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nbo.cpp
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// Please see license.txt for licensing and copyright information //
// Author: Paul Zimmerman, University of Michigan //
#include "nbo.h"
#include "constants.h"
#include "zstruct.h"
using namespace std;
//TO DO:
// 1. read in/save molden GTO section (done)
// 2. read in/save hybridization data
// 3. MOPAC data (done-ish)
// NOTE:
// bmo_occ doesn't match bmo_ quantities if 3-center is added
double NBO::get_pol(int a1, int a2, double& ev1)
{
double pol1 = 0.;
for (int j=0;j<bmo;j++) //finds bond including atoms a1 and a2
if ( (bmo_atoms[2*j+0]==a1 && bmo_atoms[2*j+1]==a2)
|| (bmo_atoms[2*j+0]==a2 && bmo_atoms[2*j+1]==a1) )
{
if (mo_occ[j]>ev1) //grab highest energy localized orbital
{
ev1 = mo_occ[j];
pol1 = bmo_polar[j];
if (bmo_atoms[2*j+0]==a1)
pol1 *= -1.;
}
}
return pol1;
}
void NBO::print_molden_orbs(int norbs, int* olist, string filename)
{
printf(" printing molden output to %s \n",filename.c_str());
ofstream molfile;
molfile.open(filename.c_str());
molfile.setf(ios::scientific);
molfile.setf(ios::left);
molfile << setprecision(8);
double* diag = mo_occ; //for mopac, this is the "eigenvalue"
for (int i=0;i<mheadersize;i++)
molfile << mheader[i] << endl;
for (int i=0;i<norbs;i++)
if (olist[i])
{
int index = i;
molfile << "Sym=X" << endl;
molfile << "Ene= " << diag[index] << endl;
molfile << "Spin=Alpha" << endl;
molfile << "Occup=1" << endl;
for (int j=0;j<nao;j++)
molfile << " " << j+1 << " " << MO[index*nao+j] << endl;
}
for (int i=0;i<nao;i++)
if (!olist[i])
{
int index = i;
molfile << "Sym=X" << endl;
molfile << "Ene= " << diag[index] << endl;
molfile << "Spin=Alpha" << endl;
molfile << "Occup=0" << endl;
for (int j=0;j<nao;j++)
molfile << " " << j+1 << " " << MO[index*nao+j] << endl;
}
molfile << "[6D]" << endl;
molfile.close();
return;
}
int NBO::compare_nbo(NBO nbo1, string mfilename, int quiet)
{
nb = 0;
if (!hasNBO || !nbo1.hasNBO || nao<1)
{
printf(" missing data in compare_nbo \n");
return -1;
}
// printf(" bmo: %2i bmo': %2i \n",bmo,nbo1.bmo);
// printf(" vmo: %2i vmo': %2i \n",vmo,nbo1.vmo);
if (blist!=NULL) delete [] blist;
blist = new int[bmo+1];
for (int i=0;i<bmo;i++) blist[i] = 0;
int* foundbmo = new int[bmo+1];
int* used = new int[nbo1.bmo+1];
for (int i=0;i<bmo;i++) foundbmo[i] = 0;
for (int i=0;i<nbo1.bmo;i++) used[i] = 0;
for (int i=0;i<bmo;i++)
{
int found = 0;
double pol1 = bmo_polar[i];
int b1 = bmo_atoms[2*i+0];
int b2 = bmo_atoms[2*i+1];
for (int j=0;j<nbo1.bmo;j++)
if (!used[j])
{
double pol2 = nbo1.bmo_polar[j];
int c1 = nbo1.bmo_atoms[2*j+0];
int c2 = nbo1.bmo_atoms[2*j+1];
if (c1==b1 && c2==b2) found = 1;
if (c1==b2 && c2==b1) found = 1;
if (!found && b2==0) //need to check this block
{
if (b1==c1 && pol2<-0.9)
found = 1;
else if (b1==c2 && pol2>0.9)
found = 1;
}
if (!found && pol1<-0.9) //need to check this block
{
if (b1==c1 && pol2<-0.9)
found = 1;
else if (b1==c2 && pol2>0.9)
found = 1;
}
if (found) { used[j] = 1; break; }
}
foundbmo[i] = found;
}
if (!quiet)
for (int i=0;i<bmo;i++)
if (!foundbmo[i])
printf(" orbital %2i: %2i-%2i \n",i+1,bmo_atoms[2*i+0],bmo_atoms[2*i+1]);
int* saveorb = new int[nao];
for (int i=0;i<bmo;i++) blist[i] = 0;
for (int i=0;i<nao;i++) saveorb[i] = 0;
for (int i=0;i<bmo;i++)
if (!foundbmo[i])
{
if (bmo_num[i]-1<0 || bmo_num[i]>nao)
{ printf(" ERROR bmo_num out of bounds: %i \n",bmo_num[i]); exit(1); }
saveorb[bmo_num[i]-1] = 1;
blist[nb++] = i;
}
if (mfilename!="none")
print_molden_orbs(nao,saveorb,mfilename);
delete [] foundbmo;
delete [] saveorb;
return 0;
}
void NBO::print_nbo()
{
printf("\n Printing NBO data! \n");
for (int i=0;i<natoms;i++)
printf(" q[%2i]: %8.5f \n",i+1,q[i]);
printf(" nalpha: %2i nbeta: %2i nelec: %2i nao: %2i \n",nalpha,nbeta,nelec,nao);
printf("\n");
printf(" now printing NBO bonding analysis \n");
for (int i=0;i<bmo;i++)
{
printf(" BMO[%2i] %2i-%2i occ: %5.3f polarization: %6.3f \n",i+1,bmo_atoms[2*i+0],bmo_atoms[2*i+1],bmo_occ[i],bmo_polar[i]);
}
for (int i=0;i<vmo;i++)
{
printf(" VMO[%2i] %2i-%2i occ: %5.3f \n",i+1,vmo_atoms[2*i+0],vmo_atoms[2*i+1],vmo_occ[i]);
}
printf("\n");
}
void NBO::alloc_nbo()
{
//printf(" in alloc_nbo for nao: %2i \n",nao);
int resetnao = 0;
if (nao<1)
{
//printf(" nao reset from: %i \n",nao);
nao = 10;
resetnao = 1;
}
nao+=1000;
mo_occ = new double[nao];
bmo_occ = new double[nao];
bmo_atoms = new int[2*nao];
bmo_polar = new double[nao];
bmo_num = new int[nao];
vmo_occ = new double[nao];
vmo_atoms = new int[2*nao];
vmo_num = new int[nao];
for (int i=0;i<nao;i++) bmo_occ[i] = 0;
for (int i=0;i<2*nao;i++) bmo_atoms[i] = 0;
for (int i=0;i<nao;i++) bmo_num[i] = 0;
for (int i=0;i<nao;i++) vmo_occ[i] = 0;
for (int i=0;i<2*nao;i++) vmo_atoms[i] = 0;
for (int i=0;i<nao;i++) vmo_num[i] = 0;
nao-=1000;
if (resetnao) nao = 0;
return;
}
double NBO::distance(int i, int j)
{
return sqrt((xyz[3*i+0]-xyz[3*j+0])*(xyz[3*i+0]-xyz[3*j+0])+
(xyz[3*i+1]-xyz[3*j+1])*(xyz[3*i+1]-xyz[3*j+1])+
(xyz[3*i+2]-xyz[3*j+2])*(xyz[3*i+2]-xyz[3*j+2]));
}
void NBO::clean_long_bonds()
{
//printf(" removing long distance \"bonds\" \n");
for (int i=0;i<bmo;i++)
{
int a1 = bmo_atoms[2*i+0]-1;
int a2 = bmo_atoms[2*i+1]-1;
double d1 = 0.;
//printf(" a1,a2: %2i %2i anumbers: %i %i \n",a1,a2,anumbers[a1],anumbers[a2]);
double d0 = 10.;
if (a1>-1 && a2>-1)
{
d0 = getRa(anumbers,a1) + getRa(anumbers,a2);
d1 = distance(a1,a2);
}
//printf(" d0: %8.5f d1: %8.5f \n",d0,d1);
if (d1 > d0)
{
//printf(" long: %2i-%2i dist: %5.2f \n",a1,a2,d1);
for (int j=i;j<bmo-1;j++)
{
int jp = j+1;
bmo_num[j] = bmo_num[jp];
bmo_atoms[2*j+0] = bmo_atoms[2*jp+0];
bmo_atoms[2*j+1] = bmo_atoms[2*jp+1];
bmo_occ[j] = bmo_occ[jp];
bmo_polar[j] = bmo_polar[jp];
}
bmo--;
}
}
return;
}
int NBO::read_nbo_file(string filename)
{
hasNBO = 0;
bmo = vmo = 0;
#if USE_MOPAC
int done1 = read_mopac_mo(filename);
if (done1) hasNBO = 1;
clean_long_bonds();
return done1;
printf(" SHOULDN'T BE HERE \n");
exit(1);
#endif
int done = read_mo(filename);
if (!done)
{
printf(" couldn't read MO's \n");
return 0;
}
alloc_nbo();
string oname = filename;
ifstream output(oname.c_str(),ios::in);
if (!output) { printf(" error opening NBO file: %s \n",oname.c_str()); return 0; }
string line;
vector<string> tok_line;
int cmo = 0;
while (!output.eof())
{
getline(output,line);
// cout << " RR " << line << endl;
if (line.find(" beta electrons")!=string::npos)
{
// cout << " RR1 " << line << endl;
tok_line = StringTools::tokenize(line, " \t");
nalpha = atoi(tok_line[2].c_str());
nbeta = atoi(tok_line[5].c_str());
nelec = nalpha+nbeta;
}
if (line.find("Summary of Natural Population Analysis")!=string::npos)
{
// cout << " RR1 " << line << endl;
for (int i=0;i<5;i++)
getline(output,line);
for (int i=0;i<natoms;i++)
{
getline(output,line);
// cout << " RR2 " << line << endl;
tok_line = StringTools::tokenize(line, " \t");
q[i] = atof(tok_line[2].c_str());
}
}
if (line.find("Bond orbital/ Coefficients/ Hybrids")!=string::npos)
{
while (!output.eof())
{
// cout << " RRo " << line << endl;
getline(output,line);
if (line.find("BD*")!=string::npos)
{
tok_line = StringTools::tokenize(line, "-() \t");
mo_occ[cmo++] = atof(tok_line[1].c_str());
vmo_occ[vmo] = atof(tok_line[1].c_str());
vmo_atoms[2*vmo+0] = atoi(tok_line[5].c_str());
vmo_atoms[2*vmo+1] = atoi(tok_line[7].c_str());
vmo_num[vmo] = atoi(tok_line[0].c_str());
vmo++;
}
else if (line.find("RY*")!=string::npos)
{
tok_line = StringTools::tokenize(line, "-() \t");
mo_occ[cmo++] = atof(tok_line[1].c_str());
}
else if (line.find("CR")!=string::npos)
{
tok_line = StringTools::tokenize(line, "-() \t");
mo_occ[cmo++] = atof(tok_line[1].c_str());
}
else if (line.find("BD")!=string::npos)
{
tok_line = StringTools::tokenize(line, "-() \t");
mo_occ[cmo++] = atof(tok_line[1].c_str());
bmo_occ[bmo] = atof(tok_line[1].c_str());
bmo_atoms[2*bmo+0] = atoi(tok_line[5].c_str());
bmo_atoms[2*bmo+1] = atoi(tok_line[7].c_str());
bmo_num[bmo] = atoi(tok_line[0].c_str());
bmo++;
}
else if (line.find("LP")!=string::npos)
{
tok_line = StringTools::tokenize(line, "-() \t");
mo_occ[cmo++] = atof(tok_line[1].c_str());
bmo_occ[bmo] = atof(tok_line[1].c_str());
bmo_atoms[2*bmo+0] = atoi(tok_line[5].c_str());
bmo_atoms[2*bmo+1] = 0;
bmo_num[bmo] = atoi(tok_line[0].c_str());
bmo++;
}
else if (line.find("****************")!=string::npos)
break;
}
}
}
output.close();
hasNBO = 1;
return 1;
}
void NBO::alloc(int natoms_i)
{
hasNBO = 0;
bmo = 0;
vmo = 0;
natoms = natoms_i;
anumbers = new int[natoms];
anames = new string[natoms];
xyz = new double[3*natoms];
q = new double[natoms];
MO = NULL;
mo_occ = NULL;
bmo_occ = NULL;
bmo_atoms = NULL;
vmo_occ = NULL;
vmo_atoms = NULL;
wAO = NULL;
tAO = NULL;
return;
}
void NBO::init(int natoms_i, int* anumbers_i, string* anames_i, double* xyz_i)
{
hasNBO = 0;
bmo = 0;
vmo = 0;
nao = 0;
nalpha = nbeta = nelec = 0;
natoms = natoms_i;
anumbers = new int[natoms];
anames = new string[natoms];
xyz = new double[3*natoms];
q = new double[natoms];
spratio = new double[natoms];
MO = NULL;
mo_occ = NULL;
bmo_occ = NULL;
bmo_polar = NULL;
bmo_atoms = NULL;
bmo_num = NULL;
vmo_occ = NULL;
vmo_atoms = NULL;
vmo_num = NULL;
wAO = NULL;
tAO = NULL;
nb = 0;
blist = NULL;
for (int i=0;i<natoms;i++)
anumbers[i] = anumbers_i[i];
for (int i=0;i<natoms;i++)
anames[i] = anames_i[i];
for (int i=0;i<3*natoms;i++)
xyz[i] = xyz_i[i];
for (int i=0;i<natoms;i++)
q[i] = 0.;
return;
}
void NBO::reset(int natoms_i, int* anumbers_i, string* anames_i, double* xyz_i)
{
hasNBO = 0;
natoms = natoms_i;
bmo = 0;
for (int i=0;i<natoms;i++)
anumbers[i] = anumbers_i[i];
for (int i=0;i<natoms;i++)
anames[i] = anames_i[i];
for (int i=0;i<3*natoms;i++)
xyz[i] = xyz_i[i];
for (int i=0;i<natoms;i++)
q[i] = 0.;
return;
}
void NBO::freemem()
{
hasNBO = 0;
natoms = 0;
bmo = 0;
delete [] xyz;
delete [] anumbers;
delete [] anames;
delete [] q;
if (MO!=NULL)
delete [] MO;
if (mo_occ!=NULL)
delete [] mo_occ;
if (bmo_occ!=NULL)
delete [] bmo_occ;
if (bmo_atoms!=NULL)
delete [] bmo_atoms;
if (bmo_polar!=NULL)
delete [] bmo_polar;
if (bmo_num!=NULL)
delete [] bmo_num;
if (vmo_occ!=NULL)
delete [] vmo_occ;
if (vmo_atoms!=NULL)
delete [] vmo_atoms;
if (vmo_num!=NULL)
delete [] vmo_num;
return;
}
int NBO::read_mopac_mo(string filename)
{
//printf(" reading MO from MOPAC file %s \n",filename.c_str());
ifstream infile;
infile.open(filename.c_str());
if (!infile){
printf(" error opening MO file (MOPAC type): %s \n",filename.c_str());
//exit(-1);
return 0;
}
//build basis set
nao = 0;
mheadersize = 4 + natoms;
for (int i=0;i<natoms;i++)
{
if (anumbers[i]==1)
{
nao += 1;
mheadersize += 6;
}
else if (anumbers[i] > 1 && anumbers[i]<=10)
{
nao += 4;
mheadersize += 6;
}
else
{
printf(" NBO: later row elements not supported yet! \n");
exit(1);
}
}
mheader = new string[mheadersize];
mheader[0] = "[Molden Format]";
mheader[1] = "[Atoms] (Angs)";
char* str = new char[250];
for (int i=0;i<natoms;i++)
{
sprintf(str," %2s %2i %2i %8.5f %8.5f %8.5f ",anames[i].c_str(),i+1,anumbers[i],xyz[3*i+0],xyz[3*i+1],xyz[3*i+2]);
mheader[i+2] = str;
}
int mc = 2 + natoms;
mheader[mc++] = "[GTO]";
for (int i=0;i<natoms;i++)
{
sprintf(str," %2i 0",i+1);
mheader[mc++] = str;
if (anumbers[i]==1)
{
mheader[mc++] = "S 3 1.000000";
mheader[mc++] = " 3.42525091E+00 1.54328970E-01 ";
mheader[mc++] = " 6.23913730E-01 5.35328140E-01 ";
mheader[mc++] = " 1.68855400E-01 4.44634540E-01 ";
mheader[mc++] = " ";
}
else if (anumbers[i]==5)
{
mheader[mc++] = "SP 3 1.000000";
mheader[mc++] = " 2.23695610E+00 -9.99672300E-02 1.55916270E-01 ";
mheader[mc++] = " 5.19820500E-01 3.99512830E-01 6.07683720E-01 ";
mheader[mc++] = " 1.69061800E-01 7.00115470E-01 3.91957390E-01 ";
mheader[mc++] = " ";
}
else if (anumbers[i]==6)
{
// mheader[mc++] = "S 3 1.000000";
// mheader[mc++] = " 7.16168370E+01 1.54328970E-01 ";
// mheader[mc++] = " 1.30450960E+01 5.35328140E-01 ";
// mheader[mc++] = " 3.53051220E+00 4.44634540E-01 ";
mheader[mc++] = "SP 3 1.000000";
mheader[mc++] = " 2.94124940E+00 -9.99672300E-02 1.55916270E-01 ";
mheader[mc++] = " 6.83483100E-01 3.99512830E-01 6.07683720E-01 ";
mheader[mc++] = " 2.22289900E-01 7.00115470E-01 3.91957390E-01 ";
mheader[mc++] = " ";
}
else if (anumbers[i]==7)
{
// mheader[mc++] = "S 3 1.000000";
// mheader[mc++] = " 9.91061690E+01 1.54328970E-01 ";
// mheader[mc++] = " 1.80523120E+01 5.35328140E-01 ";
// mheader[mc++] = " 4.88566020E+00 4.44634540E-01 ";
mheader[mc++] = "SP 3 1.000000";
mheader[mc++] = " 3.78045590E+00 -9.99672300E-02 1.55916270E-01 ";
mheader[mc++] = " 8.78496600E-01 3.99512830E-01 6.07683720E-01 ";
mheader[mc++] = " 2.85714400E-01 7.00115470E-01 3.91957390E-01 ";
mheader[mc++] = " ";
}
else if (anumbers[i]==8)
{
mheader[mc++] = "SP 3 1.000000";
mheader[mc++] = " 5.03315130E+00 -9.99672300E-02 1.55916270E-01 ";
mheader[mc++] = " 1.16959610E+00 3.99512830E-01 6.07683720E-01 ";
mheader[mc++] = " 3.80389000E-01 7.00115470E-01 3.91957390E-01 ";
mheader[mc++] = " ";
}
else if (anumbers[i]==9)
{
mheader[mc++] = "SP 3 1.000000";
mheader[mc++] = " 6.46480320E+00 -9.99672300E-02 1.55916270E-01 ";
mheader[mc++] = " 1.50228120E+00 3.99512830E-01 6.07683720E-01 ";
mheader[mc++] = " 4.88588500E-01 7.00115470E-01 3.91957390E-01 ";
mheader[mc++] = " ";
}
else
{
printf(" element # %i not implemented! \n",anumbers[i]);
exit(1);
}
}
mheader[mc++] = "[MO]";
string line;
bool success=true;
vector<string> tok_line;
//allocate for all NBO and MO data
alloc_nbo();
MO = new double[nao*nao];
for (int i=0;i<nao*nao;i++) MO[i] = 0.;
//get MO's
int found1 = 0;
int cao = 0;
int offset = 0;
while(!infile.eof())
{
success = (bool)getline(infile,line);
if (line.find("NO. OF FILLED LEVELS")!=string::npos)
{
tok_line = StringTools::tokenize(line, " \t");
nalpha = atoi(tok_line[5].c_str());
nbeta = nalpha;
nelec = nalpha + nbeta;
}
if (line.find("LOCALIZED ORBITALS")!=string::npos)
{
//cout << " RR: " << line << endl;
found1 = 1;
}
if (found1)
if (line.find("ROOT NO")!=string::npos)
{
// printf(" found ROOT NO, cao: %2i \n",cao);
//cout << " RR1: " << line << endl;
success = (bool)getline(infile,line);
//cout << " RR2: " << line << endl;
success = (bool)getline(infile,line);
//cout << " RR3: " << line << endl;
tok_line = StringTools::tokenize(line, " \t");
//this line is orbital energies
int nnew = tok_line.size();
//tok_line = StringTools::tokenize(line, " \t");
//printf(" about to write mo_occ. nnew: %2i offset: %2i \n",nnew,offset); fflush(stdout);
for (int i=0;i<nnew;i++)
mo_occ[offset+i] = atof(tok_line[i].c_str());
success = (bool)getline(infile,line);
//cout << " RR4: " << line << endl;
success = (bool)getline(infile,line);
//cout << " RR5: " << line << endl;
//starting here, MO coefs
for (int i=0;i<natoms;i++)
{
success = (bool)getline(infile,line);
//cout << " RRat: " << line << endl;
tok_line = StringTools::tokenize(line, " \t");
nnew = tok_line.size() - 3;
if (tok_line[1]=="H")
{
// printf(" found H \n");
// printf(" offset: %2i cao: %2i nnew: %2i \n",offset,cao,nnew);
tok_line = StringTools::tokenize(line, " \t");
for (int j=0;j<nnew;j++)
MO[(offset+j)*nao+cao] = atof(tok_line[3+j].c_str());
cao += 1;
success = (bool)getline(infile,line);
}
else if (tok_line[1]=="B" || tok_line[1]=="C" || tok_line[1]=="N" || tok_line[1]=="O" || tok_line[1]=="F")
{
// printf(" found C \n");
// printf(" C offset: %2i cao: %2i nnew: %2i \n",offset,cao,nnew);
for (int n=0;n<4;n++)
{
tok_line = StringTools::tokenize(line, " \t");
for (int j=0;j<nnew;j++)
MO[(offset+j)*nao+cao] = atof(tok_line[3+j].c_str());
cao += 1;
success = (bool)getline(infile,line);
}
}
}
cao = 0;
offset += 6;
} //if "ROOT NO" && found1
}
infile.close();
nmo = nao;
delete [] str;
#if 0
printf(" printing MO coeff matrix (%2i mo's %2i ao's) \n",nmo,nao);
for (int i=0;i<nmo;i++)
{
for (int j=0;j<nao;j++)
printf(" %8.5f",MO[i*nao+j]);
printf("\n");
}
#endif
//now get other NBO data
infile.open(filename.c_str());
int cmo = 0;
int nhp = 0;
while (!infile.eof())
{
success = (bool)getline(infile,line);
if (line.find("NET ATOMIC CHARGES")!=string::npos)
{
success = (bool)getline(infile,line);
success = (bool)getline(infile,line);
for (int i=0;i<natoms;i++)
{
success = (bool)getline(infile,line);
// cout << " RR1: " << line << endl;
tok_line = StringTools::tokenize(line, " \t");
q[i] = atof(tok_line[2].c_str());
double s1 = atof(tok_line[4].c_str());
if (fabs(s1)<0.01) s1 = 0.01;
double s2 = 0.;
if (tok_line.size()>5)
s2 = atof(tok_line[5].c_str());
spratio[i] = s2/s1;
//printf(" spratio[%2i]: %8.5f \n",i+1,spratio[i]);
}
}
if (line.find("NUMBER OF CENTERS")!=string::npos)
{
success = (bool)getline(infile,line);
success = (bool)getline(infile,line);
while (!infile.eof())
{
success = (bool)getline(infile,line);
tok_line = StringTools::tokenize(line, " \t");
int lsize = tok_line.size();
if (lsize>0)
{
if (line.find("LOCALIZED ORBITALS")!=string::npos)
break;
bmo_occ[cmo] = atof(tok_line[0].c_str());
if (lsize==3 && bmo_occ[cmo]>100.) //was bmo_occ[cmo] == 1.0, handling bad mopac printing
{
tok_line = StringTools::tokenize(line, " .");
bmo_atoms[2*cmo+0] = atoi(tok_line[2].c_str())/1000;
bmo_polar[cmo] = -1.0;
bmo_num[cmo] = cmo+1;
//printf(" bmo_num: %i (cmo: %i) \n",bmo_num[cmo],cmo);
//if (abs(bmo_num[bmo])>100) printf(" WARNING: bad bmo_num: %i \n",bmo_num[cmo]);
cmo++;
}
else if (lsize==4)
{
// cout << " RR1: " << line << endl;
bmo_atoms[2*cmo+0] = atoi(tok_line[2].c_str());
bmo_polar[cmo] = -1.0;
bmo_num[cmo] = cmo+1;
//printf(" bmo_num: %i (cmo: %i) \n",bmo_num[cmo],cmo);
//if (abs(bmo_num[bmo])>100) printf(" WARNING: bad bmo_num: %i \n",bmo_num[cmo]);
cmo++;
}
else if (lsize==7)
{
bmo_atoms[2*cmo+0] = atoi(tok_line[2].c_str());
bmo_atoms[2*cmo+1] = atoi(tok_line[5].c_str());
double pl = atof(tok_line[3].c_str()) - atof(tok_line[6].c_str());
bmo_polar[cmo] = -pl/100.;
bmo_num[cmo] = cmo+1;
//printf(" bmo_num: %i (cmo: %i) \n",bmo_num[cmo],cmo);
//if (abs(bmo_num[cmo])>100) printf(" WARNING: bad bmo_num: %i \n",bmo_num[cmo]);
#if 0
//for now, leave in highly polarized cases
if (fabs(pl)>95.)
{
//printf(" highly polarized bond: %2i - %2i \n",bmo_atoms[2*cmo+0],bmo_atoms[2*cmo+1]);
bmo_atoms[2*cmo+1] = 0;
nhp++;
}
#endif
cmo++;
}
else if (lsize>9)
{
get_three_center(cmo,tok_line);
}
} //if line contains data
} //while reading
} //found localized orbital data
} //while reading
//printf(" found %2i highly polarized bonds \n",nhp);
bmo = cmo;
return 1;
}
void NBO::get_three_center(int& cmo, vector<string> tok_line)
{
double wb3 = atof(tok_line[9].c_str());
//third contributor is small
if (wb3<10.)
{
bmo_atoms[2*cmo+0] = atoi(tok_line[2].c_str());
bmo_atoms[2*cmo+1] = atoi(tok_line[5].c_str());
double pl = atof(tok_line[3].c_str()) - atof(tok_line[6].c_str());
bmo_polar[cmo] = -pl/100.;
bmo_num[cmo] = cmo+1;
cmo++;
return;
}
else
{
int b1,b2,b3;
b1 = atoi(tok_line[2].c_str());
b2 = atoi(tok_line[5].c_str());
b3 = atoi(tok_line[8].c_str());
double p1a = atof(tok_line[3].c_str());
double p2a = atof(tok_line[6].c_str());
double p3a = atof(tok_line[9].c_str());
double pl1 = p1a - p2a;
double pl2 = p2a - p3a;
//put H in the middle
if (anumbers[b2-1]!=1)
{
int t1 = b2;
if (anumbers[b1-1]==1)
{
b2 = b1;
b1 = t1;
pl1 = p2a - p1a;
pl2 = p1a - p3a;
}
if (anumbers[b3-1]==1)
{
b2 = b3;
b3 = t1;
pl1 = p1a - p3a;
pl2 = p3a - p2a;
}
}
bmo_atoms[2*cmo+0] = b1;
bmo_atoms[2*cmo+1] = b2;
bmo_num[cmo] = cmo+1;
bmo_polar[cmo] = -pl1/100.;
cmo++;
bmo_atoms[2*cmo+0] = b2;
bmo_atoms[2*cmo+1] = b3;
bmo_num[cmo] = cmo+1;
bmo_polar[cmo] = -pl2/100.;
cmo++;
}
return;
}
int NBO::read_mo(string filename)
{
printf(" reading MO from Molden file %s. ",filename.c_str());
ifstream infile;
infile.open(filename.c_str());
if (!infile){
printf(" error opening MO file (Molden formatted): %s \n",filename.c_str());
return 0;
}
#if ISOMER_DB || 1
alloc_nbo();
printf(" read_mo not working right now, not using \n");
return 1;
#endif
string line;
bool success=true;
vector<string> tok_line;
int MAX_BASIS = 25 * natoms;
wAO = new int[MAX_BASIS];
tAO = new int[MAX_BASIS];
int w = 0;
nao = 0;
//save header information
int mcounting = 0;
mheadersize = 0;
while(!infile.eof())
{
success = (bool)getline(infile,line);
if (line.find("[MO]")!=string::npos)
break;
if (mcounting)
mheadersize++;
if (line.find("[Molden Format]")!=string::npos)
mcounting = 1;
}
infile.close();
int mc = 0;
mcounting = 0;
mheader = new string[mheadersize+2];
infile.open(filename.c_str());
while(!infile.eof())
{
success = (bool)getline(infile,line);
if (line.find("[Molden Format]")!=string::npos)
mcounting = 1;
if (mcounting)
mheader[mc++] = line;
if (mc>=mheadersize) break;
}
mheader[mc++] = " ";
mheader[mc++] = "[MO]";
mheadersize += 2;
infile.close();
//get basis and MO data
infile.open(filename.c_str());
while(!infile.eof())
{
success = (bool)getline(infile,line);
if (line.find("[GTO]")!=string::npos)
{
// cout << " RR00: " << line << endl;
while(line.find("[MO]")==string::npos)
{
success = (bool)getline(infile,line);
// cout << " RR0: " << line << endl;
tok_line = StringTools::tokenize(line, " \t");
if (tok_line.size()>1)
{
int isAO = atoi(tok_line[1].c_str());
if (isAO==0)
{
int cont = 1;
while(cont)
{
success = (bool)getline(infile,line);
tok_line = StringTools::tokenize(line, " \t");
//cout << " RR0: " << line << endl;
if (line.find("S")!=string::npos)
{
tAO[nao] = 0;
wAO[nao++] = w;
}
if (line.find("P")!=string::npos)
{
for (int i=0;i<3;i++)
{
tAO[nao] = 1;
wAO[nao++] = w;
}
}
if (line.find("D")!=string::npos) //spd only
{
for (int i=0;i<6;i++) //hardcoded: 6D functions
{
tAO[nao] = 2;
wAO[nao++] = w;
}
}
if (tok_line.size()<1)
break;
}
w++;
}
}
} //Reading AO basis
if (nao>MAX_BASIS)
{
printf(" nao exceeds MAX_BASIS in nbo.cpp! nao: %3i MAX_BASIS: %3i \n",nao,MAX_BASIS);
exit(1);
}
break;
}
}
for (int i=0;i<4;i++)
success = (bool)getline(infile,line);
printf(" found %i ao's (with 3p 5d etc) \n",nao);
double* jMO1 = new double[MAX_BASIS]; //Note max basis limit
int dim = 0;
while (!infile.eof())
{
success = (bool)getline(infile,line);
if (line.find("Sym")!=string::npos)