void Molecular_system::calcLocWithTestPos(Sample_point * sample,
Array1 <doublevar> & tpos,
Array1 <doublevar> & Vtest) {
int nions=sample->ionSize();
int nelectrons=sample->electronSize();
Vtest.Resize(nelectrons + 1);
Vtest = 0;
Array1 <doublevar> oldpos(3);
//cout << "Calculating local energy\n";
sample->getElectronPos(0, oldpos);
sample->setElectronPosNoNotify(0, tpos);
Array1 <doublevar> R(5);
sample->updateEIDist();
sample->updateEEDist();
for(int i=0; i < nions; i++) {
sample->getEIDist(0, i, R);
Vtest(nelectrons)+=-sample->getIonCharge(i)/R(0);
}
doublevar dist = 0.0;
for(int d=0; d<3; d++) {
dist += (oldpos(d) - tpos(d))*(oldpos(d) - tpos(d));
}
dist = sqrt(dist);
Vtest(0) = 1/dist;
Array1 <doublevar> R2(5);
for(int i=1; i< nelectrons; i++) {
sample->getEEDist(0,i,R2);
Vtest(i)= 1/R2(0);
}
sample->setElectronPosNoNotify(0, oldpos);
sample->updateEIDist();
sample->updateEEDist();
//cout << "elec-elec: " << elecElec << endl;
//cout << "pot " << pot << endl;
for(int d=0; d< 3; d++)
Vtest(nelectrons) -=electric_field(d)*tpos(d);
}
void wxWindowDFB::DoMoveWindow(int x, int y, int width, int height)
{
// NB: [x,y] arguments are in (parent's) window coordinates, while
// m_rect.{x,y} are in (parent's) client coordinates. That's why we
// offset by parentOrigin in some places below
wxPoint parentOrigin(0, 0);
AdjustForParentClientOrigin(parentOrigin.x, parentOrigin.y);
wxRect oldpos(m_rect);
oldpos.Offset(parentOrigin);
wxRect newpos(x, y, width, height);
// input [x,y] is in window coords, but we store client coords in m_rect:
m_rect = newpos;
m_rect.Offset(-parentOrigin);
// window's position+size changed and so did the subsurface that covers it
InvalidateDfbSurface();
if ( IsShown() )
{
// queue both former and new position of the window for repainting:
wxWindow *parent = GetParent();
// only refresh the visible parts:
if ( !CanBeOutsideClientArea() )
{
wxRect parentClient(parent->GetClientSize());
oldpos.Intersect(parentClient);
newpos.Intersect(parentClient);
}
parent->RefreshRect(oldpos);
parent->RefreshRect(newpos);
}
}
// Do the actual move
int psLinearMovement::MoveV (float delta)
{
if (velBody < SMALL_EPSILON && velWorld < SMALL_EPSILON && (!colldet || colldet->IsOnGround ()))
return PS_MOVE_DONTMOVE; // didn't move anywhere
int ret = PS_MOVE_SUCCEED;
iMovable* movable = mesh->GetMovable ();
if (movable->GetSectors ()->GetCount () <= 0)
return PS_MOVE_DONTMOVE; // didn't move anywhere
csMatrix3 mat;
// To test collision detection we use absolute position and transformation
// (this is relevant if we are anchored). Later on we will correct that.
csReversibleTransform fulltransf = movable->GetFullTransform ();
mat = fulltransf.GetT2O ();
csVector3 worldVel (fulltransf.This2OtherRelative (velBody) + velWorld);
csVector3 oldpos (fulltransf.GetOrigin ());
csVector3 newpos (worldVel*delta + oldpos);
csVector3 bufpos = newpos;
float dist = (newpos - oldpos).Norm ();
// @@@ Magodra: In some cases the newpos seams to be invalid. Not sure about
// the reason, but the FollowSegment function will not work later
// in this function. So check for that condidtion, give warning,
// and halt the movement.
if (CS::IsNaN(newpos.x) || CS::IsNaN(newpos.y) || CS::IsNaN(newpos.z))
{
printf("From old position %s ",toString(oldpos,movable->GetSectors()->Get(0)).GetDataSafe());
StackTrace("LinearMovement to a NAN position.");
return PS_MOVE_DONTMOVE; // didn't move anywhere
}
// Check for collisions and adjust position
if (colldet)
{
if (!colldet->AdjustForCollisions (oldpos, newpos, worldVel,
delta, movable))
{
ret = PS_MOVE_FAIL;
newpos = oldpos;
}
else
{
// check if we collided, did move less than 9/10 of the distance
if ((newpos - bufpos).Norm () > dist/10.0)
{
ret = PS_MOVE_PARTIAL;
}
}
}
csVector3 origNewpos = newpos;
bool mirror = false;
// Update position to account for portals
iSector* new_sector = movable->GetSectors ()->Get (0);
iSector* old_sector = new_sector;
// @@@ Jorrit: had to do this add!
// We need to measure slightly above the position of the actor or else
// we won't really cross a portal.
float height5 = (bottomSize.y + topSize.y) / 10.0f;
newpos.y += height5;
csMatrix3 id;
csOrthoTransform transform_oldpos (id, oldpos +
csVector3 (0.0f, height5, 0.0f));
new_sector = new_sector->FollowSegment (transform_oldpos, newpos, mirror,
PS_LINMOVE_FOLLOW_ONLY_PORTALS);
newpos.y -= height5;
if (new_sector != old_sector)
movable->SetSector (new_sector);
portalDisplaced += newpos - origNewpos;
if(!IsOnGround ())
{
//printf("Applying gravity: velY: %g.\n", velWorld.y);
// gravity! move down!
velWorld.y -= gravity * delta;
/*
* Terminal velocity
* ((120 miles/hour / 3600 second/hour) * 5280 feet/mile)
* / 3.28 feet/meter = 53.65 m/s
*/
// The body velocity is figured in here too.
if (velWorld.y < 0)
{
if (fulltransf.This2OtherRelative (velBody).y
+ velWorld.y < -(ABS_MAX_FREEFALL_VELOCITY))
velWorld.y = -(ABS_MAX_FREEFALL_VELOCITY)
- fulltransf.This2OtherRelative (velBody).y;
if (velWorld.y > 0)
{
// printf("Reset other y %g\n", fulltransf.This2OtherRelative (velBody).y);
velWorld.y = 0;
}
}
}
else
{
if(velWorld.y < 0)
{
velWorld.y = 0;
}
if (hugGround)
HugGround (newpos, new_sector);
}
// Move to the new position. If we have an anchor we have to convert
// the new position from absolute to relative.
movable->GetTransform ().SetOrigin (newpos);
movable->GetTransform ().SetT2O(
movable->GetTransform ().GetT2O () * transform_oldpos.GetT2O ());
if (colldet)
{
// Part 4: Add us to all nearby sectors.
mesh->PlaceMesh ();
}
movable->UpdateMove ();
return ret;
}
int psLinearMovement::MoveSprite (float delta)
{
int ret = PS_MOVE_SUCCEED;
csReversibleTransform fulltransf = mesh->GetMovable ()
->GetFullTransform ();
// const csMatrix3& transf = fulltransf.GetT2O ();
// Calculate the total velocity (body and world) in OBJECT space.
csVector3 bodyVel (fulltransf.Other2ThisRelative (velWorld) + velBody);
float local_max_interval =
csMin(csMin((bodyVel.y==0.0f) ? MAX_CD_INTERVAL : ABS (intervalSize.y/bodyVel.y),
(bodyVel.x==0.0f) ? MAX_CD_INTERVAL : ABS (intervalSize.x/bodyVel.x)
),(bodyVel.z==0.0f) ? MAX_CD_INTERVAL : ABS (intervalSize.z/bodyVel.z)
);
// Err on the side of safety (95% error margin)
local_max_interval *= 0.95f;
//printf("local_max_interval=%f, bodyVel is %1.2f, %1.2f, %1.2f\n",local_max_interval, bodyVel.x, bodyVel.y, bodyVel.z);
//printf("velWorld is %1.2f, %1.2f, %1.2f\n", velWorld.x, velWorld.y, velWorld.z);
//printf("velBody is %1.2f, %1.2f, %1.2f\n", velBody.x, velBody.y, velBody.z);
// Sanity check on time interval here. Something is messing it up. -KWF
//local_max_interval = csMax(local_max_interval, 0.1F);
if (colldet)
{
while (delta > local_max_interval)
{
csVector3 oldpos(mesh->GetMovable ()->GetFullTransform ().GetOrigin());
// Perform brutal optimisation here for falling with no obstacles
if(velWorld.y < -20.0f && mesh->GetMovable()->GetSectors()->GetCount() > 0)
{
csVector3 worldVel (fulltransf.This2OtherRelative (velBody) + velWorld);
bool hit = false;
// We check for other meshes at the start and end of the box with radius * 2 to be on the safe side
{
csRef<iMeshWrapperIterator> objectIter = engine->GetNearbyMeshes(mesh->GetMovable()->GetSectors()->Get(0),
oldpos + boundingBox.GetCenter(), boundingBox.GetSize().Norm() * 2);
if(objectIter->HasNext())
hit = true;
}
if(!hit)
{
csRef<iMeshWrapperIterator> objectIter = engine->GetNearbyMeshes(mesh->GetMovable()->GetSectors()->Get(0),
oldpos + worldVel * delta + boundingBox.GetCenter(), boundingBox.GetSize().Norm() * 2);
if(objectIter->HasNext())
hit = true;
}
if(!hit)
{
csOrthoTransform transform_newpos(csMatrix3(), oldpos + worldVel * delta);
csBox3 fullBox(fulltransf.This2OtherRelative(boundingBox.Min()), fulltransf.This2OtherRelative(boundingBox.Max()));
csBox3 newBox( transform_newpos.This2OtherRelative(boundingBox.Min()), transform_newpos.This2OtherRelative(boundingBox.Max()));
fullBox.AddBoundingBox(newBox);
csRef<iMeshWrapperIterator> objectIter = engine->GetNearbyMeshes(mesh->GetMovable()->GetSectors()->Get(0), fullBox);
if(objectIter->HasNext())
hit = true;
}
if(!hit)
local_max_interval = delta;
}
ret = MoveV (local_max_interval);
csVector3 displacement(fulltransf.GetOrigin() - oldpos);
displacement = fulltransf.Other2ThisRelative(displacement);
// Check the invariants still hold otherwise we may jump walls
if(!(fabs(displacement.x) <= intervalSize.x))
{
printf("X (%g) out of bounds when performing CD > %g!\n", fabs(displacement.x), intervalSize.x);
CS_ASSERT(false);
}
if(!(fabs(displacement.z) <= intervalSize.z))
{
printf("Z (%g) out of bounds when performing CD > %g!\n", fabs(displacement.y), intervalSize.y);
CS_ASSERT(false);
}
if(!(fabs(displacement.y) <= intervalSize.y))
{
printf("Y (%g) out of bounds when performing CD > %g!\n", fabs(displacement.z), intervalSize.z);
CS_ASSERT(false);
}
RotateV (local_max_interval);
// We must update the transform after every rotation!
fulltransf = mesh->GetMovable ()->GetFullTransform ();
if (ret == PS_MOVE_FAIL)
return ret;
// The velocity may have changed by now
bodyVel = fulltransf.Other2ThisRelative(velWorld) + velBody;
delta -= local_max_interval;
local_max_interval = csMin(csMin((bodyVel.y==0.0f)
? MAX_CD_INTERVAL
: ABS (intervalSize.y/bodyVel.y), (bodyVel.x==0.0f)
? MAX_CD_INTERVAL
: ABS (intervalSize.x/bodyVel.x)), (bodyVel.z==0.0f)
? MAX_CD_INTERVAL
: ABS (intervalSize.z/bodyVel.z));
// Err on the side of safety (95% error margin)
local_max_interval *= 0.95f;
// Sanity check on time interval here. Something is messing it up. -KWF
// local_max_interval = csMax(local_max_interval, 0.1F);
}
}
if (!colldet || delta)
{
ret = MoveV (delta);
RotateV(delta);
}
return ret;
}
void Average_ekt::evaluate_obdm(Wavefunction_data * wfdata, Wavefunction * wf,
System * sys, Sample_point * sample, Average_return & avg) {
wf->updateVal(wfdata,sample);
Wf_return wfval_base(wf->nfunc(),2);
wf->getVal(wfdata,0,wfval_base);
int nup=sys->nelectrons(0);
int ndown=sys->nelectrons(1);
int nelectrons=nup+ndown;
Array1 <Array2 <dcomplex> > movals1_base(nelectrons);
for(int e=0; e< nelectrons; e++) {
movals1_base(e).Resize(nmo,1);
calc_mos(sample,e,movals1_base(e));
/*! Huihuo
Here, permutation symmetry has been applied, the real evaluation quantity is
sum_(e=1)^N phi_i* (r_e) phi_j(r') psi(r_1,... r',...r_N)/psi(r_1, ..., r_n, ..., r_N)
Therefore, movals1_base[e, i] = phi_i(r_e), where e is the index of the electron.
!!!One need to be careful about the off-gamma point 1 RDM
*/
}
// avg.vals.Resize(nmo+4*nmo*nmo);
// avg.vals=0;
Array2 <dcomplex> movals1(nmo,1);
Array1 <Wf_return> wfs(nelectrons);
Wavefunction_storage * store;
wf->generateStorage(store);
for(int i=0; i< npoints_eval; i++) {
Array1 <doublevar> oldpos(3);
sample->getElectronPos(0,oldpos);
sample->setElectronPosNoNotify(0,saved_r(i));
calc_mos(sample,0,movals1);
/*!
This is simply to calculate phi_j(r'): Noted that r' has been given, therefore, movals1 is a one dimentional array, with matrix element to be
phi_j(r') -- j is the index
*/
sample->setElectronPosNoNotify(0,oldpos);
Array1 <Wf_return> wf_eval;
wf->evalTestPos(saved_r(i),sample,wfs);
//Testing the evalTestPos
//for(int e=0; e< nelectrons; e++) {
// Wf_return test_wf(wf->nfunc(),2);
// sample->getElectronPos(e,oldpos);
// wf->saveUpdate(sample,e,store);
// sample->setElectronPos(e,saved_r(i));
// wf->updateVal(wfdata,sample);
// wf->getVal(wfdata,e,test_wf);
// sample->setElectronPos(e,oldpos);
// wf->restoreUpdate(sample,e,store);
// cout << "e " << e << " test " << test_wf.amp(0,0) << " evalTestPos " << wfs(e).amp(0,0) << endl;
//}
doublevar dist1=0;
for(int m=0; m < nmo; m++)
dist1+=norm(movals1(m,0));
for(int orbnum=0; orbnum < nmo; orbnum++) {
avg.vals(orbnum)+=norm(movals1(orbnum,0))/(dist1*npoints_eval);
}
for(int e=0; e< nelectrons; e++) {
dcomplex psiratio_1b=exp(dcomplex(wfs(e).amp(0,0)-wfval_base.amp(0,0),
wfs(e).phase(0,0)-wfval_base.phase(0,0)));
/*!
psi(r_1,...,r',...,r_N)/psi(r_1,...,r_e,...,r_N), the ratio of the new with respect to the old if one change the position of the e-th electron from
r_e to r'
*/
int which_obdm=0;
if(e >= nup) { which_obdm=1; }
dcomplex tmp;
int place=0;
dcomplex prefactor=psiratio_1b/(dist1*npoints_eval);
for(int orbnum=0; orbnum < nmo; orbnum++) {
for(int orbnum2=0; orbnum2 < nmo; orbnum2++) {
//tmp=movals1(orbnum,0)*conj(movals1_base(e)(orbnum2,0))*prefactor;
/*! Huihuo Zheng
This is to based on my new definition:
\rho(r, r') = N\int dR psi*(r, R) psi(r', R) = \sum rho_{ij} phi_i*(r) phi_j(r')
in this way, one will find that, the phase factor is cancelled
*/
tmp=conj(movals1(orbnum,0))*movals1_base(e)(orbnum2,0)*prefactor;
avg.vals(nmo+2*which_obdm*nmo*nmo+place)+=tmp.real();
avg.vals(nmo+2*which_obdm*nmo*nmo+place+1)+=tmp.imag();
place+=2;
}
}
}
}
delete store;
}
void Average_ekt::evaluate_valence(Wavefunction_data * wfdata, Wavefunction * wf,
System * sys, Pseudopotential *psp, Sample_point * sample, Average_return & avg) {
/*
This is to evaluate the v_ij in extended Koopmans' theorem -- for valence bands
*/
wf->updateVal(wfdata,sample);
Wf_return wfval_base(wf->nfunc(),2);
wf->getVal(wfdata,0,wfval_base);
int nup=sys->nelectrons(0);
int ndown=sys->nelectrons(1);
int nelectrons=nup+ndown;
Array1 <doublevar> rn(3), rnp(3), rnpp(3);
Array1 <Array2 <dcomplex> > movals1_base(nelectrons);
Array2 <dcomplex> movals_p(nmo, 1);
Array1 <doublevar> VLoc(nelectrons);
Array1 <doublevar> VLoc0(nelectrons);
Array1 <doublevar> Vtest(nelectrons+1);
Array1 <dcomplex> pseudo_t(nmo);
/***************************************
Routines to get Kin and Vloc
****************************************/
Array2<doublevar> Kin(nelectrons, wf->nfunc());
//Array2<doublevar> Kin0(nelectrons, wf->nfunc());
Array2<dcomplex> movals_lap(nmo, 5);
for(int e=0; e< nelectrons; e++) {
movals1_base(e).Resize(nmo,1);
//Kin(e).Resize(1); //The Kinetic energy
calc_mos(sample, e, movals1_base(e));
}
// sys->calcKineticSeparated(sample,saved_r(i),Kin);
//***** calculate kinetic energy and potential energy
sys->calcKineticSeparated(wfdata, sample, wf, Kin);
sys->calcLocSeparated(sample, VLoc);
Array1 <Wf_return> wfs(nelectrons);
Wavefunction_storage * store;
wf->generateStorage(store);
for(int i=0; i< npoints_eval; i++) {
Array1 <doublevar> oldpos(3);
sample->getElectronPos(0,oldpos);
sample->setElectronPosNoNotify(0, saved_r(i));
calc_mosLap(sample, 0, movals_lap);
int nrandvar=psp->nTest();
Array1 <doublevar> rand_num(nrandvar);
for(int l=0; l< nrandvar; l++)
rand_num(l)=rng.ulec();
calc_mos(sample,0,movals_p);
calcPseudoMo(sys, sample, psp, rand_num, pseudo_t);
sample->setElectronPosNoNotify(0,oldpos);
Array1 <Wf_return> wf_eval;
wf->evalTestPos(saved_r(i),sample,wfs);
sys->calcLocWithTestPos(sample, saved_r(i), Vtest);
doublevar vtot = 0.0;
for (int e=0; e<nelectrons; e++) {
vtot += Vtest(e);
}
doublevar dist1=0;
for(int m=0; m < nmo; m++)
dist1+=norm(movals_p(m,0));
for(int orbnum=0; orbnum < nmo; orbnum++) {
avg.vals(orbnum)+=norm(movals_p(orbnum,0))/(dist1*npoints_eval);//this is the normalization
}
Array2<doublevar> totalv(nelectrons, wf->nfunc());
totalv = 0.0;
psp->calcNonlocSeparated(wfdata, sys, sample, wf, totalv);
int place = 0;
for (int orbnum = 0; orbnum < nmo; orbnum++ ) {
for (int orbnum2 = 0; orbnum2 < nmo; orbnum2++ ) {
dcomplex tmp3=conj(movals_p(orbnum, 0))*
(pseudo_t(orbnum2) +
Vtest(nelectrons)*movals_p(orbnum2, 0)
-0.5*movals_lap(orbnum2, 4)
+movals_p(orbnum2, 0)*vtot)
/(dist1*npoints_eval);
// tmp3=conj(movals_p(orbnum, 0))*(movals_p(orbnum2, 0))/(dist1*npoints_eval);
//dcomplex tmp3=conj(movals_p(orbnum, 0))*(pseudo_t(orbnum2))/(dist1*npoints_eval);
int which_obdm = 0;
avg.vals(nmo+8*nmo*nmo + 2*which_obdm*nmo*nmo+place) += tmp3.real();
avg.vals(nmo+8*nmo*nmo + 2*which_obdm*nmo*nmo+place+1) += tmp3.imag();
which_obdm = 1;
//tmp3=conj(movals_p(orbnum, 0))*(-0.5*movals_lap(orbnum2, 4))/(dist1*npoints_eval);
avg.vals(nmo+8*nmo*nmo + 2*which_obdm*nmo*nmo+place) += tmp3.real();
avg.vals(nmo+8*nmo*nmo + 2*which_obdm*nmo*nmo+place+1) += tmp3.imag();
place += 2;
}
}
ofstream dump;
if(dump_data) {
dump.open("EKT_DUMP",ios::app);
}
for(int e=0; e< nelectrons; e++) {
dcomplex psiratio_1b=conj(exp(dcomplex(wfs(e).amp(0,0)
-wfval_base.amp(0,0),
wfs(e).phase(0,0)
-wfval_base.phase(0,0))));
int which_obdm=0;
if(e >= nup) { which_obdm=1; }
dcomplex tmp, tmp2, tmp3;
int place=0;
dcomplex prefactor=psiratio_1b/(dist1*npoints_eval);
//cout << "Local potential" << " Kinetic" << " Pseudo" << endl;
// cout << VLoc(e) << " " << Kin(e, 0) << " " << totalv(e, 0) << endl;
for(int orbnum=0; orbnum < nmo; orbnum++) {
for(int orbnum2=0; orbnum2 < nmo; orbnum2++) {
// assert(wf->nfunc()==1);
tmp = 0.5*(movals_p(orbnum,0)*conj(movals1_base(e)(orbnum2,0))*prefactor
+ movals1_base(e)(orbnum, 0)*conj(movals_p(orbnum2, 0))*conj(prefactor));
tmp2 = tmp*(VLoc(e) + Kin(e, 0) + totalv(e, 0));
//rho_ij part the one body reduced density matrix
doublevar tmp2_mag=abs(tmp2);
if(tmp2_mag > ekt_cutoff) {
tmp2*=ekt_cutoff/tmp2_mag;
}
avg.vals(nmo+2*which_obdm*nmo*nmo+place) += tmp.real();
avg.vals(nmo+2*which_obdm*nmo*nmo+place+1) += tmp.imag();
//v_ij^v part
//tmp3 = 0.0;
avg.vals(nmo+4*nmo*nmo + 2*which_obdm*nmo*nmo+place)+=tmp2.real();
avg.vals(nmo+4*nmo*nmo + 2*which_obdm*nmo*nmo+place+1)+=tmp2.imag();
if(dump_data) {
if(orbnum==orbnum2 and orbnum==0) {
sample->getElectronPos(e,oldpos);
dump << which_obdm << "," << tmp2.real() << "," << tmp.real() << ","
<< VLoc(e) << "," << Kin(e,0) << "," << totalv(e,0) <<
"," << oldpos(0) << "," << oldpos(1) << "," << oldpos(2) << endl;
}
}
if (eval_conduction) {
//tmp3 = -1.0*psiratio_1b*conj(movals1_base(e)(orbnum, 0))*(vtot*movals_lap(orbnum2, 0)
// + pseudo_t(orbnum2) - 0.5*movals_lap(orbnum2, 4) + Vtest(nelectrons)*movals_lap(orbnum2, 0))/(dist1*npoints_eval);
tmp3 = -1.0*conj(movals1_base(e)(orbnum, 0))*movals_p(orbnum2, 0)*prefactor*(VLoc(e) + Kin(e, 0) + totalv(e, 0) + Vtest(e));
doublevar tmp3_mag=abs(tmp3);
if(tmp3_mag > ekt_cutoff) {
tmp3*=ekt_cutoff/tmp3_mag;
}
avg.vals(nmo+8*nmo*nmo + 2*which_obdm*nmo*nmo+place) += tmp3.real();
avg.vals(nmo+8*nmo*nmo + 2*which_obdm*nmo*nmo+place+1) += tmp3.imag();
}
place+=2;
}
}
}
}
delete store;
}
void Average_ekt::calcPseudoMo(System * sys,
Sample_point * sample,
Pseudopotential *psp,
const Array1 <doublevar> & accept_var,
Array1 <dcomplex> & totalv)//,
{
int natoms=sample->ionSize();
assert(accept_var.GetDim(0) >= nTest());
//assert(totalv.GetDim(0) >= nwf);
assert(nelectrons == sample->electronSize());
Array1 <doublevar> ionpos(3), oldpos(3), newpos(3);
Array1 <doublevar> newdist(5), olddist(5);
int accept_counter=0;
//deriv.Resize(natoms, 3);
//deriv=0;
dcomplex nonlocal;
Array1 <doublevar> rDotR(psp->getMaxAIP());
Array2 <dcomplex> movals_t(nmo, 1);
Array2 <dcomplex> movals(nmo, 1);
sample->getElectronPos(0, oldpos);
calc_mos(sample, 0, movals);
dcomplex local;
for (int jmo = 0; jmo < nmo; jmo ++) {
nonlocal=0.0;
local = 0.0;
for(int at = 0; at< natoms; at++){
if(psp->getNumL(at) != 0) {
Array1 <doublevar> v_l(psp->getNumL(at));
sample->getIonPos(at, ionpos);
sample->updateEIDist();
sample->getEIDist(0, at, olddist);
int spin=1;
// if(e < sys->nelectrons(0)) spin=0;
spin = 0;
psp->getRadialOut(at, spin, sample, olddist, v_l);
//----------------------------------------
//Start integral
int accept;
if(psp->getDeterministic()) {
accept= olddist(0) < psp->getCutoff(at);
}
else {
doublevar strength=0;
const doublevar calculate_threshold=10;
for(int l=0; l<psp->getNumL(at)-1; l++) {
strength+=calculate_threshold*(2*l+1)*fabs(v_l(l));
}
strength=min((doublevar) 1.0, strength);
doublevar rand=accept_var(accept_counter++);
//cout << at <<" random number " << rand
// << " p_eval " << strength << endl;
if ( strength > 0.0 ) {
for(int l=0; l<psp->getNumL(at)-1; l++)
v_l(l)/=strength;
}
accept=strength>rand;
}
//bool localonly = true;
if(accept) {
for(int i=0; i< psp->getAIP(at); i++) {
for(int d=0; d < 3; d++)
newpos(d)=psp->getIntegralPt(at,i,d)*olddist(0)-olddist(d+2);
sample->translateElectron(0, newpos);
sample->updateEIDist();
sample->getEIDist(0,at,newdist);
rDotR(i)=0;
for(int d=0; d < 3; d++)
rDotR(i)+=newdist(d+2)*olddist(d+2);
rDotR(i)/=(newdist(0)*olddist(0)); //divide by the magnitudes
calc_mos(sample, 0, movals_t);//update value
//----
//cout << "signs " << base_sign << " " << new_sign << endl;;
for(int l=0; l< psp->getNumL(at)-1; l++) {
nonlocal+=(2*l+1)*v_l(l)*legendre(rDotR(i), l)*psp->getIntegralWeight(at, i)*movals_t(jmo, 0);
}
sample->setElectronPos(0, oldpos);
}
}
int localL=psp->getNumL(at)-1; //The l-value of the local part is
local += v_l(localL);
} // if atom has psp
} //atom loop
// cout << "Local:" << local << endl;
//cout << "Nonlocal: " << nonlocal/movals(jmo, 0) << endl;
totalv(jmo) = local*movals(jmo, 0)+nonlocal;
//totalv(jmo) =0.0;
} //nmo loop
//cout << "psp: local part " << accum_local
// << " nonlocal part " << accum_nonlocal << endl;
}
void Actor::update()
{
if(!validRender()) return;
Game *gptr = NULL;
gptr = Game::getInstance();
float movespeed = 0.1;
//handle key presses
if(sf::Keyboard::isKeyPressed(sf::Keyboard::D))
{
m_Velocity = sf::Vector2f(movespeed, 0);
m_CurrentDirection = FACE_EAST;
}
else if(sf::Keyboard::isKeyPressed(sf::Keyboard::A))
{
m_Velocity = sf::Vector2f(-movespeed, 0);
m_CurrentDirection = FACE_WEST;
}
else if(sf::Keyboard::isKeyPressed(sf::Keyboard::W))
{
m_Velocity = sf::Vector2f(0, -movespeed);
m_CurrentDirection = FACE_NORTH;
}
else if(sf::Keyboard::isKeyPressed(sf::Keyboard::S))
{
m_Velocity = sf::Vector2f(0, movespeed);
m_CurrentDirection = FACE_SOUTH;
}
else if(sf::Mouse::isButtonPressed(sf::Mouse::Right) && !gptr->isEditingMap())
{
float angle = getAngle(gptr->isoPositionToScreenPosition(m_Position), gptr->mousePosGlobal, false);
if(angle >=0 && angle < 90)
{
m_Velocity = sf::Vector2f(0, -movespeed);
m_CurrentDirection = FACE_NORTH;
}
else if(angle >= 90 && angle < 180)
{
m_Velocity = sf::Vector2f(-movespeed, 0);
m_CurrentDirection = FACE_WEST;
}
else if(angle >= 180 && angle < 270)
{
m_Velocity = sf::Vector2f(0, movespeed);
m_CurrentDirection = FACE_SOUTH;
}
else
{
m_Velocity = sf::Vector2f(movespeed, 0);
m_CurrentDirection = FACE_EAST;
}
}
else
{
m_Velocity = sf::Vector2f(0,0);
}
sf::Vector3f oldpos(m_Position);
//update player position based on velocity
m_Position.x += m_Velocity.x;
m_Position.y += m_Velocity.y;
//if new player position is not valid, set back to original position
if(!gptr->validPosition(m_Position))
{
//is position not valid because it is not within current map?
if(gptr->positionOutsideOfCurrentMap(m_Position))
{
sf::Vector2f mapsize = gptr->getCurrentMapSize();
sf::Vector2f shiftdir;
//which direction to shift?
if(m_Position.x < 0) shiftdir.x = -1;
else if(m_Position.x >= mapsize.x ) shiftdir.x = 1;
if(m_Position.y < 0) shiftdir.y = -1;
else if(m_Position.y >= mapsize.y ) shiftdir.y = 1;
if(gptr->shiftMapChunkInDirection(shiftdir))
{
//adjust current position
m_Position = sf::Vector3f( m_Position.x + (-shiftdir.x*mapsize.x), m_Position.y + (-shiftdir.y*mapsize.y), m_Position.z);
//std::cout << "mposition:" << m_Position.x << "," << m_Position.y << "," << m_Position.z << std::endl;
}
else m_Position = oldpos;
}
else m_Position = oldpos;
}
if(m_AnimationClock.getElapsedTime().asMilliseconds() >= m_Animations[m_CurrentAnimation]->getFrameTime(m_AnimationFrame))
{
m_AnimationFrame++;
m_AnimationClock.restart();
if(m_AnimationFrame >= m_Animations[m_CurrentAnimation]->getFrameCount()) m_AnimationFrame = 0;
}
}
int FileContents::getField(int lineNum, int field, char *dest, int len)
{
int curfield = field;
int curline = lineNum;
dest[0] = '\0';
if (lineNum >= numLinesInFile) {
return 0;
}
if (printfFile) {
curline %= realLinesInFile;
}
const string & line = fileLines[curline];
size_t pos(0), oldpos(0);
do {
oldpos = pos;
size_t localpos = line.find(';', oldpos);
if (localpos != string::npos) {
pos = localpos + 1;
} else {
pos = localpos;
break;
}
if (curfield == 0) {
break;
}
curfield --;
} while (oldpos != string::npos);
if (curfield) {
WARNING("Field %d not found in the file %s", field, fileName);
return 0;
}
if (string::npos == oldpos) {
return 0;
}
if (string::npos != pos) {
// should not be decremented for fieldN
pos -= (oldpos + 1);
}
string x = line.substr(oldpos, pos);
if (x.length()) {
if (printfFile) {
const char *s = x.c_str();
size_t l = strlen(s);
int copied = 0;
if (l>INT_MAX)
WARNING("length of string exceeds INT_MAX: %ld",l);
for (int i = 0; i < (int)l; i++) {
if (s[i] == '%') {
if (s[i + 1] == '%') {
dest[copied++] = s[i];
} else {
const char *format = s + i;
i++;
while (s[i] != 'd') {
if (i == (int)l) {
REPORT_ERROR("Invalid printf injection field (ran off end of line): %s", s);
}
if (!(isdigit(s[i]) || s[i] == '.' || s[i] == '-')) {
REPORT_ERROR("Invalid printf injection field (only decimal values allowed '%c'): %s", s[i], s);
}
i++;
}
assert(s[i] == 'd');
char *tmp = (char *)malloc(s + i + 2 - format);
if (!tmp) {
REPORT_ERROR("Out of memory!\n");
}
memcpy(tmp, format, s + i + 1 - format);
tmp[s + i + 1 - format] = '\0';
copied += sprintf(dest + copied, tmp, printfOffset + (lineNum * printfMultiple));
free(tmp);
}
} else {
dest[copied++] = s[i];
}
}
dest[copied] = '\0';
return copied;
} else {
return snprintf(dest, len, "%s", x.c_str());
}
} else {
return 0;
}
}
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;
}
