/// takes a Python list of spheres with position and velocity vectors and returns the classical kinetic energy of the system
static PyObject *
total_ke(PyObject *self, PyObject *args)
{
/*
def total_ke(molecules):
ke = 0.0
for mol in molecules:
ke += abs(mol.vel) ** 2
return ke / 2
*/
double ke = 0.0;
PyObject *mol_list;
if (!PyArg_ParseTuple(args, "O", &mol_list)) return NULL;
if (!PyList_Check(mol_list)) return NULL;
long size = PyList_Size(mol_list);
for (long i = 0; i < size; i++) {
PyObject *mol, *vel, *abs;
if (!(mol = PyList_GetItem(mol_list, i))) return NULL;
if (!(vel = PyObject_GetAttrString(mol, "vel"))) return NULL;
if (!(abs = PyNumber_Absolute(vel))) return NULL;
double tke = PyFloat_AsDouble(abs);
ke += pow(tke, 2);
Py_DECREF(vel);
Py_DECREF(abs);
}
return Py_BuildValue("d", ke / 2);
}
inline CObject abs(const CObject& a)
{
PyObject* tmp_obj = PyNumber_Absolute(a.Get());
if ( !tmp_obj ) {
throw CArithmeticError("PyNumber_Absolute");
}
return CObject(tmp_obj, eTakeOwnership);
}
static PyObject *bip_abs(term_t t) {
PyObject *pVal, *nVal;
if (!PL_get_arg(1, t, t))
return NULL;
pVal = term_to_python(t, true);
nVal = PyNumber_Absolute(pVal);
Py_DecRef(pVal);
return nVal;
}
/// takes a Python list of spheres with position and velocity vectors and returns the Lennard-Jones potential of the system
static PyObject *
total_pe(PyObject *self, PyObject *args)
{
/*
def total_pe():
pe = 0.0
for m1 in range(len(molecules)):
mol1 = molecules[m1]
for m2 in range(m1 + 1, len(molecules)):
mol2 = molecules[m2]
r12 = abs(mol1.pos - mol2.pos)
assert abs(mol2.pos - mol1.pos) == r12
pe += r12 ** -6 * (r12 ** -6 - 2)
return pe
*/
double pe = 0.0;
PyObject *mol_list;
if (!PyArg_ParseTuple(args, "O", &mol_list)) return NULL;
if (!PyList_Check(mol_list)) return NULL;
long size = PyList_Size(mol_list);
for (long m1 = 0; m1 < size; m1++) {
PyObject *mol1, *mol1pos;
if (!(mol1 = PyList_GetItem(mol_list, m1))) return NULL;
if (!(mol1pos = PyObject_GetAttrString(mol1, "pos"))) return NULL;
for (long m2 = m1 + 1; m2 < size; m2++) {
PyObject *mol2, *mol2pos, *r12vec, *pysep;
if (!(mol2 = PyList_GetItem(mol_list, m2))) return NULL;
if (!(mol2pos = PyObject_GetAttrString(mol2, "pos"))) return NULL;
if (!(r12vec = PyNumber_Subtract(mol1pos, mol2pos))) return NULL;
if (!(pysep = PyNumber_Absolute(r12vec))) return NULL;
double r12 = PyFloat_AsDouble(pysep);
pe += pow(r12, -6) * (pow(r12, -6) - 2);
Py_DECREF(mol2pos);
Py_DECREF(r12vec);
Py_DECREF(pysep);
}
Py_DECREF(mol1pos);
}
return Py_BuildValue("d", pe);
}
static PyObject *Proxy_absolute(ProxyObject *self)
{
Proxy__ENSURE_WRAPPED_OR_RETURN_NULL(self);
return PyNumber_Absolute(self->wrapped);
}
