summaryrefslogtreecommitdiff
path: root/src
diff options
context:
space:
mode:
Diffstat (limited to 'src')
-rw-r--r--src/lib/tng_io.c100
1 files changed, 82 insertions, 18 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index 01ef8f0..d7c8b8b 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -7283,8 +7283,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_bond_add
{
int64_t i;
tng_bond_t new_bonds;
-
- TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
+ (void)tng_data;
for(i = 0; i < molecule->n_bonds; i++)
{
@@ -7709,7 +7708,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(name, "TNG library: name must not be a NULL pointer.");
- tng_molecule_cnt_list_get(tng_data, molecule_cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
for(i = 0; i < tng_data->n_molecules; i++)
{
@@ -7749,7 +7748,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_id_of_particle_nr_get
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(id, "TNG library: id must not be a NULL pointer.");
- tng_molecule_cnt_list_get(tng_data, molecule_cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
for(i = 0; i < tng_data->n_molecules; i++)
{
@@ -7788,7 +7787,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molsystem_bonds_get
TNG_ASSERT(from_atoms, "TNG library: from_atoms must not be a NULL pointer.");
TNG_ASSERT(to_atoms, "TNG library: to_atoms must not be a NULL pointer.");
- tng_molecule_cnt_list_get(tng_data, molecule_cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
*n_bonds = 0;
/* First count the total number of bonds to allocate memory */
@@ -7851,7 +7850,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_of_particle_nr_get
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(name, "TNG library: name must not be a NULL pointer.");
- tng_molecule_cnt_list_get(tng_data, molecule_cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
for(i = 0; i < tng_data->n_molecules; i++)
{
@@ -7898,7 +7897,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(name, "TNG library: name must not be a NULL pointer.");
- tng_molecule_cnt_list_get(tng_data, molecule_cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
for(i = 0; i < tng_data->n_molecules; i++)
{
@@ -7944,7 +7943,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_id_of_particle_nr_get
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(id, "TNG library: id must not be a NULL pointer.");
- tng_molecule_cnt_list_get(tng_data, molecule_cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
for(i = 0; i < tng_data->n_molecules; i++)
{
@@ -7985,7 +7984,7 @@ tng_function_status DECLSPECDLLEXPORT tng_global_residue_id_of_particle_nr_get
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(id, "TNG library: id must not be a NULL pointer.");
- tng_molecule_cnt_list_get(tng_data, molecule_cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
for(i = 0; i < tng_data->n_molecules; i++)
{
@@ -8030,7 +8029,7 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(name, "TNG library: name must not be a NULL pointer.");
- tng_molecule_cnt_list_get(tng_data, molecule_cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
for(i = 0; i < tng_data->n_molecules; i++)
{
@@ -8073,7 +8072,7 @@ tng_function_status tng_atom_type_of_particle_nr_get
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(type, "TNG library: type must not be a NULL pointer.");
- tng_molecule_cnt_list_get(tng_data, molecule_cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
for(i = 0; i < tng_data->n_molecules; i++)
{
@@ -9696,7 +9695,72 @@ tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set
(tng_trajectory_t tng_data,
const int64_t n)
{
- tng_data->n_particles = n;
+ tng_molecule_t mol;
+ tng_chain_t chain;
+ tng_residue_t res;
+ tng_atom_t atom;
+ tng_function_status stat;
+ int64_t diff, n_mod;
+
+ TNG_ASSERT(n >= 0, "TNG library: The number of molecules must be >= 0");
+
+ diff = n - tng_data->n_particles;
+
+ if(diff == 0)
+ {
+ return(TNG_SUCCESS);
+ }
+ if(diff < 0)
+ {
+ printf("TNG library: Already more particles than requested implicit ");
+ printf("particle count.\n");
+ printf("TNG library: Cannot set implicit particle count. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+
+ if(diff > 0)
+ {
+ stat = tng_molecule_find(tng_data, "TNG_IMPLICIT_MOL", -1, &mol);
+ if(stat != TNG_SUCCESS)
+ {
+ stat = tng_util_trajectory_molecule_add(tng_data,
+ "TNG_IMPLICIT_MOL",
+ diff,
+ &mol);
+ if(stat != TNG_SUCCESS)
+ {
+ return(stat);
+ }
+ stat = tng_molecule_chain_add(tng_data, mol, "", &chain);
+ if(stat != TNG_SUCCESS)
+ {
+ return(stat);
+ }
+ stat = tng_chain_residue_add(tng_data, chain, "", &res);
+ if(stat != TNG_SUCCESS)
+ {
+ return(stat);
+ }
+ tng_residue_atom_add(tng_data, res, "", "", &atom);
+ }
+ else
+ {
+ if(mol->n_atoms != 1)
+ {
+ n_mod = diff % mol->n_atoms;
+ if(n_mod != 0)
+ {
+ printf("TNG library: Number of atoms in implicit molecule ");
+ printf("not compatible with requested implicit particle cnt.\n");
+ printf("TNG library: Cannot set implicit particle count. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_FAILURE);
+ }
+ diff /= mol->n_atoms;
+ }
+ tng_molecule_cnt_set(tng_data, mol, diff);
+ }
+ }
return(TNG_SUCCESS);
}
@@ -9729,7 +9793,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(n, "TNG library: n must not be a NULL pointer");
- tng_molecule_cnt_list_get(tng_data, cnt_list);
+ tng_molecule_cnt_list_get(tng_data, &cnt_list);
for(i = tng_data->n_molecules; i --;)
{
@@ -9743,20 +9807,20 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get
tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_list_get
(const tng_trajectory_t tng_data,
- int64_t *mol_cnt_list)
+ int64_t **mol_cnt_list)
{
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
if(tng_data->var_num_atoms_flag)
{
- mol_cnt_list = tng_data->current_trajectory_frame_set.
+ *mol_cnt_list = tng_data->current_trajectory_frame_set.
molecule_cnt_list;
}
else
{
- mol_cnt_list = tng_data->molecule_cnt_list;
+ *mol_cnt_list = tng_data->molecule_cnt_list;
}
- if(mol_cnt_list == 0)
+ if(*mol_cnt_list == 0)
{
return(TNG_FAILURE);
}
@@ -14399,7 +14463,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add
tng_function_status stat;
TNG_ASSERT(name, "TNG library: name must not be a NULL pointer");
- TNG_ASSERT(cnt>=0, "TNG library: cnt must be a positive integer");
+ TNG_ASSERT(cnt>=0, "TNG library: cnt must be >= 0");
stat = tng_molecule_add(tng_data, name, mol);
if(stat != TNG_SUCCESS)
contact: Jan Huwald // Impressum