From 4da425087f165b30b25d772982e455845bac0fb0 Mon Sep 17 00:00:00 2001 From: Carsten Kutzner Date: Wed, 22 May 2013 15:47:47 +0200 Subject: [PATCH] Code cleanup in enforced rotation module, remove warnings. Change-Id: Iceb458b06f2c003c6325c77c3258edb112e449f6 --- include/pull_rotation.h | 4 +-- src/contrib/runner_openmm.c | 2 +- src/kernel/runner.c | 2 +- src/mdlib/pull_rotation.c | 50 +++++++++++++------------------------ 4 files changed, 22 insertions(+), 36 deletions(-) diff --git a/include/pull_rotation.h b/include/pull_rotation.h index b889e5bf34..9b9c33046d 100644 --- a/include/pull_rotation.h +++ b/include/pull_rotation.h @@ -70,6 +70,7 @@ extern "C" { * of the rotation output files. * \param cr Pointer to MPI communication data. * \param x The positions of all MD particles. + * \param box The simulation box. * \param mtop Molecular topology. * \param oenv Needed to open the rotation output xvgr file. * \param Flags Flags passed over from main, used to determine @@ -134,11 +135,10 @@ extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, gmx_large_int_t /*! \brief Close the enforced rotation output files. * - * \param fplog General output file, normally md.log. * \param rot Pointer to all the enforced rotation data. */ GMX_LIBMD_EXPORT -extern void finish_rot(FILE *fplog, t_rot *rot); +extern void finish_rot(t_rot *rot); #ifdef __cplusplus diff --git a/src/contrib/runner_openmm.c b/src/contrib/runner_openmm.c index 72a5c4858b..9272ef3bb7 100644 --- a/src/contrib/runner_openmm.c +++ b/src/contrib/runner_openmm.c @@ -1909,7 +1909,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt, if (inputrec->bRot) { - finish_rot(fplog,inputrec->rot); + finish_rot(inputrec->rot); } } diff --git a/src/kernel/runner.c b/src/kernel/runner.c index 765be55653..d9bfae0482 100644 --- a/src/kernel/runner.c +++ b/src/kernel/runner.c @@ -1603,7 +1603,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt, if (inputrec->bRot) { - finish_rot(fplog, inputrec->rot); + finish_rot(inputrec->rot); } } diff --git a/src/mdlib/pull_rotation.c b/src/mdlib/pull_rotation.c index 5b600b908e..8fbe2272fa 100644 --- a/src/mdlib/pull_rotation.c +++ b/src/mdlib/pull_rotation.c @@ -782,7 +782,7 @@ static FILE *open_output_file(const char *fn, int steps, const char what[]) /* Open output file for slab center data. Call on master only */ -static FILE *open_slab_out(const char *fn, t_rot *rot, const output_env_t oenv) +static FILE *open_slab_out(const char *fn, t_rot *rot) { FILE *fp; int g, i; @@ -997,7 +997,7 @@ static FILE *open_rot_out(const char *fn, t_rot *rot, const output_env_t oenv) /* Call on master only */ -static FILE *open_angles_out(const char *fn, t_rot *rot, const output_env_t oenv) +static FILE *open_angles_out(const char *fn, t_rot *rot) { int g, i; FILE *fp; @@ -1083,7 +1083,7 @@ static FILE *open_angles_out(const char *fn, t_rot *rot, const output_env_t oenv /* Open torque output file and write some information about it's structure. * Call on master only */ -static FILE *open_torque_out(const char *fn, t_rot *rot, const output_env_t oenv) +static FILE *open_torque_out(const char *fn, t_rot *rot) { FILE *fp; int g; @@ -1692,7 +1692,7 @@ static int get_single_atom_gaussians( } count--; - /* Determine the max slab */ + /* Determine the min slab */ slab = homeslab; do { @@ -2467,8 +2467,7 @@ static void get_firstlast_slab_check( t_rotgrp *rotg, /* The rotation group (inputrec data) */ t_gmx_enfrotgrp *erg, /* The rotation group (data only accessible in this file) */ rvec firstatom, /* First atom after sorting along the rotation vector v */ - rvec lastatom, /* Last atom along v */ - int g) /* The rotation group number */ + rvec lastatom) /* Last atom along v */ { erg->slab_first = get_first_slab(rotg, erg->max_beta, firstatom); erg->slab_last = get_last_slab(rotg, erg->max_beta, lastatom); @@ -2498,7 +2497,6 @@ static void do_flexible( rvec x[], /* The local positions */ matrix box, double t, /* Time in picoseconds */ - gmx_large_int_t step, /* The time step */ gmx_bool bOutstepRot, /* Output to main rotation output file */ gmx_bool bOutstepSlab) /* Output per-slab data */ { @@ -2518,7 +2516,7 @@ static void do_flexible( /* Determine the first relevant slab for the first atom and the last * relevant slab for the last atom */ - get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1], g); + get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1]); /* Determine for each slab depending on the min_gaussian cutoff criterium, * a first and a last atom index inbetween stuff needs to be calculated */ @@ -2630,10 +2628,6 @@ static gmx_inline void project_onto_plane(rvec dr, const rvec v) /* springs to the reference atoms. */ static void do_fixed( t_rotgrp *rotg, /* The rotation group */ - rvec x[], /* The positions */ - matrix box, /* The simulation box */ - double t, /* Time in picoseconds */ - gmx_large_int_t step, /* The time step */ gmx_bool bOutstepRot, /* Output to main rotation output file */ gmx_bool bOutstepSlab) /* Output per-slab data */ { @@ -2744,10 +2738,6 @@ static void do_fixed( /* Calculate the radial motion potential and forces */ static void do_radial_motion( t_rotgrp *rotg, /* The rotation group */ - rvec x[], /* The positions */ - matrix box, /* The simulation box */ - double t, /* Time in picoseconds */ - gmx_large_int_t step, /* The time step */ gmx_bool bOutstepRot, /* Output to main rotation output file */ gmx_bool bOutstepSlab) /* Output per-slab data */ { @@ -2847,8 +2837,6 @@ static void do_radial_motion_pf( t_rotgrp *rotg, /* The rotation group */ rvec x[], /* The positions */ matrix box, /* The simulation box */ - double t, /* Time in picoseconds */ - gmx_large_int_t step, /* The time step */ gmx_bool bOutstepRot, /* Output to main rotation output file */ gmx_bool bOutstepSlab) /* Output per-slab data */ { @@ -3059,8 +3047,6 @@ static void do_radial_motion2( t_rotgrp *rotg, /* The rotation group */ rvec x[], /* The positions */ matrix box, /* The simulation box */ - double t, /* Time in picoseconds */ - gmx_large_int_t step, /* The time step */ gmx_bool bOutstepRot, /* Output to main rotation output file */ gmx_bool bOutstepSlab) /* Output per-slab data */ { @@ -3307,7 +3293,7 @@ static void allocate_slabs( } -/* From the extreme coordinates of the reference group, determine the first +/* From the extreme positions of the reference group, determine the first * and last slab of the reference. We can never have more slabs in the real * simulation than calculated here for the reference. */ @@ -3583,7 +3569,7 @@ static void init_rot_group(FILE *fplog, t_commrec *cr, int g, t_rotgrp *rotg, /* Determine the smallest and largest coordinate with respect to the rotation vector */ get_firstlast_atom_ref(rotg, &ref_firstindex, &ref_lastindex); - /* From the extreme coordinates of the reference group, determine the first + /* From the extreme positions of the reference group, determine the first * and last slab of the reference. */ get_firstlast_slab_ref(rotg, erg->mc, ref_firstindex, ref_lastindex); @@ -3724,7 +3710,7 @@ extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[ er->out_slabs = NULL; if (MASTER(cr) && HaveFlexibleGroups(rot) ) { - er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), rot, oenv); + er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), rot); } if (MASTER(cr)) @@ -3806,11 +3792,11 @@ extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[ { if (HaveFlexibleGroups(rot) || HavePotFitGroups(rot) ) { - er->out_angles = open_angles_out(opt2fn("-ra", nfile, fnm), rot, oenv); + er->out_angles = open_angles_out(opt2fn("-ra", nfile, fnm), rot); } if (HaveFlexibleGroups(rot) ) { - er->out_torque = open_torque_out(opt2fn("-rt", nfile, fnm), rot, oenv); + er->out_torque = open_torque_out(opt2fn("-rt", nfile, fnm), rot); } } @@ -3819,7 +3805,7 @@ extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[ } -extern void finish_rot(FILE *fplog, t_rot *rot) +extern void finish_rot(t_rot *rot) { gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */ @@ -4043,17 +4029,17 @@ extern void do_rotation( case erotgISOPF: case erotgPM: case erotgPMPF: - do_fixed(rotg, x, box, t, step, outstep_rot, outstep_slab); + do_fixed(rotg, outstep_rot, outstep_slab); break; case erotgRM: - do_radial_motion(rotg, x, box, t, step, outstep_rot, outstep_slab); + do_radial_motion(rotg, outstep_rot, outstep_slab); break; case erotgRMPF: - do_radial_motion_pf(rotg, x, box, t, step, outstep_rot, outstep_slab); + do_radial_motion_pf(rotg, x, box, outstep_rot, outstep_slab); break; case erotgRM2: case erotgRM2PF: - do_radial_motion2(rotg, x, box, t, step, outstep_rot, outstep_slab); + do_radial_motion2(rotg, x, box, outstep_rot, outstep_slab); break; case erotgFLEXT: case erotgFLEX2T: @@ -4063,13 +4049,13 @@ extern void do_rotation( get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center); svmul(-1.0, erg->xc_center, transvec); translate_x(erg->xc, rotg->nat, transvec); - do_flexible(MASTER(cr), er, rotg, g, x, box, t, step, outstep_rot, outstep_slab); + do_flexible(MASTER(cr), er, rotg, g, x, box, t, outstep_rot, outstep_slab); break; case erotgFLEX: case erotgFLEX2: /* Do NOT subtract the center of mass in the low level routines! */ clear_rvec(erg->xc_center); - do_flexible(MASTER(cr), er, rotg, g, x, box, t, step, outstep_rot, outstep_slab); + do_flexible(MASTER(cr), er, rotg, g, x, box, t, outstep_rot, outstep_slab); break; default: gmx_fatal(FARGS, "No such rotation potential."); -- 2.22.0