From 12019ef4691316f886d9a5b188f7db2eab445192 Mon Sep 17 00:00:00 2001 From: David van der Spoel Date: Wed, 23 Sep 2015 22:11:12 +0200 Subject: [PATCH] Removed include of types/ifunc.h from typedefs.h In the process some other definitions had to be introduced in particular struct t_fcdata. Change-Id: I3d80a9c482d5d7abf0566f0a13d5795cf611bf3b --- src/gromacs/fileio/tpxio.cpp | 1 + src/gromacs/gmxana/edittop.cpp | 1 + src/gromacs/gmxana/gmx_disre.cpp | 1 + src/gromacs/gmxana/gmx_energy.cpp | 1 + src/gromacs/gmxana/gmx_hbond.cpp | 1 + src/gromacs/gmxana/gmx_lie.cpp | 1 + src/gromacs/gmxana/gmx_mk_angndx.cpp | 1 + src/gromacs/gmxana/gmx_nmeig.cpp | 1 + src/gromacs/gmxana/gmx_rms.cpp | 1 + src/gromacs/gmxlib/disre.cpp | 1 + src/gromacs/gmxlib/orires.cpp | 2 ++ src/gromacs/gmxlib/txtdump.cpp | 1 + src/gromacs/gmxpreprocess/convparm.cpp | 1 + src/gromacs/gmxpreprocess/gen_ad.cpp | 1 + src/gromacs/gmxpreprocess/gen_vsite.cpp | 1 + src/gromacs/gmxpreprocess/gpp_atomtype.cpp | 1 + src/gromacs/gmxpreprocess/gpp_nextnb.cpp | 1 + src/gromacs/gmxpreprocess/grompp.cpp | 1 + src/gromacs/gmxpreprocess/readir.cpp | 1 + src/gromacs/gmxpreprocess/tomorse.cpp | 1 + src/gromacs/gmxpreprocess/topio.cpp | 1 + src/gromacs/gmxpreprocess/toppush.cpp | 1 + src/gromacs/gmxpreprocess/topshake.cpp | 1 + src/gromacs/gmxpreprocess/toputil.cpp | 1 + src/gromacs/gmxpreprocess/vsite_parm.cpp | 1 + src/gromacs/legacyheaders/disre.h | 1 + src/gromacs/legacyheaders/force.h | 16 +++++----- src/gromacs/legacyheaders/mdebin.h | 1 + src/gromacs/legacyheaders/orires.h | 6 ++-- src/gromacs/legacyheaders/shellfc.h | 1 + src/gromacs/legacyheaders/typedefs.h | 1 - src/gromacs/legacyheaders/types/fcdata.h | 10 +++---- src/gromacs/legacyheaders/types/ifunc.h | 8 ++--- src/gromacs/legacyheaders/types/mdatom.h | 4 +-- src/gromacs/legacyheaders/update.h | 1 + src/gromacs/listed-forces/listed-forces.cpp | 1 + src/gromacs/listed-forces/listed-forces.h | 41 +++++++++++++------------- src/gromacs/listed-forces/manage-threading.cpp | 1 + src/gromacs/mdlib/adress.cpp | 1 + src/gromacs/mdlib/calc_verletbuf.cpp | 1 + src/gromacs/mdlib/ebin.cpp | 1 + src/gromacs/mdlib/forcerec.cpp | 1 + src/gromacs/mdlib/forcerec.h | 32 ++++++++++---------- src/gromacs/mdlib/mdebin.cpp | 1 + src/gromacs/mdlib/perf_est.cpp | 1 + src/gromacs/mdlib/tables.c | 9 +++--- src/gromacs/pbcutil/mshift.cpp | 1 + src/gromacs/tools/check.cpp | 1 + src/gromacs/tools/compare.cpp | 1 + src/gromacs/tools/convert_tpr.cpp | 1 + src/programs/view/manager.cpp | 1 + 51 files changed, 110 insertions(+), 60 deletions(-) diff --git a/src/gromacs/fileio/tpxio.cpp b/src/gromacs/fileio/tpxio.cpp index 25cf4c036b..a80ffe01e6 100644 --- a/src/gromacs/fileio/tpxio.cpp +++ b/src/gromacs/fileio/tpxio.cpp @@ -50,6 +50,7 @@ #include "gromacs/fileio/gmxfio-xdr.h" #include "gromacs/legacyheaders/copyrite.h" #include "gromacs/legacyheaders/names.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/vec.h" #include "gromacs/topology/block.h" #include "gromacs/topology/mtop_util.h" diff --git a/src/gromacs/gmxana/edittop.cpp b/src/gromacs/gmxana/edittop.cpp index bc7db85fb7..d7b55b6baf 100644 --- a/src/gromacs/gmxana/edittop.cpp +++ b/src/gromacs/gmxana/edittop.cpp @@ -37,6 +37,7 @@ #include "gmxpre.h" #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/topology/symtab.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp index 21c8395bf6..9e9b776850 100644 --- a/src/gromacs/gmxana/gmx_disre.cpp +++ b/src/gromacs/gmxana/gmx_disre.cpp @@ -60,6 +60,7 @@ #include "gromacs/legacyheaders/nrnb.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/viewit.h" +#include "gromacs/legacyheaders/types/fcdata.h" #include "gromacs/math/do_fit.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/ishift.h" diff --git a/src/gromacs/gmxana/gmx_energy.cpp b/src/gromacs/gmxana/gmx_energy.cpp index 133f50a65e..f9e10ffbcb 100644 --- a/src/gromacs/gmxana/gmx_energy.cpp +++ b/src/gromacs/gmxana/gmx_energy.cpp @@ -56,6 +56,7 @@ #include "gromacs/legacyheaders/names.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/viewit.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/topology/mtop_util.h" diff --git a/src/gromacs/gmxana/gmx_hbond.cpp b/src/gromacs/gmxana/gmx_hbond.cpp index 0bee366420..41de7bf2dd 100644 --- a/src/gromacs/gmxana/gmx_hbond.cpp +++ b/src/gromacs/gmxana/gmx_hbond.cpp @@ -58,6 +58,7 @@ #include "gromacs/legacyheaders/copyrite.h" #include "gromacs/legacyheaders/txtdump.h" #include "gromacs/legacyheaders/viewit.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/pbc.h" diff --git a/src/gromacs/gmxana/gmx_lie.cpp b/src/gromacs/gmxana/gmx_lie.cpp index 039881e7ad..11ab5e3e8f 100644 --- a/src/gromacs/gmxana/gmx_lie.cpp +++ b/src/gromacs/gmxana/gmx_lie.cpp @@ -50,6 +50,7 @@ #include "gromacs/legacyheaders/txtdump.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/viewit.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/vec.h" #include "gromacs/utility/arraysize.h" #include "gromacs/utility/futil.h" diff --git a/src/gromacs/gmxana/gmx_mk_angndx.cpp b/src/gromacs/gmxana/gmx_mk_angndx.cpp index 085edb708b..4554e216d1 100644 --- a/src/gromacs/gmxana/gmx_mk_angndx.cpp +++ b/src/gromacs/gmxana/gmx_mk_angndx.cpp @@ -42,6 +42,7 @@ #include "gromacs/fileio/trxio.h" #include "gromacs/gmxana/gmx_ana.h" #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/utility/arraysize.h" #include "gromacs/utility/cstringutil.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/gmxana/gmx_nmeig.cpp b/src/gromacs/gmxana/gmx_nmeig.cpp index 537e77a150..f3deec3f41 100644 --- a/src/gromacs/gmxana/gmx_nmeig.cpp +++ b/src/gromacs/gmxana/gmx_nmeig.cpp @@ -48,6 +48,7 @@ #include "gromacs/legacyheaders/copyrite.h" #include "gromacs/legacyheaders/txtdump.h" #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/linearalgebra/eigensolver.h" #include "gromacs/linearalgebra/sparsematrix.h" #include "gromacs/math/units.h" diff --git a/src/gromacs/gmxana/gmx_rms.cpp b/src/gromacs/gmxana/gmx_rms.cpp index 705095d8d1..fdb963632e 100644 --- a/src/gromacs/gmxana/gmx_rms.cpp +++ b/src/gromacs/gmxana/gmx_rms.cpp @@ -52,6 +52,7 @@ #include "gromacs/legacyheaders/copyrite.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/viewit.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/do_fit.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/rmpbc.h" diff --git a/src/gromacs/gmxlib/disre.cpp b/src/gromacs/gmxlib/disre.cpp index 4c1f046528..b28658ad5c 100644 --- a/src/gromacs/gmxlib/disre.cpp +++ b/src/gromacs/gmxlib/disre.cpp @@ -51,6 +51,7 @@ #include "gromacs/legacyheaders/main.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/fcdata.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/ishift.h" #include "gromacs/pbcutil/mshift.h" diff --git a/src/gromacs/gmxlib/orires.cpp b/src/gromacs/gmxlib/orires.cpp index 656417268f..7e8f5bdf5d 100644 --- a/src/gromacs/gmxlib/orires.cpp +++ b/src/gromacs/gmxlib/orires.cpp @@ -45,6 +45,8 @@ #include "gromacs/legacyheaders/network.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/fcdata.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/linearalgebra/nrjac.h" #include "gromacs/math/do_fit.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/gmxlib/txtdump.cpp b/src/gromacs/gmxlib/txtdump.cpp index c4258e283a..432fa5a0cb 100644 --- a/src/gromacs/gmxlib/txtdump.cpp +++ b/src/gromacs/gmxlib/txtdump.cpp @@ -48,6 +48,7 @@ #include "gromacs/legacyheaders/names.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/vec.h" #include "gromacs/utility/cstringutil.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/gmxpreprocess/convparm.cpp b/src/gromacs/gmxpreprocess/convparm.cpp index 84fda24234..dd8efa2ad3 100644 --- a/src/gromacs/gmxpreprocess/convparm.cpp +++ b/src/gromacs/gmxpreprocess/convparm.cpp @@ -48,6 +48,7 @@ #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/legacyheaders/names.h" #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/gmxpreprocess/gen_ad.cpp b/src/gromacs/gmxpreprocess/gen_ad.cpp index e50b76b179..08305e8b51 100644 --- a/src/gromacs/gmxpreprocess/gen_ad.cpp +++ b/src/gromacs/gmxpreprocess/gen_ad.cpp @@ -53,6 +53,7 @@ #include "gromacs/gmxpreprocess/resall.h" #include "gromacs/gmxpreprocess/topio.h" #include "gromacs/gmxpreprocess/toputil.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/vec.h" #include "gromacs/utility/cstringutil.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/gmxpreprocess/gen_vsite.cpp b/src/gromacs/gmxpreprocess/gen_vsite.cpp index 8393dced18..b1821f8a57 100644 --- a/src/gromacs/gmxpreprocess/gen_vsite.cpp +++ b/src/gromacs/gmxpreprocess/gen_vsite.cpp @@ -50,6 +50,7 @@ #include "gromacs/gmxpreprocess/resall.h" #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/legacyheaders/names.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/topology/residuetypes.h" diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp index 5748ae79d2..7c5601ed5a 100644 --- a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp +++ b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp @@ -45,6 +45,7 @@ #include "gromacs/gmxpreprocess/topdirs.h" #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/legacyheaders/txtdump.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/topology/symtab.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.cpp b/src/gromacs/gmxpreprocess/gpp_nextnb.cpp index 2277109fc4..a5b76b80cf 100644 --- a/src/gromacs/gmxpreprocess/gpp_nextnb.cpp +++ b/src/gromacs/gmxpreprocess/gpp_nextnb.cpp @@ -42,6 +42,7 @@ #include #include "gromacs/gmxpreprocess/toputil.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp index 3f7b4d497f..04cba38e47 100644 --- a/src/gromacs/gmxpreprocess/grompp.cpp +++ b/src/gromacs/gmxpreprocess/grompp.cpp @@ -73,6 +73,7 @@ #include "gromacs/legacyheaders/splitter.h" #include "gromacs/legacyheaders/txtdump.h" #include "gromacs/legacyheaders/warninp.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/calc_verletbuf.h" #include "gromacs/mdlib/compute_io.h" diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp index e436e7bd9b..f2af500673 100644 --- a/src/gromacs/gmxpreprocess/readir.cpp +++ b/src/gromacs/gmxpreprocess/readir.cpp @@ -54,6 +54,7 @@ #include "gromacs/legacyheaders/readinp.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/warninp.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/calc_verletbuf.h" diff --git a/src/gromacs/gmxpreprocess/tomorse.cpp b/src/gromacs/gmxpreprocess/tomorse.cpp index 6401deeda1..b60355903b 100644 --- a/src/gromacs/gmxpreprocess/tomorse.cpp +++ b/src/gromacs/gmxpreprocess/tomorse.cpp @@ -49,6 +49,7 @@ #include "gromacs/gmxpreprocess/grompp-impl.h" #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/utility/cstringutil.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/futil.h" diff --git a/src/gromacs/gmxpreprocess/topio.cpp b/src/gromacs/gmxpreprocess/topio.cpp index 3ead64e11f..b92fe2087a 100644 --- a/src/gromacs/gmxpreprocess/topio.cpp +++ b/src/gromacs/gmxpreprocess/topio.cpp @@ -63,6 +63,7 @@ #include "gromacs/legacyheaders/txtdump.h" #include "gromacs/legacyheaders/typedefs.h" #include "gromacs/legacyheaders/warninp.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" #include "gromacs/topology/block.h" diff --git a/src/gromacs/gmxpreprocess/toppush.cpp b/src/gromacs/gmxpreprocess/toppush.cpp index 803c03ae3e..5c2e8c21e8 100644 --- a/src/gromacs/gmxpreprocess/toppush.cpp +++ b/src/gromacs/gmxpreprocess/toppush.cpp @@ -52,6 +52,7 @@ #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/legacyheaders/names.h" #include "gromacs/legacyheaders/warninp.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/topology/symtab.h" #include "gromacs/utility/cstringutil.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/gmxpreprocess/topshake.cpp b/src/gromacs/gmxpreprocess/topshake.cpp index 253f2b24aa..587cce4dbe 100644 --- a/src/gromacs/gmxpreprocess/topshake.cpp +++ b/src/gromacs/gmxpreprocess/topshake.cpp @@ -48,6 +48,7 @@ #include "gromacs/gmxpreprocess/toppush.h" #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" diff --git a/src/gromacs/gmxpreprocess/toputil.cpp b/src/gromacs/gmxpreprocess/toputil.cpp index 28240a56f1..010bbf1c92 100644 --- a/src/gromacs/gmxpreprocess/toputil.cpp +++ b/src/gromacs/gmxpreprocess/toputil.cpp @@ -46,6 +46,7 @@ #include "gromacs/gmxpreprocess/gpp_atomtype.h" #include "gromacs/gmxpreprocess/topdirs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/topology/block.h" #include "gromacs/topology/symtab.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/gmxpreprocess/vsite_parm.cpp b/src/gromacs/gmxpreprocess/vsite_parm.cpp index 7bfbf6094a..328c0e1d79 100644 --- a/src/gromacs/gmxpreprocess/vsite_parm.cpp +++ b/src/gromacs/gmxpreprocess/vsite_parm.cpp @@ -49,6 +49,7 @@ #include "gromacs/gmxpreprocess/resall.h" #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/legacyheaders/names.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/utility/cstringutil.h" diff --git a/src/gromacs/legacyheaders/disre.h b/src/gromacs/legacyheaders/disre.h index f8c36254e4..549aaf422d 100644 --- a/src/gromacs/legacyheaders/disre.h +++ b/src/gromacs/legacyheaders/disre.h @@ -41,6 +41,7 @@ #include #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" struct gmx_mtop_t; struct t_commrec; diff --git a/src/gromacs/legacyheaders/force.h b/src/gromacs/legacyheaders/force.h index db2a292e67..647171e908 100644 --- a/src/gromacs/legacyheaders/force.h +++ b/src/gromacs/legacyheaders/force.h @@ -43,10 +43,12 @@ #include "gromacs/legacyheaders/tgroup.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/timing/wallcycle.h" struct t_commrec; +struct t_fcdata; struct t_graph; struct t_pbc; struct gmx_edsam; @@ -104,7 +106,7 @@ t_forcetable make_tables(FILE *fp, const output_env_t oenv, */ bondedtable_t make_bonded_table(FILE *fplog, char *fn, int angle); -/* Return a table for bonded interactions, +/* Fill a table for bonded interactions, * angle should be: bonds 0, angles 1, dihedrals 2 */ @@ -113,10 +115,10 @@ t_forcetable make_gb_table(const output_env_t oenv, const t_forcerec *fr); /* Read a table for AdResS Thermo Force calculations */ -extern t_forcetable make_atf_table(FILE *out, const output_env_t oenv, - const t_forcerec *fr, - const char *fn, - matrix box); +t_forcetable make_atf_table(FILE *out, const output_env_t oenv, + const t_forcerec *fr, + const char *fn, + matrix box); gmx_bool can_use_allvsall(const t_inputrec *ir, gmx_bool bPrintNote, struct t_commrec *cr, FILE *fp); @@ -176,7 +178,7 @@ extern void do_force(FILE *log, struct t_commrec *cr, rvec f[], tensor vir_force, t_mdatoms *mdatoms, - gmx_enerdata_t *enerd, t_fcdata *fcd, + gmx_enerdata_t *enerd, struct t_fcdata *fcd, real *lambda, struct t_graph *graph, t_forcerec *fr, gmx_vsite_t *vsite, rvec mu_tot, @@ -217,7 +219,7 @@ extern void do_force_lowlevel(t_forcerec *fr, rvec f_shortrange[], rvec f_longrange[], gmx_enerdata_t *enerd, - t_fcdata *fcd, + struct t_fcdata *fcd, gmx_localtop_t *top, gmx_genborn_t *born, gmx_bool bBornRadii, diff --git a/src/gromacs/legacyheaders/mdebin.h b/src/gromacs/legacyheaders/mdebin.h index 2628802ad5..769daa5e2a 100644 --- a/src/gromacs/legacyheaders/mdebin.h +++ b/src/gromacs/legacyheaders/mdebin.h @@ -48,6 +48,7 @@ struct gmx_constr; struct gmx_ekindata_t; struct gmx_output_env_t; +struct t_fcdata; #ifdef __cplusplus extern "C" { diff --git a/src/gromacs/legacyheaders/orires.h b/src/gromacs/legacyheaders/orires.h index db4d684e8c..a36d5ca095 100644 --- a/src/gromacs/legacyheaders/orires.h +++ b/src/gromacs/legacyheaders/orires.h @@ -41,15 +41,17 @@ #include #include "gromacs/legacyheaders/typedefs.h" - +#include "gromacs/legacyheaders/types/ifunc.h" #ifdef __cplusplus extern "C" { #endif +struct gmx_multisim_t; struct t_pbc; struct t_commrec; -struct gmx_multisim_t; +struct t_fcdata; +struct t_oriresdata; void init_orires(FILE *fplog, const gmx_mtop_t *mtop, rvec x[], diff --git a/src/gromacs/legacyheaders/shellfc.h b/src/gromacs/legacyheaders/shellfc.h index 06f11e0d15..062f11708d 100644 --- a/src/gromacs/legacyheaders/shellfc.h +++ b/src/gromacs/legacyheaders/shellfc.h @@ -45,6 +45,7 @@ struct gmx_constr; extern "C" { #endif +struct t_fcdata; struct t_graph; /* Initialization function, also predicts the initial shell postions. diff --git a/src/gromacs/legacyheaders/typedefs.h b/src/gromacs/legacyheaders/typedefs.h index 8eab587dff..5c68982690 100644 --- a/src/gromacs/legacyheaders/typedefs.h +++ b/src/gromacs/legacyheaders/typedefs.h @@ -43,7 +43,6 @@ #define NOTSET -12345 #include "gromacs/legacyheaders/types/forcerec.h" -#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/legacyheaders/types/inputrec.h" #include "gromacs/legacyheaders/types/mdatom.h" #include "gromacs/legacyheaders/types/nblist.h" diff --git a/src/gromacs/legacyheaders/types/fcdata.h b/src/gromacs/legacyheaders/types/fcdata.h index bde3a32226..d0e1d029e8 100644 --- a/src/gromacs/legacyheaders/types/fcdata.h +++ b/src/gromacs/legacyheaders/types/fcdata.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2012,2014, by the GROMACS development team, led by + * Copyright (c) 2012,2014,2015, 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. @@ -48,7 +48,7 @@ extern "C" { typedef real rvec5[5]; /* Distance restraining stuff */ -typedef struct { +typedef struct t_disresdata { int dr_weighting; /* Weighting of pairs in one restraint */ gmx_bool dr_bMixed; /* Use sqrt of the instantaneous times * * the time averaged violation */ @@ -72,7 +72,7 @@ typedef struct { /* Orientation restraining stuff */ -typedef struct { +typedef struct t_oriresdata { real fc; /* Force constant for the restraints */ real edt; /* Multiplication factor for time averaging */ real edt_1; /* 1 - edt */ @@ -102,7 +102,7 @@ typedef struct { double **v; } t_oriresdata; -typedef struct { +typedef struct bondedtable_t { int n; /* n+1 is the number of points */ real scale; /* distance between two points */ real *data; /* the actual table data, per point there are 4 numbers */ @@ -115,7 +115,7 @@ typedef struct { * (for instance for time averaging in distance retraints) * or for storing output, since force routines only return the potential. */ -typedef struct { +typedef struct t_fcdata { bondedtable_t *bondtab; bondedtable_t *angletab; bondedtable_t *dihtab; diff --git a/src/gromacs/legacyheaders/types/ifunc.h b/src/gromacs/legacyheaders/types/ifunc.h index 25d13c6f58..3d4b4b8b5a 100644 --- a/src/gromacs/legacyheaders/types/ifunc.h +++ b/src/gromacs/legacyheaders/types/ifunc.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2012,2014, by the GROMACS development team, led by + * Copyright (c) 2012,2014,2015, 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. @@ -39,15 +39,15 @@ #ifndef _ifunc_h #define _ifunc_h -#include "gromacs/legacyheaders/types/fcdata.h" -#include "gromacs/legacyheaders/types/mdatom.h" #include "gromacs/topology/idef.h" #ifdef __cplusplus extern "C" { #endif +struct t_fcdata; struct t_graph; +struct t_mdatoms; struct t_pbc; typedef real t_ifunc (int nbonds, const t_iatom iatoms[], @@ -55,7 +55,7 @@ typedef real t_ifunc (int nbonds, const t_iatom iatoms[], const rvec x[], rvec f[], rvec fshift[], const struct t_pbc *pbc, const struct t_graph *g, real lambda, real *dvdlambda, - const t_mdatoms *md, t_fcdata *fcd, + const struct t_mdatoms *md, struct t_fcdata *fcd, int *ddgatindex); /* diff --git a/src/gromacs/legacyheaders/types/mdatom.h b/src/gromacs/legacyheaders/types/mdatom.h index 34179fa88b..faebfbdb18 100644 --- a/src/gromacs/legacyheaders/types/mdatom.h +++ b/src/gromacs/legacyheaders/types/mdatom.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by + * Copyright (c) 2012,2013,2014,2015, 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. @@ -48,7 +48,7 @@ extern "C" { #define NO_TF_TABLE 255 #define DEFAULT_TF_TABLE 0 -typedef struct { +typedef struct t_mdatoms { real tmassA, tmassB, tmass; int nr; int nalloc; diff --git a/src/gromacs/legacyheaders/update.h b/src/gromacs/legacyheaders/update.h index 0f24039446..04c199f4a7 100644 --- a/src/gromacs/legacyheaders/update.h +++ b/src/gromacs/legacyheaders/update.h @@ -44,6 +44,7 @@ #include "gromacs/timing/wallcycle.h" struct gmx_constr; +struct t_fcdata; #ifdef __cplusplus extern "C" { diff --git a/src/gromacs/listed-forces/listed-forces.cpp b/src/gromacs/listed-forces/listed-forces.cpp index 4b2dabf732..ba841d264d 100644 --- a/src/gromacs/listed-forces/listed-forces.cpp +++ b/src/gromacs/listed-forces/listed-forces.cpp @@ -56,6 +56,7 @@ #include "gromacs/legacyheaders/network.h" #include "gromacs/legacyheaders/nrnb.h" #include "gromacs/legacyheaders/orires.h" +#include "gromacs/legacyheaders/types/fcdata.h" #include "gromacs/legacyheaders/types/force_flags.h" #include "gromacs/listed-forces/bonded.h" #include "gromacs/listed-forces/position-restraints.h" diff --git a/src/gromacs/listed-forces/listed-forces.h b/src/gromacs/listed-forces/listed-forces.h index 863f29b5ac..acb13fdfe0 100644 --- a/src/gromacs/listed-forces/listed-forces.h +++ b/src/gromacs/listed-forces/listed-forces.h @@ -69,6 +69,7 @@ #include "gromacs/legacyheaders/typedefs.h" struct gmx_multisim_t; +struct t_fcdata; #ifdef __cplusplus extern "C" { @@ -96,7 +97,7 @@ void calc_listed(const struct gmx_multisim_t *ms, const struct t_graph *g, gmx_enerdata_t *enerd, t_nrnb *nrnb, real *lambda, const t_mdatoms *md, - t_fcdata *fcd, int *ddgatindex, + struct t_fcdata *fcd, int *ddgatindex, int force_flags); /*! \brief As calc_listed(), but only determines the potential energy @@ -110,29 +111,29 @@ void calc_listed_lambda(const t_idef *idef, gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb, real *lambda, const t_mdatoms *md, - t_fcdata *fcd, int *global_atom_index); + struct t_fcdata *fcd, int *global_atom_index); /*! \brief Do all aspects of energy and force calculations for mdrun * on the set of listed interactions */ void -do_force_listed(struct gmx_wallcycle *wcycle, - matrix box, - const t_lambda *fepvals, - const struct gmx_multisim_t *ms, - const t_idef *idef, - const rvec x[], - history_t *hist, - rvec f[], - t_forcerec *fr, - const struct t_pbc *pbc, - const struct t_graph *graph, - gmx_enerdata_t *enerd, - t_nrnb *nrnb, - real *lambda, - const t_mdatoms *md, - t_fcdata *fcd, - int *global_atom_index, - int flags); +do_force_listed(struct gmx_wallcycle *wcycle, + matrix box, + const t_lambda *fepvals, + const struct gmx_multisim_t *ms, + const t_idef *idef, + const rvec x[], + history_t *hist, + rvec f[], + t_forcerec *fr, + const struct t_pbc *pbc, + const struct t_graph *graph, + gmx_enerdata_t *enerd, + t_nrnb *nrnb, + real *lambda, + const t_mdatoms *md, + struct t_fcdata *fcd, + int *global_atom_index, + int flags); #ifdef __cplusplus } diff --git a/src/gromacs/listed-forces/manage-threading.cpp b/src/gromacs/listed-forces/manage-threading.cpp index 183b819bef..f6a1aa08a4 100644 --- a/src/gromacs/listed-forces/manage-threading.cpp +++ b/src/gromacs/listed-forces/manage-threading.cpp @@ -52,6 +52,7 @@ #include #include "gromacs/legacyheaders/gmx_omp_nthreads.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/listed-forces/listed-forces.h" #include "gromacs/pbcutil/ishift.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/mdlib/adress.cpp b/src/gromacs/mdlib/adress.cpp index 4f5fb2a471..fb08b7ea3a 100644 --- a/src/gromacs/mdlib/adress.cpp +++ b/src/gromacs/mdlib/adress.cpp @@ -41,6 +41,7 @@ #include #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/legacyheaders/types/simple.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdlib/calc_verletbuf.cpp b/src/gromacs/mdlib/calc_verletbuf.cpp index 6326f5377e..f21b102c6f 100644 --- a/src/gromacs/mdlib/calc_verletbuf.cpp +++ b/src/gromacs/mdlib/calc_verletbuf.cpp @@ -43,6 +43,7 @@ #include #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/calculate-ewald-splitting-coefficient.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdlib/ebin.cpp b/src/gromacs/mdlib/ebin.cpp index f77fa07cbf..22b21d4251 100644 --- a/src/gromacs/mdlib/ebin.cpp +++ b/src/gromacs/mdlib/ebin.cpp @@ -43,6 +43,7 @@ #include #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp index 809125189b..66f7512f2a 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/fcdata.h" #include "gromacs/legacyheaders/types/group.h" #include "gromacs/listed-forces/manage-threading.h" #include "gromacs/math/calculate-ewald-splitting-coefficient.h" diff --git a/src/gromacs/mdlib/forcerec.h b/src/gromacs/mdlib/forcerec.h index a2915b646c..46d2eab05c 100644 --- a/src/gromacs/mdlib/forcerec.h +++ b/src/gromacs/mdlib/forcerec.h @@ -45,6 +45,8 @@ #include "gromacs/legacyheaders/types/force_flags.h" #include "gromacs/timing/wallcycle.h" +struct t_fcdata; + /*! \brief Create a new forcerec structure */ t_forcerec *mk_forcerec(void); @@ -103,21 +105,21 @@ void init_interaction_const_tables(FILE *fp, * \param[in] bNoSolvOpt Do not use solvent optimization * \param[in] print_force Print forces for atoms with force >= print_force */ -void init_forcerec(FILE *fplog, - const output_env_t oenv, - t_forcerec *fr, - t_fcdata *fcd, - const t_inputrec *ir, - const gmx_mtop_t *mtop, - const t_commrec *cr, - matrix box, - const char *tabfn, - const char *tabafn, - const char *tabpfn, - const char *tabbfn, - const char *nbpu_opt, - gmx_bool bNoSolvOpt, - real print_force); +void init_forcerec(FILE *fplog, + const output_env_t oenv, + t_forcerec *fr, + struct t_fcdata *fcd, + const t_inputrec *ir, + const gmx_mtop_t *mtop, + const t_commrec *cr, + matrix box, + const char *tabfn, + const char *tabafn, + const char *tabpfn, + const char *tabbfn, + const char *nbpu_opt, + gmx_bool bNoSolvOpt, + real print_force); /*! \brief Divide exclusions over threads * diff --git a/src/gromacs/mdlib/mdebin.cpp b/src/gromacs/mdlib/mdebin.cpp index 808f1490b4..4a11853d47 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/fcdata.h" #include "gromacs/legacyheaders/types/group.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdlib/perf_est.cpp b/src/gromacs/mdlib/perf_est.cpp index 3a93213890..5dd73f215b 100644 --- a/src/gromacs/mdlib/perf_est.cpp +++ b/src/gromacs/mdlib/perf_est.cpp @@ -41,6 +41,7 @@ #include #include "gromacs/legacyheaders/types/commrec.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/nbnxn_consts.h" #include "gromacs/mdlib/nbnxn_search.h" diff --git a/src/gromacs/mdlib/tables.c b/src/gromacs/mdlib/tables.c index c883d4afab..c764c1bb7c 100644 --- a/src/gromacs/mdlib/tables.c +++ b/src/gromacs/mdlib/tables.c @@ -46,6 +46,7 @@ #include "gromacs/legacyheaders/names.h" #include "gromacs/legacyheaders/network.h" #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/fcdata.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" @@ -1802,10 +1803,10 @@ t_forcetable make_atf_table(FILE *out, const output_env_t oenv, bondedtable_t make_bonded_table(FILE *fplog, char *fn, int angle) { - t_tabledata td; - double start; - int i; - bondedtable_t tab; + t_tabledata td; + double start; + int i; + bondedtable_t tab; if (angle < 2) { diff --git a/src/gromacs/pbcutil/mshift.cpp b/src/gromacs/pbcutil/mshift.cpp index 1f23a9b6e0..7962ba78b7 100644 --- a/src/gromacs/pbcutil/mshift.cpp +++ b/src/gromacs/pbcutil/mshift.cpp @@ -45,6 +45,7 @@ #include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/pbc.h" +#include "gromacs/topology/idef.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" diff --git a/src/gromacs/tools/check.cpp b/src/gromacs/tools/check.cpp index 28745c418a..7e58d7747e 100644 --- a/src/gromacs/tools/check.cpp +++ b/src/gromacs/tools/check.cpp @@ -50,6 +50,7 @@ #include "gromacs/fileio/xtcio.h" #include "gromacs/legacyheaders/names.h" #include "gromacs/legacyheaders/txtdump.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/pbc.h" diff --git a/src/gromacs/tools/compare.cpp b/src/gromacs/tools/compare.cpp index eac3c8e99e..2ede70dbe6 100644 --- a/src/gromacs/tools/compare.cpp +++ b/src/gromacs/tools/compare.cpp @@ -50,6 +50,7 @@ #include "gromacs/fileio/trxio.h" #include "gromacs/legacyheaders/names.h" #include "gromacs/legacyheaders/txtdump.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/topology/mtop_util.h" #include "gromacs/utility/cstringutil.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/tools/convert_tpr.cpp b/src/gromacs/tools/convert_tpr.cpp index 220f4eb447..3854ff4e77 100644 --- a/src/gromacs/tools/convert_tpr.cpp +++ b/src/gromacs/tools/convert_tpr.cpp @@ -45,6 +45,7 @@ #include "gromacs/gmxpreprocess/readir.h" #include "gromacs/legacyheaders/checkpoint.h" #include "gromacs/legacyheaders/names.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/legacyheaders/types/inputrec.h" #include "gromacs/legacyheaders/types/simple.h" #include "gromacs/legacyheaders/types/state.h" diff --git a/src/programs/view/manager.cpp b/src/programs/view/manager.cpp index 127ba80167..acbf63f0f3 100644 --- a/src/programs/view/manager.cpp +++ b/src/programs/view/manager.cpp @@ -53,6 +53,7 @@ #include "gromacs/legacyheaders/copyrite.h" #include "gromacs/legacyheaders/names.h" #include "gromacs/legacyheaders/typedefs.h" +#include "gromacs/legacyheaders/types/ifunc.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/pbc.h" -- 2.11.4.GIT