X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=blobdiff_plain;f=src%2Fgromacs%2Fmdlib%2Fns.c;h=3a1396cd40ac57bec8a893dedd78d758d470e6dc;hb=19d3c2e5d0c401eb59010960d11a18b6ba2c54c6;hp=430e26d304780b5b3f828efdad076163127cff1d;hpb=a349e4beffcbe43be945226384d2a590b27263f0;p=alexxy%2Fgromacs.git diff --git a/src/gromacs/mdlib/ns.c b/src/gromacs/mdlib/ns.c index 430e26d304..3a1396cd40 100644 --- a/src/gromacs/mdlib/ns.c +++ b/src/gromacs/mdlib/ns.c @@ -34,33 +34,33 @@ * To help us fund GROMACS development, we humbly ask that you cite * the research papers on the package. Check out http://www.gromacs.org. */ -#ifdef HAVE_CONFIG_H -#include -#endif +#include "gmxpre.h" + +#include "gromacs/legacyheaders/ns.h" #include +#include #include -#include "sysstuff.h" -#include "gromacs/utility/smalloc.h" -#include "macros.h" + +#include "gromacs/legacyheaders/domdec.h" +#include "gromacs/legacyheaders/force.h" +#include "gromacs/legacyheaders/macros.h" +#include "gromacs/legacyheaders/names.h" +#include "gromacs/legacyheaders/network.h" +#include "gromacs/legacyheaders/nonbonded.h" +#include "gromacs/legacyheaders/nrnb.h" +#include "gromacs/legacyheaders/nsgrid.h" +#include "gromacs/legacyheaders/txtdump.h" +#include "gromacs/legacyheaders/types/commrec.h" #include "gromacs/math/utilities.h" -#include "vec.h" -#include "types/commrec.h" -#include "network.h" -#include "nsgrid.h" -#include "force.h" -#include "nonbonded.h" -#include "ns.h" -#include "pbc.h" -#include "names.h" -#include "gmx_fatal.h" -#include "nrnb.h" -#include "txtdump.h" -#include "mtop_util.h" - -#include "domdec.h" -#include "adress.h" +#include "gromacs/math/vec.h" +#include "gromacs/pbcutil/ishift.h" +#include "gromacs/pbcutil/pbc.h" +#include "gromacs/topology/mtop_util.h" +#include "gromacs/utility/fatalerror.h" +#include "gromacs/utility/smalloc.h" +#include "adress.h" /* * E X C L U S I O N H A N D L I N G @@ -287,11 +287,8 @@ void init_neighbor_list(FILE *log, t_forcerec *fr, int homenr) /* Did we get the solvent loops so we can use optimized water kernels? */ if (nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf == NULL || nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf == NULL -#ifndef DISABLE_WATERWATER_NLIST || nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf == NULL - || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL -#endif - ) + || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL) { fr->solvent_opt = esolNO; if (log != NULL) @@ -672,13 +669,11 @@ put_in_list_at(gmx_bool bHaveVdW[], if (iwater != esolNO) { - vdwc = &nlist[eNL_VDWQQ_WATER]; - vdw = &nlist[eNL_VDW]; - coul = &nlist[eNL_QQ_WATER]; -#ifndef DISABLE_WATERWATER_NLIST + vdwc = &nlist[eNL_VDWQQ_WATER]; + vdw = &nlist[eNL_VDW]; + coul = &nlist[eNL_QQ_WATER]; vdwc_ww = &nlist[eNL_VDWQQ_WATERWATER]; coul_ww = &nlist[eNL_QQ_WATERWATER]; -#endif } else { @@ -698,9 +693,7 @@ put_in_list_at(gmx_bool bHaveVdW[], if (bDoCoul && bDoVdW) { new_i_nblist(vdwc, i_atom, shift, gid); -#ifndef DISABLE_WATERWATER_NLIST new_i_nblist(vdwc_ww, i_atom, shift, gid); -#endif } if (bDoVdW) { @@ -709,9 +702,7 @@ put_in_list_at(gmx_bool bHaveVdW[], if (bDoCoul) { new_i_nblist(coul, i_atom, shift, gid); -#ifndef DISABLE_WATERWATER_NLIST new_i_nblist(coul_ww, i_atom, shift, gid); -#endif } /* Loop over the j charge groups */ for (j = 0; (j < nj); j++) @@ -736,19 +727,6 @@ put_in_list_at(gmx_bool bHaveVdW[], } else { -#ifdef DISABLE_WATERWATER_NLIST - /* Add entries for the three atoms - only do VdW if we need to */ - if (!bDoVdW) - { - add_j_to_nblist(coul, jj0, bLR); - } - else - { - add_j_to_nblist(vdwc, jj0, bLR); - } - add_j_to_nblist(coul, jj0+1, bLR); - add_j_to_nblist(coul, jj0+2, bLR); -#else /* One entry for the entire water-water interaction */ if (!bDoVdW) { @@ -758,7 +736,6 @@ put_in_list_at(gmx_bool bHaveVdW[], { add_j_to_nblist(vdwc_ww, jj0, bLR); } -#endif } } else if (iwater == esolTIP4P && jwater == esolTIP4P) @@ -771,16 +748,6 @@ put_in_list_at(gmx_bool bHaveVdW[], } else { -#ifdef DISABLE_WATERWATER_NLIST - /* Add entries for the four atoms - only do VdW if we need to */ - if (bDoVdW) - { - add_j_to_nblist(vdw, jj0, bLR); - } - add_j_to_nblist(coul, jj0+1, bLR); - add_j_to_nblist(coul, jj0+2, bLR); - add_j_to_nblist(coul, jj0+3, bLR); -#else /* One entry for the entire water-water interaction */ if (!bDoVdW) { @@ -790,7 +757,6 @@ put_in_list_at(gmx_bool bHaveVdW[], { add_j_to_nblist(vdwc_ww, jj0, bLR); } -#endif } } else @@ -851,10 +817,8 @@ put_in_list_at(gmx_bool bHaveVdW[], close_i_nblist(vdw); close_i_nblist(coul); close_i_nblist(vdwc); -#ifndef DISABLE_WATERWATER_NLIST close_i_nblist(coul_ww); close_i_nblist(vdwc_ww); -#endif } else { @@ -2131,7 +2095,7 @@ static int nsgrid_core(t_commrec *cr, t_forcerec *fr, gmx_ns_t *ns; atom_id **nl_lr_ljc, **nl_lr_one, **nl_sr; int *nlr_ljc, *nlr_one, *nsr; - gmx_domdec_t *dd = NULL; + gmx_domdec_t *dd; t_block *cgs = &(top->cgs); int *cginfo = fr->cginfo; /* atom_id *i_atoms,*cgsindex=cgs->index; */ @@ -2159,10 +2123,7 @@ static int nsgrid_core(t_commrec *cr, t_forcerec *fr, ns = &fr->ns; bDomDec = DOMAINDECOMP(cr); - if (bDomDec) - { - dd = cr->dd; - } + dd = cr->dd; bTriclinicX = ((YY < grid->npbcdim && (!bDomDec || dd->nc[YY] == 1) && box[YY][XX] != 0) ||