#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/statistics/statistics.h"
#include "gromacs/topology/index.h"
-#include "gromacs/topology/topology.h"
+#include "gromacs/trajectoryanalysis/topologyinformation.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
int **ndata; /* the number of msds (particles/mols) per data
point. */
t_corr(int nrgrp, int type, int axis, real dim_factor, int nmol,
- gmx_bool bTen, gmx_bool bMass, real dt, const t_topology *top,
+ gmx_bool bTen, gmx_bool bMass, real dt,
+ const gmx::TopologyInformation &topologyInformation,
real beginfit, real endfit) :
t0(0),
delta_t(dt),
{
if (bMass)
{
- const t_atoms *atoms = &top->atoms;
+ const t_atoms *atoms = topologyInformation.atoms();
snew(mass, atoms->nr);
- for (int i = 0; (i < atoms->nr); i++)
+ for (int i = 0; i < atoms->nr; i++)
{
mass[i] = atoms->atom[i].m;
}
}
/* calculate the com of molecules in x and put it into xa */
-static void calc_mol_com(int nmol, const int *molindex, const t_block *mols, const t_atoms *atoms,
+static void calc_mol_com(const gmx::RangePartitioning &molindex,
+ const t_atoms *atoms,
rvec *x, rvec *xa)
{
- int m, mol, i, d;
rvec xm;
- real mass, mtot;
- for (m = 0; m < nmol; m++)
+ for (int mol = 0; mol < molindex.numBlocks(); mol++)
{
- mol = molindex[m];
clear_rvec(xm);
- mtot = 0;
- for (i = mols->index[mol]; i < mols->index[mol+1]; i++)
+ real mtot = 0;
+ for (auto i = molindex.block(mol).begin(); i < molindex.block(mol).end(); i++)
{
- mass = atoms->atom[i].m;
- for (d = 0; d < DIM; d++)
+ real mass = atoms->atom[i].m;
+ for (int d = 0; d < DIM; d++)
{
xm[d] += mass*x[i][d];
}
mtot += mass;
}
- svmul(1/mtot, xm, xa[m]);
+ svmul(1/mtot, xm, xa[mol]);
}
}
}
static void printmol(t_corr *curr, const char *fn,
- const char *fn_pdb, const int *molindex, const t_topology *top,
+ const char *fn_pdb,
+ const gmx::RangePartitioning &molindex,
+ const t_atoms *atoms,
rvec *x, int ePBC, matrix box, const gmx_output_env_t *oenv)
{
#define NDIST 100
gmx_stats_t lsq1;
int i, j;
real a, b, D, Dav, D2av, VarD, sqrtD, sqrtD_max, scale;
- t_pdbinfo *pdbinfo = nullptr;
- const int *mol2a = nullptr;
-
- out = xvgropen(fn, "Diffusion Coefficients / Molecule", "Molecule", "D", oenv);
-
- if (fn_pdb)
- {
- pdbinfo = top->atoms.pdbinfo;
- mol2a = top->mols.index;
- }
+ out = xvgropen(fn, "Diffusion Coefficients / Molecule", "Molecule", "D", oenv);
Dav = D2av = 0;
sqrtD_max = 0;
+ t_atoms *newatoms = copy_t_atoms(atoms);
+ if (!newatoms->pdbinfo)
+ {
+ snew(newatoms->pdbinfo, newatoms->nr);
+ }
for (i = 0; (i < curr->nmol); i++)
{
lsq1 = gmx_stats_init();
Dav += D;
D2av += gmx::square(D);
fprintf(out, "%10d %10g\n", i, D);
- if (pdbinfo)
+ sqrtD = std::sqrt(D);
+ if (sqrtD > sqrtD_max)
{
- sqrtD = std::sqrt(D);
- if (sqrtD > sqrtD_max)
- {
- sqrtD_max = sqrtD;
- }
- for (j = mol2a[molindex[i]]; j < mol2a[molindex[i]+1]; j++)
- {
- pdbinfo[j].bfac = sqrtD;
- }
+ sqrtD_max = sqrtD;
+ }
+ for (auto j : molindex.block(i))
+ {
+ newatoms->pdbinfo[j].bfac = sqrtD;
}
}
xvgrclose(out);
{
scale *= 10;
}
- GMX_RELEASE_ASSERT(pdbinfo != nullptr, "Internal error - pdbinfo not set for PDB input");
- for (i = 0; i < top->atoms.nr; i++)
+ for (i = 0; i < atoms->nr; i++)
{
- pdbinfo[i].bfac *= scale;
+ newatoms->pdbinfo[i].bfac *= scale;
}
- write_sto_conf(fn_pdb, "molecular MSD", &top->atoms, x, nullptr, ePBC, box);
+ write_sto_conf(fn_pdb, "molecular MSD", newatoms, x, nullptr, ePBC, box);
}
+ done_and_delete_atoms(newatoms);
}
/* this is the main loop for the correlation type functions
* fx and nx are file pointers to things like read_first_x and
* read_next_x
*/
-static int corr_loop(t_corr *curr, const char *fn, const t_topology *top, int ePBC,
- gmx_bool bMol, int gnx[], int *index[],
- t_calc_func *calc1, gmx_bool bTen, int *gnx_com, int *index_com[],
- real dt, real t_pdb, rvec **x_pdb, matrix box_pdb,
- const gmx_output_env_t *oenv)
+static void corr_loop(t_corr *curr, const char *fn,
+ const t_atoms *atoms,
+ const t_idef *idef, int ePBC,
+ const gmx::RangePartitioning &molindex,
+ gmx_bool bMol, int gnx[], int *index[],
+ t_calc_func *calc1, gmx_bool bTen, int *gnx_com, int *index_com[],
+ real dt, real t_pdb, rvec **x_pdb, matrix box_pdb,
+ const gmx_output_env_t *oenv)
{
rvec *x[2]; /* the coordinates to read */
rvec *xa[2]; /* the coordinates to calculate displacements for */
#ifdef DEBUG
fprintf(stderr, "Read %d atoms for first frame\n", natoms);
#endif
- if ((gnx_com != nullptr) && natoms < top->atoms.nr)
+ if ((gnx_com != nullptr) && natoms < atoms->nr)
{
- fprintf(stderr, "WARNING: The trajectory only contains part of the system (%d of %d atoms) and therefore the COM motion of only this part of the system will be removed\n", natoms, top->atoms.nr);
+ fprintf(stderr, "WARNING: The trajectory only contains part of the system (%d of %d atoms) and therefore the COM motion of only this part of the system will be removed\n", natoms, atoms->nr);
}
snew(x[prev], natoms);
if (bMol)
{
- gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
+ gpbc = gmx_rmpbc_init(idef, ePBC, natoms);
}
/* the loop over all frames */
// data becomes overwritten by the molecule data.
if (bMol)
{
- calc_mol_com(gnx[0], index[0], &top->mols, &top->atoms, x[cur], xa[cur]);
+ calc_mol_com(molindex, atoms, x[cur], xa[cur]);
}
/* for the first frame, the previous frame is a copy of the first frame */
if (gnx_com)
{
calc_com(bMol, gnx_com[0], index_com[0], xa[cur], xa[prev], box,
- &top->atoms, com);
+ atoms, com);
}
/* loop over all groups in index file */
}
close_trx(status);
-
- return natoms;
}
-static void index_atom2mol(int *n, int *index, const t_block *mols)
+static void index_atom2mol(const gmx::RangePartitioning &molindex,
+ std::vector<int> *index)
{
- int nat, i, nmol, mol, j;
-
- nat = *n;
- i = 0;
- nmol = 0;
- mol = 0;
- while (i < nat)
+ for (int m = 0; m < molindex.numBlocks(); m++)
{
- while (index[i] > mols->index[mol])
- {
- mol++;
- if (mol >= mols->nr)
- {
- gmx_fatal(FARGS, "Atom index out of range: %d", index[i]+1);
- }
- }
- for (j = mols->index[mol]; j < mols->index[mol+1]; j++)
+ for (gmx_unused int k : molindex.block(m))
{
- if (i >= nat || index[i] != j)
- {
- gmx_fatal(FARGS, "The index group does not consist of whole molecules");
- }
- i++;
+ index->push_back(m);
}
- index[nmol++] = mol;
}
-
- fprintf(stderr, "Split group of %d atoms into %d molecules\n", nat, nmol);
-
- *n = nmol;
}
static void do_corr(const char *trx_file, const char *ndx_file, const char *msd_file,
const char *mol_file, const char *pdb_file, real t_pdb,
- int nrgrp, t_topology *top, int ePBC,
+ int nrgrp,
+ const gmx::TopologyInformation &topologyInformation,
gmx_bool bTen, gmx_bool bMW, gmx_bool bRmCOMM,
int type, real dim_factor, int axis,
real dt, real beginfit, real endfit, const gmx_output_env_t *oenv)
int *gnx; /* the selected groups' sizes */
int **index; /* selected groups' indices */
char **grpname;
- int i, i0, i1, j, N, nat_trx;
+ int i, i0, i1, j, N;
real *DD, *SigmaD, a, a2, b, r, chi2;
rvec *x = nullptr;
matrix box;
int *gnx_com = nullptr; /* the COM removal group size */
int **index_com = nullptr; /* the COM removal group atom indices */
char **grpname_com = nullptr; /* the COM removal group name */
+ std::vector<int> atom2mol;
snew(gnx, nrgrp);
snew(index, nrgrp);
snew(grpname, nrgrp);
+ const t_atoms *atoms = topologyInformation.atoms();
fprintf(stderr, "\nSelect a group to calculate mean squared displacement for:\n");
- get_index(&top->atoms, ndx_file, nrgrp, gnx, index, grpname);
+ get_index(atoms, ndx_file, nrgrp, gnx, index, grpname);
if (bRmCOMM)
{
snew(grpname_com, 1);
fprintf(stderr, "\nNow select a group for center of mass removal:\n");
- get_index(&top->atoms, ndx_file, 1, gnx_com, index_com, grpname_com);
+ get_index(atoms, ndx_file, 1, gnx_com, index_com, grpname_com);
}
-
+ gmx::RangePartitioning molindex;
+ const auto *mtop = topologyInformation.mtop();
+ for (auto &mb : mtop->molblock)
+ {
+ int type = mb.type;
+ for (int j = 0; j < mb.nmol; j++)
+ {
+ molindex.appendBlock(mtop->moltype[type].atoms.nr);
+ }
+ }
+ std::vector<int> atoms2mol;
if (mol_file)
{
- index_atom2mol(&gnx[0], index[0], &top->mols);
+ index_atom2mol(molindex, &atoms2mol);
}
-
+ auto *local_top = topologyInformation.expandedTopology();
msd = gmx::compat::make_unique<t_corr>(nrgrp, type, axis, dim_factor,
mol_file == nullptr ? 0 : gnx[0],
- bTen, bMW, dt, top, beginfit, endfit);
-
- nat_trx =
- corr_loop(msd.get(), trx_file, top, ePBC, mol_file ? gnx[0] != 0 : false, gnx, index,
- (mol_file != nullptr) ? calc1_mol : (bMW ? calc1_mw : calc1_norm),
- bTen, gnx_com, index_com, dt, t_pdb,
- pdb_file ? &x : nullptr, box, oenv);
+ bTen, bMW, dt, topologyInformation,
+ beginfit, endfit);
+ topologyInformation.getBox(box);
+ corr_loop(msd.get(), trx_file, atoms, &local_top->idef,
+ topologyInformation.ePBC(), molindex,
+ mol_file ? gnx[0] != 0 : false, gnx, index,
+ (mol_file != nullptr) ? calc1_mol : (bMW ? calc1_mw : calc1_norm),
+ bTen, gnx_com, index_com, dt, t_pdb,
+ pdb_file ? &x : nullptr, box, oenv);
/* Correct for the number of points */
for (j = 0; (j < msd->ngrp); j++)
fprintf(stderr, "\nNo frame found need time tpdb = %g ps\n"
"Can not write %s\n\n", t_pdb, pdb_file);
}
- i = top->atoms.nr;
- top->atoms.nr = nat_trx;
- if (pdb_file && top->atoms.pdbinfo == nullptr)
- {
- snew(top->atoms.pdbinfo, top->atoms.nr);
- }
- printmol(msd.get(), mol_file, pdb_file, index[0], top, x, ePBC, box, oenv);
- top->atoms.nr = i;
+ printmol(msd.get(), mol_file, pdb_file, molindex, atoms,
+ x, topologyInformation.ePBC(), box, oenv);
}
DD = nullptr;
};
#define NFILE asize(fnm)
- t_topology top;
- int ePBC;
- matrix box;
+ gmx_mtop_t mtop;
const char *trx_file, *tps_file, *ndx_file, *msd_file, *mol_file, *pdb_file;
- rvec *xdum;
- gmx_bool bTop;
int axis, type;
real dim_factor;
gmx_output_env_t *oenv;
{
gmx_fatal(FARGS, "Can only calculate the full tensor for 3D msd");
}
-
- bTop = read_tps_conf(tps_file, &top, &ePBC, &xdum, nullptr, box, bMW || bRmCOMM);
- if (mol_file && !bTop)
+ gmx::TopologyInformation topologyInformation;
+ topologyInformation.fillFromInputFile(tps_file);
+ if (mol_file && !topologyInformation.hasTopology())
{
gmx_fatal(FARGS,
"Could not read a topology from %s. Try a tpr file instead.",
}
do_corr(trx_file, ndx_file, msd_file, mol_file, pdb_file, t_pdb, ngroup,
- &top, ePBC, bTen, bMW, bRmCOMM, type, dim_factor, axis, dt, beginfit, endfit,
- oenv);
+ topologyInformation, bTen, bMW, bRmCOMM, type,
+ dim_factor, axis, dt, beginfit, endfit, oenv);
view_all(oenv, NFILE, fnm);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff