int main(void) {
CHFL_TRAJECTORY* file = chfl_trajectory_open("tests/files/xyz/helium.xyz", 'r');
CHFL_FRAME* frame = chfl_frame(0);
unsigned* indexes = NULL;
if (chfl_trajectory_read(file, frame) != CHFL_SUCCESS) {/*Handle error*/}
size_t natoms = 0;
float (*positions)[3] = NULL;
chfl_frame_positions(frame, &positions, &natoms);
indexes = malloc(natoms * sizeof(unsigned));
if (indexes == NULL) {/*Handle error*/}
for (unsigned i=0; i<natoms; i++) {
indexes[i] = (unsigned)-1;
}
unsigned last_index = 0;
for (unsigned i=0; i<natoms; i++) {
if (positions[i][0] < 5) {
indexes[last_index] = i;
last_index++;
}
}
printf("Atoms with x < 5:\n");
unsigned i = 0;
while(indexes[i] != (unsigned)-1 && i < natoms) {
printf(" - %d\n", indexes[i]);
i++;
}
printf("Number of atoms: %d\n", i);
chfl_trajectory_close(file);
chfl_frame_free(frame);
free(indexes);
return EXIT_SUCCESS;
}
int main() {
CHFL_TRAJECTORY* traj = chfl_trajectory_open("filename.nc", "r");
CHFL_FRAME* frame = chfl_frame(0);
float (*positions)[3] = NULL;
double* distances = NULL;
if(traj == NULL || frame == NULL)
goto error;
size_t nsteps = 0;
chfl_trajectory_nsteps(traj, &nsteps);
distances = (double*)malloc(sizeof(double)*nsteps);
if (distances == NULL)
goto error;
// Accumulate the distances to the origin of the 10th atom throughtout the
// trajectory
for (size_t i=0; i<nsteps; i++) {
if(!chfl_trajectory_read(traj, frame))
goto error;
// Only allocate on the first iteration. This assume a constant number
// of particles
size_t natoms = 0;
if (i == 0) {
chfl_frame_atoms_count(frame, &natoms);
positions = (float(*)[3])malloc(natoms*3*sizeof(float));
if (positions == NULL)
goto error;
}
// Position of the 10th atom
chfl_frame_positions(frame, positions, natoms);
double distance = sqrt(positions[9][0]*positions[9][0] +
positions[9][1]*positions[9][1] +
positions[9][2]*positions[9][2]);
distances[i] = distance;
}
double mean = 0;
for (size_t i=0; i<nsteps; i++) {
mean += distances[i];
}
mean /= nsteps;
double rmsd = 0.0;
for (size_t i=0; i<nsteps; i++) {
rmsd += (mean - distances[i])*(mean - distances[i]);
}
rmsd /= nsteps;
rmsd = sqrt(rmsd);
printf("Root-mean square displacement is: %f", rmsd);
// Free the memory
chfl_trajectory_close(traj);
chfl_frame_free(frame);
free(distances);
free(positions);
return 0;
error:
printf("Error, cleaning up …\n");
chfl_trajectory_close(traj);
chfl_frame_free(frame);
free(distances);
free(positions);
return 1;
}
int main() {
CHFL_FRAME* frame = chfl_frame(5);
size_t natoms=0, step=0;
assert(!chfl_frame_atoms_count(frame, &natoms));
assert(natoms == 5);
assert(!chfl_frame_step(frame, &step));
assert(step == 0);
assert(!chfl_frame_set_step(frame, 42));
assert(!chfl_frame_step(frame, &step));
assert(step == 42);
float data[4][3];
float pos[4][3];
for (unsigned i=0; i<4; i++)
for (unsigned j=0; j<3; j++)
data[i][j] = i*j;
assert(!chfl_frame_set_positions(frame, data, 4));
assert(!chfl_frame_atoms_count(frame, &natoms));
assert(natoms == 4);
assert(!chfl_frame_positions(frame, pos, 4));
for (unsigned i=0; i<4; i++)
for (unsigned j=0; j<3; j++)
assert(fabs(data[i][j] - pos[i][j]) < 1e-9);
bool has_vel = true;
assert(!chfl_frame_has_velocities(frame, &has_vel));
assert(has_vel == false);
assert(!chfl_frame_set_velocities(frame, data, 4));
float vel[4][3];
assert(!chfl_frame_velocities(frame, vel, 4));
for (unsigned i=0; i<4; i++)
for (unsigned j=0; j<3; j++)
assert(fabs(data[i][j] - vel[i][j]) < 1e-9);
assert(!chfl_frame_has_velocities(frame, &has_vel));
assert(has_vel == true);
/*********************/
CHFL_CELL* cell = chfl_cell(3, 4, 5);
assert(!chfl_frame_set_cell(frame, cell));
chfl_cell_free(cell);
cell = chfl_cell_from_frame(frame);
double a, b, c;
assert(!chfl_cell_lengths(cell, &a, &b, &c));
assert(fabs(a - 3.0) < 1e-9);
assert(fabs(b - 4.0) < 1e-9);
assert(fabs(c - 5.0) < 1e-9);
chfl_cell_free(cell);
/*********************/
/*********************/
CHFL_TOPOLOGY* top = chfl_topology();
CHFL_ATOM* Zn = chfl_atom("Zn");
CHFL_ATOM* Ar = chfl_atom("Ar");
assert(!chfl_topology_append(top, Zn));
assert(!chfl_topology_append(top, Ar));
assert(!chfl_frame_set_topology(frame, top));
chfl_topology_free(top);
chfl_atom_free(Zn);
chfl_atom_free(Ar);
/*********************/
top = chfl_topology_from_frame(frame);
CHFL_ATOM* atom = chfl_atom_from_topology(top, 0);
char name[32];
assert(!chfl_atom_name(atom, name, sizeof(name)));
assert(strcmp(name, "Zn") == 0);
atom = chfl_atom_from_frame(frame, 1);
assert(!chfl_atom_name(atom, name, sizeof(name)));
assert(strcmp(name, "Ar") == 0);
chfl_atom_free(atom);
assert(!chfl_frame_free(frame));
return EXIT_SUCCESS;
}
