void colorTest()
{
ofColor rgb1 = ofColor::fromHex(0xe20bca);
ofColor rgb2 = ofColor::fromHex(0x17bb04);
ColorXYZ xyz1(rgb1);
ColorXYZ xyz2(rgb2);
for (int i = 0; i < 1024; ++i)
{
float f = i / 1024.0f;
ofColor tmp(rgb1);
ofSetColor(tmp.lerp(rgb2, f));
ofRect(i, 0, i + 1, 384);
ofSetColor(xyz1.lerp(xyz2, f).getRgb());
ofRect(i, 384, i + 1, 768);
}
}
void Nodes_method::run(Program_options & options, ostream & output)
{
ofstream os; //for writing to *.plt files
string pltfile; //name of plotfile being written
string confile; //name of configuration of electrons to be being written
double max_value,min_value;
int count;
Array1 <doublevar> xyz(3), xyz2(3),
resolution_array(3); //position of electron "in" MO
Array1 <int> D_array1(3); //dummy array1
Array2 <doublevar> oldpos(mywalker->electronSize(),3);
Array1 <doublevar> tmp(3);
D_array1=0; //sets all 3 components to 0. use as counter for gridpoints
D_array1(0)=roundoff((minmax(1)-minmax(0))/resolution);
D_array1(1)=roundoff((minmax(3)-minmax(2))/resolution);
D_array1(2)=roundoff((minmax(5)-minmax(4))/resolution);
resolution_array(0)=(minmax(1)-minmax(0))/(D_array1(0)-1);
resolution_array(1)=(minmax(3)-minmax(2))/(D_array1(1)-1);
resolution_array(2)=(minmax(5)-minmax(4))/(D_array1(2)-1);
Array2 <doublevar> grid(plots.GetSize(),D_array1(0)*D_array1(1)*D_array1(2));
Wf_return wfvals(wf->nfunc(), 2); //where wfval fist index labels
//wf number ie. ground state
// excited state and so on, and second label is for two values, sign and log(wf).
//scan electron positions
cout << "Using these electron positions:"<<endl;
for(int i=0; i<mywalker->electronSize(); i++){
mywalker->getElectronPos(i, tmp);
cout.precision(5);
cout.width(8);
cout <<i+1<<" "<<tmp(0)<<" "<<tmp(1)<<" "<<tmp(2)<<endl;
for (int d=0;d<3;d++)
oldpos(i,d)=tmp(d);
// cout << "pos " << oldpos(i,0) << " " << oldpos(i,1) << " " << oldpos(i,2)
// << endl;
}
//generate .xyz file for gOpenMol to view coordinates
pltfile=options.runid + ".xyz";
os.open(pltfile.c_str());
cout<<"writing to "<<pltfile<<endl;
vector <string> atomlabels;
sysprop->getAtomicLabels(atomlabels);
os<<atomlabels.size()+mywalker->electronSize()<<endl;
os<<endl;
int spin_up=sysprop->nelectrons(0);
//cout << "Up electrons "<<spin_up<<endl;
for(unsigned int i=0; i<atomlabels.size(); i++){
Array1 <doublevar> pos(3);
mywalker->getIonPos(i, pos);
os<<atomlabels[i] <<" "<< pos(0)
<<" "<<pos(1)
<<" "<< pos(2)<<endl;
}
for(int j=0; j<mywalker->electronSize(); j++){
if (j<spin_up) os<<"Eu";
else os<<"Ed";
// mywalker->getElectronPos(j, pos);
os<<" "<< oldpos(j,0)<<" "<<oldpos(j,1) <<" "<< oldpos(j,2)<<endl;
}
os.close();
if (!doublemove) {
//calculate value of each molecular orbital at each grid point and store in an Array1
// grid values with x=fastest running variable, and z=slowest
cout<<"calculating "<<D_array1(0)*D_array1(1)*D_array1(2)
<<" grid points"<<endl;
cout<<"for "<< plots.GetDim(0) <<" 3D projections of wavefunction"<<endl;
count=0;
xyz(0)=minmax(0);
xyz(1)=minmax(2);
xyz(2)=minmax(4); //init elec probe to xmin ymin zmin
//Array1 <doublevar> oldpos(3)
for(int i=0; i<plots.GetSize(); i++){
cout.width(3);
cout <<"============================="<<plots(i)
<<"=============================="
<<endl;
count=0;
for(int xx=0; xx<D_array1(0);xx++){
xyz(0)=minmax(0)+xx*resolution_array(0); //move forward on x axis one resolution unit
max_value=min_value=0.0;
cout << "x ";
cout.precision(5);
cout.width(8);
cout<< xyz(0);
for(int yy=0; yy<D_array1(1);yy++){
xyz(1)=minmax(2)+yy*resolution_array(1); //move forward on y axis one resolution unit
for(int zz=0;zz<D_array1(2);zz++){
xyz(2)=minmax(4)+zz*resolution_array(2); //move forward on z axis one resolution unit
// mywalker->getElectronPos(plots(i), oldpos);
mywalker->setElectronPos(plots(i)-1,xyz); //move elec#plots(i) to point specified by xyz
wf->updateVal(wfdata, mywalker); //update wfdata
wf->getVal(wfdata, 0, wfvals); //get wf value
const doublevar cutoff=15;
if(wfvals.amp(0,0)<cutoff) {
grid(i,count)=wfvals.sign(0)*exp(wfvals.amp(0,0));
}
else { //cut off the maximum value output so that there aren't overflow errors
grid(i,count)=wfvals.sign(0)*exp(cutoff);
}
//grid(i,count)=exp(2.0*wfvals(0,1));//!square of wavefunction
if (grid(i,count)>max_value) max_value=grid(i,count);
if (grid(i,count)<min_value) min_value=grid(i,count);
// cout << "grid " << grid(i,count)<< " " << xyz(0) << endl;
count++; //index for cycling through grid points
}
}
cout.setf(ios::scientific| ios:: showpos);
cout <<", max. value "<<max_value<<", min. value "<<min_value<< endl;
cout.unsetf(ios::scientific| ios:: showpos);
}
mywalker->setElectronPos(plots(i)-1, oldpos(plots(i)-1));
}
//Loop through and generate plot files for each orbital requested
if(plots.GetSize()<=0)
error("Number of requested plots is not a positive number");
cout<<"saving data for "<<plots.GetSize()<<" 3D projections of wavefunction"<<endl;
for(int i=0; i<plots.GetSize(); i++)
{
//output to file with orbital number in it
char strbuff[40];
sprintf(strbuff, "%d", plots(i));
confile=pltfile = options.runid;
confile += ".orb.";
pltfile += ".orb.";
pltfile += strbuff;
confile += strbuff;
pltfile += ".cube"; /*FIGURE OUT HOW TO CONVERT INT TO STRING*/
confile += ".xyz";
os.open(pltfile.c_str());
cout<<"writing to "<<pltfile<<endl;
os << "QWalk nodes output\n";
os << "Wavefunction single scan with " << plots(i) <<" electron"<<endl;
int natoms=sysprop->nIons();
os << " " << natoms+ mywalker->electronSize()-1 << " " << minmax(0) << " "
<< minmax(2) << " " << minmax(4) << endl;
os << D_array1(0) << " " << resolution_array(0) << " 0.0000 0.0000" << endl;
os << D_array1(1) << " 0.0000 " << resolution_array(1) << " 0.0000" << endl;
os << D_array1(2) << " 0.0000 0.0000 " << resolution_array(2) << endl;
Array1 <doublevar> pos(3);
for(int at=0; at< natoms; at++) {
mywalker->getIonPos(at,pos);
os << " " << mywalker->getIonCharge(at) << " 0.0000 " << pos(0)
<<" " << pos(1) << " " << pos(2) << endl;
}
for(int j=0; j<mywalker->electronSize(); j++){
if (j!=plots(i)-1){
if (j<spin_up) os<<" 3 0.0000 ";
else os<<" 3 0.0000 ";
os<< oldpos(j,0)<<" "<<oldpos(j,1)<<" "<< oldpos(j,2)<<endl;
}
}
os.setf(ios::scientific);
for(int j=0; j< D_array1(0)*D_array1(1)*D_array1(2); j++) {
os <<setw(16)<<setprecision(8)<<grid(i,j);
if(j%6 ==5) os << endl;
}
os << endl;
os.unsetf(ios::scientific);
os<<setprecision(6);
os.close();
/*
old plt file plots
// http://www.csc.fi/gopenmol/developers/plt_format.phtml
os<<"3 "; //rank=3 always
os<<"2\n"; //dummy variable => "Orbital/density surface"
//number of grid points for x, y, & z direction
os <<D_array1(2)<<" "<<D_array1(1)<<" "<<D_array1(0)<<endl;
os <<minmax(4)<<" "<<minmax(5)<<" "<<minmax(2)<<" "<<minmax(3)
<<" "<<minmax(0)<<" "<<minmax(1)<<endl;
for(int j=0; j<(D_array1(0)*D_array1(1)*D_array1(2)); j++)
os<<grid(i,j)<<endl;
os.close();
os.open(confile.c_str());
cout<<"writing to "<<confile<<endl;
Array1 <doublevar> pos(3);
sysprop->getAtomicLabels(atomlabels);
os<<atomlabels.size()+ mywalker->electronSize()-1 <<endl;
os << endl;
for(unsigned int j=0; j<atomlabels.size();j++){
mywalker->getIonPos(j, pos);
os<<atomlabels[j] <<" "<< pos(0)
<<" "<<pos(1)
<<" "<< pos(2)<<endl;
}
for(int j=0; j<mywalker->electronSize(); j++){
if (j!=plots(i)-1){
if (j<spin_up) os<<"Eu";
else os<<"Ed";
// mywalker->getElectronPos(j, pos);
os<<" "<< oldpos(j,0)<<" "<<oldpos(j,1)
<<" "<< oldpos(j,2)<<endl;
}
}
os.close();
*/
}
}
else {
cout << "Using translation vector(s): "<<endl;
for(int i=0;i<dxyz.GetDim(0);i++)
cout<<"( "<<dxyz(i,0)<<" , "<<dxyz(i,1)<<" , "<<dxyz(i,2)<<" )"<<endl;
for(int i=0; i<plots.GetSize(); i=i+2){
count=0;
xyz(0)=minmax(0);
xyz(1)=minmax(2);
xyz(2)=minmax(4); //init elec probe to xmin ymin zmin
//Array1 <doublevar> oldpos(3)
cout.width(3);
cout <<"============================="<<plots(i)<<" and "<<plots(i+1)
<<"=============================="
<<endl;
for(int xx=0; xx<D_array1(0);xx++){
max_value=min_value=0.0;
xyz(0)=minmax(0)+xx*resolution_array(0);
xyz2(0)=xyz(0)+dxyz(i/2,0);
cout << "x ";
cout.precision(5);
cout.width(8);
cout<< xyz(0);
for(int yy=0; yy<D_array1(1);yy++){
xyz(1)=minmax(2)+yy*resolution_array(1);
xyz2(1)=xyz(1)+dxyz(i/2,1);
for(int zz=0;zz<D_array1(2);zz++){
xyz(2)=minmax(4)+zz*resolution_array(2);
xyz2(2)=xyz(2)+dxyz(i/2,2);
// mywalker->getElectronPos(plots(i), oldpos);
mywalker->setElectronPos(plots(i)-1,xyz);//move elec#plots(i)
//to point specified by xyz
mywalker->setElectronPos(plots(i+1)-1,xyz2);//move elec#plots(i)
//to point specified by xyz
wf->updateVal(wfdata, mywalker); //update wfdata
wf->getVal(wfdata, 0, wfvals); //get wf value
grid(i,count)=wfvals.sign(0)*exp(wfvals.amp(0,0));
//grid(i,count)=exp(2.0*wfvals(0,1));//!square of wavefunction
// cout << "grid " << grid(i,count)<< " " << xyz(0) << endl;
if (grid(i,count)>max_value) max_value=grid(i,count);
if (grid(i,count)<min_value) min_value=grid(i,count);
count++; //index for cycling through grid points
}
}
cout.setf(ios::scientific| ios:: showpos);
cout <<", max. value "<<max_value<<", min. value "<<min_value<< endl;
cout.unsetf(ios::scientific| ios:: showpos);
}
mywalker->setElectronPos(plots(i)-1, oldpos(plots(i)-1));
mywalker->setElectronPos(plots(i+1)-1, oldpos(plots(i+1)-1));
}
//Loop through and generate plot files for each orbital requested
if(plots.GetSize()<=0)
error("Number of requested plots is not a positive number");
cout<<"saving data for "<<plots.GetSize()<<" 3D projections of wavefunction"<<endl;
for(int i=0; i<plots.GetSize(); i=i+2)
{
char strbuff2[40],strbuff[40];
//output to file with orbital number in it
sprintf(strbuff, "%d", plots(i));
sprintf(strbuff2, "%d", plots(i+1));
confile=pltfile = options.runid;
confile += ".orb.";
pltfile += ".orb.";
pltfile += strbuff;
confile += strbuff;
pltfile += "with";
confile += "with";
pltfile += strbuff2;
confile += strbuff2;
pltfile += ".cube"; /*FIGURE OUT HOW TO CONVERT INT TO STRING*/
confile += ".xyz";
os.open(pltfile.c_str());
cout<<"writing to "<<pltfile<<endl;
os << "GOS nodes output\n";
os << "Wave function double scan with "<< plots(i) <<" & "<<plots(i+1)<<" electrons"<< endl;
int natoms=sysprop->nIons();
os << " " << natoms + mywalker->electronSize()-2 << " " << minmax(0) << " "
<< minmax(2) << " " << minmax(4) << endl;
os << D_array1(0) << " " << resolution_array(0) << " 0.0000 0.0000" << endl;
os << D_array1(1) << " 0.0000 " << resolution_array(1) << " 0.0000" << endl;
os << D_array1(2) << " 0.0000 0.0000 " << resolution_array(2) << endl;
Array1 <doublevar> pos(3);
for(int at=0; at< natoms; at++) {
mywalker->getIonPos(at,pos);
os << " " << mywalker->getIonCharge(at) << " 0.0000 " << pos(0)
<<" " << pos(1) << " " << pos(2) << endl;
}
for(int j=0; j<mywalker->electronSize(); j++){
if ((j!=plots(i)-1)&&(j!=plots(i+1)-1)){
if (j<spin_up) os<<" 3 0.0000 ";
else os<<" 3 0.0000 ";
os<< oldpos(j,0)<<" "<<oldpos(j,1)<<" "<< oldpos(j,2)<<endl;
}
}
os.setf(ios::scientific);
for(int j=0; j< D_array1(0)*D_array1(1)*D_array1(2); j++) {
os << setw(16) << setprecision(8) << grid(i,j);
if(j%6 ==5) os << endl;
}
os << endl;
os.unsetf(ios::scientific);
os<<setprecision(6);
os.close();
/*
old plot to plt file version
// http://www.csc.fi/gopenmol/developers/plt_format.phtml
os<<"3 "; //rank=3 always
os<<"2\n"; //dummy variable => "Orbital/density surface"
//number of grid points for x, y, & z direction
os <<D_array1(2)<<" "<<D_array1(1)<<" "<<D_array1(0)<<endl;
os <<minmax(4)<<" "<<minmax(5)<<" "<<minmax(2)<<" "<<minmax(3)
<<" "<<minmax(0)<<" "<<minmax(1)<<endl;
for(int j=0; j<(D_array1(0)*D_array1(1)*D_array1(2)); j++)
os<<grid(i,j)<<endl;
os.close();
os.open(confile.c_str());
cout<<"writing to "<<confile<<endl;
Array1 <doublevar> pos(3);
sysprop->getAtomicLabels(atomlabels);
os<<atomlabels.size()+ mywalker->electronSize()-2 <<endl;
os << endl;
for(unsigned int j=0; j<atomlabels.size();j++){
mywalker->getIonPos(j, pos);
os<<atomlabels[j] <<" "<< pos(0)
<<" "<<pos(1)
<<" "<< pos(2)<<endl;
}
for(int j=0; j<mywalker->electronSize(); j++){
if ((j!=plots(i)-1)&&(j!=plots(i+1)-1)){
if (j<spin_up) os<<"Eu";
else os<<"Ed";
// mywalker->getElectronPos(j, pos);
os<<" "<< oldpos(j,0)<<" "<<oldpos(j,1)
<<" "<< oldpos(j,2)<<endl;
}
}
os.close();
*/
}
}
cout <<"End of Nodes Method"<<endl;
}
