void AtomTable::fill(const std::vector<bf_t> & basis, bool verbose) {
// Amount of basis functions is
Nbf=basis.size();
// Amount of integrals is (complex functions, so symmetry is different..)
size_t N=Nbf*Nbf*Nbf*Nbf;
// Make pairs helper
pairs.clear();
for(size_t i=0;i<Nbf;i++)
for(size_t j=0;j<=i;j++) {
bfpair_t tmp;
tmp.i=i;
tmp.j=j;
pairs.push_back(tmp);
}
try {
ints.reserve(N);
ints.resize(N);
} catch(std::bad_alloc err) {
std::ostringstream oss;
ERROR_INFO();
oss << "Was unable to reserve " << memory_size(N*sizeof(double)) << " of memory.\n";
throw std::runtime_error(oss.str());
}
// Initialize with zeros
for(size_t i=0;i<N;i++)
ints[i]=0.0;
Timer t;
if(verbose) {
printf("Filling table of integrals ... ");
fflush(stdout);
}
// Fill integrals table
#ifdef _OPENMP
#pragma omp parallel for schedule(dynamic)
#endif
for(size_t i=0;i<Nbf;i++)
for(size_t j=0;j<Nbf;j++)
for(size_t k=0;k<Nbf;k++)
for(size_t l=0;l<Nbf;l++) {
ints[idx(i,j,k,l)]=ERI(basis[i],basis[j],basis[k],basis[l]);
}
if(verbose) {
printf("done (%s)\n",t.elapsed().c_str());
fflush(stdout);
}
}
int main()
{
size_t NElec = 10;
size_t NOcc = NElec / 2;
size_t NBasis = 26;
size_t M = idx4(NBasis, NBasis, NBasis, NBasis);
size_t i, j, k, l;
double val;
size_t mu, nu, lam, sig;
FILE *enuc_file;
enuc_file = fopen("h2o_dzp_enuc.dat", "r");
double Vnn;
fscanf(enuc_file, "%lf", &Vnn);
fclose(enuc_file);
printf("Nuclear repulsion energy = %12f\n", Vnn);
arma::mat S(NBasis, NBasis);
arma::mat T(NBasis, NBasis);
arma::mat V(NBasis, NBasis);
arma::mat H(NBasis, NBasis);
arma::mat F(NBasis, NBasis, arma::fill::zeros);
arma::mat F_prime(NBasis, NBasis, arma::fill::zeros);
arma::mat D(NBasis, NBasis, arma::fill::zeros);
arma::mat D_old(NBasis, NBasis, arma::fill::zeros);
arma::mat C(NBasis, NBasis);
arma::vec eps_vec(NBasis);
arma::mat C_prime(NBasis, NBasis);
arma::vec Lam_S_vec(NBasis);
arma::mat Lam_S_mat(NBasis, NBasis);
arma::mat L_S(NBasis, NBasis);
FILE *S_file, *T_file, *V_file;
S_file = fopen("h2o_dzp_s.dat", "r");
T_file = fopen("h2o_dzp_t.dat", "r");
V_file = fopen("h2o_dzp_v.dat", "r");
while (fscanf(S_file, "%d %d %lf", &i, &j, &val) != EOF)
S(i-1, j-1) = S(j-1, i-1) = val;
while (fscanf(T_file, "%d %d %lf", &i, &j, &val) != EOF)
T(i-1, j-1) = T(j-1, i-1) = val;
while (fscanf(V_file, "%d %d %lf", &i, &j, &val) != EOF)
V(i-1, j-1) = V(j-1, i-1) = val;
fclose(S_file);
fclose(T_file);
fclose(V_file);
arma::vec ERI = arma::vec(M, arma::fill::zeros);
FILE *ERI_file;
ERI_file = fopen("h2o_dzp_eri.dat", "r");
while (fscanf(ERI_file, "%d %d %d %d %lf", &i, &j, &k, &l, &val) != EOF) {
mu = i-1; nu = j-1; lam = k-1; sig = l-1;
ERI(idx4(mu,nu,lam,sig)) = val;
}
fclose(ERI_file);
double thresh_E = 1.0e-15;
double thresh_D = 1.0e-10;
size_t iteration = 0;
size_t max_iterations = 1024;
double E_total, E_elec_old, E_elec_new, delta_E, rmsd_D;
printf("Overlap Integrals:\n");
print_arma_mat(S);
printf("Kinetic-Energy Integrals:\n");
print_arma_mat(T);
printf("Nuclear Attraction Integrals\n");
print_arma_mat(V);
H = T + V;
printf("Core Hamiltonian:\n");
print_arma_mat(H);
arma::eig_sym(Lam_S_vec, L_S, S);
// What's wrong with this?
// Lam_S_mat = Lam_S_vec * arma::eye<arma::mat>(Lam_S_vec.n_elem, Lam_S_vec.n_elem);
Lam_S_mat = arma::diagmat(Lam_S_vec);
arma::mat Lam_sqrt_inv = arma::sqrt(arma::inv(Lam_S_mat));
arma::mat symm_orthog = L_S * Lam_sqrt_inv * L_S.t();
F_prime = symm_orthog.t() * H * symm_orthog;
arma::eig_sym(eps_vec, C_prime, F_prime);
C = symm_orthog * C_prime;
build_density(D, C, NOcc);
printf("S^-1/2 Matrix:\n");
print_arma_mat(symm_orthog);
printf("Initial F' Matrix:\n");
print_arma_mat(F_prime);
printf("Initial C Matrix:\n");
print_arma_mat(C);
printf("Initial Density Matrix:\n");
print_arma_mat(D);
E_elec_new = calc_elec_energy(D, H, H);
E_total = E_elec_new + Vnn;
delta_E = E_total;
printf(" Iter E(elec) E(tot) Delta(E) RMS(D)\n");
printf("%4d %20.12f %20.12f %20.12f\n",
iteration, E_elec_new, E_total, delta_E);
iteration++;
while (iteration < max_iterations) {
build_fock(F, D, H, ERI);
F_prime = symm_orthog.t() * F * symm_orthog;
arma::eig_sym(eps_vec, C_prime, F_prime);
C = symm_orthog * C_prime;
D_old = D;
build_density(D, C, NOcc);
E_elec_old = E_elec_new;
E_elec_new = calc_elec_energy(D, H, F);
E_total = E_elec_new + Vnn;
if (iteration == 1) {
printf("Fock Matrix:\n");
print_arma_mat(F);
printf("%4d %20.12f %20.12f %20.12f\n",
iteration, E_elec_new, E_total, delta_E);
} else {
printf("%4d %20.12f %20.12f %20.12f %20.12f\n",
iteration, E_elec_new, E_total, delta_E, rmsd_D);
}
delta_E = E_elec_new - E_elec_old;
rmsd_D = rmsd_density(D, D_old);
if (delta_E < thresh_E && rmsd_D < thresh_D) {
printf("Convergence achieved.\n");
break;
}
F = F_prime;
iteration++;
}
arma::mat F_MO = C.t() * F * C;
// Save the TEIs and MO coefficients/energies to disk
// for use in other routines.
H.save("H.mat", arma::arma_ascii);
ERI.save("TEI_AO.mat", arma::arma_ascii);
C.save("C.mat", arma::arma_ascii);
F_MO.save("F_MO.mat", arma::arma_ascii);
return 0;
}
