static void *open_tng_read(const char *filename, const char*,
int *natoms)
{
tngdata *tng;
tng_function_status stat;
int64_t n, exp;
tng = new tngdata;
stat = tng_util_trajectory_open(filename, 'r', &tng->tng_traj);
if(stat != TNG_SUCCESS)
{
fprintf(stderr, "tngplugin) Cannot open file '%s'\n", filename);
return NULL;
}
tng_num_particles_get(tng->tng_traj, &n);
*natoms = (int)n;
tng->natoms = (int)n;
tng->step = 0;
tng_num_frames_get(tng->tng_traj, &n);
tng->n_frames = n;
tng->has_velocities = 0;
tng_distance_unit_exponential_get(tng->tng_traj, &exp);
tng->coord_exponential = (int) exp;
return tng;
}
void gmx_fwrite_tng(tng_trajectory_t tng,
const gmx_bool bUseLossyCompression,
int step,
real elapsedPicoSeconds,
real lambda,
const rvec *box,
int nAtoms,
const rvec *x,
const rvec *v,
const rvec *f)
{
#ifdef GMX_USE_TNG
typedef tng_function_status (*write_data_func_pointer)(tng_trajectory_t,
const gmx_int64_t,
const double,
const real*,
const gmx_int64_t,
const gmx_int64_t,
const char*,
const char,
const char);
#ifdef GMX_DOUBLE
static write_data_func_pointer write_data = tng_util_generic_with_time_double_write;
#else
static write_data_func_pointer write_data = tng_util_generic_with_time_write;
#endif
double elapsedSeconds = elapsedPicoSeconds * PICO;
gmx_int64_t nParticles;
char compression;
if (!tng)
{
/* This function might get called when the type of the
compressed trajectory is actually XTC. So we exit and move
on. */
return;
}
tng_num_particles_get(tng, &nParticles);
if (nAtoms != (int)nParticles)
{
tng_implicit_num_particles_set(tng, nAtoms);
}
if (bUseLossyCompression)
{
compression = TNG_TNG_COMPRESSION;
}
else
{
compression = TNG_GZIP_COMPRESSION;
}
/* The writing is done using write_data, which writes float or double
* depending on the GROMACS compilation. */
if (x)
{
GMX_ASSERT(box, "Need a non-NULL box if positions are written");
if (write_data(tng, step, elapsedSeconds,
reinterpret_cast<const real *>(x),
3, TNG_TRAJ_POSITIONS, "POSITIONS",
TNG_PARTICLE_BLOCK_DATA,
compression) != TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
}
/* TNG-MF1 compression only compresses positions and velocities. Use lossless
* compression for box shape regardless of output mode */
if (write_data(tng, step, elapsedSeconds,
reinterpret_cast<const real *>(box),
9, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE",
TNG_NON_PARTICLE_BLOCK_DATA,
TNG_GZIP_COMPRESSION) != TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
}
}
if (v)
{
if (write_data(tng, step, elapsedSeconds,
reinterpret_cast<const real *>(v),
3, TNG_TRAJ_VELOCITIES, "VELOCITIES",
TNG_PARTICLE_BLOCK_DATA,
compression) != TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
}
}
if (f)
{
/* TNG-MF1 compression only compresses positions and velocities. Use lossless
* compression for forces regardless of output mode */
if (write_data(tng, step, elapsedSeconds,
reinterpret_cast<const real *>(f),
3, TNG_TRAJ_FORCES, "FORCES",
TNG_PARTICLE_BLOCK_DATA,
TNG_GZIP_COMPRESSION) != TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
}
}
/* TNG-MF1 compression only compresses positions and velocities. Use lossless
* compression for lambdas regardless of output mode */
if (write_data(tng, step, elapsedSeconds,
reinterpret_cast<const real *>(&lambda),
1, TNG_GMX_LAMBDA, "LAMBDAS",
TNG_NON_PARTICLE_BLOCK_DATA,
TNG_GZIP_COMPRESSION) != TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
}
#else
GMX_UNUSED_VALUE(tng);
GMX_UNUSED_VALUE(bUseLossyCompression);
GMX_UNUSED_VALUE(step);
GMX_UNUSED_VALUE(elapsedPicoSeconds);
GMX_UNUSED_VALUE(lambda);
GMX_UNUSED_VALUE(box);
GMX_UNUSED_VALUE(nAtoms);
GMX_UNUSED_VALUE(x);
GMX_UNUSED_VALUE(v);
GMX_UNUSED_VALUE(f);
#endif
}
static int read_tng_timestep(void *v, int natoms, molfile_timestep_t *ts)
{
/* The pointers that will be allocated by the TNG must be NULL before allocation. */
void *values = 0;
char datatype;
float box_shape[9], vmd_box[6];
float fact = 1;
int64_t frame, n, temp, temp2;
double temp_time;
tng_function_status stat;
tngdata *tng = (tngdata *)v;
if(!ts)
{
return MOLFILE_ERROR;
}
// fprintf(stderr, "Reading framestep from TNG\n");
stat = tng_util_particle_data_next_frame_read(tng->tng_traj, TNG_TRAJ_POSITIONS, &values,
&datatype, &frame, &temp_time);
ts->physical_time = temp_time / PICO;
if(stat != TNG_SUCCESS)
{
if(values)
{
free(values);
}
return MOLFILE_ERROR;
}
// fprintf(stderr, "tngplugin) Timestep %d (%f), frame %d (%d), %d atoms\n",
// tng->step, ts->physical_time, (int)frame, (int)tng->n_frames, natoms);
/* TODO: Here it would be possible to add reading of the energy and pressure
* measurements supported in VMD if they are present in the TNG file */
tng_num_particles_get(tng->tng_traj, &n);
if(n != natoms)
{
fprintf(stderr, "tngplugin) Timestep in file contains wrong number of atoms\n");
fprintf(stderr, "tngplugin) Found %d, expected %d\n", (int)n, natoms);
return MOLFILE_ERROR;
}
if(tng->coord_exponential != -10)
{
fact = pow(10.0, tng->coord_exponential + 10);
}
convert_to_float(values, ts->coords, fact, natoms, 3, datatype);
if(ts->velocities)
{
// fprintf(stderr, "tngplugin) Reading velocities\n");
stat = tng_particle_data_vector_interval_get(tng->tng_traj, TNG_TRAJ_VELOCITIES, frame,
frame, TNG_USE_HASH, &values,
&n, &temp, &temp2, &datatype);
if(stat == TNG_CRITICAL)
{
if(values)
{
free(values);
}
return MOLFILE_ERROR;
}
if(stat == TNG_SUCCESS)
{
convert_to_float(values, ts->velocities, fact, natoms, 3, datatype);
}
}
stat = tng_data_vector_interval_get(tng->tng_traj, TNG_TRAJ_BOX_SHAPE,
frame, frame, TNG_USE_HASH, &values,
&temp, &temp2, &datatype);
if(stat == TNG_CRITICAL)
{
if(values)
{
free(values);
}
return MOLFILE_ERROR;
}
if(stat == TNG_SUCCESS)
{
convert_to_float(values, box_shape, fact, 1, 9, datatype);
convert_tng_box_shape_to_vmd(box_shape, vmd_box);
if(ts)
{
ts->A = vmd_box[0];
ts->B = vmd_box[1];
ts->C = vmd_box[2];
ts->alpha = vmd_box[3];
ts->beta = vmd_box[4];
ts->gamma = vmd_box[5];
}
}
++tng->step;
if(values)
{
free(values);
}
return MOLFILE_SUCCESS;
}
gmx_bool gmx_get_tng_data_next_frame_of_block_type(tng_trajectory_t input,
gmx_int64_t blockId,
real **values,
gmx_int64_t *frameNumber,
double *frameTime,
gmx_int64_t *nValuesPerFrame,
gmx_int64_t *nAtoms,
real *prec,
char *name,
int maxLen,
gmx_bool *bOK)
{
#if GMX_USE_TNG
tng_function_status stat;
char datatype = -1;
gmx_int64_t codecId;
int blockDependency;
void *data = 0;
double localPrec;
stat = tng_data_block_name_get(input, blockId, name, maxLen);
if (stat != TNG_SUCCESS)
{
gmx_file("Cannot read next frame of TNG file");
}
stat = tng_data_block_dependency_get(input, blockId, &blockDependency);
if (stat != TNG_SUCCESS)
{
gmx_file("Cannot read next frame of TNG file");
}
if (blockDependency & TNG_PARTICLE_DEPENDENT)
{
tng_num_particles_get(input, nAtoms);
stat = tng_util_particle_data_next_frame_read(input,
blockId,
&data,
&datatype,
frameNumber,
frameTime);
}
else
{
*nAtoms = 1; /* There are not actually any atoms, but it is used for
allocating memory */
stat = tng_util_non_particle_data_next_frame_read(input,
blockId,
&data,
&datatype,
frameNumber,
frameTime);
}
if (stat == TNG_CRITICAL)
{
gmx_file("Cannot read next frame of TNG file");
}
if (stat == TNG_FAILURE)
{
*bOK = TRUE;
return FALSE;
}
stat = tng_data_block_num_values_per_frame_get(input, blockId, nValuesPerFrame);
if (stat != TNG_SUCCESS)
{
gmx_file("Cannot read next frame of TNG file");
}
snew(*values, sizeof(real) * *nValuesPerFrame * *nAtoms);
convert_array_to_real_array(data,
*values,
getDistanceScaleFactor(input),
*nAtoms,
*nValuesPerFrame,
datatype);
tng_util_frame_current_compression_get(input, blockId, &codecId, &localPrec);
/* This must be updated if/when more lossy compression methods are added */
if (codecId != TNG_TNG_COMPRESSION)
{
*prec = -1.0;
}
else
{
*prec = localPrec;
}
*bOK = TRUE;
return TRUE;
#else
GMX_UNUSED_VALUE(input);
GMX_UNUSED_VALUE(blockId);
GMX_UNUSED_VALUE(values);
GMX_UNUSED_VALUE(frameNumber);
GMX_UNUSED_VALUE(frameTime);
GMX_UNUSED_VALUE(nValuesPerFrame);
GMX_UNUSED_VALUE(nAtoms);
GMX_UNUSED_VALUE(prec);
GMX_UNUSED_VALUE(name);
GMX_UNUSED_VALUE(maxLen);
GMX_UNUSED_VALUE(bOK);
return FALSE;
#endif
}
/* TODO: If/when TNG acquires the ability to copy data blocks without
* uncompressing them, then this implemenation should be reconsidered.
* Ideally, gmx trjconv -f a.tng -o b.tng -b 10 -e 20 would be fast
* and lose no information. */
gmx_bool gmx_read_next_tng_frame(tng_trajectory_t input,
t_trxframe *fr,
gmx_int64_t *requestedIds,
int numRequestedIds)
{
#if GMX_USE_TNG
gmx_bool bOK = TRUE;
tng_function_status stat;
gmx_int64_t numberOfAtoms = -1, frameNumber = -1;
gmx_int64_t nBlocks, blockId, *blockIds = NULL, codecId;
char datatype = -1;
void *values = NULL;
double frameTime = -1.0;
int size, blockDependency;
double prec;
const int defaultNumIds = 5;
static gmx_int64_t fallbackRequestedIds[defaultNumIds] =
{
TNG_TRAJ_BOX_SHAPE, TNG_TRAJ_POSITIONS,
TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES,
TNG_GMX_LAMBDA
};
fr->bStep = FALSE;
fr->bTime = FALSE;
fr->bLambda = FALSE;
fr->bAtoms = FALSE;
fr->bPrec = FALSE;
fr->bX = FALSE;
fr->bV = FALSE;
fr->bF = FALSE;
fr->bBox = FALSE;
/* If no specific IDs were requested read all block types that can
* currently be interpreted */
if (!requestedIds || numRequestedIds == 0)
{
numRequestedIds = defaultNumIds;
requestedIds = fallbackRequestedIds;
}
stat = tng_num_particles_get(input, &numberOfAtoms);
if (stat != TNG_SUCCESS)
{
gmx_file("Cannot determine number of atoms from TNG file.");
}
fr->natoms = numberOfAtoms;
if (!gmx_get_tng_data_block_types_of_next_frame(input,
fr->step,
numRequestedIds,
requestedIds,
&frameNumber,
&nBlocks,
&blockIds))
{
return FALSE;
}
if (nBlocks == 0)
{
return FALSE;
}
for (gmx_int64_t i = 0; i < nBlocks; i++)
{
blockId = blockIds[i];
tng_data_block_dependency_get(input, blockId, &blockDependency);
if (blockDependency & TNG_PARTICLE_DEPENDENT)
{
stat = tng_util_particle_data_next_frame_read(input,
blockId,
&values,
&datatype,
&frameNumber,
&frameTime);
}
else
{
stat = tng_util_non_particle_data_next_frame_read(input,
blockId,
&values,
&datatype,
&frameNumber,
&frameTime);
}
if (stat == TNG_CRITICAL)
{
gmx_file("Cannot read positions from TNG file.");
return FALSE;
}
else if (stat == TNG_FAILURE)
{
continue;
}
switch (blockId)
{
case TNG_TRAJ_BOX_SHAPE:
switch (datatype)
{
case TNG_INT_DATA:
size = sizeof(gmx_int64_t);
break;
case TNG_FLOAT_DATA:
size = sizeof(float);
break;
case TNG_DOUBLE_DATA:
size = sizeof(double);
break;
default:
gmx_incons("Illegal datatype of box shape values!");
}
for (int i = 0; i < DIM; i++)
{
convert_array_to_real_array(reinterpret_cast<char *>(values) + size * i * DIM,
reinterpret_cast<real *>(fr->box[i]),
getDistanceScaleFactor(input),
1,
DIM,
datatype);
}
fr->bBox = TRUE;
break;
case TNG_TRAJ_POSITIONS:
srenew(fr->x, fr->natoms);
convert_array_to_real_array(values,
reinterpret_cast<real *>(fr->x),
getDistanceScaleFactor(input),
fr->natoms,
DIM,
datatype);
fr->bX = TRUE;
tng_util_frame_current_compression_get(input, blockId, &codecId, &prec);
/* This must be updated if/when more lossy compression methods are added */
if (codecId == TNG_TNG_COMPRESSION)
{
fr->prec = prec;
fr->bPrec = TRUE;
}
break;
case TNG_TRAJ_VELOCITIES:
srenew(fr->v, fr->natoms);
convert_array_to_real_array(values,
(real *) fr->v,
getDistanceScaleFactor(input),
fr->natoms,
DIM,
datatype);
fr->bV = TRUE;
tng_util_frame_current_compression_get(input, blockId, &codecId, &prec);
/* This must be updated if/when more lossy compression methods are added */
if (codecId == TNG_TNG_COMPRESSION)
{
fr->prec = prec;
fr->bPrec = TRUE;
}
break;
case TNG_TRAJ_FORCES:
srenew(fr->f, fr->natoms);
convert_array_to_real_array(values,
reinterpret_cast<real *>(fr->f),
getDistanceScaleFactor(input),
fr->natoms,
DIM,
datatype);
fr->bF = TRUE;
break;
case TNG_GMX_LAMBDA:
switch (datatype)
{
case TNG_FLOAT_DATA:
fr->lambda = *(reinterpret_cast<float *>(values));
break;
case TNG_DOUBLE_DATA:
fr->lambda = *(reinterpret_cast<double *>(values));
break;
default:
gmx_incons("Illegal datatype lambda value!");
}
fr->bLambda = TRUE;
break;
default:
gmx_warning("Illegal block type! Currently GROMACS tools can only handle certain data types. Skipping block.");
}
/* values does not have to be freed before reading next frame. It will
* be reallocated if it is not NULL. */
}
fr->step = static_cast<int>(frameNumber);
fr->bStep = TRUE;
// Convert the time to ps
fr->time = frameTime / PICO;
fr->bTime = TRUE;
/* values must be freed before leaving this function */
sfree(values);
return bOK;
#else
GMX_UNUSED_VALUE(input);
GMX_UNUSED_VALUE(fr);
GMX_UNUSED_VALUE(requestedIds);
GMX_UNUSED_VALUE(numRequestedIds);
return FALSE;
#endif
}
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
}