 17 00:00:00 2001 From: David van der Spoel Date: Tue, 22 Sep 2015 15:54:38 +0200 Subject: [PATCH] Removed four includes from legacyheaders/typedefs.h Removed types/energy.h types/enums.h types/fcdata.h types/group.h from typedefs.h. Change-Id: I9191a58ff65a729e01723428f61ef418bbf1e3ba --- src/gromacs/fileio/trajectory_writing.h | 47 +++++++++++++++++---------------- src/gromacs/legacyheaders/mdebin.h | 35 ++++++++++++------------ src/gromacs/legacyheaders/tgroup.h | 11 ++++---- src/gromacs/legacyheaders/typedefs.h | 4 --- src/gromacs/legacyheaders/types/group.h | 4 +-- src/gromacs/mdlib/coupling.cpp | 2 ++ src/gromacs/mdlib/forcerec.cpp | 1 + src/gromacs/mdlib/md_support.cpp | 1 + src/gromacs/mdlib/mdebin.cpp | 1 + src/gromacs/mdlib/nbnxn_search.cpp | 1 + src/gromacs/mdlib/ns.cpp | 1 + src/gromacs/mdlib/stat.cpp | 1 + src/gromacs/mdlib/tgroup.cpp | 1 + src/gromacs/mdlib/tpi.cpp | 1 + src/gromacs/mdlib/update.cpp | 1 + 15 files changed, 61 insertions(+), 51 deletions(-) diff --git a/src/gromacs/fileio/trajectory_writing.h b/src/gromacs/fileio/trajectory_writing.h index b1d88e35cd..aaf75ecab6 100644 --- a/src/gromacs/fileio/trajectory_writing.h +++ b/src/gromacs/fileio/trajectory_writing.h @@ -45,6 +45,7 @@ #include "gromacs/legacyheaders/mdebin.h" #include "gromacs/timing/wallcycle.h" +struct gmx_ekindata_t; struct gmx_mtop_t; struct t_commrec; @@ -57,29 +58,29 @@ extern "C" { * This routine does communication (e.g. collecting distributed coordinates) */ void -do_md_trajectory_writing(FILE *fplog, - struct t_commrec *cr, - int nfile, - const t_filenm fnm[], - gmx_int64_t step, - gmx_int64_t step_rel, - double t, - t_inputrec *ir, - t_state *state, - t_state *state_global, - struct gmx_mtop_t *top_global, - t_forcerec *fr, - gmx_mdoutf_t outf, - t_mdebin *mdebin, - gmx_ekindata_t *ekind, - rvec *f, - rvec *f_global, - int *nchkpt, - gmx_bool bCPT, - gmx_bool bRerunMD, - gmx_bool bLastStep, - gmx_bool bDoConfOut, - gmx_bool bSumEkinhOld +do_md_trajectory_writing(FILE *fplog, + struct t_commrec *cr, + int nfile, + const t_filenm fnm[], + gmx_int64_t step, + gmx_int64_t step_rel, + double t, + t_inputrec *ir, + t_state *state, + t_state *state_global, + struct gmx_mtop_t *top_global, + t_forcerec *fr, + gmx_mdoutf_t outf, + t_mdebin *mdebin, + struct gmx_ekindata_t *ekind, + rvec *f, + rvec *f_global, + int *nchkpt, + gmx_bool bCPT, + gmx_bool bRerunMD, + gmx_bool bLastStep, + gmx_bool bDoConfOut, + gmx_bool bSumEkinhOld ); diff --git a/src/gromacs/legacyheaders/mdebin.h b/src/gromacs/legacyheaders/mdebin.h index fe75031c4c..2628802ad5 100644 --- a/src/gromacs/legacyheaders/mdebin.h +++ b/src/gromacs/legacyheaders/mdebin.h @@ -46,6 +46,7 @@ #include "gromacs/legacyheaders/types/state.h" struct gmx_constr; +struct gmx_ekindata_t; struct gmx_output_env_t; #ifdef __cplusplus @@ -127,23 +128,23 @@ FILE *open_dhdl(const char *filename, const t_inputrec *ir, /* update the averaging structures. Called every time the energies are evaluated. */ -void upd_mdebin(t_mdebin *md, - gmx_bool bDoDHDL, - gmx_bool bSum, - double time, - real tmass, - gmx_enerdata_t *enerd, - t_state *state, - t_lambda *fep, - t_expanded *expand, - matrix lastbox, - tensor svir, - tensor fvir, - tensor vir, - tensor pres, - gmx_ekindata_t *ekind, - rvec mu_tot, - struct gmx_constr *constr); +void upd_mdebin(t_mdebin *md, + gmx_bool bDoDHDL, + gmx_bool bSum, + double time, + real tmass, + gmx_enerdata_t *enerd, + t_state *state, + t_lambda *fep, + t_expanded *expand, + matrix lastbox, + tensor svir, + tensor fvir, + tensor vir, + tensor pres, + struct gmx_ekindata_t *ekind, + rvec mu_tot, + struct gmx_constr *constr); void upd_mdebin_step(t_mdebin *md); /* Updates only the step count in md */ diff --git a/src/gromacs/legacyheaders/tgroup.h b/src/gromacs/legacyheaders/tgroup.h index 2b6dff0418..9d2568a21d 100644 --- a/src/gromacs/legacyheaders/tgroup.h +++ b/src/gromacs/legacyheaders/tgroup.h @@ -41,6 +41,7 @@ #include "gromacs/legacyheaders/network.h" #include "gromacs/legacyheaders/typedefs.h" +struct gmx_ekindata_t; struct t_commrec; #ifdef __cplusplus @@ -48,27 +49,27 @@ extern "C" { #endif void init_ekindata(FILE *log, gmx_mtop_t *mtop, t_grpopts *opts, - gmx_ekindata_t *ekind); + struct gmx_ekindata_t *ekind); /* Allocate memory and set the grpnr array. */ -void done_ekindata(gmx_ekindata_t *ekind); +void done_ekindata(struct gmx_ekindata_t *ekind); /* Free the memory */ void accumulate_u(struct t_commrec *cr, t_grpopts *opts, - gmx_ekindata_t *ekind); + struct gmx_ekindata_t *ekind); /*extern void accumulate_ekin(struct t_commrec *cr,t_grpopts *opts,t_groups *grps);*/ /* Communicate subsystem - group velocities and subsystem ekin respectively * and sum them up. Return them in grps. */ -real sum_ekin(t_grpopts *opts, gmx_ekindata_t *ekind, real *dekindlambda, +real sum_ekin(t_grpopts *opts, struct gmx_ekindata_t *ekind, real *dekindlambda, gmx_bool bEkinFullStep, gmx_bool bScaleEkin); /* Sum the group ekins into total ekin and calc temp per group, * return total temperature. */ -void update_ekindata(int start, int homenr, gmx_ekindata_t *ekind, +void update_ekindata(int start, int homenr, struct gmx_ekindata_t *ekind, t_grpopts *opts, rvec v[], t_mdatoms *md, real lambda); /* Do the update of group velocities (if bNEMD) and * (partial) group ekin. diff --git a/src/gromacs/legacyheaders/typedefs.h b/src/gromacs/legacyheaders/typedefs.h index 1204719dac..8eab587dff 100644 --- a/src/gromacs/legacyheaders/typedefs.h +++ b/src/gromacs/legacyheaders/typedefs.h @@ -42,11 +42,7 @@ /* DEPRECATED! value for signaling unitialized variables */ #define NOTSET -12345 -#include "gromacs/legacyheaders/types/energy.h" -#include "gromacs/legacyheaders/types/enums.h" -#include "gromacs/legacyheaders/types/fcdata.h" #include "gromacs/legacyheaders/types/forcerec.h" -#include "gromacs/legacyheaders/types/group.h" #include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/legacyheaders/types/inputrec.h" #include "gromacs/legacyheaders/types/mdatom.h" diff --git a/src/gromacs/legacyheaders/types/group.h b/src/gromacs/legacyheaders/types/group.h index 1ad37bad7f..26cda6efe1 100644 --- a/src/gromacs/legacyheaders/types/group.h +++ b/src/gromacs/legacyheaders/types/group.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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015, 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. @@ -72,7 +72,7 @@ typedef struct { real vcos; /* The velocity of the cosine profile */ } t_cos_acc; -typedef struct { +typedef struct gmx_ekindata_t { gmx_bool bNEMD; int ngtc; /* The number of T-coupling groups */ t_grp_tcstat *tcstat; /* T-coupling data */ diff --git a/src/gromacs/mdlib/coupling.cpp b/src/gromacs/mdlib/coupling.cpp index 30a5942d32..2a1c8eb5c3 100644 --- a/src/gromacs/mdlib/coupling.cpp +++ b/src/gromacs/mdlib/coupling.cpp @@ -48,6 +48,8 @@ #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/update.h" #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/energy.h" +#include "gromacs/legacyheaders/types/group.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/random/random.h" diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp index 6847eb92c7..809125189b 100644 --- a/src/gromacs/mdlib/forcerec.cpp +++ b/src/gromacs/mdlib/forcerec.cpp @@ -67,6 +67,7 @@ #include "gromacs/legacyheaders/txtdump.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/group.h" #include "gromacs/listed-forces/manage-threading.h" #include "gromacs/math/calculate-ewald-splitting-coefficient.h" #include "gromacs/math/units.h" diff --git a/src/gromacs/mdlib/md_support.cpp b/src/gromacs/mdlib/md_support.cpp index e781a77fb9..5aceded430 100644 --- a/src/gromacs/mdlib/md_support.cpp +++ b/src/gromacs/mdlib/md_support.cpp @@ -50,6 +50,7 @@ #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/vcm.h" #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/group.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/mdrun_signalling.h" #include "gromacs/timing/wallcycle.h" diff --git a/src/gromacs/mdlib/mdebin.cpp b/src/gromacs/mdlib/mdebin.cpp index a880ff0435..808f1490b4 100644 --- a/src/gromacs/mdlib/mdebin.cpp +++ b/src/gromacs/mdlib/mdebin.cpp @@ -51,6 +51,7 @@ #include "gromacs/legacyheaders/network.h" #include "gromacs/legacyheaders/orires.h" #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/group.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/constr.h" diff --git a/src/gromacs/mdlib/nbnxn_search.cpp b/src/gromacs/mdlib/nbnxn_search.cpp index 69d712539d..9429ddf89d 100644 --- a/src/gromacs/mdlib/nbnxn_search.cpp +++ b/src/gromacs/mdlib/nbnxn_search.cpp @@ -50,6 +50,7 @@ #include "gromacs/legacyheaders/nrnb.h" #include "gromacs/legacyheaders/ns.h" #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/group.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/nb_verlet.h" diff --git a/src/gromacs/mdlib/ns.cpp b/src/gromacs/mdlib/ns.cpp index f3120478f6..fc26ea39fe 100644 --- a/src/gromacs/mdlib/ns.cpp +++ b/src/gromacs/mdlib/ns.cpp @@ -55,6 +55,7 @@ #include "gromacs/legacyheaders/nsgrid.h" #include "gromacs/legacyheaders/txtdump.h" #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/group.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/ishift.h" diff --git a/src/gromacs/mdlib/stat.cpp b/src/gromacs/mdlib/stat.cpp index b2fb398f43..d60ceb6f76 100644 --- a/src/gromacs/mdlib/stat.cpp +++ b/src/gromacs/mdlib/stat.cpp @@ -54,6 +54,7 @@ #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/vcm.h" #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/group.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/constr.h" diff --git a/src/gromacs/mdlib/tgroup.cpp b/src/gromacs/mdlib/tgroup.cpp index 263c16ce1c..7b3a45a294 100644 --- a/src/gromacs/mdlib/tgroup.cpp +++ b/src/gromacs/mdlib/tgroup.cpp @@ -45,6 +45,7 @@ #include "gromacs/legacyheaders/network.h" #include "gromacs/legacyheaders/rbin.h" #include "gromacs/legacyheaders/update.h" +#include "gromacs/legacyheaders/types/group.h" #include "gromacs/math/vec.h" #include "gromacs/topology/mtop_util.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/mdlib/tpi.cpp b/src/gromacs/mdlib/tpi.cpp index 8360184120..7902941f9a 100644 --- a/src/gromacs/mdlib/tpi.cpp +++ b/src/gromacs/mdlib/tpi.cpp @@ -74,6 +74,7 @@ #include "gromacs/legacyheaders/update.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" diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp index accdad3168..e5a7517f1c 100644 --- a/src/gromacs/mdlib/update.cpp +++ b/src/gromacs/mdlib/update.cpp @@ -55,6 +55,7 @@ #include "gromacs/legacyheaders/txtdump.h" #include "gromacs/legacyheaders/typedefs.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" -- 2.11.4.GIT