void eval(MonteCarloNode& n) {
auto& b = n.board;
auto sym = n.orientation;
feats.fill(Features());
oriented.fill(Features());
extractFeatures(b,feats);
dihedralTranspose(feats,oriented,sym);
inVec.clear();
convertToTCNNInput(oriented,inVec);
result = &nn.fprop(inVec);
std::vector<size_t> inds;
inds.assign(n.moves.size(),0);
double total = 0;
for(size_t i = 0; i < n.moves.size(); ++i) {
inds[i] = /*IX(n.moves[i]);*/IX(dihedral(n.moves[i],sym));
total += (*result)[inds[i]];
}
for(size_t i = 0; i < n.moves.size(); ++i) {
n.probabilities[i].store((*result)[inds[i]]/total);
}
}
int main(int argc, char** argv) {
int i, t;
int n_frames = 10;
int n_atoms = 5;
int n_sphere_points = 960;
int* pairs = calloc(2, sizeof(int));
pairs[0] = 0;
pairs[1] = 1;
int triplets[3] = {0, 1, 2};
int quartets[4] = {0, 1, 2, 3};
float * box_matrix = calloc(n_frames*9, sizeof(float));
for (t = 0; t < n_frames; t++)
for (i = 0; i < 3; i++)
box_matrix[t*9 + i*3+i] = 1;
float * atom_radii = calloc(n_atoms, sizeof(float));
float * xyzlist = calloc(n_frames*n_atoms*3, sizeof(float));
float * geom_out = calloc(n_frames, sizeof(float));
float * displacement_out = calloc(n_frames*1*3, sizeof(float));
float * array_of_areas = calloc(n_frames*n_atoms, sizeof(float));
for (i = 0; i < n_frames*n_atoms*3; i++)
xyzlist[i] = i;
sasa(n_frames, n_atoms, xyzlist, atom_radii, n_sphere_points, array_of_areas);
printf("Finished sasa\n");
dihedral(xyzlist, quartets, geom_out, n_frames, n_atoms, 1);
printf("finished dihedral\n");
dist(xyzlist, pairs, geom_out, NULL, n_frames, n_atoms, 1);
printf("finished dist 1\n");
dist(xyzlist, pairs, NULL, displacement_out, n_frames, n_atoms, 1);
printf("finished dist 2\n");
dist_mic(xyzlist, pairs, box_matrix, geom_out, NULL, n_frames, n_atoms, 1);
printf("finished mic 1\n");
dist_mic(xyzlist, pairs, box_matrix, NULL, displacement_out, n_frames, n_atoms, 1);
printf("finished mic 2\n");
angle(xyzlist, triplets, geom_out, n_frames, n_atoms, 1);
printf("finished angle\n");
// example: this is an invalid read that should trigger valgrid
// or the clang address tool
// __m128 f = _mm_loadu_ps(atom_radii+(n_atoms-3));
free(atom_radii);
free(xyzlist);
free(array_of_areas);
free(geom_out);
free(displacement_out);
free(pairs);
free(box_matrix);
return 0;
}
// recalculate the value of this geometry, and return it
float GeometryDihedral::calculate(void) {
// get coords to calculate distance
float pos1[3], pos2[3], pos3[3], pos4[3];
if(!normal_atom_coord(0, pos1))
return 0.0;
if(!normal_atom_coord(1, pos2))
return 0.0;
if(!normal_atom_coord(2, pos3))
return 0.0;
if(!normal_atom_coord(3, pos4))
return 0.0;
return (geomValue = dihedral(pos1, pos2, pos3, pos4));
}
PyObject *wrap_dihedral(PyObject *self,PyObject *args)
{
PyObject *cs1, *cs2,*cs3, *cs4;
if(!PyArg_ParseTuple(args,"OOOO",&cs1,&cs2,&cs3,&cs4))
return NULL;
rvec r1,r2,r3,r4;
int i;
for(i=0;i<DIM;i++){
r1[i]=PyFloat_AsDouble(PySequence_GetItem(cs1,i));
r2[i]=PyFloat_AsDouble(PySequence_GetItem(cs2,i));
r3[i]=PyFloat_AsDouble(PySequence_GetItem(cs3,i));
r4[i]=PyFloat_AsDouble(PySequence_GetItem(cs4,i));
}
real d = dihedral(r1,r2,r3,r4);
PyObject *ret;
ret=Py_BuildValue("d",d);
return ret;
}