Removed include of types/ifunc.h from typedefs.h

[gromacs.git] / src / gromacs / tools / convert_tpr.cpp

/*
 * 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) 2013,2014,2015, 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.
 */
#include "gmxpre.h"

#include <cmath>

#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/gmxpreprocess/readir.h"
#include "gromacs/legacyheaders/checkpoint.h"
#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/types/ifunc.h"
#include "gromacs/legacyheaders/types/inputrec.h"
#include "gromacs/legacyheaders/types/simple.h"
#include "gromacs/legacyheaders/types/state.h"
#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"

#define RANGECHK(i, n) if ((i) >= (n)) gmx_fatal(FARGS, "Your index file contains atomnumbers (e.g. %d)\nthat are larger than the number of atoms in the tpr file (%d)", (i), (n))

static gmx_bool *bKeepIt(int gnx, int natoms, atom_id index[])
{
    gmx_bool *b;
    int       i;

    snew(b, natoms);
    for (i = 0; (i < gnx); i++)
    {
        RANGECHK(index[i], natoms);
        b[index[i]] = TRUE;
    }

    return b;
}

static atom_id *invind(int gnx, int natoms, atom_id index[])
{
    atom_id *inv;
    int      i;

    snew(inv, natoms);
    for (i = 0; (i < gnx); i++)
    {
        RANGECHK(index[i], natoms);
        inv[index[i]] = i;
    }

    return inv;
}

static void reduce_block(gmx_bool bKeep[], t_block *block,
                         const char *name)
{
    atom_id *index;
    int      i, j, newi, newj;

    snew(index, block->nr);

    newi = newj = 0;
    for (i = 0; (i < block->nr); i++)
    {
        for (j = block->index[i]; (j < block->index[i+1]); j++)
        {
            if (bKeep[j])
            {
                newj++;
            }
        }
        if (newj > index[newi])
        {
            newi++;
            index[newi] = newj;
        }
    }

    fprintf(stderr, "Reduced block %8s from %6d to %6d index-, %6d to %6d a-entries\n",
            name, block->nr, newi, block->index[block->nr], newj);
    block->index = index;
    block->nr    = newi;
}

static void reduce_blocka(atom_id invindex[], gmx_bool bKeep[], t_blocka *block,
                          const char *name)
{
    atom_id *index, *a;
    int      i, j, k, newi, newj;

    snew(index, block->nr);
    snew(a, block->nra);

    newi = newj = 0;
    for (i = 0; (i < block->nr); i++)
    {
        for (j = block->index[i]; (j < block->index[i+1]); j++)
        {
            k = block->a[j];
            if (bKeep[k])
            {
                a[newj] = invindex[k];
                newj++;
            }
        }
        if (newj > index[newi])
        {
            newi++;
            index[newi] = newj;
        }
    }

    fprintf(stderr, "Reduced block %8s from %6d to %6d index-, %6d to %6d a-entries\n",
            name, block->nr, newi, block->nra, newj);
    block->index = index;
    block->a     = a;
    block->nr    = newi;
    block->nra   = newj;
}

static void reduce_rvec(int gnx, atom_id index[], rvec vv[])
{
    rvec *ptr;
    int   i;

    snew(ptr, gnx);
    for (i = 0; (i < gnx); i++)
    {
        copy_rvec(vv[index[i]], ptr[i]);
    }
    for (i = 0; (i < gnx); i++)
    {
        copy_rvec(ptr[i], vv[i]);
    }
    sfree(ptr);
}

static void reduce_atom(int gnx, atom_id index[], t_atom atom[], char ***atomname,
                        int *nres, t_resinfo *resinfo)
{
    t_atom    *ptr;
    char    ***aname;
    t_resinfo *rinfo;
    int        i, nr;

    snew(ptr, gnx);
    snew(aname, gnx);
    snew(rinfo, atom[index[gnx-1]].resind+1);
    for (i = 0; (i < gnx); i++)
    {
        ptr[i]   = atom[index[i]];
        aname[i] = atomname[index[i]];
    }
    nr = -1;
    for (i = 0; (i < gnx); i++)
    {
        atom[i]     = ptr[i];
        atomname[i] = aname[i];
        if ((i == 0) || (atom[i].resind != atom[i-1].resind))
        {
            nr++;
            rinfo[nr] = resinfo[atom[i].resind];
        }
        atom[i].resind = nr;
    }
    nr++;
    for (i = 0; (i < nr); i++)
    {
        resinfo[i] = rinfo[i];
    }
    *nres = nr;

    sfree(aname);
    sfree(ptr);
    sfree(rinfo);
}

static void reduce_ilist(atom_id invindex[], gmx_bool bKeep[],
                         t_ilist *il, int nratoms, const char *name)
{
    t_iatom *ia;
    int      i, j, newnr;
    gmx_bool bB;

    if (il->nr)
    {
        snew(ia, il->nr);
        newnr = 0;
        for (i = 0; (i < il->nr); i += nratoms+1)
        {
            bB = TRUE;
            for (j = 1; (j <= nratoms); j++)
            {
                bB = bB && bKeep[il->iatoms[i+j]];
            }
            if (bB)
            {
                ia[newnr++] = il->iatoms[i];
                for (j = 1; (j <= nratoms); j++)
                {
                    ia[newnr++] = invindex[il->iatoms[i+j]];
                }
            }
        }
        fprintf(stderr, "Reduced ilist %8s from %6d to %6d entries\n",
                name, il->nr/(nratoms+1),
                newnr/(nratoms+1));

        il->nr = newnr;
        for (i = 0; (i < newnr); i++)
        {
            il->iatoms[i] = ia[i];
        }

        sfree(ia);
    }
}

static void reduce_topology_x(int gnx, atom_id index[],
                              gmx_mtop_t *mtop, rvec x[], rvec v[])
{
    t_topology   top;
    gmx_bool    *bKeep;
    atom_id     *invindex;
    int          i;

    top      = gmx_mtop_t_to_t_topology(mtop);
    bKeep    = bKeepIt(gnx, top.atoms.nr, index);
    invindex = invind(gnx, top.atoms.nr, index);

    reduce_block(bKeep, &(top.cgs), "cgs");
    reduce_block(bKeep, &(top.mols), "mols");
    reduce_blocka(invindex, bKeep, &(top.excls), "excls");
    reduce_rvec(gnx, index, x);
    reduce_rvec(gnx, index, v);
    reduce_atom(gnx, index, top.atoms.atom, top.atoms.atomname,
                &(top.atoms.nres), top.atoms.resinfo);

    for (i = 0; (i < F_NRE); i++)
    {
        reduce_ilist(invindex, bKeep, &(top.idef.il[i]),
                     interaction_function[i].nratoms,
                     interaction_function[i].name);
    }

    top.atoms.nr = gnx;

    mtop->nmoltype = 1;
    snew(mtop->moltype, mtop->nmoltype);
    mtop->moltype[0].name  = mtop->name;
    mtop->moltype[0].atoms = top.atoms;
    for (i = 0; i < F_NRE; i++)
    {
        mtop->moltype[0].ilist[i] = top.idef.il[i];
    }
    mtop->moltype[0].atoms = top.atoms;
    mtop->moltype[0].cgs   = top.cgs;
    mtop->moltype[0].excls = top.excls;

    mtop->nmolblock = 1;
    snew(mtop->molblock, mtop->nmolblock);
    mtop->molblock[0].type       = 0;
    mtop->molblock[0].nmol       = 1;
    mtop->molblock[0].natoms_mol = top.atoms.nr;
    mtop->molblock[0].nposres_xA = 0;
    mtop->molblock[0].nposres_xB = 0;

    mtop->natoms                 = top.atoms.nr;
}

static void zeroq(atom_id index[], gmx_mtop_t *mtop)
{
    int mt, i;

    for (mt = 0; mt < mtop->nmoltype; mt++)
    {
        for (i = 0; (i < mtop->moltype[mt].atoms.nr); i++)
        {
            mtop->moltype[mt].atoms.atom[index[i]].q  = 0;
            mtop->moltype[mt].atoms.atom[index[i]].qB = 0;
        }
    }
}

int gmx_convert_tpr(int argc, char *argv[])
{
    const char       *desc[] = {
        "[THISMODULE] can edit run input files in four ways.[PAR]",
        "[BB]1.[bb] by modifying the number of steps in a run input file",
        "with options [TT]-extend[tt], [TT]-until[tt] or [TT]-nsteps[tt]",
        "(nsteps=-1 means unlimited number of steps)[PAR]",
        "[BB]2.[bb] (OBSOLETE) by creating a run input file",
        "for a continuation run when your simulation has crashed due to e.g.",
        "a full disk, or by making a continuation run input file.",
        "This option is obsolete, since mdrun now writes and reads",
        "checkpoint files.",
        "[BB]Note[bb] that a frame with coordinates and velocities is needed.",
        "When pressure and/or Nose-Hoover temperature coupling is used",
        "an energy file can be supplied to get an exact continuation",
        "of the original run.[PAR]",
        "[BB]3.[bb] by creating a [REF].tpx[ref] file for a subset of your original",
        "tpx file, which is useful when you want to remove the solvent from",
        "your [REF].tpx[ref] file, or when you want to make e.g. a pure C[GRK]alpha[grk] [REF].tpx[ref] file.",
        "Note that you may need to use [TT]-nsteps -1[tt] (or similar) to get",
        "this to work.",
        "[BB]WARNING: this [REF].tpx[ref] file is not fully functional[bb].[PAR]",
        "[BB]4.[bb] by setting the charges of a specified group",
        "to zero. This is useful when doing free energy estimates",
        "using the LIE (Linear Interaction Energy) method."
    };

    const char       *top_fn, *frame_fn;
    struct t_fileio  *fp;
    ener_file_t       fp_ener = NULL;
    gmx_trr_header_t  head;
    int               i;
    gmx_int64_t       nsteps_req, run_step, frame;
    double            run_t, state_t;
    gmx_bool          bOK, bNsteps, bExtend, bUntil, bTime, bTraj;
    gmx_bool          bFrame, bUse, bSel, bNeedEner, bReadEner, bScanEner, bFepState;
    gmx_mtop_t        mtop;
    t_atoms           atoms;
    t_inputrec       *ir;
    t_state           state;
    rvec             *newx = NULL, *newv = NULL, *tmpx, *tmpv;
    matrix            newbox;
    int               gnx;
    char             *grpname;
    atom_id          *index = NULL;
    int               nre;
    gmx_enxnm_t      *enm     = NULL;
    t_enxframe       *fr_ener = NULL;
    char              buf[200], buf2[200];
    output_env_t      oenv;
    t_filenm          fnm[] = {
        { efTPR, NULL,  NULL,    ffREAD  },
        { efTRN, "-f",  NULL,    ffOPTRD },
        { efEDR, "-e",  NULL,    ffOPTRD },
        { efNDX, NULL,  NULL,    ffOPTRD },
        { efTPR, "-o",  "tprout", ffWRITE }
    };
#define NFILE asize(fnm)

    /* Command line options */
    static int      nsteps_req_int = 0;
    static real     start_t        = -1.0, extend_t = 0.0, until_t = 0.0;
    static int      init_fep_state = 0;
    static gmx_bool bContinuation  = TRUE, bZeroQ = FALSE, bVel = TRUE;
    static t_pargs  pa[]           = {
        { "-extend",        FALSE, etREAL, {&extend_t},
          "Extend runtime by this amount (ps)" },
        { "-until",         FALSE, etREAL, {&until_t},
          "Extend runtime until this ending time (ps)" },
        { "-nsteps",        FALSE, etINT,  {&nsteps_req_int},
          "Change the number of steps" },
        { "-time",          FALSE, etREAL, {&start_t},
          "Continue from frame at this time (ps) instead of the last frame" },
        { "-zeroq",         FALSE, etBOOL, {&bZeroQ},
          "Set the charges of a group (from the index) to zero" },
        { "-vel",           FALSE, etBOOL, {&bVel},
          "Require velocities from trajectory" },
        { "-cont",          FALSE, etBOOL, {&bContinuation},
          "For exact continuation, the constraints should not be applied before the first step" },
        { "-init_fep_state", FALSE, etINT, {&init_fep_state},
          "fep state to initialize from" },
    };

    /* Parse the command line */
    if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
                           asize(desc), desc, 0, NULL, &oenv))
    {
        return 0;
    }

    /* Convert int to gmx_int64_t */
    nsteps_req = nsteps_req_int;
    bNsteps    = opt2parg_bSet("-nsteps", asize(pa), pa);
    bExtend    = opt2parg_bSet("-extend", asize(pa), pa);
    bUntil     = opt2parg_bSet("-until", asize(pa), pa);
    bFepState  = opt2parg_bSet("-init_fep_state", asize(pa), pa);
    bTime      = opt2parg_bSet("-time", asize(pa), pa);
    bTraj      = (opt2bSet("-f", NFILE, fnm) || bTime);

    top_fn = ftp2fn(efTPR, NFILE, fnm);
    fprintf(stderr, "Reading toplogy and stuff from %s\n", top_fn);

    snew(ir, 1);
    read_tpx_state(top_fn, ir, &state, &mtop);
    run_step = ir->init_step;
    run_t    = ir->init_step*ir->delta_t + ir->init_t;

    if (!EI_STATE_VELOCITY(ir->eI))
    {
        bVel = FALSE;
    }

    if (bTraj)
    {
        fprintf(stderr, "\n"
                "NOTE: Reading the state from trajectory is an obsolete feature of gmx convert-tpr.\n"
                "      Continuation should be done by loading a checkpoint file with mdrun -cpi\n"
                "      This guarantees that all state variables are transferred.\n"
                "      gmx convert-tpr is now only useful for increasing nsteps,\n"
                "      but even that can often be avoided by using mdrun -maxh\n"
                "\n");

        if (ir->bContinuation != bContinuation)
        {
            fprintf(stderr, "Modifying ir->bContinuation to %s\n",
                    bool_names[bContinuation]);
        }
        ir->bContinuation = bContinuation;


        bNeedEner = (ir->epc == epcPARRINELLORAHMAN || ir->etc == etcNOSEHOOVER);
        bReadEner = (bNeedEner && ftp2bSet(efEDR, NFILE, fnm));
        bScanEner = (bReadEner && !bTime);

        if (ir->epc != epcNO || EI_SD(ir->eI) || ir->eI == eiBD)
        {
            fprintf(stderr, "NOTE: The simulation uses pressure coupling and/or stochastic dynamics.\n"
                    "gmx convert-tpr can not provide binary identical continuation.\n"
                    "If you want that, supply a checkpoint file to mdrun\n\n");
        }

        if (EI_SD(ir->eI) || ir->eI == eiBD)
        {
            fprintf(stderr, "\nChanging ld-seed from %" GMX_PRId64 " ", ir->ld_seed);
            ir->ld_seed = (gmx_int64_t)gmx_rng_make_seed();
            fprintf(stderr, "to %" GMX_PRId64 "\n\n", ir->ld_seed);
        }

        frame_fn = ftp2fn(efTRN, NFILE, fnm);

        if (fn2ftp(frame_fn) == efCPT)
        {
            int sim_part;

            fprintf(stderr,
                    "\nREADING STATE FROM CHECKPOINT %s...\n\n",
                    frame_fn);

            read_checkpoint_state(frame_fn, &sim_part,
                                  &run_step, &run_t, &state);
        }
        else
        {
            fprintf(stderr,
                    "\nREADING COORDS, VELS AND BOX FROM TRAJECTORY %s...\n\n",
                    frame_fn);

            fp = gmx_trr_open(frame_fn, "r");
            if (bScanEner)
            {
                fp_ener = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
                do_enxnms(fp_ener, &nre, &enm);
                snew(fr_ener, 1);
                fr_ener->t = -1e-12;
            }

            /* Now scan until the last set of x and v (step == 0)
             * or the ones at step step.
             */
            bFrame = TRUE;
            frame  = 0;
            while (bFrame)
            {
                bFrame = gmx_trr_read_frame_header(fp, &head, &bOK);
                if (bOK && frame == 0)
                {
                    if (mtop.natoms != head.natoms)
                    {
                        gmx_fatal(FARGS, "Number of atoms in Topology (%d) "
                                  "is not the same as in Trajectory (%d)\n",
                                  mtop.natoms, head.natoms);
                    }
                    snew(newx, head.natoms);
                    snew(newv, head.natoms);
                }
                bFrame = bFrame && bOK;
                if (bFrame)
                {
                    bOK = gmx_trr_read_frame_data(fp, &head, newbox, newx, newv, NULL);
                }
                bFrame = bFrame && bOK;
                bUse   = FALSE;
                if (bFrame &&
                    (head.x_size) && (head.v_size || !bVel))
                {
                    bUse = TRUE;
                    if (bScanEner)
                    {
                        /* Read until the energy time is >= the trajectory time */
                        while (fr_ener->t < head.t && do_enx(fp_ener, fr_ener))
                        {
                            ;
                        }
                        bUse = (fr_ener->t == head.t);
                    }
                    if (bUse)
                    {
                        tmpx                  = newx;
                        newx                  = state.x;
                        state.x               = tmpx;
                        tmpv                  = newv;
                        newv                  = state.v;
                        state.v               = tmpv;
                        run_t                 = head.t;
                        run_step              = head.step;
                        state.fep_state       = head.fep_state;
                        state.lambda[efptFEP] = head.lambda;
                        copy_mat(newbox, state.box);
                    }
                }
                if (bFrame || !bOK)
                {
                    sprintf(buf, "\r%s %s frame %s%s: step %s%s time %s",
                            "%s", "%s", "%6", GMX_PRId64, "%6", GMX_PRId64, " %8.3f");
                    fprintf(stderr, buf,
                            bUse ? "Read   " : "Skipped", ftp2ext(fn2ftp(frame_fn)),
                            frame, head.step, head.t);
                    frame++;
                    if (bTime && (head.t >= start_t))
                    {
                        bFrame = FALSE;
                    }
                }
            }
            if (bScanEner)
            {
                close_enx(fp_ener);
                free_enxframe(fr_ener);
                free_enxnms(nre, enm);
            }
            gmx_trr_close(fp);
            fprintf(stderr, "\n");

            if (!bOK)
            {
                fprintf(stderr, "%s frame %s (step %s, time %g) is incomplete\n",
                        ftp2ext(fn2ftp(frame_fn)), gmx_step_str(frame-1, buf2),
                        gmx_step_str(head.step, buf), head.t);
            }
            fprintf(stderr, "\nUsing frame of step %s time %g\n",
                    gmx_step_str(run_step, buf), run_t);

            if (bNeedEner)
            {
                if (bReadEner)
                {
                    get_enx_state(ftp2fn(efEDR, NFILE, fnm), run_t, &mtop.groups, ir, &state);
                }
                else
                {
                    fprintf(stderr, "\nWARNING: The simulation uses %s temperature and/or %s pressure coupling,\n"
                            "         the continuation will only be exact when an energy file is supplied\n\n",
                            ETCOUPLTYPE(etcNOSEHOOVER),
                            EPCOUPLTYPE(epcPARRINELLORAHMAN));
                }
            }
            if (bFepState)
            {
                ir->fepvals->init_fep_state = init_fep_state;
            }
        }
    }

    if (bNsteps)
    {
        fprintf(stderr, "Setting nsteps to %s\n", gmx_step_str(nsteps_req, buf));
        ir->nsteps = nsteps_req;
    }
    else
    {
        /* Determine total number of steps remaining */
        if (bExtend)
        {
            ir->nsteps = ir->nsteps - (run_step - ir->init_step) + (gmx_int64_t)(extend_t/ir->delta_t + 0.5);
            printf("Extending remaining runtime of by %g ps (now %s steps)\n",
                   extend_t, gmx_step_str(ir->nsteps, buf));
        }
        else if (bUntil)
        {
            printf("nsteps = %s, run_step = %s, current_t = %g, until = %g\n",
                   gmx_step_str(ir->nsteps, buf),
                   gmx_step_str(run_step, buf2),
                   run_t, until_t);
            ir->nsteps = (gmx_int64_t)((until_t - run_t)/ir->delta_t + 0.5);
            printf("Extending remaining runtime until %g ps (now %s steps)\n",
                   until_t, gmx_step_str(ir->nsteps, buf));
        }
        else
        {
            ir->nsteps -= run_step - ir->init_step;
            /* Print message */
            printf("%s steps (%g ps) remaining from first run.\n",
                   gmx_step_str(ir->nsteps, buf), ir->nsteps*ir->delta_t);
        }
    }

    if (bNsteps || bZeroQ || (ir->nsteps > 0))
    {
        ir->init_step = run_step;

        if (ftp2bSet(efNDX, NFILE, fnm) ||
            !(bNsteps || bExtend || bUntil || bTraj))
        {
            atoms = gmx_mtop_global_atoms(&mtop);
            get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1,
                      &gnx, &index, &grpname);
            if (!bZeroQ)
            {
                bSel = (gnx != state.natoms);
                for (i = 0; ((i < gnx) && (!bSel)); i++)
                {
                    bSel = (i != index[i]);
                }
            }
            else
            {
                bSel = FALSE;
            }
            if (bSel)
            {
                fprintf(stderr, "Will write subset %s of original tpx containing %d "
                        "atoms\n", grpname, gnx);
                reduce_topology_x(gnx, index, &mtop, state.x, state.v);
                state.natoms = gnx;
            }
            else if (bZeroQ)
            {
                zeroq(index, &mtop);
                fprintf(stderr, "Zero-ing charges for group %s\n", grpname);
            }
            else
            {
                fprintf(stderr, "Will write full tpx file (no selection)\n");
            }
        }

        state_t = ir->init_t + ir->init_step*ir->delta_t;
        sprintf(buf,   "Writing statusfile with starting step %s%s and length %s%s steps...\n", "%10", GMX_PRId64, "%10", GMX_PRId64);
        fprintf(stderr, buf, ir->init_step, ir->nsteps);
        fprintf(stderr, "                                 time %10.3f and length %10.3f ps\n",
                state_t, ir->nsteps*ir->delta_t);
        write_tpx_state(opt2fn("-o", NFILE, fnm), ir, &state, &mtop);
    }
    else
    {
        printf("You've simulated long enough. Not writing tpr file\n");
    }

    return 0;
}