예제 #1
0
static void insert_mols(int nmol_insrt, int ntry, int seed,
                        t_atoms *atoms, rvec **x, real **exclusionDistances,
                        t_atoms *atoms_insrt, rvec *x_insrt, real *exclusionDistances_insrt,
                        int ePBC, matrix box,
                        const char* posfn, const rvec deltaR, int enum_rot)
{
    t_pbc            pbc;
    rvec            *x_n;
    int              mol;
    int              trial;
    double         **rpos;

    const real       maxInsertRadius
        = *std::max_element(exclusionDistances_insrt,
                            exclusionDistances_insrt + atoms_insrt->nr);
    real             maxRadius = maxInsertRadius;
    if (atoms->nr > 0)
    {
        const real maxExistingRadius
            = *std::max_element(*exclusionDistances,
                                *exclusionDistances + atoms->nr);
        maxRadius = std::max(maxInsertRadius, maxExistingRadius);
    }

    // TODO: Make all of this exception-safe.
    gmx::AnalysisNeighborhood nb;
    nb.setCutoff(maxInsertRadius + maxRadius);

    gmx_rng_t        rng = gmx_rng_init(seed);
    set_pbc(&pbc, ePBC, box);

    snew(x_n, atoms_insrt->nr);

    /* With -ip, take nmol_insrt from file posfn */
    if (posfn != NULL)
    {
        int ncol;
        nmol_insrt = read_xvg(posfn, &rpos, &ncol);
        if (ncol != 3)
        {
            gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n", ncol, posfn);
        }
        fprintf(stderr, "Read %d positions from file %s\n\n", nmol_insrt, posfn);
    }

    {
        const int finalAtomCount    = atoms->nr + nmol_insrt * atoms_insrt->nr;
        const int finalResidueCount = atoms->nres + nmol_insrt * atoms_insrt->nres;
        srenew(atoms->resinfo,      finalResidueCount);
        srenew(atoms->atomname,     finalAtomCount);
        srenew(atoms->atom,         finalAtomCount);
        srenew(*x,                  finalAtomCount);
        srenew(*exclusionDistances, finalAtomCount);
    }

    trial = mol = 0;
    while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
    {
        fprintf(stderr, "\rTry %d", trial++);
        rvec offset_x;
        if (posfn == NULL)
        {
            /* insert at random positions */
            offset_x[XX] = box[XX][XX] * gmx_rng_uniform_real(rng);
            offset_x[YY] = box[YY][YY] * gmx_rng_uniform_real(rng);
            offset_x[ZZ] = box[ZZ][ZZ] * gmx_rng_uniform_real(rng);
        }
        else
        {
            /* Insert at positions taken from option -ip file */
            offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2 * gmx_rng_uniform_real(rng)-1);
            offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2 * gmx_rng_uniform_real(rng)-1);
            offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2 * gmx_rng_uniform_real(rng)-1);
        }
        generate_trial_conf(atoms_insrt->nr, x_insrt, offset_x, enum_rot, rng,
                            x_n);
        gmx::AnalysisNeighborhoodPositions pos(*x, atoms->nr);
        gmx::AnalysisNeighborhoodSearch    search = nb.initSearch(&pbc, pos);
        if (is_insertion_allowed(&search, *exclusionDistances, atoms_insrt->nr,
                                 x_n, exclusionDistances_insrt))
        {
            const int firstIndex = atoms->nr;
            for (int i = 0; i < atoms_insrt->nr; ++i)
            {
                copy_rvec(x_n[i], (*x)[firstIndex + i]);
                (*exclusionDistances)[firstIndex + i] = exclusionDistances_insrt[i];
            }
            merge_atoms_noalloc(atoms, atoms_insrt);
            ++mol;
            fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
        }
    }
    gmx_rng_destroy(rng);
    srenew(atoms->resinfo,  atoms->nres);
    srenew(atoms->atomname, atoms->nr);
    srenew(atoms->atom,     atoms->nr);
    srenew(*x,              atoms->nr);
    srenew(*exclusionDistances, atoms->nr);

    fprintf(stderr, "\n");
    /* print number of molecules added */
    fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
            mol, nmol_insrt, *atoms_insrt->resinfo[0].name);

    sfree(x_n);
}
예제 #2
0
static void insert_mols(int nmol_insrt, int ntry, int seed,
                        real defaultDistance, real scaleFactor,
                        t_atoms *atoms, rvec **x,
                        const t_atoms *atoms_insrt, const rvec *x_insrt,
                        int ePBC, matrix box,
                        const std::string &posfn, const rvec deltaR, int enum_rot)
{
    t_pbc            pbc;
    rvec            *x_n;

    fprintf(stderr, "Initialising inter-atomic distances...\n");
    gmx_atomprop_t   aps = gmx_atomprop_init();
    real            *exclusionDistances
        = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
    real            *exclusionDistances_insrt
        = makeExclusionDistances(atoms_insrt, aps, defaultDistance, scaleFactor);
    gmx_atomprop_destroy(aps);

    const real       maxInsertRadius
        = *std::max_element(exclusionDistances_insrt,
                            exclusionDistances_insrt + atoms_insrt->nr);
    real             maxRadius = maxInsertRadius;
    if (atoms->nr > 0)
    {
        const real maxExistingRadius
            = *std::max_element(exclusionDistances,
                                exclusionDistances + atoms->nr);
        maxRadius = std::max(maxInsertRadius, maxExistingRadius);
    }

    // TODO: Make all of this exception-safe.
    gmx::AnalysisNeighborhood nb;
    nb.setCutoff(maxInsertRadius + maxRadius);

    gmx_rng_t        rng = gmx_rng_init(seed);
    set_pbc(&pbc, ePBC, box);

    snew(x_n, atoms_insrt->nr);

    /* With -ip, take nmol_insrt from file posfn */
    double         **rpos = NULL;
    if (!posfn.empty())
    {
        int ncol;
        nmol_insrt = read_xvg(posfn.c_str(), &rpos, &ncol);
        if (ncol != 3)
        {
            gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n",
                      posfn.c_str());
        }
        fprintf(stderr, "Read %d positions from file %s\n\n",
                nmol_insrt, posfn.c_str());
    }

    {
        const int finalAtomCount    = atoms->nr + nmol_insrt * atoms_insrt->nr;
        const int finalResidueCount = atoms->nres + nmol_insrt * atoms_insrt->nres;
        srenew(atoms->resinfo,      finalResidueCount);
        srenew(atoms->atomname,     finalAtomCount);
        srenew(atoms->atom,         finalAtomCount);
        srenew(*x,                  finalAtomCount);
        srenew(exclusionDistances,  finalAtomCount);
    }

    int mol        = 0;
    int trial      = 0;
    int firstTrial = 0;
    int failed     = 0;
    while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
    {
        rvec offset_x;
        if (posfn.empty())
        {
            // Insert at random positions.
            offset_x[XX] = box[XX][XX] * gmx_rng_uniform_real(rng);
            offset_x[YY] = box[YY][YY] * gmx_rng_uniform_real(rng);
            offset_x[ZZ] = box[ZZ][ZZ] * gmx_rng_uniform_real(rng);
        }
        else
        {
            // Skip a position if ntry trials were not successful.
            if (trial >= firstTrial + ntry)
            {
                fprintf(stderr, " skipped position (%.3f, %.3f, %.3f)\n",
                        rpos[XX][mol], rpos[YY][mol], rpos[ZZ][mol]);
                ++mol;
                ++failed;
            }
            // Insert at positions taken from option -ip file.
            offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2 * gmx_rng_uniform_real(rng)-1);
            offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2 * gmx_rng_uniform_real(rng)-1);
            offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2 * gmx_rng_uniform_real(rng)-1);
        }
        fprintf(stderr, "\rTry %d", ++trial);
        generate_trial_conf(atoms_insrt->nr, x_insrt, offset_x, enum_rot, rng,
                            x_n);
        gmx::AnalysisNeighborhoodPositions pos(*x, atoms->nr);
        gmx::AnalysisNeighborhoodSearch    search = nb.initSearch(&pbc, pos);
        if (is_insertion_allowed(&search, exclusionDistances, atoms_insrt->nr,
                                 x_n, exclusionDistances_insrt))
        {
            const int firstIndex = atoms->nr;
            for (int i = 0; i < atoms_insrt->nr; ++i)
            {
                copy_rvec(x_n[i], (*x)[firstIndex + i]);
                exclusionDistances[firstIndex + i] = exclusionDistances_insrt[i];
            }
            merge_atoms_noalloc(atoms, atoms_insrt);
            ++mol;
            firstTrial = trial;
            fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
        }
    }
    gmx_rng_destroy(rng);
    srenew(atoms->resinfo,  atoms->nres);
    srenew(atoms->atomname, atoms->nr);
    srenew(atoms->atom,     atoms->nr);
    srenew(*x,              atoms->nr);

    fprintf(stderr, "\n");
    /* print number of molecules added */
    fprintf(stderr, "Added %d molecules (out of %d requested)\n",
            mol - failed, nmol_insrt);

    sfree(x_n);
    sfree(exclusionDistances);
    sfree(exclusionDistances_insrt);
    if (rpos != NULL)
    {
        for (int i = 0; i < DIM; ++i)
        {
            sfree(rpos[i]);
        }
        sfree(rpos);
    }
}