From b5c9f851184f69fdc4533f272f6b0a598e8552ca Mon Sep 17 00:00:00 2001 From: Berk Hess Date: Thu, 2 Jul 2015 14:05:26 +0200 Subject: [PATCH] Correct grompp pull warning message A warning full pull-coord?-groups referred to pull-coord?-geometry instead. This is fixed by changing the order of proceses the pull options, which better reflects the dependencies. Also reordered the options in the mdp manual. Change-Id: I6309d021282156cd3409af35bcfa38dc2cab1c67 --- docs/user-guide/mdp-options.rst | 20 ++++++++++---------- src/gromacs/gmxpreprocess/readpull.c | 4 ++-- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst index 5767bd4f99..4fb9c0b204 100644 --- a/docs/user-guide/mdp-options.rst +++ b/docs/user-guide/mdp-options.rst @@ -1695,16 +1695,6 @@ applicable pulling coordinate. system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B 2010). -.. mdp:: pull-coord1-groups - - The two groups indices should be given on which this pull - coordinate will operate. The first index can be 0, in which case an - absolute reference of :mdp:`pull-coord1-origin` is used. With an - absolute reference the system is no longer translation invariant - and one should think about what to do with the center of mass - motion. Note that (only) for :mdp:`pull-coord1-geometry` = - :mdp-value:`direction-relative` four groups are required. - .. mdp:: pull-coord1-type: .. mdp-value:: umbrella @@ -1780,6 +1770,16 @@ applicable pulling coordinate. component. This geometry is not supported with constraint pulling. +.. mdp:: pull-coord1-groups + + The two groups indices should be given on which this pull + coordinate will operate. The first index can be 0, in which case an + absolute reference of :mdp:`pull-coord1-origin` is used. With an + absolute reference the system is no longer translation invariant + and one should think about what to do with the center of mass + motion. Note that (only) for :mdp:`pull-coord1-geometry` = + :mdp-value:`direction-relative` four groups are required. + .. mdp:: pull-coord1-dim (Y Y Y) diff --git a/src/gromacs/gmxpreprocess/readpull.c b/src/gromacs/gmxpreprocess/readpull.c index 49793283cc..f2fb2d2203 100644 --- a/src/gromacs/gmxpreprocess/readpull.c +++ b/src/gromacs/gmxpreprocess/readpull.c @@ -262,12 +262,12 @@ char **read_pullparams(int *ninp_p, t_inpfile **inp_p, int ngroup; pcrd = &pull->coord[i-1]; - sprintf(buf, "pull-coord%d-groups", i); - STYPE(buf, groups, ""); sprintf(buf, "pull-coord%d-type", i); EETYPE(buf, pcrd->eType, epull_names); sprintf(buf, "pull-coord%d-geometry", i); EETYPE(buf, pcrd->eGeom, epullg_names); + sprintf(buf, "pull-coord%d-groups", i); + STYPE(buf, groups, ""); nscan = sscanf(groups, "%d %d %d %d %d", &pcrd->group[0], &pcrd->group[1], &pcrd->group[2], &pcrd->group[3], &idum); ngroup = (pcrd->eGeom == epullgDIRRELATIVE) ? 4 : 2; -- 2.22.0