PNOGuessFunctions.h

Go to the documentation of this file.

/*
 * BasisFunctions.h
 *
 *  Created on: Apr 18, 2018
 *      Author: kottmanj
 */
 
#ifndef PAPER_CODE_BASISFUNCTIONS_H_
#define PAPER_CODE_BASISFUNCTIONS_H_
 
 
#include <exception>
#include <stdlib.h>
#include <cassert>
#include <cmath>
#include <numeric>
#include <valarray>
#include <stdio.h>
#include <madness.h>
#include<madness/chem/PNOStructures.h>
#include<madness/chem/projector.h>
#include<madness/chem/GuessFactory.h>
#include<madness/chem/molecule.h>
 
#include <tuple>
 
 
namespace madness {
 
 
/// class which provides guess functions for pnos and cabs basis sets
/// the guess functions are not orthonormalized or Q-projected
class BasisFunctions{
public:
    typedef std::vector<std::tuple<int, std::vector<double>, std::vector<double> > > cbfT;
    BasisFunctions(World& world,const Molecule& mol, const size_t& l): world(world), molecule(mol), lmax(l) {}
    World& world;
    const Molecule& molecule;
    const size_t lmax;
 
    // print out a basis of contracted orbitals
    void print_contracted_basis(std::map<std::string, cbfT >& molbas)const{
        for(const auto& tmp:molbas){
        cbfT abf=tmp.second;
        for(const auto& bf:abf){
            const int type = std::get<0>(bf);
            const std::vector<double> ex=std::get<1>(bf);
            const std::vector<double> c=std::get<2>(bf);
            std::cout << ex.size() << " " << type << "\n";
            for(size_t k=0;k<ex.size();++k) std::cout << ex[k] << "  " << c[k] << "\n";
 
        }
        }
    }
 
    vector_real_function_3d guess_virtuals_from_file() const;
    vector_real_function_3d guess_contracted_virtuals_from_file() const {
        MyTimer time_1 = MyTimer(world).start();
        // Read Exponents from file
        std::map<std::string, cbfT > molbas = read_contracted_basis_from_file("bas", molecule.get_atoms());
        print("Exponents from file bas:");
        print_contracted_basis(molbas);
        time_1.stop().print("Read Exponents From File");
        vector_real_function_3d virtuals;
 
        MyTimer time_2 = MyTimer(world).start();
        for (const madness::Atom& atom : molecule.get_atoms()) {
            cbfT abf = molbas.at(atomic_number_to_symbol(atom.atomic_number));
            for(const auto& bf:abf){
            const int type = std::get<0>(bf);
            const std::vector<double> ex=std::get<1>(bf);
            const std::vector<double> c=std::get<2>(bf);
            MADNESS_ASSERT(ex.size()==c.size());
            vector_real_function_3d contracted_function;
            for(size_t k=0;k<ex.size();++k){
                vector_real_function_3d gshell = guess_virtual_gaussian_shell(atom, type, ex[k]);
                print_size(world,gshell,"ex="+std::to_string(ex[k]));
                normalize(world,gshell);
                truncate(world,gshell,FunctionDefaults<3>::get_thresh());
                print_size(world,gshell,"ex="+std::to_string(ex[k]));
                if(contracted_function.empty()) contracted_function=c[k]*gshell;
                else contracted_function += c[k]*gshell;
            }
            normalize(world,contracted_function);
            virtuals=append(virtuals,contracted_function);
 
            }
//          for (size_t l = 0; l < exp_atom.size(); ++l) {
//              for (const double e : exp_atom[l]) {
//                  virtuals=append(virtuals, guess_virtual_gaussian_shell(atom, l, e));
//              }
//          }
        }
        time_2.stop().print("Creating Contracted Guess Basis");
        return virtuals;
    }
 
    vector_real_function_3d guess_with_psi4(const vector_real_function_3d& mos)const{
        MADNESS_EXCEPTION("Not there for new madness version",1);
    }
 
    /// make guess virtuals by exciting with polynomials: v = poly*f
    vector_real_function_3d guess_with_exop(const vector_real_function_3d& f, const std::string& type="dipole+", const bool trigo=true)const{
        if(world.rank()==0) std::cout << "Create guess functions by multiplying plane-waves to " << f.size() << " functions \n";
        MADNESS_ASSERT(not f.empty());
 
        std::vector<coord_3d> centers = guessfactory::compute_centroids(f);
        std::vector<std::string> exop_list =  guessfactory::make_predefined_exop_strings(type);
 
 
 
        // make the list with seeds and excitation operators
        std::vector<std::pair<vector_real_function_3d,std::string> > init_list;
 
        for(const auto& exop:exop_list){
            vector_real_function_3d cs=copy(world,f,false);
            init_list.push_back(std::make_pair(cs,exop));
        }
        world.gop.fence();
 
        vector_real_function_3d virtuals;
        if(trigo) for(auto& it:init_list) virtuals=append(virtuals, guessfactory::apply_trigonometric_exop(it.first,it.second,centers,false));
        else for(auto& it:init_list){
            if(world.rank()==0) std::cout << "polynomial guess!\n";
            virtuals=append(virtuals, guessfactory::apply_polynomial_exop(it.first,it.second,centers,false));
        }
        world.gop.fence();
 
        return (virtuals);
    }
 
    vector_real_function_3d guess_virtuals_internal(const std::map<std::string, std::vector<int> > guess_map) const;
    vector_real_function_3d predefined_guess(const std::string name)const{
        // determine start zeta value
        size_t start=0;
        bool empty=false;
        if(name=="pvdz") start=2;
        else if(name=="pvtz") start=3;
        else if(name=="pvqz") start=4;
        else if(name=="pv5z") start=5;
        else if(name=="pv6z") start=6;
        else if(name=="pv7z") start=7;
        else if(name=="zero" or name=="0" or name=="void" or name=="none" or name=="empty") empty=true;
        else MADNESS_EXCEPTION(("unknown predefined guess:"+name).c_str(),1);
 
        std::map<std::string, std::vector<int> > guess_map;
        for(const auto& atom :molecule.get_atoms()){// (int i = 0; i < nemo.molecule().natom(); ++i) {
            const std::string symbol = atomic_number_to_symbol(atom.atomic_number);
            const std::size_t n=atom.atomic_number;
            if(empty) guess_map[symbol]=std::vector<int>(lmax,0);
            else{
                if(n<3) guess_map[symbol]=fill_peterson(start); // first row
                else if(n<11) guess_map[symbol]=fill_peterson(start+1); // first row
                else if(n<19) guess_map[symbol]=fill_peterson(start+2); // third row
                else MADNESS_EXCEPTION("Predefined guesses only up to third row",1);
            }
 
        }
        return guess_virtuals_internal(guess_map);
    }
 
    // helper to fill up l numbers (Peterson Style)
    std::vector<int> fill_peterson(const size_t& s)const{
        std::vector<int> result(lmax,0);
        for(size_t i=0;i<lmax;i++){
            const int tmp=(s-i);
            if(tmp>0) result[i]=tmp;
            else result[i]=0;
        }
        return result;
    }
 
    // helper to get vectors of right size
    std::vector<int> fill_up(std::vector<int> v)const{
        std::vector<int> result(lmax,0);
        for(size_t i=0;i<(lmax>v.size() ? v.size() : lmax);++i) result[i]=v[i];
        return result;
    }
 
    /// return a shell of l-quantum l and exponent e, including all cartesian
    /// components
    vector_real_function_3d guess_virtual_gaussian_shell(const Atom& atom, const int l, const double e) const;
 
    /// read external CABS
    std::map<std::string, std::vector<std::vector<double> > > read_basis_from_file(const std::string& filename, const std::vector<madness::Atom> atoms) const;
    std::vector<std::vector<double> > read_basis_from_file(const std::string& filename, const std::string& atom) const;
 
 
 
 
    std::map<std::string, cbfT > read_contracted_basis_from_file(const std::string& filename, const std::vector<madness::Atom> atoms) const {
        std::map<std::string, cbfT > molbas;
        for (const madness::Atom& atom : atoms) {
            const std::string symbol = atomic_number_to_symbol(atom.atomic_number);
            if (molbas.find(symbol) == molbas.end()) {
                cbfT tmpbas = read_contracted_basis_from_file(filename, symbol);
                molbas[symbol] = tmpbas;
            }
        }
        return molbas;
    }
 
    cbfT read_contracted_basis_from_file(const std::string& filename, const std::string& atom) const {
        std::ifstream f(filename.c_str());
        position_stream(f, atom);
        std::string s;
        int n=-1;
        std::string str_pw_guess, symbol;
        cbfT result;
        std::size_t stars = 0;
        while (f >> s) {
            if (s == "*") {
                f>>n; // initial step
                ++stars;
                if (stars == 2)
                    break;
            }else{
                n=std::stoi(s);
                MADNESS_ASSERT(n>0);
            }
            if(n>0){
                f>>s;
                if (s == "s" || s == "p" || s == "d" || s == "f" || s == "g" || s == "h" || s == "i" || s == "k") {
                    std::vector<double> exponents;
                    std::vector<double> coeff;
                    for(int i=0;i<n;++i){
                        double ex,c;
                        f>>ex;
                        f>>c;
                        exponents.push_back(ex);
                        coeff.push_back(c);
                    }
 
                    result.push_back(std::make_tuple(lqtoint(s),exponents,coeff));
                } else MADNESS_EXCEPTION("UNKNOWN ANGULAR QUANTUM NUMBER",1);
            }
        }
 
        return result;
    }
 
    /// little helper function for l-quantum numbers
    size_t lqtoint(const std::string& l) const;
 
    class CartesianGaussian : public FunctionFunctorInterface<double, 3> {
    public:
        CartesianGaussian(const Atom& atom, const double e, const int i, const int j, const int k);
 
        double x, y, z;   ///< origin
        double exponent;  ///< exponent
        int i, j, k;      ///< cartesian exponents
 
        double operator()(const coord_3d& xyz) const {
            double xx = xyz[0] - x;
            double yy = xyz[1] - y;
            double zz = xyz[2] - z;
            const double e = exponent * (xx * xx + yy * yy + zz * zz);
            return pow(xx, i) * pow(yy, j) * pow(zz, k) * exp(-e);
        }
    };
 
    /// make a set of Cartesian Gaussian functions located on atom
 
    /// @param[in]  atom    where the Cartesian Gaussian function is located
    /// @param[in]  l       the l-quantum number
    /// @param[in]  exponent    exponent of the Cartesian Gaussian function
    std::vector<CartesianGaussian> make_cartesian_guess(const Atom& atom, int l,
            const double exponent) {
        std::vector<CartesianGaussian> gg;
 
        // loop over all Cartesian components of l
        for (int kx = l; kx >= 0; kx--) {
            for (int ky = l - kx; ky >= 0; ky--) {
                int kz = l - kx - ky;
                gg.push_back(CartesianGaussian(atom, exponent, kx, ky, kz));
            }
        }
 
        return gg;
    }
 
    /// real solid harmonic Gaussian
    /// \note see https://en.wikipedia.org/wiki/Spherical_harmonics and https://en.wikipedia.org/wiki/Solid_harmonics
    class SolidHarmonicGaussian : public FunctionFunctorInterface<double, 3> {
    public:
        SolidHarmonicGaussian(const Atom& atom, const double e, int l, int m)
    : x(atom.x), y(atom.y), z(atom.z), exponent(e), Z(atom.atomic_number), l(l), m(m) {}
 
        double x, y, z;   ///< origin
        double exponent;  ///< exponent
        double Z;
        int l, m;         ///< (real) solid harmonic quanta
 
        template <typename T> int sgn(T val) const {
            return (T(0) < val) - (val < T(0));
        }
 
        double operator ()(const coord_3d& xyz) const;
 
        std::vector<coord_3d> special_points() const final {
            coord_3d coord;
            coord[0]=x;
            coord[1]=y;
            coord[2]=z;
            return std::vector<coord_3d>(1,coord);
        }
 
        Level special_level() const final {
            const double width = 1.0/sqrt(2.0*exponent); //  with width of the gaussian
            const int level = FunctionDefaults<3>::set_length_scale(width); // length scale for special points (center)
            return level;
        }
    };
 
    /// make a set of Cartesian Gaussian functions located on atom
 
    /// @param[in]  atom    where the Cartesian Gaussian function is located
    /// @param[in]  l       the l-quantum number
    /// @param[in]  exponent    exponent of the Cartesian Gaussian function
    std::vector<SolidHarmonicGaussian> make_solidharmonic_guess(const Atom& atom, int l,
            const double exponent)const {
        std::vector<SolidHarmonicGaussian> gg;
 
        // loop over all angular components of l
        for(int m=-l; m<=l; ++m) {
            gg.push_back(SolidHarmonicGaussian(atom, exponent, l, m));
        }
 
        return gg;
    }
 
};
 
}// namespace madness
 
#endif /* PAPER_CODE_BASISFUNCTIONS_H_ */