void TileMap::set_cell(int p_x,int p_y,int p_tile,bool p_flip_x,bool p_flip_y,bool p_transpose) {
PosKey pk(p_x,p_y);
Map<PosKey,Cell>::Element *E=tile_map.find(pk);
if (!E && p_tile==INVALID_CELL)
return; //nothing to do
PosKey qk(p_x/_get_quadrant_size(),p_y/_get_quadrant_size());
if (p_tile==INVALID_CELL) {
//erase existing
tile_map.erase(pk);
Map<PosKey,Quadrant>::Element *Q = quadrant_map.find(qk);
ERR_FAIL_COND(!Q);
Quadrant &q=Q->get();
q.cells.erase(pk);
if (q.cells.size()==0)
_erase_quadrant(Q);
else
_make_quadrant_dirty(Q);
return;
}
Map<PosKey,Quadrant>::Element *Q = quadrant_map.find(qk);
if (!E) {
E=tile_map.insert(pk,Cell());
if (!Q) {
Q=_create_quadrant(qk);
}
Quadrant &q=Q->get();
q.cells.insert(pk);
} else {
ERR_FAIL_COND(!Q); // quadrant should exist...
if (E->get().id==p_tile && E->get().flip_h==p_flip_x && E->get().flip_v==p_flip_y && E->get().transpose==p_transpose)
return; //nothing changed
}
Cell &c = E->get();
c.id=p_tile;
c.flip_h=p_flip_x;
c.flip_v=p_flip_y;
c.transpose=p_transpose;
_make_quadrant_dirty(Q);
}
void TileMap::_recreate_quadrants() {
_clear_quadrants();
for (Map<PosKey,Cell>::Element *E=tile_map.front();E;E=E->next()) {
PosKey qk(E->key().x/quadrant_size,E->key().y/quadrant_size);
Map<PosKey,Quadrant>::Element *Q=quadrant_map.find(qk);
if (!Q) {
Q=_create_quadrant(qk);
dirty_quadrant_list.add(&Q->get().dirty_list);
}
Q->get().cells.insert(E->key());
}
}
bool MomentumEstimator::putSpecial(xmlNodePtr cur, ParticleSet& elns, bool rootNode)
{
OhmmsAttributeSet pAttrib;
string hdf5_flag="yes";
pAttrib.add(hdf5_flag,"hdf5");
pAttrib.add(M,"samples");
pAttrib.put(cur);
hdf5_out = (hdf5_flag=="yes");
// app_log()<<" MomentumEstimator::putSpecial "<<endl;
xmlNodePtr kids=cur->children;
while (kids!=NULL)
{
string cname((const char*)(kids->name));
// app_log()<<" MomentumEstimator::cname : "<<cname<<endl;
if (cname=="kpoints")
{
string ctype("manual");
OhmmsAttributeSet pAttrib;
pAttrib.add(ctype,"mode");
pAttrib.add(kgrid,"grid");
pAttrib.put(kids);
#if OHMMS_DIM==3
int numqtwists(6*kgrid+3);
std::vector<int> qk(0);
mappedQtonofK.resize(numqtwists,qk);
compQ.resize(numqtwists);
RealType qn(4.0*M_PI*M_PI*std::pow(Lattice.Volume,-2.0/3.0));
mappedQnorms.resize(numqtwists,qn*0.5/RealType(M));
if (twist[0]==0)
mappedQnorms[kgrid]=qn/RealType(M);
if (twist[1]==0)
mappedQnorms[3*kgrid+1]=qn/RealType(M);
if (twist[2]==0)
mappedQnorms[5*kgrid+2]=qn/RealType(M);
// app_log()<<" Jnorm="<<qn<<endl;
Q.resize(numqtwists);
for (int i=-kgrid; i<(kgrid+1); i++)
{
PosType kpt;
kpt[0]=i-twist[0];
kpt[1]=i-twist[1];
kpt[2]=i-twist[2];
kpt=Lattice.k_cart(kpt);
Q[i+kgrid]=abs(kpt[0]);
Q[i+kgrid+(2*kgrid+1)]=abs(kpt[1]);
Q[i+kgrid+(4*kgrid+2)]=abs(kpt[2]);
}
app_log()<<" Using all k-space points with (nx^2+ny^2+nz^2)^0.5 < "<< kgrid <<" for Momentum Distribution."<<endl;
app_log()<<" My twist is:"<<twist[0]<<" "<<twist[1]<<" "<<twist[2]<<endl;
int indx(0);
int kgrid_squared=kgrid*kgrid;
for (int i=-kgrid; i<(kgrid+1); i++)
{
for (int j=-kgrid; j<(kgrid+1); j++)
{
for (int k=-kgrid; k<(kgrid+1); k++)
{
if (i*i+j*j+k*k<=kgrid_squared) //if (std::sqrt(i*i+j*j+k*k)<=kgrid)
{
PosType kpt;
kpt[0]=i-twist[0];
kpt[1]=j-twist[1];
kpt[2]=k-twist[2];
//convert to Cartesian: note that 2Pi is multiplied
kpt=Lattice.k_cart(kpt);
kPoints.push_back(kpt);
mappedQtonofK[i+kgrid].push_back(indx);
mappedQtonofK[j+kgrid+(2*kgrid+1)].push_back(indx);
mappedQtonofK[k+kgrid+(4*kgrid+2)].push_back(indx);
indx++;
}
}
}
}
#endif
#if OHMMS_DIM==2
int numqtwists(4*kgrid+2);
std::vector<int> qk(0);
mappedQtonofK.resize(numqtwists,qk);
compQ.resize(numqtwists);
RealType qn(2.0*M_PI/std::sqrt(Lattice.Volume));
mappedQnorms.resize(numqtwists,qn*0.5/RealType(M));
if (twist[0]==0)
mappedQnorms[kgrid]=qn/RealType(M);
if (twist[1]==0)
mappedQnorms[3*kgrid+1]=qn/RealType(M);
// app_log()<<" Jnorm="<<qn<<endl;
Q.resize(numqtwists);
for (int i=-kgrid; i<(kgrid+1); i++)
{
PosType kpt;
kpt[0]=i-twist[0];
kpt[1]=i-twist[1];
kpt=Lattice.k_cart(kpt);
Q[i+kgrid]=abs(kpt[0]);
Q[i+kgrid+(2*kgrid+1)]=abs(kpt[1]);
}
app_log()<<" Using all k-space points with (nx^2+ny^2)^0.5 < "<< kgrid <<" for Momentum Distribution."<<endl;
app_log()<<" My twist is:"<<twist[0]<<" "<<twist[1]<<endl;
int indx(0);
int kgrid_squared=kgrid*kgrid;
for (int i=-kgrid; i<(kgrid+1); i++)
{
for (int j=-kgrid; j<(kgrid+1); j++)
{
if (i*i+j*j<=kgrid_squared) //if (std::sqrt(i*i+j*j+k*k)<=kgrid)
{
PosType kpt;
kpt[0]=i-twist[0];
kpt[1]=j-twist[1];
//convert to Cartesian: note that 2Pi is multiplied
kpt=Lattice.k_cart(kpt);
kPoints.push_back(kpt);
mappedQtonofK[i+kgrid].push_back(indx);
mappedQtonofK[j+kgrid+(2*kgrid+1)].push_back(indx);
indx++;
}
}
}
#endif
}
kids=kids->next;
}
if (rootNode)
{
std::stringstream sstr;
sstr<<"Kpoints";
for(int i(0); i<OHMMS_DIM; i++)
sstr<<"_"<<round(100.0*twist[i]);
sstr<<".dat";
ofstream fout(sstr.str().c_str());
fout.setf(ios::scientific, ios::floatfield);
fout << "# mag_k ";
for(int i(0); i<OHMMS_DIM; i++)
fout << "k_"<<i<<" ";
fout <<endl;
for (int i=0; i<kPoints.size(); i++)
{
float khere(std::sqrt(dot(kPoints[i],kPoints[i])));
fout<<khere;
for(int j(0); j<OHMMS_DIM; j++)
fout<<" "<<kPoints[i][j];
fout<<endl;
}
fout.close();
sstr.str("");
sstr<<"Qpoints";
for(int i(0); i<OHMMS_DIM; i++)
sstr<<"_"<<round(100.0*twist[i]);
sstr<<".dat";
ofstream qout(sstr.str().c_str());
qout.setf(ios::scientific, ios::floatfield);
qout << "# mag_q" << endl;
for (int i=0; i<Q.size(); i++)
{
qout<<Q[i]<<endl;
}
qout.close();
}
nofK.resize(kPoints.size());
norm_nofK=1.0/RealType(M);
return true;
}
void runGenTest(RunParameters &r) {
// Define variables
Vector J, expJ;
std::vector<int> cons;
std::vector<double> weight;
if (r.useGI) {
epsilonP2_ptr=&epsilonP2_GI;
epsilonC_ptr=&epsilonC_GI;
getMaxError_ptr=&getMaxError_GI;
}
else {
epsilonP2_ptr=&epsilonP2;
epsilonC_ptr=&epsilonC;
getMaxError_ptr=&getMaxError;
}
// Get reference sequence from file
FILE *consIn = fopen(r.getConsensusInfile().c_str(),"r");
if (consIn!=NULL) getConsensus(consIn,cons);
else { printf("Error reading input from file %s\n\n",r.getConsensusInfile().c_str()); exit(1); }
fclose(consIn);
if (r.useVerbose) {
printf("Reference sequence: ");
for (int i=0;i<cons.size();i++) printf(" %d",cons[i]);
printf("\n\n");
}
// Retrieve couplings from file
FILE *dataIn=fopen(r.getInfile().c_str(),"r");
if (dataIn!=NULL) getCouplings(dataIn,J);
else { printf("Error reading input from file %s",r.getInfile().c_str()); exit(1); }
fclose(dataIn);
// Resize expJ
for (int i=0;i<J.size();i++) expJ.push_back(std::vector<double>(J[i].size(),0));
for (int i=0;i<J.size();i++) { for (int j=0;j<J[i].size();j++) expJ[i][j] = exp(J[i][j]); }
// Declare 2-point correlations, 3-point correlations, P(k) and magnetisations
bool ThreePoints = (r.p3red || r.p3);
int N = sizetolength(J.size()); // System size
double alpha = 0.01; // Field regularization multiplier
double gamma = 0; // Regularization strength (L2, set below)
if (r.useGamma) {
if (r.gamma==0) gamma=1/(r.sampleB);
else gamma=r.gamma;
}
Vector p(J.size(),std::vector<double>()); // MC magnetisations and 2-point correlations
Vector cc(J.size(),std::vector<double>()); // MC connected 2-point correlations
Vector q(J.size(),std::vector<double>()); // MSA magnetisations and 2-point correlations
Vector qcc(J.size(),std::vector<double>()); // MSA connected 2-point correlations
std::vector<std::vector<std::vector<std::vector<double> > > > p3(N); // MC 3-point correlations
std::vector<std::vector<std::vector<std::vector<double> > > > c3(N); // MC connected 3-point correlations
std::vector<std::vector<std::vector<std::vector<double> > > > q3(N); // MSA 3-point correlations
std::vector<std::vector<std::vector<std::vector<double> > > > qc3(N); // MSA connected 3-point correlations
std::vector<double> pk(N+1,0); // MC mutation probability
std::vector<double> qk(N+1,0); // MSA mutation probability
std::vector<double> absErr(2,0); // Absolute errors on magnetisation and 2-point correlations
for (int i=0;i<J.size();i++) {
cc[i].resize(J[i].size(),0);
p[i].resize(J[i].size(),0);
qcc[i].resize(J[i].size(),0);
q[i].resize(J[i].size(),0);
}
if (ThreePoints) { for (int i=0;i<N;i++) {
p3[i].resize(N);
c3[i].resize(N);
q3[i].resize(N);
qc3[i].resize(N);
for (int j=0;j<N;j++) {
p3[i][j].resize(N);
c3[i][j].resize(N);
q3[i][j].resize(N);
qc3[i][j].resize(N);
for (int k=0;k<N;k++) {
p3[i][j][k].resize(p[i].size()*p[j].size()*p[k].size(),0);
c3[i][j][k].resize(p[i].size()*p[j].size()*p[k].size(),0);
q3[i][j][k].resize(p[i].size()*p[j].size()*p[k].size(),0);
qc3[i][j][k].resize(p[i].size()*p[j].size()*p[k].size(),0);
}
}
} }
// Get sequences from MSA file and compute correlations
FILE *alIn=fopen(r.getInfileAl().c_str(),"r");
FILE *weightIn=fopen(r.getWeights().c_str(),"r");
if (alIn!=NULL){
if (ThreePoints) getAlignment(alIn,weightIn,J,q,q3,qk,cons);
else getAlignment(alIn,weightIn,J,q,qk,cons);
}
else { printf("Error reading input from file %s\n\n",r.getInfileAl().c_str()); exit(1); }
fclose(alIn);
if (weightIn!=NULL) fclose(weightIn);
if (r.useVerbose) printf("Got N=%d, len(h[0])=%d\n",N,(int)J[0].size());
// Get default starting configuration, if nontrivial
std::vector<int> lattice(N);
if (r.useStart) {
FILE *startIn=fopen(r.getStartInfile().c_str(),"r");
for (int i=0;i<N;i++) fscanf(startIn,"%d",&lattice[i]);
}
else { for (int i=0;i<N;i++) lattice[i]=(int) p[i].size(); }
// Prepare to simulate
srand((unsigned)time(0));
// Run MC and get correlations
if (ThreePoints) getErrorGenTest(J, expJ, r.sampleB, r.b, r.runs, p, lattice, pk, p3, cons); // compute errors on P P2 and MAX
else getErrorGenTest(J, expJ, r.sampleB, r.b, r.runs, p, lattice, pk, cons); // compute errors on P P2 and MAX
//Compute connected correlations
double Neff = 0;
double NJeff = 0;
// estimate the threshold for correlations to print out
double meanq = 0;
for (int i=0;i<lattice.size();i++) { for (int a=0;a<p[i].size();a++) {
Neff++;
meanq+=q[i][a];
absErr[0] += (p[i][a] - q[i][a]) * (p[i][a] - q[i][a]);
for (int j=i+1;j<lattice.size();j++) { for (int b=0;b<p[j].size();b++) {
NJeff++;
int idx = index(i,j,lattice.size());
int sab = sindex(a,b,J[i].size(),J[j].size());
absErr[1] += (p[idx][sab] - q[idx][sab]) * (p[idx][sab] - q[idx][sab]);
cc[idx][sab] = p[idx][sab] - (p[i][a] * p[j][b]);
qcc[idx][sab] = q[idx][sab] - (q[i][a] * q[j][b]);
if (ThreePoints) { for (int k=j+1;k<lattice.size();k++) { for (int c=0;c<p[k].size();c++) {
int ijx = idx;
int ikx = index(i,k,lattice.size());
int jkx = index(j,k,lattice.size());
int sac = sindex(a,c,J[i].size(),J[k].size());
int sbc = sindex(b,c,J[j].size(),J[k].size());
int sabc = sindex3(a,b,c,J[i].size(),J[j].size(),J[k].size());
c3[i][j][k][sabc] = p3[i][j][k][sabc] - (p[i][a]*p[jkx][sbc]) - (p[j][b]*p[ikx][sac]) - (p[k][c]*p[ijx][sab]) + (2*(p[i][a]*p[j][b]*p[k][c]));
qc3[i][j][k][sabc] = q3[i][j][k][sabc] - (q[i][a]*q[jkx][sbc]) - (q[j][b]*q[ikx][sac]) - (q[k][c]*q[ijx][sab]) + (2*(q[i][a]*q[j][b]*q[k][c]));
} } }
} }
} }
absErr[0] = sqrt(absErr[0]/Neff);
absErr[1] = sqrt(absErr[1]/NJeff);
meanq=meanq/Neff;
// Print out errors
double maxPrecision=1/(r.sampleB);
double ep1 = epsilonP(q, p, N, maxPrecision, J, gamma, alpha);
double ep2 = (*epsilonP2_ptr)(q, p, N, maxPrecision, J, gamma);
double em = (*getMaxError_ptr)( q, p, maxPrecision, J, gamma, alpha);
printf("\nRelative errors: P %f, P2 %f MAX %f gamma %f\n",ep1,ep2,em,gamma);
printf("Absolute errors: P %f, P2 %f \n\n",absErr[0],absErr[1]);
//Print results for comparison
FILE *mOut = fopen(r.getMOutfile().c_str(),"w");
FILE *pOut = fopen(r.getP2Outfile().c_str(),"w");
FILE *ccOut = fopen(r.getCCOutfile().c_str(),"w");
FILE *pkOut = fopen(r.getPKOutfile().c_str(),"w");
printMagnetisations(mOut, q, p);
double num=0;
printCorrelations(ccOut, qcc, cc,pOut, q, p);
if (ThreePoints){
FILE *p3Out = fopen(r.getP3Outfile().c_str(),"w");
FILE *c3Out = fopen(r.getC3Outfile().c_str(),"w");
if (r.p3red) num=meanq*meanq*meanq;
if (r.p3) num=0;
print3points(c3Out, qc3, c3,p3Out, q3, p3, num);
}
for (int sit=0;sit<N;sit++) fprintf(pkOut,"%d %le %le\n",sit,qk[sit],pk[sit]);
fflush(pkOut);
}