apps/periodic_old/molecularbasis.h

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/*
  This file is part of MADNESS.
  
  Copyright (C) 2007,2010 Oak Ridge National Laboratory
  
  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version.
  
  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  GNU General Public License for more details.
  
  You should have received a copy of the GNU General Public License
  along with this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
  
  For more information please contact:
  
  Robert J. Harrison
  Oak Ridge National Laboratory
  One Bethel Valley Road
  P.O. Box 2008, MS-6367
  
  email: harrisonrj@ornl.gov
  tel:   865-241-3937
  fax:   865-572-0680
*/
 
#ifndef MOLECULAR_BASIS_H
#define MOLECULAR_BASIS_H
 
#include <madness/madness_config.h>
#include <madness/constants.h>
#include "mentity.h"
#include <madness/external/tinyxml/tinyxml.h>
#include <madness/tensor/tensor.h>
 
#include <vector>
#include <algorithm>
#include <iostream>
#include <sstream>
#include <iomanip>
#include <cstdio>
 
/// Represents a single shell of contracted, Cartesian, Gaussian primitives
class ContractedGaussianShell {
    int type;  ///< Angular momentum = 0, 1, 2, ...
    std::vector<double> coeff;
    std::vector<double> expnt;
    double rsqmax;
    int numbf;  ///< Number of basis functions in shell (type+1)*(type+2)/2
 
    void normalize() {
        // nwcchem cartesian normalization conventions
        // translation of nmcoeff.F into python and thence to c++
        int np = coeff.size();
        if (np == 1) coeff[0] = 1.0e0;
 
        double pi32=pow(madness::constants::pi,1.5);
        int l_lim = 2*type - 1;
        double f = 1.0e00;
        for (int n=l_lim; n>1; n-=2) f *= n;
 
        for (int n=0; n<np; n++)
            coeff[n] *= pow(2.e0*expnt[n]/madness::constants::pi,0.75e0)*pow(4.e0*expnt[n],0.5E0*type)/sqrt(f);
 
        double sum = 0.0;
        for (int n1=0; n1<np; n1++) {
            for (int n2=0; n2<np; n2++) {
                double S =pi32/pow(expnt[n1]+expnt[n2],1.5e0+type)/pow(2e0,type);
                sum = sum + coeff[n1]*coeff[n2]*S;
            }
        }
        sum *= f;
 
        f = 1e0/sqrt(sum);
        for (int n=0; n<np; n++) coeff[n] *= f;
    }
 
public:
    ContractedGaussianShell()
            : type(-1), coeff(), expnt(), rsqmax(0.0), numbf(0) {};
 
    ContractedGaussianShell(int type,
                            const std::vector<double>& coeff,
                            const std::vector<double>& expnt,
                            bool donorm=true)
            : type(type), coeff(coeff), expnt(expnt), numbf((type+1)*(type+2)/2) {
        if (donorm) normalize();
        double minexpnt = expnt[0];
        for (unsigned int i=1; i<expnt.size(); i++)
            minexpnt = std::min(minexpnt,expnt[i]);
        rsqmax = 18.4/minexpnt;  // 18.4 = 8*ln(10)
    }
 
 
    /// Returns square of the distance beyond which function is less than 1e-8.
    double rangesq() const {
        return rsqmax;
    }
 
 
    /// Evaluates the radial part of the contracted function
    double eval_radial(double rsq) const {
        if (rsq > rsqmax) return 0.0;
        double sum = 0.0;
        for (unsigned int i=0; i<coeff.size(); i++) {
            double ersq = expnt[i]*rsq;
            if (ersq < 18.4) sum += coeff[i]*exp(-ersq);
        }
        return sum;
    }
 
 
    /// Evaluates the entire shell returning the incremented result pointer
    double* eval(double rsq, double x, double y, double z, double* bf) const {
        double R = eval_radial(rsq);
        if (fabs(R) < 1e-8) {
            for (int i=0; i<numbf; i++) bf[i] = 0.0;
 
        }
        else {
            switch (type) {
            case 0:
                bf[0] =  R;
                break;
            case 1:
                bf[0] =  R*x;
                bf[1] =  R*y;
                bf[2] =  R*z;
                break;
            case 2:
                bf[0] = R*x*x;
                bf[1] = R*x*y;
                bf[2] = R*x*z ;
                bf[3] = R*y*y ;
                bf[4] = R*y*z ;
                bf[5] = R*z*z;
                break;
            case 3:
                bf[0] = R*x*x*x;
                bf[1] = R*x*x*y;
                bf[2] = R*x*x*z;
                bf[3] = R*x*y*y;
                bf[4] = R*x*y*z;
                bf[5] = R*x*z*z;
                bf[6] = R*y*y*y;
                bf[7] = R*y*y*z;
                bf[8] = R*y*z*z;
                bf[9] = R*z*z*z;
                break;
 
            default:
                throw "UNKNOWN ANGULAR MOMENTUM";
            }
        }
        return bf+numbf;
    }
 
 
    /// Returns the shell angular momentum
    int angular_momentum() const {
        return type;
    }
 
    /// Returns the number of basis functions in the shell
    int nbf() const {
        return numbf;
    }
 
    /// Returns the number of primitives in the contraction
    int nprim() const {
        return coeff.size();
    }
 
    /// Returns a const reference to the coefficients
    const std::vector<double>& get_coeff() const {
        return coeff;
    }
 
    /// Returns a const reference to the exponents
    const std::vector<double>& get_expnt() const {
        return expnt;
    }
 
    /// Returns a string description of the basis function type
    const char* get_desc(int ibf) const {
        static const char* tags[4][10] = {
            {"s"   ,""    ,""    ,""    ,""    ,""    ,""    ,""    ,""    ,""    } ,
            {"px"  ,"py"  ,"pz"  ,""    ,""    ,""    ,""    ,""    ,""    ,""    } ,
            {"dxx" ,"dxy" ,"dxz" ,"dyy" ,"dyz" ,"dzz" ,""    ,""    ,""    ,""    } ,
            {"fxxx","fxxy","fxxz","fxyy","fxyz","fxzz","fxzz","fyyy","fyzz","fzzz"}
        };
        MADNESS_ASSERT(ibf<numbf && ibf >= 0);
        return tags[type][ibf];
    }
 
    template <typename Archive>
    void serialize(Archive& ar) {
        ar & type & coeff & expnt & rsqmax & numbf;
    }
};
 
 
std::ostream& operator<<(std::ostream& s, const ContractedGaussianShell& c) {
    static const char* tag[] = {"s","p","d","f","g"};
    char buf[32768];
    char* p = buf;
    const std::vector<double>& coeff = c.get_coeff();
    const std::vector<double>& expnt = c.get_expnt();
 
    p += sprintf(p,"%s [",tag[c.angular_momentum()]);
    for (int i=0; i<c.nprim(); i++) {
        p += sprintf(p, "%.6f(%.6f)",coeff[i],expnt[i]);
        if (i != (c.nprim()-1)) p += sprintf(p, ", ");
    }
    p += sprintf(p, "]");
    s << buf;
    return s;
}
 
 
/// Represents multiple shells of contracted gaussians on a single center
class AtomicBasis {
    std::vector<ContractedGaussianShell> g;
    double rmaxsq;
    int numbf;
    Tensor<double> dmat, avec, bvec;
 
public:
    AtomicBasis() : g(), rmaxsq(0.0), numbf(0) {};
 
    AtomicBasis(const std::vector<ContractedGaussianShell>& g)
            : g(g) {
        rmaxsq = 0.0;
        numbf = 0;
        for (unsigned int i=0; i<g.size(); i++) {
            rmaxsq = std::max(rmaxsq, g[i].rangesq());
            numbf += g[i].nbf();
        }
    }
 
    void set_guess_info(const Tensor<double>& dmat,
                        const Tensor<double>& avec, const Tensor<double>& bvec) {
        this->dmat = copy(dmat);
        this->avec = copy(avec);
        this->bvec = copy(bvec);
    }
 
    /// Returns the number of basis functions on the center
    int nbf() const {
        return numbf;
    }
 
    /// Returns the number of shells on the center
    int nshell() const {
        return g.size();
    }
 
    /// Returns a const reference to the shells
    const std::vector<ContractedGaussianShell>& get_shells() const {
        return g;
    };
 
    /// Evaluates the basis functions at point x, y, z relative to atomic center
 
    /// The array bf[] must be large enough to hold nbf() values.
    ///
    /// Returned is the incremented pointer.
    double* eval(double x, double y, double z, double* bf) const {
        double rsq = x*x + y*y + z*z;
        if (rsq > rmaxsq) {
            for (int i=0; i<numbf; i++) bf[i] = 0.0;
            return bf+numbf;
        }
 
        double* bfstart = bf;
        for (unsigned int i=0; i<g.size(); i++) {
            bf = g[i].eval(rsq, x, y, z, bf);
        }
        // paranoia is good
        MADNESS_ASSERT(bf-bfstart == numbf);
        return bf;
    }
 
    /// Evaluates the guess atomic density at point x, y, z relative to atomic center
    double eval_guess_density(double x, double y, double z) const {
        MADNESS_ASSERT(has_guess_info());
        double rsq = x*x + y*y + z*z;
        if (rsq > rmaxsq) return 0.0;
 
        double bf[numbf];
        eval(x, y, z, bf);
        const double* p = dmat.ptr();
        double sum = 0.0;
        for (int i=0; i<numbf; i++, p+=numbf) {
            double sumj = 0.0;
            for (int j=0; j<numbf; ++j)
                sumj += p[j]*bf[j];
            sum += bf[i]*sumj;
        }
        return sum;
    }
 
    /// Return shell that contains basis function ibf and also return index of function in the shell
    const ContractedGaussianShell& get_shell_from_basis_function(int ibf, int& ibf_in_shell) const {
        int n=0;
        for (unsigned int i=0; i<g.size(); i++) {
            int nbf_in_shell = g[i].nbf();
            if (ibf>=n && ibf<(n+nbf_in_shell)) {
                ibf_in_shell = ibf-n;
                return g[i];
            }
            else {
                n += g[i].nbf();
            }
        }
        MADNESS_EXCEPTION("AtomicBasis: get_shell_from_basis_function", ibf*100000 + nbf());
    }
 
    bool has_guess_info() const {
        return dmat.size()>0;
    }
 
    const Tensor<double>& get_dmat() const {
        return dmat;
    };
 
    const Tensor<double>& get_avec() const {
        return avec;
    };
 
    const Tensor<double>& get_bvec() const {
        return bvec;
    };
 
    template <typename Archive>
    void serialize(Archive& ar) {
        ar & g & rmaxsq & numbf & dmat & avec & bvec;
    }
 
};
 
std::ostream& operator<<(std::ostream& s, const AtomicBasis& c) {
    const std::vector<ContractedGaussianShell>& shells = c.get_shells();
    for (int i=0; i<c.nshell(); i++) {
        s << "     " << shells[i] << std::endl;
    }
    if (c.has_guess_info()) {
        s << "     " << "Guess density matrix" << std::endl;
        s << c.get_dmat();
    }
 
    return s;
}
 
/// Used to represent one basis function from a shell on a specific center
class AtomicBasisFunction {
private:
    const double xx, yy, zz; // Coordinates of the center
    const ContractedGaussianShell& shell; // Reference to the underlying atomic shell
    const int ibf; // Index of basis function in the shell (0, 1, ...)
    const int nbf; // Number of functions in the shell
 
public:
    AtomicBasisFunction(double x, double y, double z,
                        const ContractedGaussianShell& shell, int ibf)
            : xx(x), yy(y), zz(z), shell(shell), ibf(ibf), nbf(shell.nbf()) {}
 
 
    AtomicBasisFunction(const AtomicBasisFunction& aofunc)
            : xx(aofunc.xx)
            , yy(aofunc.yy)
            , zz(aofunc.zz)
            , shell(aofunc.shell)
            , ibf(aofunc.ibf)
            , nbf(aofunc.nbf) {}
 
    double operator()(double x, double y, double z) const {
        double bf[nbf];
        x-=xx;
        y-=yy;
        z-=zz;
        double rsq = x*x + y*y + z*z;
        shell.eval(rsq, x, y, z, bf);
        return bf[ibf];
    }
 
    void print_me(std::ostream& s) const {
        s << "atomic basis function: center " << xx << " " << yy << " " << zz << " : ibf " << ibf << " nbf " << nbf << " : shell " << shell << std::endl;
    }
 
    const ContractedGaussianShell& get_shell() const {
        return shell;
    }
 
    int get_index() const {
        return ibf;
    }
 
    const char* get_desc() const {
        return shell.get_desc(ibf);
    }
    
    void get_coords(double& x, double& y, double& z) const {
        x=xx; y=yy; z=zz;
        return;
    }
 
    double rangesq() const {
        return shell.rangesq();
    }
};
 
std::ostream& operator<<(std::ostream& s, const AtomicBasisFunction& a) {
    a.print_me(s);
    return s;
};
 
/// Contracted Gaussian basis
class AtomicBasisSet {
    std::string name;
    std::vector<AtomicBasis> ag;  //< Basis associated by atomic number = 1, 2, ...; 0=Bq.
 
    template <typename T>
    std::vector<T> load_tixml_vector(TiXmlElement* node, int n, const char* name) {
        TiXmlElement* child = node->FirstChildElement(name);
        MADNESS_ASSERT(child);
        std::istringstream s(child->GetText());
        std::vector<T> r(n);
        for (int i=0; i<n; i++) {
            MADNESS_ASSERT(s >> r[i]);
        }
        return r;
    }
 
    template <typename T>
    Tensor<T> load_tixml_matrix(TiXmlElement* node, int n, int m, const char* name) {
        TiXmlElement* child = node->FirstChildElement(name);
        MADNESS_ASSERT(child);
        std::istringstream s(child->GetText());
        Tensor<T> r(n,m);
        for (int i=0; i<n; i++) {
            for (int j=0; j<m; j++) {
                MADNESS_ASSERT(s >> r(i,j));
            }
        }
        return r;
    }
 
public:
    AtomicBasisSet() : name("unknown"), ag(110) {}
 
 
    AtomicBasisSet(std::string filename) : name(""), ag(110) {
        read_file(filename);
    }
 
    void read_file(std::string filename) {
        static const bool debug = false;
        TiXmlDocument doc(filename);
        if (!doc.LoadFile()) {
            std::cout << "AtomicBasisSet: Failed loading from file " << filename
                      << " : ErrorDesc  " << doc.ErrorDesc()
                      << " : Row " << doc.ErrorRow()
                      << " : Col " << doc.ErrorCol() << std::endl;
            MADNESS_EXCEPTION("AtomicBasisSet: Failed loading basis set",0);
        }
        for (TiXmlElement* node=doc.FirstChildElement(); node; node=node->NextSiblingElement()) {
            if (strcmp(node->Value(),"name") == 0) {
                name = node->GetText();
                if (debug) std::cout << "Loading basis set " << name << std::endl;
            }
            else if (strcmp(node->Value(), "basis") == 0) {
                const char* symbol = node->Attribute("symbol");
                if (debug) std::cout << "  found basis set for " << symbol << std::endl;
                int atn = symbol_to_atomic_number(symbol);
                std::vector<ContractedGaussianShell> g;
                for (TiXmlElement* shell=node->FirstChildElement(); shell; shell=shell->NextSiblingElement()) {
                    const char* type = shell->Attribute("type");
                    int nprim=-1;
                    shell->Attribute("nprim",&nprim);
                    if (debug) std::cout << "      found shell " << type << " " << nprim << std::endl;
                    std::vector<double> expnt = load_tixml_vector<double>(shell, nprim, "exponents");
                    if (strcmp(type,"L") == 0) {
                        std::vector<double> scoeff = load_tixml_vector<double>(shell, nprim, "scoefficients");
                        std::vector<double> pcoeff = load_tixml_vector<double>(shell, nprim, "pcoefficients");
                        g.push_back(ContractedGaussianShell(0,scoeff,expnt));
                        g.push_back(ContractedGaussianShell(1,pcoeff,expnt));
                    }
                    else {
                        static const char* tag[] = {"S","P","D","F","G"};
                        int i;
                        for (i=0; i<5; i++) {
                            if (strcmp(type,tag[i]) == 0) goto foundit;
                        }
                        MADNESS_EXCEPTION("Loading atomic basis set: bad shell type?",0);
foundit:
                        std::vector<double> coeff = load_tixml_vector<double>(shell, nprim, "coefficients");
                        g.push_back(ContractedGaussianShell(i, coeff, expnt));
                    }
                }
                ag[atn] = AtomicBasis(g);
            }
            else if (strcmp(node->Value(), "atomicguess") == 0) {
                const char* symbol = node->Attribute("symbol");
                if (debug) std::cout << "  atomic guess info for " << symbol << std::endl;
                int atn = symbol_to_atomic_number(symbol);
                MADNESS_ASSERT(is_supported(atn));
                int nbf = ag[atn].nbf();
                Tensor<double> dmat = load_tixml_matrix<double>(node, nbf, nbf, "guessdensitymatrix");
                Tensor<double> avec = load_tixml_matrix<double>(node, nbf, nbf, "alphavectors");
                Tensor<double> bvec = load_tixml_matrix<double>(node, nbf, nbf, "betavectors");
                ag[atn].set_guess_info(dmat, avec, bvec);
            }
            else {
                MADNESS_EXCEPTION("Loading atomic basis set: unexpected XML element", 0);
            }
        }
 
    }
 
 
    /// Makes map from atoms to first basis function on atom and number of basis functions on atom
    void atoms_to_bfn(const MolecularEntity& mentity, std::vector<int>& at_to_bf, std::vector<int>& at_nbf) {
        at_to_bf = std::vector<int>(mentity.natom());
        at_nbf   = std::vector<int>(mentity.natom());
 
        int n = 0;
        for (int i=0; i<mentity.natom(); i++) {
            const Atom& atom = mentity.get_atom(i);
            const int atn = atom.atomic_number;
            MADNESS_ASSERT(is_supported(atn));
            at_to_bf[i] = n;
            at_nbf[i] = ag[atn].nbf();
            n += at_nbf[i];
        }
    }
 
 
    /// Returns the number of the atom the ibf'th basis function is on
    int basisfn_to_atom(const MolecularEntity& mentity, int ibf) const {
        MADNESS_ASSERT(ibf >= 0);
        int n = 0;
        for (int i=0; i<mentity.natom(); i++) {
            // Is the desired function on this atom?
            const Atom& atom = mentity.get_atom(i);
            const int atn = atom.atomic_number;
            MADNESS_ASSERT(is_supported(atn));
            const int nbf_on_atom = ag[atn].nbf();
            if (ibf >= n  && (n+nbf_on_atom) > ibf) {
                return i;
            }
            else {
                n += nbf_on_atom;
            }
        }
        MADNESS_EXCEPTION("AtomicBasisSet: get_atomic_basis_function: confused?", ibf);
    }
 
    /// Returns the ibf'th atomic basis function
    AtomicBasisFunction get_atomic_basis_function(const MolecularEntity& mentity, int ibf) const {
        MADNESS_ASSERT(ibf >= 0);
        int n = 0;
        for (int i=0; i<mentity.natom(); i++) {
            // Is the desired function on this atom?
            const Atom& atom = mentity.get_atom(i);
            const int atn = atom.atomic_number;
            MADNESS_ASSERT(is_supported(atn));
            const int nbf_on_atom = ag[atn].nbf();
            if (ibf >= n  && (n+nbf_on_atom) > ibf) {
                int index;
                const ContractedGaussianShell& shell =
                    ag[atn].get_shell_from_basis_function(ibf-n, index);
                return AtomicBasisFunction(atom.x, atom.y, atom.z, shell, index);
            }
            else {
                n += nbf_on_atom;
            }
        }
        MADNESS_EXCEPTION("AtomicBasisSet: get_atomic_basis_function: confused?", ibf);
    }
 
 
    /// Given a molecule count the number of basis functions
    int nbf(const MolecularEntity& mentity) const {
        int n = 0;
        for (int i=0; i<mentity.natom(); i++) {
            const Atom& atom = mentity.get_atom(i);
            const int atn = atom.atomic_number;
            MADNESS_ASSERT(is_supported(atn));
            n += ag[atn].nbf();
        }
        return n;
    }
 
    /// Evaluates the basis functions
    void eval(const MolecularEntity& mentity, double x, double y, double z, double *bf) const {
        for (int i=0; i<mentity.natom(); i++) {
            const Atom& atom = mentity.get_atom(i);
            const int atn = atom.atomic_number;
            bf = ag[atn].eval(x-atom.x, y-atom.y, z-atom.z, bf);
        }
    }
 
 
    /// Evaluates the guess density
    double eval_guess_density(const MolecularEntity& mentity, double x, double y, double z) const {
        double sum = 0.0;
        for (int i=0; i<mentity.natom(); i++) {
            const Atom& atom = mentity.get_atom(i);
            const int atn = atom.atomic_number;
            sum += ag[atn].eval_guess_density(x-atom.x, y-atom.y, z-atom.z);
        }
        return sum;
    }
 
    bool is_supported(int atomic_number) const {
        return ag[atomic_number].nbf() > 0;
    }
 
    /// Print basis info for atoms in the molecule (once for each unique atom type)
    void print(const MolecularEntity& mentity) const {
        std::cout << "\n " << name << " atomic basis set" << std::endl;
        for (int i=0; i<mentity.natom(); i++) {
            const Atom& atom = mentity.get_atom(i);
            const unsigned int atn = atom.atomic_number;
            for (int j=0; j<i; j++) {
                if (mentity.get_atom(j).atomic_number == atn)
                    goto doneitalready;
            }
            std::cout << std::endl;
            std::cout << "   " <<  get_atomic_data(i).symbol << std::endl;
            std::cout << ag[atn];
doneitalready:
            ;
        }
    }
 
    template <typename T>
    class AnalysisSorter {
        const Tensor<T> v;
    public:
        AnalysisSorter(const Tensor<T>& v) : v(v) {}
        bool operator()(long i, long j) const {
            return std::abs(v[i]) > std::abs(v[j]);
        }
    };
 
    /// Given a vector of AO coefficients prints an analysis
 
    /// For each significant coeff it prints
    /// - atomic symbol
    /// - atom number
    /// - basis function type (e.g., dxy)
    /// - basis function number
    /// - MO coeff
    template <typename T>
    void print_anal(const MolecularEntity& mentity, const Tensor<T>& v) {
        const double thresh = 0.2*v.normf();
        if (thresh == 0.0) {
            printf("    zero vector\n");
            return;
        }
        long nbf = int(v.dim[0]);
        long list[nbf];
        long ngot=0;
        for (long i=0; i<nbf; i++) {
            if (std::abs(v(i)) > thresh) {
                list[ngot++] = i;
            }
        }
        std::sort(list,list+ngot,AnalysisSorter<T>(v));
 
        const char* format;
        if (mentity.natom() < 10) {
            format = "  %2s(%1d)%4s(%2ld)%6.3f  ";
        }
        else if (mentity.natom() < 100) {
            format = "  %2s(%2d)%4s(%3ld)%6.3f  ";
        }
        else if (mentity.natom() < 1000) {
            format = "  %2s(%3d)%4s(%4ld)%6.3f  ";
        }
        else {
            format = "  %2s(%4d)%4s(%5ld)%6.3f  ";
        }
        for (long ii=0; ii<ngot; ii++) {
            long ibf = list[ii];
 
            const int iat = basisfn_to_atom(mentity, ibf);
            const Atom& atom = mentity.get_atom(iat);
            const AtomicBasisFunction ao = get_atomic_basis_function(mentity, ibf);
            const char* desc = ao.get_desc();
            const char* element = get_atomic_data(atom.atomic_number).symbol;
 
            // This will need wrapping in a template for a complex MO vector
            printf(format, element, iat, desc, ibf, v[ibf]);
        }
        printf("\n");
    }
 
    /// Print basis info for all supported atoms
    void print_all() const {
        std::cout << "\n " << name << " atomic basis set" << std::endl;
        for (unsigned int i=0; i<ag.size(); i++) {
            if (ag[i].nbf() > 0) {
                std::cout << "   " <<  get_atomic_data(i).symbol << std::endl;
                std::cout << ag[i];
            }
        }
    }
 
    template <typename Archive>
    void serialize(Archive& ar) {
        ar & name & ag;
    }
};
 
 
 
#endif