static void addTngMoleculeFromTopology(tng_trajectory_t tng,
const char *moleculeName,
const t_atoms *atoms,
gmx_int64_t numMolecules,
tng_molecule_t *tngMol)
{
if (tng_molecule_add(tng, moleculeName, tngMol) != TNG_SUCCESS)
{
gmx_file("Cannot add molecule to TNG molecular system.");
}
/* FIXME: The TNG atoms should contain mass and atomB info (for free
* energy calculations), i.e. in when it's available in TNG (2.0). */
for (int atomIt = 0; atomIt < atoms->nr; atomIt++)
{
const t_atom *at = &atoms->atom[atomIt];
/* FIXME: Currently the TNG API can only add atoms belonging to a
* residue and chain. Wait for TNG 2.0*/
if (atoms->nres > 0)
{
const t_resinfo *resInfo = &atoms->resinfo[at->resind];
char chainName[2] = {resInfo->chainid, 0};
tng_chain_t tngChain = NULL;
tng_residue_t tngRes = NULL;
tng_atom_t tngAtom = NULL;
if (tng_molecule_chain_find (tng, *tngMol, chainName,
(gmx_int64_t)-1, &tngChain) !=
TNG_SUCCESS)
{
tng_molecule_chain_add (tng, *tngMol, chainName,
&tngChain);
}
/* FIXME: When TNG supports both residue index and residue
* number the latter should be used. Wait for TNG 2.0*/
if (tng_chain_residue_find(tng, tngChain, *resInfo->name,
at->resind + 1, &tngRes)
!= TNG_SUCCESS)
{
tng_chain_residue_add(tng, tngChain, *resInfo->name, &tngRes);
}
tng_residue_atom_add(tng, tngRes, *(atoms->atomname[atomIt]), *(atoms->atomtype[atomIt]), &tngAtom);
}
}
tng_molecule_cnt_set(tng, *tngMol, numMolecules);
}
/* Create a TNG molecule representing the selection groups
* to write */
static void add_selection_groups(tng_trajectory_t tng,
const gmx_mtop_t *mtop)
{
const gmx_moltype_t *molType;
const t_atoms *atoms;
const t_atom *at;
const t_resinfo *resInfo;
const t_ilist *ilist;
int nAtoms = 0, i = 0, j, molIt, atomIt, nameIndex;
int atom_offset = 0;
tng_molecule_t mol, iterMol;
tng_chain_t chain;
tng_residue_t res;
tng_atom_t atom;
tng_bond_t tngBond;
gmx_int64_t nMols;
char *groupName;
/* The name of the TNG molecule containing the selection group is the
* same as the name of the selection group. */
nameIndex = *mtop->groups.grps[egcCompressedX].nm_ind;
groupName = *mtop->groups.grpname[nameIndex];
tng_molecule_alloc(tng, &mol);
tng_molecule_name_set(tng, mol, groupName);
tng_molecule_chain_add(tng, mol, "", &chain);
for (molIt = 0; molIt < mtop->nmoltype; molIt++)
{
molType = &mtop->moltype[mtop->molblock[molIt].type];
atoms = &molType->atoms;
for (j = 0; j < mtop->molblock[molIt].nmol; j++)
{
bool bAtomsAdded = FALSE;
for (atomIt = 0; atomIt < atoms->nr; atomIt++, i++)
{
char *res_name;
int res_id;
if (ggrpnr(&mtop->groups, egcCompressedX, i) != 0)
{
continue;
}
at = &atoms->atom[atomIt];
if (atoms->nres > 0)
{
resInfo = &atoms->resinfo[at->resind];
/* FIXME: When TNG supports both residue index and residue
* number the latter should be used. */
res_name = *resInfo->name;
res_id = at->resind + 1;
}
else
{
res_name = (char *)"";
res_id = 0;
}
if (tng_chain_residue_find(tng, chain, res_name, res_id, &res)
!= TNG_SUCCESS)
{
/* Since there is ONE chain for selection groups do not keep the
* original residue IDs - otherwise there might be conflicts. */
tng_chain_residue_add(tng, chain, res_name, &res);
}
tng_residue_atom_w_id_add(tng, res, *(atoms->atomname[atomIt]),
*(atoms->atomtype[atomIt]),
atom_offset + atomIt, &atom);
nAtoms++;
bAtomsAdded = TRUE;
}
/* Add bonds. */
if (bAtomsAdded)
{
for (int k = 0; k < F_NRE; k++)
{
if (IS_CHEMBOND(k))
{
ilist = &molType->ilist[k];
if (ilist)
{
int l = 1;
while (l < ilist->nr)
{
int atom1, atom2;
atom1 = ilist->iatoms[l] + atom_offset;
atom2 = ilist->iatoms[l+1] + atom_offset;
if (ggrpnr(&mtop->groups, egcCompressedX, atom1) == 0 &&
ggrpnr(&mtop->groups, egcCompressedX, atom2) == 0)
{
tng_molecule_bond_add(tng, mol, ilist->iatoms[l],
ilist->iatoms[l+1], &tngBond);
}
l += 3;
}
}
}
}
/* Settle is described using three atoms */
ilist = &molType->ilist[F_SETTLE];
if (ilist)
{
int l = 1;
while (l < ilist->nr)
{
int atom1, atom2, atom3;
atom1 = ilist->iatoms[l] + atom_offset;
atom2 = ilist->iatoms[l+1] + atom_offset;
atom3 = ilist->iatoms[l+2] + atom_offset;
if (ggrpnr(&mtop->groups, egcCompressedX, atom1) == 0)
{
if (ggrpnr(&mtop->groups, egcCompressedX, atom2) == 0)
{
tng_molecule_bond_add(tng, mol, atom1,
atom2, &tngBond);
}
if (ggrpnr(&mtop->groups, egcCompressedX, atom3) == 0)
{
tng_molecule_bond_add(tng, mol, atom1,
atom3, &tngBond);
}
}
l += 4;
}
}
}
atom_offset += atoms->nr;
}
}
if (nAtoms != i)
{
tng_molecule_existing_add(tng, &mol);
tng_molecule_cnt_set(tng, mol, 1);
tng_num_molecule_types_get(tng, &nMols);
for (gmx_int64_t k = 0; k < nMols; k++)
{
tng_molecule_of_index_get(tng, k, &iterMol);
if (iterMol == mol)
{
continue;
}
tng_molecule_cnt_set(tng, iterMol, 0);
}
}
else
{
tng_molecule_free(tng, &mol);
}
}
int main ()
/******************************************************************************/
/*
Purpose:
MAIN is the main program for MD_OPENMP.
Discussion:
MD implements a simple molecular dynamics simulation.
The program uses Open MP directives to allow parallel computation.
The velocity Verlet time integration scheme is used.
The particles interact with a central pair potential.
Output of the program is saved in the TNG format, which is why this
code is included in the TNG API release. The high-level API of the
TNG API is used where appropriate.
Licensing:
This code is distributed under the GNU LGPL license.
Modified:
8 Jan 2013
Author:
Original FORTRAN77 version by Bill Magro.
C version by John Burkardt.
TNG trajectory output by Magnus Lundborg.
Parameters:
None
*/
{
float *acc;
float *box;
float *box_shape;
float dt = 0.0002;
float e0;
float *force;
int i;
float kinetic;
float mass = 1.0;
int nd = 3;
int np = 50;
float *pos;
float potential;
int proc_num;
int seed = 123456789;
int step;
int step_num = 50000;
int step_print;
int step_print_index;
int step_print_num;
int step_save;
float *vel;
float wtime;
tng_trajectory_t traj;
tng_molecule_t molecule;
tng_chain_t chain;
tng_residue_t residue;
tng_atom_t atom;
timestamp ( );
proc_num = omp_get_num_procs ( );
acc = ( float * ) malloc ( nd * np * sizeof ( float ) );
box = ( float * ) malloc ( nd * sizeof ( float ) );
box_shape = (float *) malloc (9 * sizeof (float));
force = ( float * ) malloc ( nd * np * sizeof ( float ) );
pos = ( float * ) malloc ( nd * np * sizeof ( float ) );
vel = ( float * ) malloc ( nd * np * sizeof ( float ) );
printf ( "\n" );
printf ( "MD_OPENMP\n" );
printf ( " C/OpenMP version\n" );
printf ( "\n" );
printf ( " A molecular dynamics program.\n" );
printf ( "\n" );
printf ( " NP, the number of particles in the simulation is %d\n", np );
printf ( " STEP_NUM, the number of time steps, is %d\n", step_num );
printf ( " DT, the size of each time step, is %f\n", dt );
printf ( "\n" );
printf ( " Number of processors available = %d\n", proc_num );
printf ( " Number of threads = %d\n", omp_get_max_threads ( ) );
printf("\n");
printf(" Initializing trajectory storage.\n");
/* Initialize the TNG trajectory */
tng_util_trajectory_open(TNG_EXAMPLE_FILES_DIR "tng_md_out.tng", 'w', &traj);
/* Set molecules data */
/* N.B. This is still not done using utility functions. The low-level API
* is used. */
printf(" Creating molecules in trajectory.\n");
tng_molecule_add(traj, "water", &molecule);
tng_molecule_chain_add(traj, molecule, "W", &chain);
tng_chain_residue_add(traj, chain, "WAT", &residue);
if(tng_residue_atom_add(traj, residue, "O", "O", &atom) == TNG_CRITICAL)
{
tng_util_trajectory_close(&traj);
printf(" Cannot create molecules.\n");
exit(1);
}
tng_molecule_cnt_set(traj, molecule, np);
/*
Set the dimensions of the box.
*/
for(i = 0; i < 9; i++)
{
box_shape[i] = 0.0;
}
for ( i = 0; i < nd; i++ )
{
box[i] = 10.0;
/* box_shape stores 9 values according to the TNG specs */
box_shape[i*nd + i] = box[i];
}
printf ( "\n" );
printf ( " Initializing positions, velocities, and accelerations.\n" );
/*
Set initial positions, velocities, and accelerations.
*/
initialize ( np, nd, box, &seed, pos, vel, acc );
/*
Compute the forces and energies.
*/
printf ( "\n" );
printf ( " Computing initial forces and energies.\n" );
compute ( np, nd, pos, vel, mass, force, &potential, &kinetic );
e0 = potential + kinetic;
/* Saving frequency */
step_save = 400;
step_print = 0;
step_print_index = 0;
step_print_num = 10;
/*
This is the main time stepping loop:
Compute forces and energies,
Update positions, velocities, accelerations.
*/
printf(" Every %d steps box shape, particle positions, velocities and forces are\n",
step_save);
printf(" saved to a TNG trajectory file.\n");
printf ( "\n" );
printf ( " At certain step intervals, we report the potential and kinetic energies.\n" );
printf ( " The sum of these energies should be a constant.\n" );
printf ( " As an accuracy check, we also print the relative error\n" );
printf ( " in the total energy.\n" );
printf ( "\n" );
printf ( " Step Potential Kinetic (P+K-E0)/E0\n" );
printf ( " Energy P Energy K Relative Energy Error\n" );
printf ( "\n" );
step = 0;
printf ( " %8d %14f %14f %14e\n",
step, potential, kinetic, ( potential + kinetic - e0 ) / e0 );
step_print_index++;
step_print = ( step_print_index * step_num ) / step_print_num;
/* Set the output frequency of box shape, positions, velocities and forces */
if(tng_util_box_shape_write_frequency_set(traj, step_save) != TNG_SUCCESS)
{
printf("Error setting writing frequency data. %s: %d\n",
__FILE__, __LINE__);
exit(1);
}
if(tng_util_pos_write_frequency_set(traj, step_save) != TNG_SUCCESS)
{
printf("Error setting writing frequency data. %s: %d\n",
__FILE__, __LINE__);
exit(1);
}
if(tng_util_vel_write_frequency_set(traj, step_save) != TNG_SUCCESS)
{
printf("Error setting writing frequency data. %s: %d\n",
__FILE__, __LINE__);
exit(1);
}
if(tng_util_force_write_frequency_set(traj, step_save) != TNG_SUCCESS)
{
printf("Error setting writing frequency data. %s: %d\n",
__FILE__, __LINE__);
exit(1);
}
/* Write the first frame of box shape, positions, velocities and forces */
if(tng_util_box_shape_write(traj, 0, box_shape) != TNG_SUCCESS)
{
printf("Error writing box shape. %s: %d\n",
__FILE__, __LINE__);
exit(1);
}
if(tng_util_pos_write(traj, 0, pos) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
exit(1);
}
if(tng_util_vel_write(traj, 0, vel) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
exit(1);
}
if(tng_util_force_write(traj, 0, force) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
exit(1);
}
wtime = omp_get_wtime ( );
for ( step = 1; step < step_num; step++ )
{
compute ( np, nd, pos, vel, mass, force, &potential, &kinetic );
if ( step == step_print )
{
printf ( " %8d %14f %14f %14e\n", step, potential, kinetic,
( potential + kinetic - e0 ) / e0 );
step_print_index++;
step_print = ( step_print_index * step_num ) / step_print_num;
}
if(step % step_save == 0)
{
/* Write box shape, positions, velocities and forces */
if(tng_util_box_shape_write(traj, step, box_shape) != TNG_SUCCESS)
{
printf("Error writing box shape. %s: %d\n",
__FILE__, __LINE__);
exit(1);
}
if(tng_util_pos_write(traj, step, pos) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
break;
}
if(tng_util_vel_write(traj, step, vel) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
break;
}
if(tng_util_force_write(traj, step, force) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
break;
}
}
update ( np, nd, pos, vel, force, acc, mass, dt );
}
wtime = omp_get_wtime ( ) - wtime;
printf ( "\n" );
printf ( " Elapsed time for main computation:\n" );
printf ( " %f seconds.\n", wtime );
free ( acc );
free ( box );
free ( box_shape );
free ( force );
free ( pos );
free ( vel );
/* Close the TNG output. */
tng_util_trajectory_close(&traj);
printf ( "\n" );
printf ( "MD_OPENMP\n" );
printf ( " Normal end of execution.\n" );
printf ( "\n" );
timestamp ( );
return 0;
}
void gmx_tng_setup_atom_subgroup(tng_trajectory_t tng,
const int nind,
const int *ind,
const char *name)
{
#if GMX_USE_TNG
gmx_int64_t nAtoms, cnt, nMols;
tng_molecule_t mol, iterMol;
tng_chain_t chain;
tng_residue_t res;
tng_atom_t atom;
tng_function_status stat;
tng_num_particles_get(tng, &nAtoms);
if (nAtoms == nind)
{
return;
}
stat = tng_molecule_find(tng, name, -1, &mol);
if (stat == TNG_SUCCESS)
{
tng_molecule_num_atoms_get(tng, mol, &nAtoms);
tng_molecule_cnt_get(tng, mol, &cnt);
if (nAtoms == nind)
{
stat = TNG_SUCCESS;
}
else
{
stat = TNG_FAILURE;
}
}
if (stat == TNG_FAILURE)
{
/* The indexed atoms are added to one separate molecule. */
tng_molecule_alloc(tng, &mol);
tng_molecule_name_set(tng, mol, name);
tng_molecule_chain_add(tng, mol, "", &chain);
for (int i = 0; i < nind; i++)
{
char temp_name[256], temp_type[256];
/* Try to retrieve the residue name of the atom */
stat = tng_residue_name_of_particle_nr_get(tng, ind[i], temp_name, 256);
if (stat != TNG_SUCCESS)
{
temp_name[0] = '\0';
}
/* Check if the molecule of the selection already contains this residue */
if (tng_chain_residue_find(tng, chain, temp_name, -1, &res)
!= TNG_SUCCESS)
{
tng_chain_residue_add(tng, chain, temp_name, &res);
}
/* Try to find the original name and type of the atom */
stat = tng_atom_name_of_particle_nr_get(tng, ind[i], temp_name, 256);
if (stat != TNG_SUCCESS)
{
temp_name[0] = '\0';
}
stat = tng_atom_type_of_particle_nr_get(tng, ind[i], temp_type, 256);
if (stat != TNG_SUCCESS)
{
temp_type[0] = '\0';
}
tng_residue_atom_w_id_add(tng, res, temp_name, temp_type, ind[i], &atom);
}
tng_molecule_existing_add(tng, &mol);
}
/* Set the count of the molecule containing the selected atoms to 1 and all
* other molecules to 0 */
tng_molecule_cnt_set(tng, mol, 1);
tng_num_molecule_types_get(tng, &nMols);
for (gmx_int64_t k = 0; k < nMols; k++)
{
tng_molecule_of_index_get(tng, k, &iterMol);
if (iterMol == mol)
{
continue;
}
tng_molecule_cnt_set(tng, iterMol, 0);
}
#else
GMX_UNUSED_VALUE(tng);
GMX_UNUSED_VALUE(nind);
GMX_UNUSED_VALUE(ind);
GMX_UNUSED_VALUE(name);
#endif
}