d = np.zeros((N,3), dtype='double')
ifail = np.zeros(1, dtype='int')
# Use above to find d. Solve Ax=b for x.
code = """
for(int i=0; i<N; i++) {
double *A = M+i*9;
double *b = F+i*3;
double *x = d+i*3;
double det=A[0]*A[4]*A[8]+A[1]*A[5]*A[6] +A[3]*A[7]*A[2]-A[2]*A[4]*A[6] -A[0]*A[5]*A[7]-A[8]*A[1]*A[3];
if (abs(det)<1.0e-14) *ifail = 1;
*(x++)=(b[0]*A[4]*A[8]+A[1]*A[5]*b[2]+b[1]*A[7]*A[2]-A[2]*A[4]*b[2]-b[0]*A[5]*A[7]-A[8]*A[1]*b[1])/det;
*(x++)=(A[0]*b[1]*A[8]+b[0]*A[5]*A[6]+A[3]*b[2]*A[2]-A[2]*b[1]*A[6]-A[0]*A[5]*b[2]-A[8]*b[0]*A[3])/det;
*(x++)=(A[0]*A[4]*b[2]+A[1]*b[1]*A[6]+A[3]*A[7]*b[0]-b[0]*A[4]*A[6]-A[0]*b[1]*A[7]-b[2]*A[1]*A[3])/det;
}
"""
W.inline(code, ['F', 'M', 'd', 'N', 'ifail']);
return d
if __name__ == '__main__':
model = eam_model('eam.tab', 7.0, 0.9)
box, coords, ityp, ityp2, typnam = readfiles.readxyz('1_1-1.xyz')
# dirty change
model.set_atoms(box, coords, ityp)
print model.get_energy()
force = model.get_force()
print force
print "Pressure", model.get_pressure(), "eV/Angstrom^3"
print "Pressure", model.get_pressure(GPa=True), "GPa"
#force_norm = np.sqrt((force*force).sum(axis=1))
code = """
for(int k=0; k<n; k++) {
int i = *(neighborlist++);
int j = *(neighborlist++);
double *Fi = F+i*3;
double *Fj = F+j*3;
*(Fi++) -= ((*dV+(*(dF+i)**(drhoj))-(*(dF+j)**(drhoi)))*(*rijhat));
*(Fi++) -= ((*dV+(*(dF+i)**(drhoj))-(*(dF+j)**(drhoi)))*(*(rijhat+1)));
*(Fi++) -= ((*dV+(*(dF+i)**(drhoj))-(*(dF+j)**(drhoi)))*(*(rijhat+2)));
*(Fj++) += ((*dV+(*(dF+j)**(drhoi))-(*(dF+i)**(drhoj)))*(*rijhat));
*(Fj++) += ((*dV+(*(dF+j)**(drhoi))-(*(dF+i)**(drhoj)))*(*(rijhat+1)));
*(Fj++) += ((*dV+(*(dF+j)**(drhoi))-(*(dF+i)**(drhoj)))*(*(rijhat+2)));
drhoi++;
drhoj++;
dV++;
rijhat+=3;
}
"""
W.inline(code, ["F", "dV", "drhoi", "drhoj", "rijhat", "dF", "n", "neighborlist"])
return F
model = eam_model("eam.tab", 7.0, 0.9)
box, coords, ityp, ityp2, typnam = readfiles.readxyz("test.xyz")
# dirty change
model.set_atoms(box, coords, ityp)
print model.get_energy()
force = model.get_force()
print force
# force_norm = np.sqrt((force*force).sum(axis=1))