CUDA cut-off kernels now shift exclusion energies

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / readir.c

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014, 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.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * 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 <config.h>
#endif

#include <ctype.h>
#include <stdlib.h>
#include <limits.h>
#include "sysstuff.h"
#include "smalloc.h"
#include "typedefs.h"
#include "physics.h"
#include "names.h"
#include "gmx_fatal.h"
#include "macros.h"
#include "index.h"
#include "symtab.h"
#include "string2.h"
#include "readinp.h"
#include "warninp.h"
#include "readir.h"
#include "toputil.h"
#include "index.h"
#include "network.h"
#include "vec.h"
#include "pbc.h"
#include "mtop_util.h"
#include "chargegroup.h"
#include "inputrec.h"
#include "calc_verletbuf.h"

#define MAXPTR 254
#define NOGID  255

/* Resource parameters
 * Do not change any of these until you read the instruction
 * in readinp.h. Some cpp's do not take spaces after the backslash
 * (like the c-shell), which will give you a very weird compiler
 * message.
 */

typedef struct t_inputrec_strings
{
    char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
         acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
         energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
         couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
         wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN];
    char   fep_lambda[efptNR][STRLEN];
    char   lambda_weights[STRLEN];
    char **pull_grp;
    char **rot_grp;
    char   anneal[STRLEN], anneal_npoints[STRLEN],
           anneal_time[STRLEN], anneal_temp[STRLEN];
    char   QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
           bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
           SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
    char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
         efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];

} gmx_inputrec_strings;

static gmx_inputrec_strings *is = NULL;

void init_inputrec_strings()
{
    if (is)
    {
        gmx_incons("Attempted to call init_inputrec_strings before calling done_inputrec_strings. Only one inputrec (i.e. .mdp file) can be parsed at a time.");
    }
    snew(is, 1);
}

void done_inputrec_strings()
{
    sfree(is);
    is = NULL;
}

static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];

enum {
    egrptpALL,         /* All particles have to be a member of a group.     */
    egrptpALL_GENREST, /* A rest group with name is generated for particles *
                        * that are not part of any group.                   */
    egrptpPART,        /* As egrptpALL_GENREST, but no name is generated    *
                        * for the rest group.                               */
    egrptpONE          /* Merge all selected groups into one group,         *
                        * make a rest group for the remaining particles.    */
};

static const char *constraints[eshNR+1]    = {
    "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
};

static const char *couple_lam[ecouplamNR+1]    = {
    "vdw-q", "vdw", "q", "none", NULL
};

void init_ir(t_inputrec *ir, t_gromppopts *opts)
{
    snew(opts->include, STRLEN);
    snew(opts->define, STRLEN);
    snew(ir->fepvals, 1);
    snew(ir->expandedvals, 1);
    snew(ir->simtempvals, 1);
}

static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
{

    int i;

    for (i = 0; i < ntemps; i++)
    {
        /* simple linear scaling -- allows more control */
        if (simtemp->eSimTempScale == esimtempLINEAR)
        {
            simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
        }
        else if (simtemp->eSimTempScale == esimtempGEOMETRIC)  /* should give roughly equal acceptance for constant heat capacity . . . */
        {
            simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
        }
        else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
        {
            simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
        }
        else
        {
            char errorstr[128];
            sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
            gmx_fatal(FARGS, errorstr);
        }
    }
}



static void _low_check(gmx_bool b, char *s, warninp_t wi)
{
    if (b)
    {
        warning_error(wi, s);
    }
}

static void check_nst(const char *desc_nst, int nst,
                      const char *desc_p, int *p,
                      warninp_t wi)
{
    char buf[STRLEN];

    if (*p > 0 && *p % nst != 0)
    {
        /* Round up to the next multiple of nst */
        *p = ((*p)/nst + 1)*nst;
        sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
                desc_p, desc_nst, desc_p, *p);
        warning(wi, buf);
    }
}

static gmx_bool ir_NVE(const t_inputrec *ir)
{
    return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
}

static int lcd(int n1, int n2)
{
    int d, i;

    d = 1;
    for (i = 2; (i <= n1 && i <= n2); i++)
    {
        if (n1 % i == 0 && n2 % i == 0)
        {
            d = i;
        }
    }

    return d;
}

static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
{
    if (*eintmod == eintmodPOTSHIFT_VERLET)
    {
        if (ir->cutoff_scheme == ecutsVERLET)
        {
            *eintmod = eintmodPOTSHIFT;
        }
        else
        {
            *eintmod = eintmodNONE;
        }
    }
}

void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
              warninp_t wi)
/* Check internal consistency */
{
    /* Strange macro: first one fills the err_buf, and then one can check
     * the condition, which will print the message and increase the error
     * counter.
     */
#define CHECK(b) _low_check(b, err_buf, wi)
    char        err_buf[256], warn_buf[STRLEN];
    int         i, j;
    int         ns_type  = 0;
    real        dt_coupl = 0;
    real        dt_pcoupl;
    int         nstcmin;
    t_lambda   *fep    = ir->fepvals;
    t_expanded *expand = ir->expandedvals;

    set_warning_line(wi, mdparin, -1);

    /* BASIC CUT-OFF STUFF */
    if (ir->rcoulomb < 0)
    {
        warning_error(wi, "rcoulomb should be >= 0");
    }
    if (ir->rvdw < 0)
    {
        warning_error(wi, "rvdw should be >= 0");
    }
    if (ir->rlist < 0 &&
        !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
    {
        warning_error(wi, "rlist should be >= 0");
    }

    process_interaction_modifier(ir, &ir->coulomb_modifier);
    process_interaction_modifier(ir, &ir->vdw_modifier);

    if (ir->cutoff_scheme == ecutsGROUP)
    {
        warning_note(wi,
                     "The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed in a future "
                     "release when all interaction forms are supported for the verlet scheme. The verlet "
                     "scheme already scales better, and it is compatible with GPUs and other accelerators.");

        /* BASIC CUT-OFF STUFF */
        if (ir->rlist == 0 ||
            !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
              (ir_vdw_might_be_zero_at_cutoff(ir)     && ir->rvdw     > ir->rlist)))
        {
            /* No switched potential and/or no twin-range:
             * we can set the long-range cut-off to the maximum of the other cut-offs.
             */
            ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
        }
        else if (ir->rlistlong < 0)
        {
            ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
            sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
                    ir->rlistlong);
            warning(wi, warn_buf);
        }
        if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
        {
            warning_error(wi, "Can not have an infinite cut-off with PBC");
        }
        if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
        {
            warning_error(wi, "rlistlong can not be shorter than rlist");
        }
        if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
        {
            warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
        }
    }

    if (ir->rlistlong == ir->rlist)
    {
        ir->nstcalclr = 0;
    }
    else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
    {
        warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
    }

    if (ir->cutoff_scheme == ecutsVERLET)
    {
        real rc_max;

        /* Normal Verlet type neighbor-list, currently only limited feature support */
        if (inputrec2nboundeddim(ir) < 3)
        {
            warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
        }
        if (ir->rcoulomb != ir->rvdw)
        {
            warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
        }
        if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
        {
            if (ir->vdw_modifier == eintmodNONE ||
                ir->vdw_modifier == eintmodPOTSHIFT)
            {
                ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);

                sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
                warning_note(wi, warn_buf);

                ir->vdwtype = evdwCUT;
            }
            else
            {
                sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
                warning_error(wi, warn_buf);
            }
        }

        if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
        {
            warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
        }
        if (!(ir->coulombtype == eelCUT ||
              (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
              EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
        {
            warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
        }
        if (!(ir->coulomb_modifier == eintmodNONE ||
              ir->coulomb_modifier == eintmodPOTSHIFT))
        {
            sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
            warning_error(wi, warn_buf);
        }

        if (ir->nstlist <= 0)
        {
            warning_error(wi, "With Verlet lists nstlist should be larger than 0");
        }

        if (ir->nstlist < 10)
        {
            warning_note(wi, "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.");
        }

        rc_max = max(ir->rvdw, ir->rcoulomb);

        if (ir->verletbuf_tol <= 0)
        {
            if (ir->verletbuf_tol == 0)
            {
                warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
            }

            if (ir->rlist < rc_max)
            {
                warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
            }

            if (ir->rlist == rc_max && ir->nstlist > 1)
            {
                warning_note(wi, "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation.");
            }
        }
        else
        {
            if (ir->rlist > rc_max)
            {
                warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.");
            }

            if (ir->nstlist == 1)
            {
                /* No buffer required */
                ir->rlist = rc_max;
            }
            else
            {
                if (EI_DYNAMICS(ir->eI))
                {
                    if (inputrec2nboundeddim(ir) < 3)
                    {
                        warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-tolerance > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-tolerance = -1.");
                    }
                    /* Set rlist temporarily so we can continue processing */
                    ir->rlist = rc_max;
                }
                else
                {
                    /* Set the buffer to 5% of the cut-off */
                    ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
                }
            }
        }

        /* No twin-range calculations with Verlet lists */
        ir->rlistlong = ir->rlist;
    }

    if (ir->nstcalclr == -1)
    {
        /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
        ir->nstcalclr = ir->nstlist;
    }
    else if (ir->nstcalclr > 0)
    {
        if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
        {
            warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
        }
    }
    else if (ir->nstcalclr < -1)
    {
        warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
    }

    if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
    {
        warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
    }

    /* GENERAL INTEGRATOR STUFF */
    if (!(ir->eI == eiMD || EI_VV(ir->eI)))
    {
        ir->etc = etcNO;
    }
    if (ir->eI == eiVVAK)
    {
        sprintf(warn_buf, "Integrator method %s is implemented primarily for validation purposes; for molecular dynamics, you should probably be using %s or %s", ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
        warning_note(wi, warn_buf);
    }
    if (!EI_DYNAMICS(ir->eI))
    {
        ir->epc = epcNO;
    }
    if (EI_DYNAMICS(ir->eI))
    {
        if (ir->nstcalcenergy < 0)
        {
            ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
            if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
            {
                /* nstcalcenergy larger than nstener does not make sense.
                 * We ideally want nstcalcenergy=nstener.
                 */
                if (ir->nstlist > 0)
                {
                    ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
                }
                else
                {
                    ir->nstcalcenergy = ir->nstenergy;
                }
            }
        }
        else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
                  (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
                   (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )

        {
            const char *nsten    = "nstenergy";
            const char *nstdh    = "nstdhdl";
            const char *min_name = nsten;
            int         min_nst  = ir->nstenergy;

            /* find the smallest of ( nstenergy, nstdhdl ) */
            if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
                (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
            {
                min_nst  = ir->fepvals->nstdhdl;
                min_name = nstdh;
            }
            /* If the user sets nstenergy small, we should respect that */
            sprintf(warn_buf,
                    "Setting nstcalcenergy (%d) equal to %s (%d)",
                    ir->nstcalcenergy, min_name, min_nst);
            warning_note(wi, warn_buf);
            ir->nstcalcenergy = min_nst;
        }

        if (ir->epc != epcNO)
        {
            if (ir->nstpcouple < 0)
            {
                ir->nstpcouple = ir_optimal_nstpcouple(ir);
            }
        }
        if (IR_TWINRANGE(*ir))
        {
            check_nst("nstlist", ir->nstlist,
                      "nstcalcenergy", &ir->nstcalcenergy, wi);
            if (ir->epc != epcNO)
            {
                check_nst("nstlist", ir->nstlist,
                          "nstpcouple", &ir->nstpcouple, wi);
            }
        }

        if (ir->nstcalcenergy > 0)
        {
            if (ir->efep != efepNO)
            {
                /* nstdhdl should be a multiple of nstcalcenergy */
                check_nst("nstcalcenergy", ir->nstcalcenergy,
                          "nstdhdl", &ir->fepvals->nstdhdl, wi);
                /* nstexpanded should be a multiple of nstcalcenergy */
                check_nst("nstcalcenergy", ir->nstcalcenergy,
                          "nstexpanded", &ir->expandedvals->nstexpanded, wi);
            }
            /* for storing exact averages nstenergy should be
             * a multiple of nstcalcenergy
             */
            check_nst("nstcalcenergy", ir->nstcalcenergy,
                      "nstenergy", &ir->nstenergy, wi);
        }
    }

    /* LD STUFF */
    if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
        ir->bContinuation && ir->ld_seed != -1)
    {
        warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
    }

    /* TPI STUFF */
    if (EI_TPI(ir->eI))
    {
        sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
        CHECK(ir->ePBC != epbcXYZ);
        sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
        CHECK(ir->ns_type != ensGRID);
        sprintf(err_buf, "with TPI nstlist should be larger than zero");
        CHECK(ir->nstlist <= 0);
        sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
        CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
    }

    /* SHAKE / LINCS */
    if ( (opts->nshake > 0) && (opts->bMorse) )
    {
        sprintf(warn_buf,
                "Using morse bond-potentials while constraining bonds is useless");
        warning(wi, warn_buf);
    }

    if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
        ir->bContinuation && ir->ld_seed != -1)
    {
        warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
    }
    /* verify simulated tempering options */

    if (ir->bSimTemp)
    {
        gmx_bool bAllTempZero = TRUE;
        for (i = 0; i < fep->n_lambda; i++)
        {
            sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
            CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
            if (fep->all_lambda[efptTEMPERATURE][i] > 0)
            {
                bAllTempZero = FALSE;
            }
        }
        sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
        CHECK(bAllTempZero == TRUE);

        sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
        CHECK(ir->eI != eiVV);

        /* check compatability of the temperature coupling with simulated tempering */

        if (ir->etc == etcNOSEHOOVER)
        {
            sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
            warning_note(wi, warn_buf);
        }

        /* check that the temperatures make sense */

        sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= than the simulated tempering lower temperature (%g)", ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
        CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);

        sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
        CHECK(ir->simtempvals->simtemp_high <= 0);

        sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
        CHECK(ir->simtempvals->simtemp_low <= 0);
    }

    /* verify free energy options */

    if (ir->efep != efepNO)
    {
        fep = ir->fepvals;
        sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
                fep->sc_power);
        CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);

        sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
                (int)fep->sc_r_power);
        CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);

        sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
        CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) ||  (fep->init_lambda > 0)));

        sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
        CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));

        sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
        CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));

        sprintf(err_buf, "Free-energy not implemented for Ewald");
        CHECK(ir->coulombtype == eelEWALD);

        /* check validty of lambda inputs */
        if (fep->n_lambda == 0)
        {
            /* Clear output in case of no states:*/
            sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
            CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
        }
        else
        {
            sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
            CHECK((fep->init_fep_state >= fep->n_lambda));
        }

        sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
        CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));

        sprintf(err_buf, "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with init-lambda-state or with init-lambda, but not both",
                fep->init_lambda, fep->init_fep_state);
        CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));



        if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
        {
            int n_lambda_terms;
            n_lambda_terms = 0;
            for (i = 0; i < efptNR; i++)
            {
                if (fep->separate_dvdl[i])
                {
                    n_lambda_terms++;
                }
            }
            if (n_lambda_terms > 1)
            {
                sprintf(warn_buf, "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't use init-lambda to set lambda state (except for slow growth). Use init-lambda-state instead.");
                warning(wi, warn_buf);
            }

            if (n_lambda_terms < 2 && fep->n_lambda > 0)
            {
                warning_note(wi,
                             "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
            }
        }

        for (j = 0; j < efptNR; j++)
        {
            for (i = 0; i < fep->n_lambda; i++)
            {
                sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[j], fep->all_lambda[j][i]);
                CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
            }
        }

        if ((fep->sc_alpha > 0) && (!fep->bScCoul))
        {
            for (i = 0; i < fep->n_lambda; i++)
            {
                sprintf(err_buf, "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to crashes, and is not supported.", i, fep->all_lambda[efptVDW][i],
                        fep->all_lambda[efptCOUL][i]);
                CHECK((fep->sc_alpha > 0) &&
                      (((fep->all_lambda[efptCOUL][i] > 0.0) &&
                        (fep->all_lambda[efptCOUL][i] < 1.0)) &&
                       ((fep->all_lambda[efptVDW][i] > 0.0) &&
                        (fep->all_lambda[efptVDW][i] < 1.0))));
            }
        }

        if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
        {
            real sigma, lambda, r_sc;

            sigma  = 0.34;
            /* Maximum estimate for A and B charges equal with lambda power 1 */
            lambda = 0.5;
            r_sc   = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
            sprintf(warn_buf, "With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of %g nm the fraction of the particle-particle potential at the cut-off at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
                    fep->sc_r_power,
                    sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
            warning_note(wi, warn_buf);
        }

        /*  Free Energy Checks -- In an ideal world, slow growth and FEP would
            be treated differently, but that's the next step */

        for (i = 0; i < efptNR; i++)
        {
            for (j = 0; j < fep->n_lambda; j++)
            {
                sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
                CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
            }
        }
    }

    if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
    {
        fep    = ir->fepvals;
        expand = ir->expandedvals;

        /* checking equilibration of weights inputs for validity */

        sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
                expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
        CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));

        sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
                expand->equil_samples, elmceq_names[elmceqSAMPLES]);
        CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));

        sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
                expand->equil_steps, elmceq_names[elmceqSTEPS]);
        CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));

        sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
                expand->equil_samples, elmceq_names[elmceqWLDELTA]);
        CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));

        sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
                expand->equil_ratio, elmceq_names[elmceqRATIO]);
        CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));

        sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
                expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
        CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));

        sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
                expand->equil_samples, elmceq_names[elmceqSAMPLES]);
        CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));

        sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
                expand->equil_steps, elmceq_names[elmceqSTEPS]);
        CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));

        sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
                expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
        CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));

        sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
                expand->equil_ratio, elmceq_names[elmceqRATIO]);
        CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));

        sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
                elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
        CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));

        sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
        CHECK((expand->lmc_repeats <= 0));
        sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
        CHECK((expand->minvarmin <= 0));
        sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
        CHECK((expand->c_range < 0));
        sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
                fep->init_fep_state, expand->lmc_forced_nstart);
        CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
        sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
        CHECK((expand->lmc_forced_nstart < 0));
        sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
        CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));

        sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
        CHECK((expand->init_wl_delta < 0));
        sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
        CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
        sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
        CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));

        /* if there is no temperature control, we need to specify an MC temperature */
        sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
        if (expand->nstTij > 0)
        {
            sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
                    expand->nstTij, ir->nstlog);
            CHECK((mod(expand->nstTij, ir->nstlog) != 0));
        }
    }

    /* PBC/WALLS */
    sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
    CHECK(ir->nwall && ir->ePBC != epbcXY);

    /* VACUUM STUFF */
    if (ir->ePBC != epbcXYZ && ir->nwall != 2)
    {
        if (ir->ePBC == epbcNONE)
        {
            if (ir->epc != epcNO)
            {
                warning(wi, "Turning off pressure coupling for vacuum system");
                ir->epc = epcNO;
            }
        }
        else
        {
            sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
                    epbc_names[ir->ePBC]);
            CHECK(ir->epc != epcNO);
        }
        sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
        CHECK(EEL_FULL(ir->coulombtype));

        sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
                epbc_names[ir->ePBC]);
        CHECK(ir->eDispCorr != edispcNO);
    }

    if (ir->rlist == 0.0)
    {
        sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
                "with coulombtype = %s or coulombtype = %s\n"
                "without periodic boundary conditions (pbc = %s) and\n"
                "rcoulomb and rvdw set to zero",
                eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
        CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
              (ir->ePBC     != epbcNONE) ||
              (ir->rcoulomb != 0.0)      || (ir->rvdw != 0.0));

        if (ir->nstlist < 0)
        {
            warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
        }
        if (ir->nstlist > 0)
        {
            warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
        }
    }

    /* COMM STUFF */
    if (ir->nstcomm == 0)
    {
        ir->comm_mode = ecmNO;
    }
    if (ir->comm_mode != ecmNO)
    {
        if (ir->nstcomm < 0)
        {
            warning(wi, "If you want to remove the rotation around the center of mass, you should set comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to its absolute value");
            ir->nstcomm = abs(ir->nstcomm);
        }

        if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
        {
            warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
            ir->nstcomm = ir->nstcalcenergy;
        }

        if (ir->comm_mode == ecmANGULAR)
        {
            sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
            CHECK(ir->bPeriodicMols);
            if (ir->ePBC != epbcNONE)
            {
                warning(wi, "Removing the rotation around the center of mass in a periodic system (this is not a problem when you have only one molecule).");
            }
        }
    }

    if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
    {
        warning_note(wi, "Tumbling and or flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR.");
    }

    sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
            " algorithm not implemented");
    CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
          && (ir->ns_type == ensSIMPLE));

    /* TEMPERATURE COUPLING */
    if (ir->etc == etcYES)
    {
        ir->etc = etcBERENDSEN;
        warning_note(wi, "Old option for temperature coupling given: "
                     "changing \"yes\" to \"Berendsen\"\n");
    }

    if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
    {
        if (ir->opts.nhchainlength < 1)
        {
            sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
            ir->opts.nhchainlength = 1;
            warning(wi, warn_buf);
        }

        if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
        {
            warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
            ir->opts.nhchainlength = 1;
        }
    }
    else
    {
        ir->opts.nhchainlength = 0;
    }

    if (ir->eI == eiVVAK)
    {
        sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
                ei_names[eiVVAK]);
        CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
    }

    if (ETC_ANDERSEN(ir->etc))
    {
        sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
        CHECK(!(EI_VV(ir->eI)));

        for (i = 0; i < ir->opts.ngtc; i++)
        {
            sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
            CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
            sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
                    i, ir->opts.tau_t[i]);
            CHECK(ir->opts.tau_t[i] < 0);
        }
        if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
        {
            sprintf(warn_buf, "Center of mass removal not necessary for %s.  All velocities of coupled groups are rerandomized periodically, so flying ice cube errors will not occur.", etcoupl_names[ir->etc]);
            warning_note(wi, warn_buf);
        }

        sprintf(err_buf, "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are randomized every time step", ir->nstcomm, etcoupl_names[ir->etc]);
        CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));

        for (i = 0; i < ir->opts.ngtc; i++)
        {
            int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
            sprintf(err_buf, "tau_t/delta_t for group %d for temperature control method %s must be a multiple of nstcomm (%d), as velocities of atoms in coupled groups are randomized every time step. The input tau_t (%8.3f) leads to %d steps per randomization", i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
            CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
        }
    }
    if (ir->etc == etcBERENDSEN)
    {
        sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
                ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
        warning_note(wi, warn_buf);
    }

    if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
        && ir->epc == epcBERENDSEN)
    {
        sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
                "true ensemble for the thermostat");
        warning(wi, warn_buf);
    }

    /* PRESSURE COUPLING */
    if (ir->epc == epcISOTROPIC)
    {
        ir->epc = epcBERENDSEN;
        warning_note(wi, "Old option for pressure coupling given: "
                     "changing \"Isotropic\" to \"Berendsen\"\n");
    }

    if (ir->epc != epcNO)
    {
        dt_pcoupl = ir->nstpcouple*ir->delta_t;

        sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
        CHECK(ir->tau_p <= 0);

        if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
        {
            sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
                    EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
            warning(wi, warn_buf);
        }

        sprintf(err_buf, "compressibility must be > 0 when using pressure"
                " coupling %s\n", EPCOUPLTYPE(ir->epc));
        CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
              ir->compress[ZZ][ZZ] < 0 ||
              (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
               ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));

        if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
        {
            sprintf(warn_buf,
                    "You are generating velocities so I am assuming you "
                    "are equilibrating a system. You are using "
                    "%s pressure coupling, but this can be "
                    "unstable for equilibration. If your system crashes, try "
                    "equilibrating first with Berendsen pressure coupling. If "
                    "you are not equilibrating the system, you can probably "
                    "ignore this warning.",
                    epcoupl_names[ir->epc]);
            warning(wi, warn_buf);
        }
    }

    if (EI_VV(ir->eI))
    {
        if (ir->epc > epcNO)
        {
            if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
            {
                warning_error(wi, "for md-vv and md-vv-avek, can only use Berendsen and Martyna-Tuckerman-Tobias-Klein (MTTK) equations for pressure control; MTTK is equivalent to Parrinello-Rahman.");
            }
        }
    }

    /* ELECTROSTATICS */
    /* More checks are in triple check (grompp.c) */

    if (ir->coulombtype == eelSWITCH)
    {
        sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
                "artifacts, advice: use coulombtype = %s",
                eel_names[ir->coulombtype],
                eel_names[eelRF_ZERO]);
        warning(wi, warn_buf);
    }

    if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
    {
        sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
        warning_note(wi, warn_buf);
    }

    if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
    {
        sprintf(warn_buf, "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old format and exchanging epsilon-r and epsilon-rf", ir->epsilon_r);
        warning(wi, warn_buf);
        ir->epsilon_rf = ir->epsilon_r;
        ir->epsilon_r  = 1.0;
    }

    if (getenv("GALACTIC_DYNAMICS") == NULL)
    {
        sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
        CHECK(ir->epsilon_r < 0);
    }

    if (EEL_RF(ir->coulombtype))
    {
        /* reaction field (at the cut-off) */

        if (ir->coulombtype == eelRF_ZERO)
        {
            sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
                    eel_names[ir->coulombtype]);
            CHECK(ir->epsilon_rf != 0);
            ir->epsilon_rf = 0.0;
        }

        sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
        CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
              (ir->epsilon_r == 0));
        if (ir->epsilon_rf == ir->epsilon_r)
        {
            sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
                    eel_names[ir->coulombtype]);
            warning(wi, warn_buf);
        }
    }
    /* Allow rlist>rcoulomb for tabulated long range stuff. This just
     * means the interaction is zero outside rcoulomb, but it helps to
     * provide accurate energy conservation.
     */
    if (ir_coulomb_might_be_zero_at_cutoff(ir))
    {
        if (ir_coulomb_switched(ir))
        {
            sprintf(err_buf,
                    "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
                    eel_names[ir->coulombtype]);
            CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
        }
    }
    else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
    {
        if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
        {
            sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
                    eel_names[ir->coulombtype]);
            CHECK(ir->rlist > ir->rcoulomb);
        }
    }

    if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
        ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
    {
        sprintf(warn_buf,
                "The switch/shift interaction settings are just for compatibility; you will get better "
                "performance from applying potential modifiers to your interactions!\n");
        warning_note(wi, warn_buf);
    }

    if (ir->coulombtype == eelPMESWITCH)
    {
        if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
        {
            sprintf(warn_buf, "The switching range for %s should be 5%% or less, energy conservation will be good anyhow, since ewald_rtol = %g",
                    eel_names[ir->coulombtype],
                    ir->ewald_rtol);
            warning(wi, warn_buf);
        }
    }

    if (EEL_FULL(ir->coulombtype))
    {
        if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
            ir->coulombtype == eelPMEUSERSWITCH)
        {
            sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
                    eel_names[ir->coulombtype]);
            CHECK(ir->rcoulomb > ir->rlist);
        }
        else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
        {
            if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
            {
                sprintf(err_buf,
                        "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
                        "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
                        "a potential modifier.", eel_names[ir->coulombtype]);
                if (ir->nstcalclr == 1)
                {
                    CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
                }
                else
                {
                    CHECK(ir->rcoulomb != ir->rlist);
                }
            }
        }
    }

    if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
    {
        if (ir->pme_order < 3)
        {
            warning_error(wi, "pme-order can not be smaller than 3");
        }
    }

    if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
    {
        if (ir->ewald_geometry == eewg3D)
        {
            sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
                    epbc_names[ir->ePBC], eewg_names[eewg3DC]);
            warning(wi, warn_buf);
        }
        /* This check avoids extra pbc coding for exclusion corrections */
        sprintf(err_buf, "wall-ewald-zfac should be >= 2");
        CHECK(ir->wall_ewald_zfac < 2);
    }

    if (ir_vdw_switched(ir))
    {
        sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
        CHECK(ir->rvdw_switch >= ir->rvdw);

        if (ir->rvdw_switch < 0.5*ir->rvdw)
        {
            sprintf(warn_buf, "You are applying a switch function to vdw forces or potentials from %g to %g nm, which is more than half the interaction range, whereas switch functions are intended to act only close to the cut-off.",
                    ir->rvdw_switch, ir->rvdw);
            warning_note(wi, warn_buf);
        }
    }
    else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
    {
        if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
        {
            sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
            CHECK(ir->rlist > ir->rvdw);
        }
    }

    if (ir->cutoff_scheme == ecutsGROUP)
    {
        if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
             (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
            ir->nstlist != 1)
        {
            warning_note(wi, "With exact cut-offs, rlist should be "
                         "larger than rcoulomb and rvdw, so that there "
                         "is a buffer region for particle motion "
                         "between neighborsearch steps");
        }

        if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
        {
            sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
                    IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
            warning_note(wi, warn_buf);
        }
        if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
        {
            sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
                    IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
            warning_note(wi, warn_buf);
        }
    }

    if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
    {
        warning_note(wi, "You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
    }

    if (ir->nstlist == -1)
    {
        sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
        CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
    }
    sprintf(err_buf, "nstlist can not be smaller than -1");
    CHECK(ir->nstlist < -1);

    if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
        && ir->rvdw != 0)
    {
        warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
    }

    if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
    {
        warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
    }

    /* ENERGY CONSERVATION */
    if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
    {
        if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
        {
            sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
                    evdw_names[evdwSHIFT]);
            warning_note(wi, warn_buf);
        }
        if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
        {
            sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
                    eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
            warning_note(wi, warn_buf);
        }
    }

    /* IMPLICIT SOLVENT */
    if (ir->coulombtype == eelGB_NOTUSED)
    {
        ir->coulombtype      = eelCUT;
        ir->implicit_solvent = eisGBSA;
        fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
                "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
                "setting implicit-solvent value to \"GBSA\" in input section.\n");
    }

    if (ir->sa_algorithm == esaSTILL)
    {
        sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
        CHECK(ir->sa_algorithm == esaSTILL);
    }

    if (ir->implicit_solvent == eisGBSA)
    {
        sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
        CHECK(ir->rgbradii != ir->rlist);

        if (ir->coulombtype != eelCUT)
        {
            sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
            CHECK(ir->coulombtype != eelCUT);
        }
        if (ir->vdwtype != evdwCUT)
        {
            sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
            CHECK(ir->vdwtype != evdwCUT);
        }
        if (ir->nstgbradii < 1)
        {
            sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
            warning_note(wi, warn_buf);
            ir->nstgbradii = 1;
        }
        if (ir->sa_algorithm == esaNO)
        {
            sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
            warning_note(wi, warn_buf);
        }
        if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
        {
            sprintf(warn_buf, "Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936 kJ/nm^2/mol for Still and HCT/OBC respectively\n");
            warning_note(wi, warn_buf);

            if (ir->gb_algorithm == egbSTILL)
            {
                ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
            }
            else
            {
                ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
            }
        }
        if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
        {
            sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
            CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
        }

    }

    if (ir->bAdress)
    {
        if (ir->cutoff_scheme != ecutsGROUP)
        {
            warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
        }
        if (!EI_SD(ir->eI))
        {
            warning_error(wi, "AdresS simulation supports only stochastic dynamics");
        }
        if (ir->epc != epcNO)
        {
            warning_error(wi, "AdresS simulation does not support pressure coupling");
        }
        if (EEL_FULL(ir->coulombtype))
        {
            warning_error(wi, "AdresS simulation does not support long-range electrostatics");
        }
    }
}

/* count the number of text elemets separated by whitespace in a string.
    str = the input string
    maxptr = the maximum number of allowed elements
    ptr = the output array of pointers to the first character of each element
    returns: the number of elements. */
int str_nelem(const char *str, int maxptr, char *ptr[])
{
    int   np = 0;
    char *copy0, *copy;

    copy0 = strdup(str);
    copy  = copy0;
    ltrim(copy);
    while (*copy != '\0')
    {
        if (np >= maxptr)
        {
            gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
                      str, maxptr);
        }
        if (ptr)
        {
            ptr[np] = copy;
        }
        np++;
        while ((*copy != '\0') && !isspace(*copy))
        {
            copy++;
        }
        if (*copy != '\0')
        {
            *copy = '\0';
            copy++;
        }
        ltrim(copy);
    }
    if (ptr == NULL)
    {
        sfree(copy0);
    }

    return np;
}

/* interpret a number of doubles from a string and put them in an array,
   after allocating space for them.
   str = the input string
   n = the (pre-allocated) number of doubles read
   r = the output array of doubles. */
static void parse_n_real(char *str, int *n, real **r)
{
    char *ptr[MAXPTR];
    int   i;

    *n = str_nelem(str, MAXPTR, ptr);

    snew(*r, *n);
    for (i = 0; i < *n; i++)
    {
        (*r)[i] = strtod(ptr[i], NULL);
    }
}

static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
{

    int         i, j, max_n_lambda, nweights, nfep[efptNR];
    t_lambda   *fep    = ir->fepvals;
    t_expanded *expand = ir->expandedvals;
    real      **count_fep_lambdas;
    gmx_bool    bOneLambda = TRUE;

    snew(count_fep_lambdas, efptNR);

    /* FEP input processing */
    /* first, identify the number of lambda values for each type.
       All that are nonzero must have the same number */

    for (i = 0; i < efptNR; i++)
    {
        parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
    }

    /* now, determine the number of components.  All must be either zero, or equal. */

    max_n_lambda = 0;
    for (i = 0; i < efptNR; i++)
    {
        if (nfep[i] > max_n_lambda)
        {
            max_n_lambda = nfep[i];  /* here's a nonzero one.  All of them
                                        must have the same number if its not zero.*/
            break;
        }
    }

    for (i = 0; i < efptNR; i++)
    {
        if (nfep[i] == 0)
        {
            ir->fepvals->separate_dvdl[i] = FALSE;
        }
        else if (nfep[i] == max_n_lambda)
        {
            if (i != efptTEMPERATURE)  /* we treat this differently -- not really a reason to compute the derivative with
                                          respect to the temperature currently */
            {
                ir->fepvals->separate_dvdl[i] = TRUE;
            }
        }
        else
        {
            gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
                      nfep[i], efpt_names[i], max_n_lambda);
        }
    }
    /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
    ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;

    /* the number of lambdas is the number we've read in, which is either zero
       or the same for all */
    fep->n_lambda = max_n_lambda;

    /* allocate space for the array of lambda values */
    snew(fep->all_lambda, efptNR);
    /* if init_lambda is defined, we need to set lambda */
    if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
    {
        ir->fepvals->separate_dvdl[efptFEP] = TRUE;
    }
    /* otherwise allocate the space for all of the lambdas, and transfer the data */
    for (i = 0; i < efptNR; i++)
    {
        snew(fep->all_lambda[i], fep->n_lambda);
        if (nfep[i] > 0)  /* if it's zero, then the count_fep_lambda arrays
                             are zero */
        {
            for (j = 0; j < fep->n_lambda; j++)
            {
                fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
            }
            sfree(count_fep_lambdas[i]);
        }
    }
    sfree(count_fep_lambdas);

    /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
       bookkeeping -- for now, init_lambda */

    if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
    {
        for (i = 0; i < fep->n_lambda; i++)
        {
            fep->all_lambda[efptFEP][i] = fep->init_lambda;
        }
    }

    /* check to see if only a single component lambda is defined, and soft core is defined.
       In this case, turn on coulomb soft core */

    if (max_n_lambda == 0)
    {
        bOneLambda = TRUE;
    }
    else
    {
        for (i = 0; i < efptNR; i++)
        {
            if ((nfep[i] != 0) && (i != efptFEP))
            {
                bOneLambda = FALSE;
            }
        }
    }
    if ((bOneLambda) && (fep->sc_alpha > 0))
    {
        fep->bScCoul = TRUE;
    }

    /* Fill in the others with the efptFEP if they are not explicitly
       specified (i.e. nfep[i] == 0).  This means if fep is not defined,
       they are all zero. */

    for (i = 0; i < efptNR; i++)
    {
        if ((nfep[i] == 0) && (i != efptFEP))
        {
            for (j = 0; j < fep->n_lambda; j++)
            {
                fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
            }
        }
    }


    /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
    if (fep->sc_r_power == 48)
    {
        if (fep->sc_alpha > 0.1)
        {
            gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
        }
    }

    expand = ir->expandedvals;
    /* now read in the weights */
    parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
    if (nweights == 0)
    {
        snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
    }
    else if (nweights != fep->n_lambda)
    {
        gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
                  nweights, fep->n_lambda);
    }
    if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
    {
        expand->nstexpanded = fep->nstdhdl;
        /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
    }
    if ((expand->nstexpanded < 0) && ir->bSimTemp)
    {
        expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
        /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
           2*tau_t just to be careful so it's not to frequent  */
    }
}


static void do_simtemp_params(t_inputrec *ir)
{

    snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
    GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);

    return;
}

static void do_wall_params(t_inputrec *ir,
                           char *wall_atomtype, char *wall_density,
                           t_gromppopts *opts)
{
    int    nstr, i;
    char  *names[MAXPTR];
    double dbl;

    opts->wall_atomtype[0] = NULL;
    opts->wall_atomtype[1] = NULL;

    ir->wall_atomtype[0] = -1;
    ir->wall_atomtype[1] = -1;
    ir->wall_density[0]  = 0;
    ir->wall_density[1]  = 0;

    if (ir->nwall > 0)
    {
        nstr = str_nelem(wall_atomtype, MAXPTR, names);
        if (nstr != ir->nwall)
        {
            gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
                      ir->nwall, nstr);
        }
        for (i = 0; i < ir->nwall; i++)
        {
            opts->wall_atomtype[i] = strdup(names[i]);
        }

        if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
        {
            nstr = str_nelem(wall_density, MAXPTR, names);
            if (nstr != ir->nwall)
            {
                gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
            }
            for (i = 0; i < ir->nwall; i++)
            {
                sscanf(names[i], "%lf", &dbl);
                if (dbl <= 0)
                {
                    gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
                }
                ir->wall_density[i] = dbl;
            }
        }
    }
}

static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
{
    int     i;
    t_grps *grps;
    char    str[STRLEN];

    if (nwall > 0)
    {
        srenew(groups->grpname, groups->ngrpname+nwall);
        grps = &(groups->grps[egcENER]);
        srenew(grps->nm_ind, grps->nr+nwall);
        for (i = 0; i < nwall; i++)
        {
            sprintf(str, "wall%d", i);
            groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
            grps->nm_ind[grps->nr++]          = groups->ngrpname++;
        }
    }
}

void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
                         t_expanded *expand, warninp_t wi)
{
    int        ninp, nerror = 0;
    t_inpfile *inp;

    ninp   = *ninp_p;
    inp    = *inp_p;

    /* read expanded ensemble parameters */
    CCTYPE ("expanded ensemble variables");
    ITYPE ("nstexpanded", expand->nstexpanded, -1);
    EETYPE("lmc-stats", expand->elamstats, elamstats_names);
    EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
    EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
    ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
    ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
    ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
    RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
    RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
    CCTYPE("Seed for Monte Carlo in lambda space");
    ITYPE ("lmc-seed", expand->lmc_seed, -1);
    RTYPE ("mc-temperature", expand->mc_temp, -1);
    ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
    ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
    ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
    EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
    ITYPE("nst-transition-matrix", expand->nstTij, -1);
    ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
    ITYPE ("weight-c-range", expand->c_range, 0);      /* default is just C=0 */
    RTYPE ("wl-scale", expand->wl_scale, 0.8);
    RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
    RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
    EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);

    *ninp_p   = ninp;
    *inp_p    = inp;

    return;
}

void get_ir(const char *mdparin, const char *mdparout,
            t_inputrec *ir, t_gromppopts *opts,
            warninp_t wi)
{
    char       *dumstr[2];
    double      dumdub[2][6];
    t_inpfile  *inp;
    const char *tmp;
    int         i, j, m, ninp;
    char        warn_buf[STRLEN];
    t_lambda   *fep    = ir->fepvals;
    t_expanded *expand = ir->expandedvals;

    init_inputrec_strings();
    inp = read_inpfile(mdparin, &ninp, wi);

    snew(dumstr[0], STRLEN);
    snew(dumstr[1], STRLEN);

    if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
    {
        sprintf(warn_buf,
                "%s did not specify a value for the .mdp option "
                "\"cutoff-scheme\". Probably it was first intended for use "
                "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
                "introduced, but the group scheme was still the default. "
                "The default is now the Verlet scheme, so you will observe "
                "different behaviour.", mdparin);
        warning_note(wi, warn_buf);
    }

    /* remove the following deprecated commands */
    REM_TYPE("title");
    REM_TYPE("cpp");
    REM_TYPE("domain-decomposition");
    REM_TYPE("andersen-seed");
    REM_TYPE("dihre");
    REM_TYPE("dihre-fc");
    REM_TYPE("dihre-tau");
    REM_TYPE("nstdihreout");
    REM_TYPE("nstcheckpoint");

    /* replace the following commands with the clearer new versions*/
    REPL_TYPE("unconstrained-start", "continuation");
    REPL_TYPE("foreign-lambda", "fep-lambdas");
    REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
    REPL_TYPE("nstxtcout", "nstxout-compressed");
    REPL_TYPE("xtc-grps", "compressed-x-grps");
    REPL_TYPE("xtc-precision", "compressed-x-precision");

    CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
    CTYPE ("Preprocessor information: use cpp syntax.");
    CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
    STYPE ("include", opts->include,  NULL);
    CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
    STYPE ("define",  opts->define,   NULL);

    CCTYPE ("RUN CONTROL PARAMETERS");
    EETYPE("integrator",  ir->eI,         ei_names);
    CTYPE ("Start time and timestep in ps");
    RTYPE ("tinit",   ir->init_t, 0.0);
    RTYPE ("dt",      ir->delta_t,    0.001);
    STEPTYPE ("nsteps",   ir->nsteps,     0);
    CTYPE ("For exact run continuation or redoing part of a run");
    STEPTYPE ("init-step", ir->init_step,  0);
    CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
    ITYPE ("simulation-part", ir->simulation_part, 1);
    CTYPE ("mode for center of mass motion removal");
    EETYPE("comm-mode",   ir->comm_mode,  ecm_names);
    CTYPE ("number of steps for center of mass motion removal");
    ITYPE ("nstcomm", ir->nstcomm,    100);
    CTYPE ("group(s) for center of mass motion removal");
    STYPE ("comm-grps",   is->vcm,            NULL);

    CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
    CTYPE ("Friction coefficient (amu/ps) and random seed");
    RTYPE ("bd-fric",     ir->bd_fric,    0.0);
    STEPTYPE ("ld-seed",  ir->ld_seed,    -1);

    /* Em stuff */
    CCTYPE ("ENERGY MINIMIZATION OPTIONS");
    CTYPE ("Force tolerance and initial step-size");
    RTYPE ("emtol",       ir->em_tol,     10.0);
    RTYPE ("emstep",      ir->em_stepsize, 0.01);
    CTYPE ("Max number of iterations in relax-shells");
    ITYPE ("niter",       ir->niter,      20);
    CTYPE ("Step size (ps^2) for minimization of flexible constraints");
    RTYPE ("fcstep",      ir->fc_stepsize, 0);
    CTYPE ("Frequency of steepest descents steps when doing CG");
    ITYPE ("nstcgsteep",  ir->nstcgsteep, 1000);
    ITYPE ("nbfgscorr",   ir->nbfgscorr,  10);

    CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
    RTYPE ("rtpi",    ir->rtpi,   0.05);

    /* Output options */
    CCTYPE ("OUTPUT CONTROL OPTIONS");
    CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
    ITYPE ("nstxout", ir->nstxout,    0);
    ITYPE ("nstvout", ir->nstvout,    0);
    ITYPE ("nstfout", ir->nstfout,    0);
    ir->nstcheckpoint = 1000;
    CTYPE ("Output frequency for energies to log file and energy file");
    ITYPE ("nstlog",  ir->nstlog, 1000);
    ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
    ITYPE ("nstenergy",   ir->nstenergy,  1000);
    CTYPE ("Output frequency and precision for .xtc file");
    ITYPE ("nstxout-compressed", ir->nstxout_compressed,  0);
    RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
    CTYPE ("This selects the subset of atoms for the compressed");
    CTYPE ("trajectory file. You can select multiple groups. By");
    CTYPE ("default, all atoms will be written.");
    STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
    CTYPE ("Selection of energy groups");
    STYPE ("energygrps",  is->energy,         NULL);

    /* Neighbor searching */
    CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
    CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
    EETYPE("cutoff-scheme",     ir->cutoff_scheme,    ecutscheme_names);
    CTYPE ("nblist update frequency");
    ITYPE ("nstlist", ir->nstlist,    10);
    CTYPE ("ns algorithm (simple or grid)");
    EETYPE("ns-type",     ir->ns_type,    ens_names);
    /* set ndelta to the optimal value of 2 */
    ir->ndelta = 2;
    CTYPE ("Periodic boundary conditions: xyz, no, xy");
    EETYPE("pbc",         ir->ePBC,       epbc_names);
    EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
    CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
    CTYPE ("a value of -1 means: use rlist");
    RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol,    0.005);
    CTYPE ("nblist cut-off");
    RTYPE ("rlist",   ir->rlist,  1.0);
    CTYPE ("long-range cut-off for switched potentials");
    RTYPE ("rlistlong",   ir->rlistlong,  -1);
    ITYPE ("nstcalclr",   ir->nstcalclr,  -1);

    /* Electrostatics */
    CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
    CTYPE ("Method for doing electrostatics");
    EETYPE("coulombtype", ir->coulombtype,    eel_names);
    EETYPE("coulomb-modifier",    ir->coulomb_modifier,    eintmod_names);
    CTYPE ("cut-off lengths");
    RTYPE ("rcoulomb-switch", ir->rcoulomb_switch,    0.0);
    RTYPE ("rcoulomb",    ir->rcoulomb,   1.0);
    CTYPE ("Relative dielectric constant for the medium and the reaction field");
    RTYPE ("epsilon-r",   ir->epsilon_r,  1.0);
    RTYPE ("epsilon-rf",  ir->epsilon_rf, 0.0);
    CTYPE ("Method for doing Van der Waals");
    EETYPE("vdw-type",    ir->vdwtype,    evdw_names);
    EETYPE("vdw-modifier",    ir->vdw_modifier,    eintmod_names);
    CTYPE ("cut-off lengths");
    RTYPE ("rvdw-switch", ir->rvdw_switch,    0.0);
    RTYPE ("rvdw",    ir->rvdw,   1.0);
    CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
    EETYPE("DispCorr",    ir->eDispCorr,  edispc_names);
    CTYPE ("Extension of the potential lookup tables beyond the cut-off");
    RTYPE ("table-extension", ir->tabext, 1.0);
    CTYPE ("Separate tables between energy group pairs");
    STYPE ("energygrp-table", is->egptable,   NULL);
    CTYPE ("Spacing for the PME/PPPM FFT grid");
    RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
    CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
    ITYPE ("fourier-nx",  ir->nkx,         0);
    ITYPE ("fourier-ny",  ir->nky,         0);
    ITYPE ("fourier-nz",  ir->nkz,         0);
    CTYPE ("EWALD/PME/PPPM parameters");
    ITYPE ("pme-order",   ir->pme_order,   4);
    RTYPE ("ewald-rtol",  ir->ewald_rtol, 0.00001);
    RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
    EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
    EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
    RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
    EETYPE("optimize-fft", ir->bOptFFT,  yesno_names);

    CCTYPE("IMPLICIT SOLVENT ALGORITHM");
    EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);

    CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
    CTYPE ("Algorithm for calculating Born radii");
    EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
    CTYPE ("Frequency of calculating the Born radii inside rlist");
    ITYPE ("nstgbradii", ir->nstgbradii, 1);
    CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
    CTYPE ("between rlist and rgbradii is updated every nstlist steps");
    RTYPE ("rgbradii",  ir->rgbradii, 1.0);
    CTYPE ("Dielectric coefficient of the implicit solvent");
    RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
    CTYPE ("Salt concentration in M for Generalized Born models");
    RTYPE ("gb-saltconc",  ir->gb_saltconc, 0.0);
    CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
    RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
    RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
    RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
    RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
    EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
    CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
    CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
    RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);

    /* Coupling stuff */
    CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
    CTYPE ("Temperature coupling");
    EETYPE("tcoupl",  ir->etc,        etcoupl_names);
    ITYPE ("nsttcouple", ir->nsttcouple,  -1);
    ITYPE("nh-chain-length",     ir->opts.nhchainlength, 10);
    EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
    CTYPE ("Groups to couple separately");
    STYPE ("tc-grps",     is->tcgrps,         NULL);
    CTYPE ("Time constant (ps) and reference temperature (K)");
    STYPE ("tau-t",   is->tau_t,      NULL);
    STYPE ("ref-t",   is->ref_t,      NULL);
    CTYPE ("pressure coupling");
    EETYPE("pcoupl",  ir->epc,        epcoupl_names);
    EETYPE("pcoupltype",  ir->epct,       epcoupltype_names);
    ITYPE ("nstpcouple", ir->nstpcouple,  -1);
    CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
    RTYPE ("tau-p",   ir->tau_p,  1.0);
    STYPE ("compressibility", dumstr[0],  NULL);
    STYPE ("ref-p",       dumstr[1],      NULL);
    CTYPE ("Scaling of reference coordinates, No, All or COM");
    EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);

    /* QMMM */
    CCTYPE ("OPTIONS FOR QMMM calculations");
    EETYPE("QMMM", ir->bQMMM, yesno_names);
    CTYPE ("Groups treated Quantum Mechanically");
    STYPE ("QMMM-grps",  is->QMMM,          NULL);
    CTYPE ("QM method");
    STYPE("QMmethod",     is->QMmethod, NULL);
    CTYPE ("QMMM scheme");
    EETYPE("QMMMscheme",  ir->QMMMscheme,    eQMMMscheme_names);
    CTYPE ("QM basisset");
    STYPE("QMbasis",      is->QMbasis, NULL);
    CTYPE ("QM charge");
    STYPE ("QMcharge",    is->QMcharge, NULL);
    CTYPE ("QM multiplicity");
    STYPE ("QMmult",      is->QMmult, NULL);
    CTYPE ("Surface Hopping");
    STYPE ("SH",          is->bSH, NULL);
    CTYPE ("CAS space options");
    STYPE ("CASorbitals",      is->CASorbitals,   NULL);
    STYPE ("CASelectrons",     is->CASelectrons,  NULL);
    STYPE ("SAon", is->SAon, NULL);
    STYPE ("SAoff", is->SAoff, NULL);
    STYPE ("SAsteps", is->SAsteps, NULL);
    CTYPE ("Scale factor for MM charges");
    RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
    CTYPE ("Optimization of QM subsystem");
    STYPE ("bOPT",          is->bOPT, NULL);
    STYPE ("bTS",          is->bTS, NULL);

    /* Simulated annealing */
    CCTYPE("SIMULATED ANNEALING");
    CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
    STYPE ("annealing",   is->anneal,      NULL);
    CTYPE ("Number of time points to use for specifying annealing in each group");
    STYPE ("annealing-npoints", is->anneal_npoints, NULL);
    CTYPE ("List of times at the annealing points for each group");
    STYPE ("annealing-time",       is->anneal_time,       NULL);
    CTYPE ("Temp. at each annealing point, for each group.");
    STYPE ("annealing-temp",  is->anneal_temp,  NULL);

    /* Startup run */
    CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
    EETYPE("gen-vel",     opts->bGenVel,  yesno_names);
    RTYPE ("gen-temp",    opts->tempi,    300.0);
    ITYPE ("gen-seed",    opts->seed,     -1);

    /* Shake stuff */
    CCTYPE ("OPTIONS FOR BONDS");
    EETYPE("constraints", opts->nshake,   constraints);
    CTYPE ("Type of constraint algorithm");
    EETYPE("constraint-algorithm",  ir->eConstrAlg, econstr_names);
    CTYPE ("Do not constrain the start configuration");
    EETYPE("continuation", ir->bContinuation, yesno_names);
    CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
    EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
    CTYPE ("Relative tolerance of shake");
    RTYPE ("shake-tol", ir->shake_tol, 0.0001);
    CTYPE ("Highest order in the expansion of the constraint coupling matrix");
    ITYPE ("lincs-order", ir->nProjOrder, 4);
    CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
    CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
    CTYPE ("For energy minimization with constraints it should be 4 to 8.");
    ITYPE ("lincs-iter", ir->nLincsIter, 1);
    CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
    CTYPE ("rotates over more degrees than");
    RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
    CTYPE ("Convert harmonic bonds to morse potentials");
    EETYPE("morse",       opts->bMorse, yesno_names);

    /* Energy group exclusions */
    CCTYPE ("ENERGY GROUP EXCLUSIONS");
    CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
    STYPE ("energygrp-excl", is->egpexcl,     NULL);

    /* Walls */
    CCTYPE ("WALLS");
    CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
    ITYPE ("nwall", ir->nwall, 0);
    EETYPE("wall-type",     ir->wall_type,   ewt_names);
    RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
    STYPE ("wall-atomtype", is->wall_atomtype, NULL);
    STYPE ("wall-density",  is->wall_density,  NULL);
    RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);

    /* COM pulling */
    CCTYPE("COM PULLING");
    CTYPE("Pull type: no, umbrella, constraint or constant-force");
    EETYPE("pull",          ir->ePull, epull_names);
    if (ir->ePull != epullNO)
    {
        snew(ir->pull, 1);
        is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
    }

    /* Enforced rotation */
    CCTYPE("ENFORCED ROTATION");
    CTYPE("Enforced rotation: No or Yes");
    EETYPE("rotation",       ir->bRot, yesno_names);
    if (ir->bRot)
    {
        snew(ir->rot, 1);
        is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
    }

    /* Refinement */
    CCTYPE("NMR refinement stuff");
    CTYPE ("Distance restraints type: No, Simple or Ensemble");
    EETYPE("disre",       ir->eDisre,     edisre_names);
    CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
    EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
    CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
    EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
    RTYPE ("disre-fc",    ir->dr_fc,  1000.0);
    RTYPE ("disre-tau",   ir->dr_tau, 0.0);
    CTYPE ("Output frequency for pair distances to energy file");
    ITYPE ("nstdisreout", ir->nstdisreout, 100);
    CTYPE ("Orientation restraints: No or Yes");
    EETYPE("orire",       opts->bOrire,   yesno_names);
    CTYPE ("Orientation restraints force constant and tau for time averaging");
    RTYPE ("orire-fc",    ir->orires_fc,  0.0);
    RTYPE ("orire-tau",   ir->orires_tau, 0.0);
    STYPE ("orire-fitgrp", is->orirefitgrp,    NULL);
    CTYPE ("Output frequency for trace(SD) and S to energy file");
    ITYPE ("nstorireout", ir->nstorireout, 100);

    /* free energy variables */
    CCTYPE ("Free energy variables");
    EETYPE("free-energy", ir->efep, efep_names);
    STYPE ("couple-moltype",  is->couple_moltype,  NULL);
    EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
    EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
    EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);

    RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
                                                    we can recognize if
                                                    it was not entered */
    ITYPE ("init-lambda-state", fep->init_fep_state, -1);
    RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
    ITYPE ("nstdhdl", fep->nstdhdl, 50);
    STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
    STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
    STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
    STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
    STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
    STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
    STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
    ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
    STYPE ("init-lambda-weights", is->lambda_weights, NULL);
    EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
    RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
    ITYPE ("sc-power", fep->sc_power, 1);
    RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
    RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
    EETYPE("sc-coul", fep->bScCoul, yesno_names);
    ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
    RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
    EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
           separate_dhdl_file_names);
    EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
    ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
    RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);

    /* Non-equilibrium MD stuff */
    CCTYPE("Non-equilibrium MD stuff");
    STYPE ("acc-grps",    is->accgrps,        NULL);
    STYPE ("accelerate",  is->acc,            NULL);
    STYPE ("freezegrps",  is->freeze,         NULL);
    STYPE ("freezedim",   is->frdim,          NULL);
    RTYPE ("cos-acceleration", ir->cos_accel, 0);
    STYPE ("deform",      is->deform,         NULL);

    /* simulated tempering variables */
    CCTYPE("simulated tempering variables");
    EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
    EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
    RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
    RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);

    /* expanded ensemble variables */
    if (ir->efep == efepEXPANDED || ir->bSimTemp)
    {
        read_expandedparams(&ninp, &inp, expand, wi);
    }

    /* Electric fields */
    CCTYPE("Electric fields");
    CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
    CTYPE ("and a phase angle (real)");
    STYPE ("E-x",     is->efield_x,   NULL);
    STYPE ("E-xt",    is->efield_xt,  NULL);
    STYPE ("E-y",     is->efield_y,   NULL);
    STYPE ("E-yt",    is->efield_yt,  NULL);
    STYPE ("E-z",     is->efield_z,   NULL);
    STYPE ("E-zt",    is->efield_zt,  NULL);

    CCTYPE("Ion/water position swapping for computational electrophysiology setups");
    CTYPE("Swap positions along direction: no, X, Y, Z");
    EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
    if (ir->eSwapCoords != eswapNO)
    {
        snew(ir->swap, 1);
        CTYPE("Swap attempt frequency");
        ITYPE("swap-frequency", ir->swap->nstswap, 1);
        CTYPE("Two index groups that contain the compartment-partitioning atoms");
        STYPE("split-group0", splitgrp0, NULL);
        STYPE("split-group1", splitgrp1, NULL);
        CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
        EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
        EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);

        CTYPE("Group name of ions that can be exchanged with solvent molecules");
        STYPE("swap-group", swapgrp, NULL);
        CTYPE("Group name of solvent molecules");
        STYPE("solvent-group", solgrp, NULL);

        CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
        CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
        CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
        RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
        RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
        RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
        RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
        RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
        RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);

        CTYPE("Average the number of ions per compartment over these many swap attempt steps");
        ITYPE("coupl-steps", ir->swap->nAverage, 10);
        CTYPE("Requested number of anions and cations for each of the two compartments");
        CTYPE("-1 means fix the numbers as found in time step 0");
        ITYPE("anionsA", ir->swap->nanions[0], -1);
        ITYPE("cationsA", ir->swap->ncations[0], -1);
        ITYPE("anionsB", ir->swap->nanions[1], -1);
        ITYPE("cationsB", ir->swap->ncations[1], -1);
        CTYPE("Start to swap ions if threshold difference to requested count is reached");
        RTYPE("threshold", ir->swap->threshold, 1.0);
    }

    /* AdResS defined thingies */
    CCTYPE ("AdResS parameters");
    EETYPE("adress",       ir->bAdress, yesno_names);
    if (ir->bAdress)
    {
        snew(ir->adress, 1);
        read_adressparams(&ninp, &inp, ir->adress, wi);
    }

    /* User defined thingies */
    CCTYPE ("User defined thingies");
    STYPE ("user1-grps",  is->user1,          NULL);
    STYPE ("user2-grps",  is->user2,          NULL);
    ITYPE ("userint1",    ir->userint1,   0);
    ITYPE ("userint2",    ir->userint2,   0);
    ITYPE ("userint3",    ir->userint3,   0);
    ITYPE ("userint4",    ir->userint4,   0);
    RTYPE ("userreal1",   ir->userreal1,  0);
    RTYPE ("userreal2",   ir->userreal2,  0);
    RTYPE ("userreal3",   ir->userreal3,  0);
    RTYPE ("userreal4",   ir->userreal4,  0);
#undef CTYPE

    write_inpfile(mdparout, ninp, inp, FALSE, wi);
    for (i = 0; (i < ninp); i++)
    {
        sfree(inp[i].name);
        sfree(inp[i].value);
    }
    sfree(inp);

    /* Process options if necessary */
    for (m = 0; m < 2; m++)
    {
        for (i = 0; i < 2*DIM; i++)
        {
            dumdub[m][i] = 0.0;
        }
        if (ir->epc)
        {
            switch (ir->epct)
            {
                case epctISOTROPIC:
                    if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
                    {
                        warning_error(wi, "Pressure coupling not enough values (I need 1)");
                    }
                    dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
                    break;
                case epctSEMIISOTROPIC:
                case epctSURFACETENSION:
                    if (sscanf(dumstr[m], "%lf%lf",
                               &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
                    {
                        warning_error(wi, "Pressure coupling not enough values (I need 2)");
                    }
                    dumdub[m][YY] = dumdub[m][XX];
                    break;
                case epctANISOTROPIC:
                    if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
                               &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
                               &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
                    {
                        warning_error(wi, "Pressure coupling not enough values (I need 6)");
                    }
                    break;
                default:
                    gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
                              epcoupltype_names[ir->epct]);
            }
        }
    }
    clear_mat(ir->ref_p);
    clear_mat(ir->compress);
    for (i = 0; i < DIM; i++)
    {
        ir->ref_p[i][i]    = dumdub[1][i];
        ir->compress[i][i] = dumdub[0][i];
    }
    if (ir->epct == epctANISOTROPIC)
    {
        ir->ref_p[XX][YY] = dumdub[1][3];
        ir->ref_p[XX][ZZ] = dumdub[1][4];
        ir->ref_p[YY][ZZ] = dumdub[1][5];
        if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
        {
            warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
        }
        ir->compress[XX][YY] = dumdub[0][3];
        ir->compress[XX][ZZ] = dumdub[0][4];
        ir->compress[YY][ZZ] = dumdub[0][5];
        for (i = 0; i < DIM; i++)
        {
            for (m = 0; m < i; m++)
            {
                ir->ref_p[i][m]    = ir->ref_p[m][i];
                ir->compress[i][m] = ir->compress[m][i];
            }
        }
    }

    if (ir->comm_mode == ecmNO)
    {
        ir->nstcomm = 0;
    }

    opts->couple_moltype = NULL;
    if (strlen(is->couple_moltype) > 0)
    {
        if (ir->efep != efepNO)
        {
            opts->couple_moltype = strdup(is->couple_moltype);
            if (opts->couple_lam0 == opts->couple_lam1)
            {
                warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
            }
            if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
                                   opts->couple_lam1 == ecouplamNONE))
            {
                warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
            }
        }
        else
        {
            warning(wi, "Can not couple a molecule with free_energy = no");
        }
    }
    /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
    if (ir->efep != efepNO)
    {
        if (fep->delta_lambda > 0)
        {
            ir->efep = efepSLOWGROWTH;
        }
    }

    if (ir->bSimTemp)
    {
        fep->bPrintEnergy = TRUE;
        /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
           if the temperature is changing. */
    }

    if ((ir->efep != efepNO) || ir->bSimTemp)
    {
        ir->bExpanded = FALSE;
        if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
        {
            ir->bExpanded = TRUE;
        }
        do_fep_params(ir, is->fep_lambda, is->lambda_weights);
        if (ir->bSimTemp) /* done after fep params */
        {
            do_simtemp_params(ir);
        }
    }
    else
    {
        ir->fepvals->n_lambda = 0;
    }

    /* WALL PARAMETERS */

    do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);

    /* ORIENTATION RESTRAINT PARAMETERS */

    if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
    {
        warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
    }

    /* DEFORMATION PARAMETERS */

    clear_mat(ir->deform);
    for (i = 0; i < 6; i++)
    {
        dumdub[0][i] = 0;
    }
    m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
               &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
               &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
    for (i = 0; i < 3; i++)
    {
        ir->deform[i][i] = dumdub[0][i];
    }
    ir->deform[YY][XX] = dumdub[0][3];
    ir->deform[ZZ][XX] = dumdub[0][4];
    ir->deform[ZZ][YY] = dumdub[0][5];
    if (ir->epc != epcNO)
    {
        for (i = 0; i < 3; i++)
        {
            for (j = 0; j <= i; j++)
            {
                if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
                {
                    warning_error(wi, "A box element has deform set and compressibility > 0");
                }
            }
        }
        for (i = 0; i < 3; i++)
        {
            for (j = 0; j < i; j++)
            {
                if (ir->deform[i][j] != 0)
                {
                    for (m = j; m < DIM; m++)
                    {
                        if (ir->compress[m][j] != 0)
                        {
                            sprintf(warn_buf, "An off-diagonal box element has deform set while compressibility > 0 for the same component of another box vector, this might lead to spurious periodicity effects.");
                            warning(wi, warn_buf);
                        }
                    }
                }
            }
        }
    }

    /* Ion/water position swapping checks */
    if (ir->eSwapCoords != eswapNO)
    {
        if (ir->swap->nstswap < 1)
        {
            warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
        }
        if (ir->swap->nAverage < 1)
        {
            warning_error(wi, "coupl_steps must be 1 or larger.\n");
        }
        if (ir->swap->threshold < 1.0)
        {
            warning_error(wi, "Ion count threshold must be at least 1.\n");
        }
    }

    sfree(dumstr[0]);
    sfree(dumstr[1]);
}

static int search_QMstring(const char *s, int ng, const char *gn[])
{
    /* same as normal search_string, but this one searches QM strings */
    int i;

    for (i = 0; (i < ng); i++)
    {
        if (gmx_strcasecmp(s, gn[i]) == 0)
        {
            return i;
        }
    }

    gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);

    return -1;

} /* search_QMstring */

/* We would like gn to be const as well, but C doesn't allow this */
int search_string(const char *s, int ng, char *gn[])
{
    int i;

    for (i = 0; (i < ng); i++)
    {
        if (gmx_strcasecmp(s, gn[i]) == 0)
        {
            return i;
        }
    }

    gmx_fatal(FARGS,
              "Group %s referenced in the .mdp file was not found in the index file.\n"
              "Group names must match either [moleculetype] names or custom index group\n"
              "names, in which case you must supply an index file to the '-n' option\n"
              "of grompp.",
              s);

    return -1;
}

static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
                             t_blocka *block, char *gnames[],
                             int gtype, int restnm,
                             int grptp, gmx_bool bVerbose,
                             warninp_t wi)
{
    unsigned short *cbuf;
    t_grps         *grps = &(groups->grps[gtype]);
    int             i, j, gid, aj, ognr, ntot = 0;
    const char     *title;
    gmx_bool        bRest;
    char            warn_buf[STRLEN];

    if (debug)
    {
        fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
    }

    title = gtypes[gtype];

    snew(cbuf, natoms);
    /* Mark all id's as not set */
    for (i = 0; (i < natoms); i++)
    {
        cbuf[i] = NOGID;
    }

    snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
    for (i = 0; (i < ng); i++)
    {
        /* Lookup the group name in the block structure */
        gid = search_string(ptrs[i], block->nr, gnames);
        if ((grptp != egrptpONE) || (i == 0))
        {
            grps->nm_ind[grps->nr++] = gid;
        }
        if (debug)
        {
            fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
        }

        /* Now go over the atoms in the group */
        for (j = block->index[gid]; (j < block->index[gid+1]); j++)
        {

            aj = block->a[j];

            /* Range checking */
            if ((aj < 0) || (aj >= natoms))
            {
                gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
            }
            /* Lookup up the old group number */
            ognr = cbuf[aj];
            if (ognr != NOGID)
            {
                gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
                          aj+1, title, ognr+1, i+1);
            }
            else
            {
                /* Store the group number in buffer */
                if (grptp == egrptpONE)
                {
                    cbuf[aj] = 0;
                }
                else
                {
                    cbuf[aj] = i;
                }
                ntot++;
            }
        }
    }

    /* Now check whether we have done all atoms */
    bRest = FALSE;
    if (ntot != natoms)
    {
        if (grptp == egrptpALL)
        {
            gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
                      natoms-ntot, title);
        }
        else if (grptp == egrptpPART)
        {
            sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
                    natoms-ntot, title);
            warning_note(wi, warn_buf);
        }
        /* Assign all atoms currently unassigned to a rest group */
        for (j = 0; (j < natoms); j++)
        {
            if (cbuf[j] == NOGID)
            {
                cbuf[j] = grps->nr;
                bRest   = TRUE;
            }
        }
        if (grptp != egrptpPART)
        {
            if (bVerbose)
            {
                fprintf(stderr,
                        "Making dummy/rest group for %s containing %d elements\n",
                        title, natoms-ntot);
            }
            /* Add group name "rest" */
            grps->nm_ind[grps->nr] = restnm;

            /* Assign the rest name to all atoms not currently assigned to a group */
            for (j = 0; (j < natoms); j++)
            {
                if (cbuf[j] == NOGID)
                {
                    cbuf[j] = grps->nr;
                }
            }
            grps->nr++;
        }
    }

    if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
    {
        /* All atoms are part of one (or no) group, no index required */
        groups->ngrpnr[gtype] = 0;
        groups->grpnr[gtype]  = NULL;
    }
    else
    {
        groups->ngrpnr[gtype] = natoms;
        snew(groups->grpnr[gtype], natoms);
        for (j = 0; (j < natoms); j++)
        {
            groups->grpnr[gtype][j] = cbuf[j];
        }
    }

    sfree(cbuf);

    return (bRest && grptp == egrptpPART);
}

static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
{
    t_grpopts              *opts;
    gmx_groups_t           *groups;
    t_pull                 *pull;
    int                     natoms, ai, aj, i, j, d, g, imin, jmin;
    t_iatom                *ia;
    int                    *nrdf2, *na_vcm, na_tot;
    double                 *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
    gmx_mtop_atomloop_all_t aloop;
    t_atom                 *atom;
    int                     mb, mol, ftype, as;
    gmx_molblock_t         *molb;
    gmx_moltype_t          *molt;

    /* Calculate nrdf.
     * First calc 3xnr-atoms for each group
     * then subtract half a degree of freedom for each constraint
     *
     * Only atoms and nuclei contribute to the degrees of freedom...
     */

    opts = &ir->opts;

    groups = &mtop->groups;
    natoms = mtop->natoms;

    /* Allocate one more for a possible rest group */
    /* We need to sum degrees of freedom into doubles,
     * since floats give too low nrdf's above 3 million atoms.
     */
    snew(nrdf_tc, groups->grps[egcTC].nr+1);
    snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
    snew(na_vcm, groups->grps[egcVCM].nr+1);

    for (i = 0; i < groups->grps[egcTC].nr; i++)
    {
        nrdf_tc[i] = 0;
    }
    for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
    {
        nrdf_vcm[i] = 0;
    }

    snew(nrdf2, natoms);
    aloop = gmx_mtop_atomloop_all_init(mtop);
    while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
    {
        nrdf2[i] = 0;
        if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
        {
            g = ggrpnr(groups, egcFREEZE, i);
            /* Double count nrdf for particle i */
            for (d = 0; d < DIM; d++)
            {
                if (opts->nFreeze[g][d] == 0)
                {
                    nrdf2[i] += 2;
                }
            }
            nrdf_tc [ggrpnr(groups, egcTC, i)]  += 0.5*nrdf2[i];
            nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
        }
    }

    as = 0;
    for (mb = 0; mb < mtop->nmolblock; mb++)
    {
        molb = &mtop->molblock[mb];
        molt = &mtop->moltype[molb->type];
        atom = molt->atoms.atom;
        for (mol = 0; mol < molb->nmol; mol++)
        {
            for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
            {
                ia = molt->ilist[ftype].iatoms;
                for (i = 0; i < molt->ilist[ftype].nr; )
                {
                    /* Subtract degrees of freedom for the constraints,
                     * if the particles still have degrees of freedom left.
                     * If one of the particles is a vsite or a shell, then all
                     * constraint motion will go there, but since they do not
                     * contribute to the constraints the degrees of freedom do not
                     * change.
                     */
                    ai = as + ia[1];
                    aj = as + ia[2];
                    if (((atom[ia[1]].ptype == eptNucleus) ||
                         (atom[ia[1]].ptype == eptAtom)) &&
                        ((atom[ia[2]].ptype == eptNucleus) ||
                         (atom[ia[2]].ptype == eptAtom)))
                    {
                        if (nrdf2[ai] > 0)
                        {
                            jmin = 1;
                        }
                        else
                        {
                            jmin = 2;
                        }
                        if (nrdf2[aj] > 0)
                        {
                            imin = 1;
                        }
                        else
                        {
                            imin = 2;
                        }
                        imin       = min(imin, nrdf2[ai]);
                        jmin       = min(jmin, nrdf2[aj]);
                        nrdf2[ai] -= imin;
                        nrdf2[aj] -= jmin;
                        nrdf_tc [ggrpnr(groups, egcTC, ai)]  -= 0.5*imin;
                        nrdf_tc [ggrpnr(groups, egcTC, aj)]  -= 0.5*jmin;
                        nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
                        nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
                    }
                    ia += interaction_function[ftype].nratoms+1;
                    i  += interaction_function[ftype].nratoms+1;
                }
            }
            ia = molt->ilist[F_SETTLE].iatoms;
            for (i = 0; i < molt->ilist[F_SETTLE].nr; )
            {
                /* Subtract 1 dof from every atom in the SETTLE */
                for (j = 0; j < 3; j++)
                {
                    ai         = as + ia[1+j];
                    imin       = min(2, nrdf2[ai]);
                    nrdf2[ai] -= imin;
                    nrdf_tc [ggrpnr(groups, egcTC, ai)]  -= 0.5*imin;
                    nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
                }
                ia += 4;
                i  += 4;
            }
            as += molt->atoms.nr;
        }
    }

    if (ir->ePull == epullCONSTRAINT)
    {
        /* Correct nrdf for the COM constraints.
         * We correct using the TC and VCM group of the first atom
         * in the reference and pull group. If atoms in one pull group
         * belong to different TC or VCM groups it is anyhow difficult
         * to determine the optimal nrdf assignment.
         */
        pull = ir->pull;

        for (i = 0; i < pull->ncoord; i++)
        {
            imin = 1;

            for (j = 0; j < 2; j++)
            {
                const t_pull_group *pgrp;

                pgrp = &pull->group[pull->coord[i].group[j]];

                if (pgrp->nat > 0)
                {
                    /* Subtract 1/2 dof from each group */
                    ai = pgrp->ind[0];
                    nrdf_tc [ggrpnr(groups, egcTC, ai)]  -= 0.5*imin;
                    nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
                    if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
                    {
                        gmx_fatal(FARGS, "Center of mass pulling constraints caused the number of degrees of freedom for temperature coupling group %s to be negative", gnames[groups->grps[egcTC].nm_ind[ggrpnr(groups, egcTC, ai)]]);
                    }
                }
                else
                {
                    /* We need to subtract the whole DOF from group j=1 */
                    imin += 1;
                }
            }
        }
    }

    if (ir->nstcomm != 0)
    {
        /* Subtract 3 from the number of degrees of freedom in each vcm group
         * when com translation is removed and 6 when rotation is removed
         * as well.
         */
        switch (ir->comm_mode)
        {
            case ecmLINEAR:
                n_sub = ndof_com(ir);
                break;
            case ecmANGULAR:
                n_sub = 6;
                break;
            default:
                n_sub = 0;
                gmx_incons("Checking comm_mode");
        }

        for (i = 0; i < groups->grps[egcTC].nr; i++)
        {
            /* Count the number of atoms of TC group i for every VCM group */
            for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
            {
                na_vcm[j] = 0;
            }
            na_tot = 0;
            for (ai = 0; ai < natoms; ai++)
            {
                if (ggrpnr(groups, egcTC, ai) == i)
                {
                    na_vcm[ggrpnr(groups, egcVCM, ai)]++;
                    na_tot++;
                }
            }
            /* Correct for VCM removal according to the fraction of each VCM
             * group present in this TC group.
             */
            nrdf_uc = nrdf_tc[i];
            if (debug)
            {
                fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
                        i, nrdf_uc, n_sub);
            }
            nrdf_tc[i] = 0;
            for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
            {
                if (nrdf_vcm[j] > n_sub)
                {
                    nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
                        (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
                }
                if (debug)
                {
                    fprintf(debug, "  nrdf_vcm[%d] = %g, nrdf = %g\n",
                            j, nrdf_vcm[j], nrdf_tc[i]);
                }
            }
        }
    }
    for (i = 0; (i < groups->grps[egcTC].nr); i++)
    {
        opts->nrdf[i] = nrdf_tc[i];
        if (opts->nrdf[i] < 0)
        {
            opts->nrdf[i] = 0;
        }
        fprintf(stderr,
                "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
                gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
    }

    sfree(nrdf2);
    sfree(nrdf_tc);
    sfree(nrdf_vcm);
    sfree(na_vcm);
}

static void decode_cos(char *s, t_cosines *cosine)
{
    char   *t;
    char    format[STRLEN], f1[STRLEN];
    double  a, phi;
    int     i;

    t = strdup(s);
    trim(t);

    cosine->n   = 0;
    cosine->a   = NULL;
    cosine->phi = NULL;
    if (strlen(t))
    {
        sscanf(t, "%d", &(cosine->n));
        if (cosine->n <= 0)
        {
            cosine->n = 0;
        }
        else
        {
            snew(cosine->a, cosine->n);
            snew(cosine->phi, cosine->n);

            sprintf(format, "%%*d");
            for (i = 0; (i < cosine->n); i++)
            {
                strcpy(f1, format);
                strcat(f1, "%lf%lf");
                if (sscanf(t, f1, &a, &phi) < 2)
                {
                    gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
                }
                cosine->a[i]   = a;
                cosine->phi[i] = phi;
                strcat(format, "%*lf%*lf");
            }
        }
    }
    sfree(t);
}

static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
                            const char *option, const char *val, int flag)
{
    /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
     * But since this is much larger than STRLEN, such a line can not be parsed.
     * The real maximum is the number of names that fit in a string: STRLEN/2.
     */
#define EGP_MAX (STRLEN/2)
    int      nelem, i, j, k, nr;
    char    *names[EGP_MAX];
    char  ***gnames;
    gmx_bool bSet;

    gnames = groups->grpname;

    nelem = str_nelem(val, EGP_MAX, names);
    if (nelem % 2 != 0)
    {
        gmx_fatal(FARGS, "The number of groups for %s is odd", option);
    }
    nr   = groups->grps[egcENER].nr;
    bSet = FALSE;
    for (i = 0; i < nelem/2; i++)
    {
        j = 0;
        while ((j < nr) &&
               gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
        {
            j++;
        }
        if (j == nr)
        {
            gmx_fatal(FARGS, "%s in %s is not an energy group\n",
                      names[2*i], option);
        }
        k = 0;
        while ((k < nr) &&
               gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
        {
            k++;
        }
        if (k == nr)
        {
            gmx_fatal(FARGS, "%s in %s is not an energy group\n",
                      names[2*i+1], option);
        }
        if ((j < nr) && (k < nr))
        {
            ir->opts.egp_flags[nr*j+k] |= flag;
            ir->opts.egp_flags[nr*k+j] |= flag;
            bSet = TRUE;
        }
    }

    return bSet;
}


static void make_swap_groups(
        t_swapcoords *swap,
        char         *swapgname,
        char         *splitg0name,
        char         *splitg1name,
        char         *solgname,
        t_blocka     *grps,
        char        **gnames)
{
    int   ig = -1, i = 0, j;
    char *splitg;


    /* Just a quick check here, more thorough checks are in mdrun */
    if (strcmp(splitg0name, splitg1name) == 0)
    {
        gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
    }

    /* First get the swap group index atoms */
    ig        = search_string(swapgname, grps->nr, gnames);
    swap->nat = grps->index[ig+1] - grps->index[ig];
    if (swap->nat > 0)
    {
        fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
        snew(swap->ind, swap->nat);
        for (i = 0; i < swap->nat; i++)
        {
            swap->ind[i] = grps->a[grps->index[ig]+i];
        }
    }
    else
    {
        gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
    }

    /* Now do so for the split groups */
    for (j = 0; j < 2; j++)
    {
        if (j == 0)
        {
            splitg = splitg0name;
        }
        else
        {
            splitg = splitg1name;
        }

        ig                 = search_string(splitg, grps->nr, gnames);
        swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
        if (swap->nat_split[j] > 0)
        {
            fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
                    j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
            snew(swap->ind_split[j], swap->nat_split[j]);
            for (i = 0; i < swap->nat_split[j]; i++)
            {
                swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
            }
        }
        else
        {
            gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
        }
    }

    /* Now get the solvent group index atoms */
    ig            = search_string(solgname, grps->nr, gnames);
    swap->nat_sol = grps->index[ig+1] - grps->index[ig];
    if (swap->nat_sol > 0)
    {
        fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
        snew(swap->ind_sol, swap->nat_sol);
        for (i = 0; i < swap->nat_sol; i++)
        {
            swap->ind_sol[i] = grps->a[grps->index[ig]+i];
        }
    }
    else
    {
        gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
    }
}


void do_index(const char* mdparin, const char *ndx,
              gmx_mtop_t *mtop,
              gmx_bool bVerbose,
              t_inputrec *ir, rvec *v,
              warninp_t wi)
{
    t_blocka     *grps;
    gmx_groups_t *groups;
    int           natoms;
    t_symtab     *symtab;
    t_atoms       atoms_all;
    char          warnbuf[STRLEN], **gnames;
    int           nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
    real          tau_min;
    int           nstcmin;
    int           nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
    char         *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
    int           i, j, k, restnm;
    real          SAtime;
    gmx_bool      bExcl, bTable, bSetTCpar, bAnneal, bRest;
    int           nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
                  nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
    char          warn_buf[STRLEN];

    if (bVerbose)
    {
        fprintf(stderr, "processing index file...\n");
    }
    debug_gmx();
    if (ndx == NULL)
    {
        snew(grps, 1);
        snew(grps->index, 1);
        snew(gnames, 1);
        atoms_all = gmx_mtop_global_atoms(mtop);
        analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
        free_t_atoms(&atoms_all, FALSE);
    }
    else
    {
        grps = init_index(ndx, &gnames);
    }

    groups = &mtop->groups;
    natoms = mtop->natoms;
    symtab = &mtop->symtab;

    snew(groups->grpname, grps->nr+1);

    for (i = 0; (i < grps->nr); i++)
    {
        groups->grpname[i] = put_symtab(symtab, gnames[i]);
    }
    groups->grpname[i] = put_symtab(symtab, "rest");
    restnm             = i;
    srenew(gnames, grps->nr+1);
    gnames[restnm]   = *(groups->grpname[i]);
    groups->ngrpname = grps->nr+1;

    set_warning_line(wi, mdparin, -1);

    ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
    nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
    ntcg   = str_nelem(is->tcgrps, MAXPTR, ptr3);
    if ((ntau_t != ntcg) || (nref_t != ntcg))
    {
        gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
                  "%d tau-t values", ntcg, nref_t, ntau_t);
    }

    bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
    do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
                 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
    nr            = groups->grps[egcTC].nr;
    ir->opts.ngtc = nr;
    snew(ir->opts.nrdf, nr);
    snew(ir->opts.tau_t, nr);
    snew(ir->opts.ref_t, nr);
    if (ir->eI == eiBD && ir->bd_fric == 0)
    {
        fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
    }

    if (bSetTCpar)
    {
        if (nr != nref_t)
        {
            gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
        }

        tau_min = 1e20;
        for (i = 0; (i < nr); i++)
        {
            ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
            if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
            {
                sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
                warning_error(wi, warn_buf);
            }

            if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
            {
                warning_note(wi, "tau-t = -1 is the value to signal that a group should not have temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
            }

            if (ir->opts.tau_t[i] >= 0)
            {
                tau_min = min(tau_min, ir->opts.tau_t[i]);
            }
        }
        if (ir->etc != etcNO && ir->nsttcouple == -1)
        {
            ir->nsttcouple = ir_optimal_nsttcouple(ir);
        }

        if (EI_VV(ir->eI))
        {
            if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
            {
                gmx_fatal(FARGS, "Cannot do Nose-Hoover temperature with Berendsen pressure control with md-vv; use either vrescale temperature with berendsen pressure or Nose-Hoover temperature with MTTK pressure");
            }
            if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
            {
                if (ir->nstpcouple != ir->nsttcouple)
                {
                    int mincouple = min(ir->nstpcouple, ir->nsttcouple);
                    ir->nstpcouple = ir->nsttcouple = mincouple;
                    sprintf(warn_buf, "for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal.  Both have been reset to min(nsttcouple,nstpcouple) = %d", mincouple);
                    warning_note(wi, warn_buf);
                }
            }
        }
        /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
           primarily for testing purposes, and does not work with temperature coupling other than 1 */

        if (ETC_ANDERSEN(ir->etc))
        {
            if (ir->nsttcouple != 1)
            {
                ir->nsttcouple = 1;
                sprintf(warn_buf, "Andersen temperature control methods assume nsttcouple = 1; there is no need for larger nsttcouple > 1, since no global parameters are computed. nsttcouple has been reset to 1");
                warning_note(wi, warn_buf);
            }
        }
        nstcmin = tcouple_min_integration_steps(ir->etc);
        if (nstcmin > 1)
        {
            if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
            {
                sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
                        ETCOUPLTYPE(ir->etc),
                        tau_min, nstcmin,
                        ir->nsttcouple*ir->delta_t);
                warning(wi, warn_buf);
            }
        }
        for (i = 0; (i < nr); i++)
        {
            ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
            if (ir->opts.ref_t[i] < 0)
            {
                gmx_fatal(FARGS, "ref-t for group %d negative", i);
            }
        }
        /* set the lambda mc temperature to the md integrator temperature (which should be defined
           if we are in this conditional) if mc_temp is negative */
        if (ir->expandedvals->mc_temp < 0)
        {
            ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
        }
    }

    /* Simulated annealing for each group. There are nr groups */
    nSA = str_nelem(is->anneal, MAXPTR, ptr1);
    if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
    {
        nSA = 0;
    }
    if (nSA > 0 && nSA != nr)
    {
        gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
    }
    else
    {
        snew(ir->opts.annealing, nr);
        snew(ir->opts.anneal_npoints, nr);
        snew(ir->opts.anneal_time, nr);
        snew(ir->opts.anneal_temp, nr);
        for (i = 0; i < nr; i++)
        {
            ir->opts.annealing[i]      = eannNO;
            ir->opts.anneal_npoints[i] = 0;
            ir->opts.anneal_time[i]    = NULL;
            ir->opts.anneal_temp[i]    = NULL;
        }
        if (nSA > 0)
        {
            bAnneal = FALSE;
            for (i = 0; i < nr; i++)
            {
                if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
                {
                    ir->opts.annealing[i] = eannNO;
                }
                else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
                {
                    ir->opts.annealing[i] = eannSINGLE;
                    bAnneal               = TRUE;
                }
                else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
                {
                    ir->opts.annealing[i] = eannPERIODIC;
                    bAnneal               = TRUE;
                }
            }
            if (bAnneal)
            {
                /* Read the other fields too */
                nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
                if (nSA_points != nSA)
                {
                    gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
                }
                for (k = 0, i = 0; i < nr; i++)
                {
                    ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
                    if (ir->opts.anneal_npoints[i] == 1)
                    {
                        gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
                    }
                    snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
                    snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
                    k += ir->opts.anneal_npoints[i];
                }

                nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
                if (nSA_time != k)
                {
                    gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
                }
                nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
                if (nSA_temp != k)
                {
                    gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
                }

                for (i = 0, k = 0; i < nr; i++)
                {

                    for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
                    {
                        ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
                        ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
                        if (j == 0)
                        {
                            if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
                            {
                                gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
                            }
                        }
                        else
                        {
                            /* j>0 */
                            if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
                            {
                                gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
                                          ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
                            }
                        }
                        if (ir->opts.anneal_temp[i][j] < 0)
                        {
                            gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
                        }
                        k++;
                    }
                }
                /* Print out some summary information, to make sure we got it right */
                for (i = 0, k = 0; i < nr; i++)
                {
                    if (ir->opts.annealing[i] != eannNO)
                    {
                        j = groups->grps[egcTC].nm_ind[i];
                        fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
                                *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
                                ir->opts.anneal_npoints[i]);
                        fprintf(stderr, "Time (ps)   Temperature (K)\n");
                        /* All terms except the last one */
                        for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
                        {
                            fprintf(stderr, "%9.1f      %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
                        }

                        /* Finally the last one */
                        j = ir->opts.anneal_npoints[i]-1;
                        if (ir->opts.annealing[i] == eannSINGLE)
                        {
                            fprintf(stderr, "%9.1f-     %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
                        }
                        else
                        {
                            fprintf(stderr, "%9.1f      %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
                            if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
                            {
                                warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
                            }
                        }
                    }
                }
            }
        }
    }

    if (ir->ePull != epullNO)
    {
        make_pull_groups(ir->pull, is->pull_grp, grps, gnames);

        make_pull_coords(ir->pull);
    }

    if (ir->bRot)
    {
        make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
    }

    if (ir->eSwapCoords != eswapNO)
    {
        make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
    }

    nacc = str_nelem(is->acc, MAXPTR, ptr1);
    nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
    if (nacg*DIM != nacc)
    {
        gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
                  nacg, nacc);
    }
    do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
                 restnm, egrptpALL_GENREST, bVerbose, wi);
    nr = groups->grps[egcACC].nr;
    snew(ir->opts.acc, nr);
    ir->opts.ngacc = nr;

    for (i = k = 0; (i < nacg); i++)
    {
        for (j = 0; (j < DIM); j++, k++)
        {
            ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
        }
    }
    for (; (i < nr); i++)
    {
        for (j = 0; (j < DIM); j++)
        {
            ir->opts.acc[i][j] = 0;
        }
    }

    nfrdim  = str_nelem(is->frdim, MAXPTR, ptr1);
    nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
    if (nfrdim != DIM*nfreeze)
    {
        gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
                  nfreeze, nfrdim);
    }
    do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
                 restnm, egrptpALL_GENREST, bVerbose, wi);
    nr             = groups->grps[egcFREEZE].nr;
    ir->opts.ngfrz = nr;
    snew(ir->opts.nFreeze, nr);
    for (i = k = 0; (i < nfreeze); i++)
    {
        for (j = 0; (j < DIM); j++, k++)
        {
            ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
            if (!ir->opts.nFreeze[i][j])
            {
                if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
                {
                    sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
                            "(not %s)", ptr1[k]);
                    warning(wi, warn_buf);
                }
            }
        }
    }
    for (; (i < nr); i++)
    {
        for (j = 0; (j < DIM); j++)
        {
            ir->opts.nFreeze[i][j] = 0;
        }
    }

    nenergy = str_nelem(is->energy, MAXPTR, ptr1);
    do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
                 restnm, egrptpALL_GENREST, bVerbose, wi);
    add_wall_energrps(groups, ir->nwall, symtab);
    ir->opts.ngener = groups->grps[egcENER].nr;
    nvcm            = str_nelem(is->vcm, MAXPTR, ptr1);
    bRest           =
        do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
                     restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
    if (bRest)
    {
        warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
                "This may lead to artifacts.\n"
                "In most cases one should use one group for the whole system.");
    }

    /* Now we have filled the freeze struct, so we can calculate NRDF */
    calc_nrdf(mtop, ir, gnames);

    if (v && NULL)
    {
        real fac, ntot = 0;

        /* Must check per group! */
        for (i = 0; (i < ir->opts.ngtc); i++)
        {
            ntot += ir->opts.nrdf[i];
        }
        if (ntot != (DIM*natoms))
        {
            fac = sqrt(ntot/(DIM*natoms));
            if (bVerbose)
            {
                fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
                        "and removal of center of mass motion\n", fac);
            }
            for (i = 0; (i < natoms); i++)
            {
                svmul(fac, v[i], v[i]);
            }
        }
    }

    nuser = str_nelem(is->user1, MAXPTR, ptr1);
    do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
                 restnm, egrptpALL_GENREST, bVerbose, wi);
    nuser = str_nelem(is->user2, MAXPTR, ptr1);
    do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
                 restnm, egrptpALL_GENREST, bVerbose, wi);
    nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
    do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
                 restnm, egrptpONE, bVerbose, wi);
    nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
    do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
                 restnm, egrptpALL_GENREST, bVerbose, wi);

    /* QMMM input processing */
    nQMg          = str_nelem(is->QMMM, MAXPTR, ptr1);
    nQMmethod     = str_nelem(is->QMmethod, MAXPTR, ptr2);
    nQMbasis      = str_nelem(is->QMbasis, MAXPTR, ptr3);
    if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
    {
        gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
                  " and %d methods\n", nQMg, nQMbasis, nQMmethod);
    }
    /* group rest, if any, is always MM! */
    do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
                 restnm, egrptpALL_GENREST, bVerbose, wi);
    nr            = nQMg; /*atoms->grps[egcQMMM].nr;*/
    ir->opts.ngQM = nQMg;
    snew(ir->opts.QMmethod, nr);
    snew(ir->opts.QMbasis, nr);
    for (i = 0; i < nr; i++)
    {
        /* input consists of strings: RHF CASSCF PM3 .. These need to be
         * converted to the corresponding enum in names.c
         */
        ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
                                               eQMmethod_names);
        ir->opts.QMbasis[i]  = search_QMstring(ptr3[i], eQMbasisNR,
                                               eQMbasis_names);

    }
    nQMmult   = str_nelem(is->QMmult, MAXPTR, ptr1);
    nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
    nbSH      = str_nelem(is->bSH, MAXPTR, ptr3);
    snew(ir->opts.QMmult, nr);
    snew(ir->opts.QMcharge, nr);
    snew(ir->opts.bSH, nr);

    for (i = 0; i < nr; i++)
    {
        ir->opts.QMmult[i]   = strtol(ptr1[i], NULL, 10);
        ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
        ir->opts.bSH[i]      = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
    }

    nCASelec  = str_nelem(is->CASelectrons, MAXPTR, ptr1);
    nCASorb   = str_nelem(is->CASorbitals, MAXPTR, ptr2);
    snew(ir->opts.CASelectrons, nr);
    snew(ir->opts.CASorbitals, nr);
    for (i = 0; i < nr; i++)
    {
        ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
        ir->opts.CASorbitals[i]  = strtol(ptr2[i], NULL, 10);
    }
    /* special optimization options */

    nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
    nbTS  = str_nelem(is->bTS, MAXPTR, ptr2);
    snew(ir->opts.bOPT, nr);
    snew(ir->opts.bTS, nr);
    for (i = 0; i < nr; i++)
    {
        ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
        ir->opts.bTS[i]  = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
    }
    nSAon     = str_nelem(is->SAon, MAXPTR, ptr1);
    nSAoff    = str_nelem(is->SAoff, MAXPTR, ptr2);
    nSAsteps  = str_nelem(is->SAsteps, MAXPTR, ptr3);
    snew(ir->opts.SAon, nr);
    snew(ir->opts.SAoff, nr);
    snew(ir->opts.SAsteps, nr);

    for (i = 0; i < nr; i++)
    {
        ir->opts.SAon[i]    = strtod(ptr1[i], NULL);
        ir->opts.SAoff[i]   = strtod(ptr2[i], NULL);
        ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
    }
    /* end of QMMM input */

    if (bVerbose)
    {
        for (i = 0; (i < egcNR); i++)
        {
            fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
            for (j = 0; (j < groups->grps[i].nr); j++)
            {
                fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
            }
            fprintf(stderr, "\n");
        }
    }

    nr = groups->grps[egcENER].nr;
    snew(ir->opts.egp_flags, nr*nr);

    bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
    if (bExcl && ir->cutoff_scheme == ecutsVERLET)
    {
        warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
    }
    if (bExcl && EEL_FULL(ir->coulombtype))
    {
        warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
    }

    bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
    if (bTable && !(ir->vdwtype == evdwUSER) &&
        !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
        !(ir->coulombtype == eelPMEUSERSWITCH))
    {
        gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
    }

    decode_cos(is->efield_x, &(ir->ex[XX]));
    decode_cos(is->efield_xt, &(ir->et[XX]));
    decode_cos(is->efield_y, &(ir->ex[YY]));
    decode_cos(is->efield_yt, &(ir->et[YY]));
    decode_cos(is->efield_z, &(ir->ex[ZZ]));
    decode_cos(is->efield_zt, &(ir->et[ZZ]));

    if (ir->bAdress)
    {
        do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
    }

    for (i = 0; (i < grps->nr); i++)
    {
        sfree(gnames[i]);
    }
    sfree(gnames);
    done_blocka(grps);
    sfree(grps);

}



static void check_disre(gmx_mtop_t *mtop)
{
    gmx_ffparams_t *ffparams;
    t_functype     *functype;
    t_iparams      *ip;
    int             i, ndouble, ftype;
    int             label, old_label;

    if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
    {
        ffparams  = &mtop->ffparams;
        functype  = ffparams->functype;
        ip        = ffparams->iparams;
        ndouble   = 0;
        old_label = -1;
        for (i = 0; i < ffparams->ntypes; i++)
        {
            ftype = functype[i];
            if (ftype == F_DISRES)
            {
                label = ip[i].disres.label;
                if (label == old_label)
                {
                    fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
                    ndouble++;
                }
                old_label = label;
            }
        }
        if (ndouble > 0)
        {
            gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
                      "probably the parameters for multiple pairs in one restraint "
                      "are not identical\n", ndouble);
        }
    }
}

static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
                                   gmx_bool posres_only,
                                   ivec AbsRef)
{
    int                  d, g, i;
    gmx_mtop_ilistloop_t iloop;
    t_ilist             *ilist;
    int                  nmol;
    t_iparams           *pr;

    clear_ivec(AbsRef);

    if (!posres_only)
    {
        /* Check the COM */
        for (d = 0; d < DIM; d++)
        {
            AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
        }
        /* Check for freeze groups */
        for (g = 0; g < ir->opts.ngfrz; g++)
        {
            for (d = 0; d < DIM; d++)
            {
                if (ir->opts.nFreeze[g][d] != 0)
                {
                    AbsRef[d] = 1;
                }
            }
        }
    }

    /* Check for position restraints */
    iloop = gmx_mtop_ilistloop_init(sys);
    while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
    {
        if (nmol > 0 &&
            (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
        {
            for (i = 0; i < ilist[F_POSRES].nr; i += 2)
            {
                pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
                for (d = 0; d < DIM; d++)
                {
                    if (pr->posres.fcA[d] != 0)
                    {
                        AbsRef[d] = 1;
                    }
                }
            }
            for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
            {
                /* Check for flat-bottom posres */
                pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
                if (pr->fbposres.k != 0)
                {
                    switch (pr->fbposres.geom)
                    {
                        case efbposresSPHERE:
                            AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
                            break;
                        case efbposresCYLINDER:
                            AbsRef[XX] = AbsRef[YY] = 1;
                            break;
                        case efbposresX: /* d=XX */
                        case efbposresY: /* d=YY */
                        case efbposresZ: /* d=ZZ */
                            d         = pr->fbposres.geom - efbposresX;
                            AbsRef[d] = 1;
                            break;
                        default:
                            gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
                                      "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
                                      pr->fbposres.geom);
                    }
                }
            }
        }
    }

    return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
}

static void
check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
                                   gmx_bool *bC6ParametersWorkWithGeometricRules,
                                   gmx_bool *bC6ParametersWorkWithLBRules,
                                   gmx_bool *bLBRulesPossible)
{
    int           ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
    int          *typecount;
    real          tol;
    double        geometricdiff, LBdiff;
    double        c6i, c6j, c12i, c12j;
    double        c6, c6_geometric, c6_LB;
    double        sigmai, sigmaj, epsi, epsj;
    gmx_bool      bCanDoLBRules, bCanDoGeometricRules;
    const char   *ptr;

    /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
     * force-field floating point parameters.
     */
    tol = 1e-5;
    ptr = getenv("GMX_LJCOMB_TOL");
    if (ptr != NULL)
    {
        double dbl;

        sscanf(ptr, "%lf", &dbl);
        tol = dbl;
    }

    *bC6ParametersWorkWithLBRules         = TRUE;
    *bC6ParametersWorkWithGeometricRules  = TRUE;
    bCanDoLBRules                         = TRUE;
    bCanDoGeometricRules                  = TRUE;
    ntypes                                = mtop->ffparams.atnr;
    snew(typecount, ntypes);
    gmx_mtop_count_atomtypes(mtop, state, typecount);
    geometricdiff           = LBdiff = 0.0;
    *bLBRulesPossible       = TRUE;
    for (tpi = 0; tpi < ntypes; ++tpi)
    {
        c6i  = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
        c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
        for (tpj = tpi; tpj < ntypes; ++tpj)
        {
            c6j          = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
            c12j         = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
            c6           = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
            c6_geometric = sqrt(c6i * c6j);
            if (!gmx_numzero(c6_geometric))
            {
                if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
                {
                    sigmai   = pow(c12i / c6i, 1.0/6.0);
                    sigmaj   = pow(c12j / c6j, 1.0/6.0);
                    epsi     = c6i * c6i /(4.0 * c12i);
                    epsj     = c6j * c6j /(4.0 * c12j);
                    c6_LB    = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
                }
                else
                {
                    *bLBRulesPossible = FALSE;
                    c6_LB             = c6_geometric;
                }
                bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
            }

            if (FALSE == bCanDoLBRules)
            {
                *bC6ParametersWorkWithLBRules = FALSE;
            }

            bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);

            if (FALSE == bCanDoGeometricRules)
            {
                *bC6ParametersWorkWithGeometricRules = FALSE;
            }
        }
    }
    sfree(typecount);
}

static void
check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
                        warninp_t wi)
{
    char     err_buf[256];
    gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;

    check_combination_rule_differences(mtop, 0,
                                       &bC6ParametersWorkWithGeometricRules,
                                       &bC6ParametersWorkWithLBRules,
                                       &bLBRulesPossible);
    if (ir->ljpme_combination_rule == eljpmeLB)
    {
        if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
        {
            warning(wi, "You are using arithmetic-geometric combination rules "
                    "in LJ-PME, but your non-bonded C6 parameters do not "
                    "follow these rules.");
        }
    }
    else
    {
        if (FALSE == bC6ParametersWorkWithGeometricRules)
        {
            if (ir->eDispCorr != edispcNO)
            {
                warning_note(wi, "You are using geometric combination rules in "
                             "LJ-PME, but your non-bonded C6 parameters do "
                             "not follow these rules. "
                             "This will introduce very small errors in the forces and energies in "
                             "your simulations. Dispersion correction will correct total energy "
                             "and/or pressure for isotropic systems, but not forces or surface tensions.");
            }
            else
            {
                warning_note(wi, "You are using geometric combination rules in "
                             "LJ-PME, but your non-bonded C6 parameters do "
                             "not follow these rules. "
                             "This will introduce very small errors in the forces and energies in "
                             "your simulations. If your system is homogeneous, consider using dispersion correction "
                             "for the total energy and pressure.");
            }
        }
    }
}

void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
                  warninp_t wi)
{
    char                      err_buf[256];
    int                       i, m, c, nmol, npct;
    gmx_bool                  bCharge, bAcc;
    real                      gdt_max, *mgrp, mt;
    rvec                      acc;
    gmx_mtop_atomloop_block_t aloopb;
    gmx_mtop_atomloop_all_t   aloop;
    t_atom                   *atom;
    ivec                      AbsRef;
    char                      warn_buf[STRLEN];

    set_warning_line(wi, mdparin, -1);

    if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
        ir->comm_mode == ecmNO &&
        !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
        !ETC_ANDERSEN(ir->etc))
    {
        warning(wi, "You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass");
    }

    /* Check for pressure coupling with absolute position restraints */
    if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
    {
        absolute_reference(ir, sys, TRUE, AbsRef);
        {
            for (m = 0; m < DIM; m++)
            {
                if (AbsRef[m] && norm2(ir->compress[m]) > 0)
                {
                    warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
                    break;
                }
            }
        }
    }

    bCharge = FALSE;
    aloopb  = gmx_mtop_atomloop_block_init(sys);
    while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
    {
        if (atom->q != 0 || atom->qB != 0)
        {
            bCharge = TRUE;
        }
    }

    if (!bCharge)
    {
        if (EEL_FULL(ir->coulombtype))
        {
            sprintf(err_buf,
                    "You are using full electrostatics treatment %s for a system without charges.\n"
                    "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
                    EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
            warning(wi, err_buf);
        }
    }
    else
    {
        if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
        {
            sprintf(err_buf,
                    "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
                    "You might want to consider using %s electrostatics.\n",
                    EELTYPE(eelPME));
            warning_note(wi, err_buf);
        }
    }

    /* Check if combination rules used in LJ-PME are the same as in the force field */
    if (EVDW_PME(ir->vdwtype))
    {
        check_combination_rules(ir, sys, wi);
    }

    /* Generalized reaction field */
    if (ir->opts.ngtc == 0)
    {
        sprintf(err_buf, "No temperature coupling while using coulombtype %s",
                eel_names[eelGRF]);
        CHECK(ir->coulombtype == eelGRF);
    }
    else
    {
        sprintf(err_buf, "When using coulombtype = %s"
                " ref-t for temperature coupling should be > 0",
                eel_names[eelGRF]);
        CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
    }

    if (ir->eI == eiSD1 &&
        (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
         gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
    {
        sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
        warning_note(wi, warn_buf);
    }

    bAcc = FALSE;
    for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
    {
        for (m = 0; (m < DIM); m++)
        {
            if (fabs(ir->opts.acc[i][m]) > 1e-6)
            {
                bAcc = TRUE;
            }
        }
    }
    if (bAcc)
    {
        clear_rvec(acc);
        snew(mgrp, sys->groups.grps[egcACC].nr);
        aloop = gmx_mtop_atomloop_all_init(sys);
        while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
        {
            mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
        }
        mt = 0.0;
        for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
        {
            for (m = 0; (m < DIM); m++)
            {
                acc[m] += ir->opts.acc[i][m]*mgrp[i];
            }
            mt += mgrp[i];
        }
        for (m = 0; (m < DIM); m++)
        {
            if (fabs(acc[m]) > 1e-6)
            {
                const char *dim[DIM] = { "X", "Y", "Z" };
                fprintf(stderr,
                        "Net Acceleration in %s direction, will %s be corrected\n",
                        dim[m], ir->nstcomm != 0 ? "" : "not");
                if (ir->nstcomm != 0 && m < ndof_com(ir))
                {
                    acc[m] /= mt;
                    for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
                    {
                        ir->opts.acc[i][m] -= acc[m];
                    }
                }
            }
        }
        sfree(mgrp);
    }

    if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
        !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
    {
        gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
    }

    if (ir->ePull != epullNO)
    {
        gmx_bool bPullAbsoluteRef;

        bPullAbsoluteRef = FALSE;
        for (i = 0; i < ir->pull->ncoord; i++)
        {
            bPullAbsoluteRef = bPullAbsoluteRef ||
                ir->pull->coord[i].group[0] == 0 ||
                ir->pull->coord[i].group[1] == 0;
        }
        if (bPullAbsoluteRef)
        {
            absolute_reference(ir, sys, FALSE, AbsRef);
            for (m = 0; m < DIM; m++)
            {
                if (ir->pull->dim[m] && !AbsRef[m])
                {
                    warning(wi, "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts.");
                    break;
                }
            }
        }

        if (ir->pull->eGeom == epullgDIRPBC)
        {
            for (i = 0; i < 3; i++)
            {
                for (m = 0; m <= i; m++)
                {
                    if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
                        ir->deform[i][m] != 0)
                    {
                        for (c = 0; c < ir->pull->ncoord; c++)
                        {
                            if (ir->pull->coord[c].vec[m] != 0)
                            {
                                gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
                            }
                        }
                    }
                }
            }
        }
    }

    check_disre(sys);
}

void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
{
    real        min_size;
    gmx_bool    bTWIN;
    char        warn_buf[STRLEN];
    const char *ptr;

    ptr = check_box(ir->ePBC, box);
    if (ptr)
    {
        warning_error(wi, ptr);
    }

    if (bConstr && ir->eConstrAlg == econtSHAKE)
    {
        if (ir->shake_tol <= 0.0)
        {
            sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
                    ir->shake_tol);
            warning_error(wi, warn_buf);
        }

        if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
        {
            sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
            if (ir->epc == epcNO)
            {
                warning(wi, warn_buf);
            }
            else
            {
                warning_error(wi, warn_buf);
            }
        }
    }

    if ( (ir->eConstrAlg == econtLINCS) && bConstr)
    {
        /* If we have Lincs constraints: */
        if (ir->eI == eiMD && ir->etc == etcNO &&
            ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
        {
            sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
            warning_note(wi, warn_buf);
        }

        if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
        {
            sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
            warning_note(wi, warn_buf);
        }
        if (ir->epc == epcMTTK)
        {
            warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
        }
    }

    if (ir->LincsWarnAngle > 90.0)
    {
        sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
        warning(wi, warn_buf);
        ir->LincsWarnAngle = 90.0;
    }

    if (ir->ePBC != epbcNONE)
    {
        if (ir->nstlist == 0)
        {
            warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
        }
        bTWIN = (ir->rlistlong > ir->rlist);
        if (ir->ns_type == ensGRID)
        {
            if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
            {
                sprintf(warn_buf, "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease %s.\n",
                        bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
                warning_error(wi, warn_buf);
            }
        }
        else
        {
            min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
            if (2*ir->rlistlong >= min_size)
            {
                sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
                warning_error(wi, warn_buf);
                if (TRICLINIC(box))
                {
                    fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
                }
            }
        }
    }
}

void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
                             rvec *x,
                             warninp_t wi)
{
    real rvdw1, rvdw2, rcoul1, rcoul2;
    char warn_buf[STRLEN];

    calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);

    if (rvdw1 > 0)
    {
        printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
               rvdw1, rvdw2);
    }
    if (rcoul1 > 0)
    {
        printf("Largest charge group radii for Coulomb:       %5.3f, %5.3f nm\n",
               rcoul1, rcoul2);
    }

    if (ir->rlist > 0)
    {
        if (rvdw1  + rvdw2  > ir->rlist ||
            rcoul1 + rcoul2 > ir->rlist)
        {
            sprintf(warn_buf,
                    "The sum of the two largest charge group radii (%f) "
                    "is larger than rlist (%f)\n",
                    max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
            warning(wi, warn_buf);
        }
        else
        {
            /* Here we do not use the zero at cut-off macro,
             * since user defined interactions might purposely
             * not be zero at the cut-off.
             */
            if (ir_vdw_is_zero_at_cutoff(ir) &&
                rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
            {
                sprintf(warn_buf, "The sum of the two largest charge group "
                        "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
                        "With exact cut-offs, better performance can be "
                        "obtained with cutoff-scheme = %s, because it "
                        "does not use charge groups at all.",
                        rvdw1+rvdw2,
                        ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
                        ir->rlistlong, ir->rvdw,
                        ecutscheme_names[ecutsVERLET]);
                if (ir_NVE(ir))
                {
                    warning(wi, warn_buf);
                }
                else
                {
                    warning_note(wi, warn_buf);
                }
            }
            if (ir_coulomb_is_zero_at_cutoff(ir) &&
                rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
            {
                sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
                        "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
                        rcoul1+rcoul2,
                        ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
                        ir->rlistlong, ir->rcoulomb,
                        ecutscheme_names[ecutsVERLET]);
                if (ir_NVE(ir))
                {
                    warning(wi, warn_buf);
                }
                else
                {
                    warning_note(wi, warn_buf);
                }
            }
        }
    }
}