/*! * \param[in] pc Position calculation data structure. * \param[out] p Output positions. * * Calls to gmx_ana_poscalc_update() using \p pc should use only positions * initialized with this function. * The \c p->g pointer is initialized to point to an internal group that * contains the maximum index group set with gmx_ana_poscalc_set_maxindex(). */ void gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p) { gmx_ana_indexmap_init(&p->m, &pc->gmax, pc->coll->top_, pc->itype); /* Only do the static optimization when there is no completion */ if (!(pc->flags & POS_DYNAMIC) && pc->b.nra == pc->gmax.isize) { gmx_ana_indexmap_set_static(&p->m, &pc->b); } gmx_ana_pos_reserve(p, p->m.nr, 0); if (pc->flags & POS_VELOCITIES) { gmx_ana_pos_reserve_velocities(p); } if (pc->flags & POS_FORCES) { gmx_ana_pos_reserve_forces(p); } gmx_ana_pos_set_nr(p, p->m.nr); gmx_ana_pos_set_evalgrp(p, &pc->gmax); }
/*! \brief * Parses the values for a parameter that takes a variable number of values. * * \param[in] nval Number of values in \p values. * \param[in] values Pointer to the list of values. * \param param Parameter to parse. * \param root Selection element to which child expressions are added. * \returns TRUE if the values were parsed successfully, FALSE otherwise. * * For integer ranges, the sequence of numbers from the first to second value * is stored, each as a separate value. */ static gmx_bool parse_values_varnum(int nval, t_selexpr_value *values, gmx_ana_selparam_t *param, t_selelem *root) { t_selexpr_value *value; int i, j; param->flags &= ~SPAR_DYNAMIC; /* Update nval if there are integer ranges. */ if (param->val.type == INT_VALUE) { value = values; while (value) { if (value->type == INT_VALUE && !value->bExpr) { nval += abs(value->u.i.i2 - value->u.i.i1); } value = value->next; } } /* Check that the value type is actually implemented */ if (param->val.type != INT_VALUE && param->val.type != REAL_VALUE && param->val.type != STR_VALUE && param->val.type != POS_VALUE) { gmx_bug("internal error"); return FALSE; } /* Reserve appropriate amount of memory */ if (param->val.type == POS_VALUE) { gmx_ana_pos_reserve(param->val.u.p, nval, 0); gmx_ana_pos_set_nr(param->val.u.p, nval); gmx_ana_indexmap_init(¶m->val.u.p->m, NULL, NULL, INDEX_UNKNOWN); } else { _gmx_selvalue_reserve(¶m->val, nval); } value = values; i = 0; while (value) { if (value->bExpr) { _gmx_selparser_error("expressions not supported within value lists"); return FALSE; } if (value->type != param->val.type) { gmx_bug("internal error"); return FALSE; } switch (param->val.type) { case INT_VALUE: if (value->u.i.i1 <= value->u.i.i2) { for (j = value->u.i.i1; j <= value->u.i.i2; ++j) { param->val.u.i[i++] = j; } } else { for (j = value->u.i.i1; j >= value->u.i.i2; --j) { param->val.u.i[i++] = j; } } break; case REAL_VALUE: if (value->u.r.r1 != value->u.r.r2) { _gmx_selparser_error("real ranges not supported for parameter '%s'", param->name); return FALSE; } param->val.u.r[i++] = value->u.r.r1; break; case STR_VALUE: param->val.u.s[i++] = strdup(value->u.s); break; case POS_VALUE: copy_rvec(value->u.x, param->val.u.p->x[i++]); break; default: /* Should not be reached */ gmx_bug("internal error"); return FALSE; } value = value->next; } param->val.nr = i; if (param->nvalptr) { *param->nvalptr = param->val.nr; } param->nvalptr = NULL; /* Create a dummy child element to store the string values. * This element is responsible for freeing the values, but carries no * other function. */ if (param->val.type == STR_VALUE) { t_selelem *child; child = _gmx_selelem_create(SEL_CONST); _gmx_selelem_set_vtype(child, STR_VALUE); child->name = param->name; child->flags &= ~SEL_ALLOCVAL; child->flags |= SEL_FLAGSSET | SEL_VARNUMVAL | SEL_ALLOCDATA; child->v.nr = param->val.nr; _gmx_selvalue_setstore(&child->v, param->val.u.s); /* Because the child is not group-valued, the u union is not used * for anything, so we can abuse it by storing the parameter value * as place_child() expects, but this is really ugly... */ child->u.param = param; place_child(root, child, param); } return TRUE; }