// Returns a checkpoint of this CFGIterator's progress.
CFGIterator::checkpoint CFGIterator::getChkpt()
{
assert(initialized);
CFGIterator::checkpoint chkpt(remainingNodes, visited);
return chkpt;
//return new CFGIterator::checkpoint::checkpoint(remainingNodes, visited);
}
// Returns a checkpoint of this CFGIterator's progress.
dataflowCFGIterator::checkpoint dataflowCFGIterator::getChkpt()
{
assert(initialized);
dataflowCFGIterator::checkpoint chkpt(CFGIterator::getChkpt(), terminator);
return chkpt;
//return new dataflowCFGIterator::checkpoint::checkpoint(CFGIterator::getChkpt(), terminator);
}
// Returns a checkpoint of this iterator's progress.
dataflow::checkpoint dataflow::getChkpt()
{
ROSE_ASSERT(initialized);
dataflow::checkpoint chkpt(iterator::getChkpt(), terminator);
return chkpt;
//return new dataflow::checkpoint::checkpoint(iterator::getChkpt(), terminator);
}
// Returns a checkpoint of this iterator's progress.
iterator::checkpoint iterator::getChkpt()
{
ROSE_ASSERT(initialized);
iterator::checkpoint chkpt(remainingNodes, visited);
return chkpt;
//return new iterator::checkpoint::checkpoint(remainingNodes, visited);
}
int xn_import(struct udf_type *t) {
struct root_entry r;
int res;
size_t nblocks, nbytes;
cap_t c;
long db;
int i, tid;
xn_cnt_t n;
da_t da;
void *p;
if((tid = sys__type_mount(t->type_name)) >= 0) {
//printf("hit in cache for %s (tid %d, class %d)\n", t->type_name, tid, t->class);
return tid;
} else
//printf("<%s> did not hit in cache\n", t->type_name);
c = (cap_t)CAP_ROOT;
/* Allocate space, place in root, import. */
if(sys__xn_mount(&r, t->type_name, c) == XN_SUCCESS) {
xn_cnt_t cnt;
ppn_t ppn;
cnt = r.nelem;
printf("reading %d\n", r.nelem);
/* alloc storage. */
for(ppn = -1, i = 0; i < r.nelem; i++, ppn++) {
ppn = sys__xn_bind(r.db+i, ppn, (cap_t)CAP_ROOT, XN_FORCE_READIN, 1);
if(ppn < 0) {
printf("ppn = %ld\n", ppn);
fatal(Death);
}
}
/* now need to load. */
if((res = sys__xn_readin(r.db, r.nelem, &cnt)) != XN_SUCCESS) {
printf("res = %d\n", res);
fatal(Death);
}
/* GROK -- not my code, but I think cnt should have been 1 */
/* going into the readin (rather than nelem), since each */
/* disk request gets notification (rather than each block */
/* read or written). */
wk_waitfor_value (&cnt, 0, 0);
printf("hit in cache for %s\n", t->type_name);
if((res = sys__type_mount(t->type_name)) < XN_SUCCESS) {
printf("res = %d\n", res);
fatal(SHould have hit);
}
return res;
}
chkpt("xn_mount");
nblocks = bytes_to_blocks(sizeof *t);
db = 0;
if(sys__install_mount(t->type_name, &db, nblocks, XN_DB, c) < 0)
fatal(Mount failed);
//printf("nblocks = %ld\n", (long)nblocks);
/* Allocate pages, and copyin. */
for(i = 0; i < nblocks; i++) {
if(sys__xn_bind(db+i, -1, c, XN_ZERO_FILL, 1) < 0)
fatal(Could not bind);
da = da_compose(db+i, 0);
p = (char *)t + i * PAGESIZ;
nbytes = (i == (nblocks - 1)) ?
(sizeof *t % XN_BLOCK_SIZE) : PAGESIZ;
if((res = sys__xn_writeb(da, p, nbytes, c)) < 0) {
printf("res = %d\n", res);
fatal(Could not write);
}
n = 1;
if(sys__xn_writeback(db+i, 1, &n) < 0)
fatal(Cannot write back);
wk_waitfor_value (&n, 0, 0);
}
chkpt("type import..");
if((tid = sys__type_import(t->type_name)) < 0)
fatal(Cannot import);
return tid;
}
int main(int argc, char **argv) {
#ifdef _OPENMP
printf("ERKALE - population from Hel, OpenMP version, running on %i cores.\n",omp_get_max_threads());
#else
printf("ERKALE - population from Hel, serial version.\n");
#endif
print_copyright();
print_license();
#ifdef SVNRELEASE
printf("At svn revision %s.\n\n",SVNREVISION);
#endif
print_hostname();
if(argc!=2) {
printf("Usage: %s runfile\n",argv[0]);
return 1;
}
// Parse settings
Settings set;
set.add_string("LoadChk","Checkpoint file to load density from","erkale.chk");
set.add_bool("Bader", "Run Bader analysis?", false);
set.add_bool("Becke", "Run Becke analysis?", false);
set.add_bool("Mulliken", "Run Mulliken analysis?", false);
set.add_bool("Lowdin", "Run Löwdin analysis?", false);
set.add_bool("IAO", "Run Intrinsic Atomic Orbital analysis?", false);
set.add_string("IAOBasis", "Minimal basis set for IAO analysis", "MINAO.gbs");
set.add_bool("Hirshfeld", "Run Hirshfeld analysis?", false);
set.add_string("HirshfeldMethod", "Method to use for Hirshfeld(-I) analysis", "HF");
set.add_bool("IterativeHirshfeld", "Run iterative Hirshfeld analysis?", false);
set.add_bool("Stockholder", "Run Stockholder analysis?", false);
set.add_bool("Voronoi", "Run Voronoi analysis?", false);
set.add_double("Tol", "Grid tolerance to use for the charges", 1e-5);
set.add_bool("OrbThr", "Compute orbital density thresholds", false);
set.add_bool("SICThr", "Compute SIC orbital density thresholds", false);
set.add_bool("DensThr", "Compute total density thresholds", false);
set.add_double("OrbThrVal", "Which density threshold to calculate", 0.85);
set.add_double("OrbThrGrid", "Accuracy of orbital density threshold integration grid", 1e-3);
// Parse settings
set.parse(argv[1]);
// Print settings
set.print();
// Initialize libint
init_libint_base();
// Load checkpoint
Checkpoint chkpt(set.get_string("LoadChk"),false);
// Load basis set
BasisSet basis;
chkpt.read(basis);
// Restricted calculation?
bool restr;
chkpt.read("Restricted",restr);
arma::mat P, Pa, Pb;
chkpt.read("P",P);
if(!restr) {
chkpt.read("Pa",Pa);
chkpt.read("Pb",Pb);
}
double tol=set.get_double("Tol");
if(set.get_bool("Bader")) {
if(restr)
bader_analysis(basis,P,tol);
else
bader_analysis(basis,Pa,Pb,tol);
}
if(set.get_bool("Becke")) {
if(restr)
becke_analysis(basis,P,tol);
else
becke_analysis(basis,Pa,Pb,tol);
}
std::string hmet=set.get_string("HirshfeldMethod");
if(set.get_bool("Hirshfeld")) {
if(restr)
hirshfeld_analysis(basis,P,hmet,tol);
else
hirshfeld_analysis(basis,Pa,Pb,hmet,tol);
}
if(set.get_bool("IterativeHirshfeld")) {
if(restr)
iterative_hirshfeld_analysis(basis,P,hmet,tol);
else
iterative_hirshfeld_analysis(basis,Pa,Pb,hmet,tol);
}
if(set.get_bool("IAO")) {
std::string minbas=set.get_string("IAOBasis");
if(restr) {
// Get amount of occupied orbitals
int Nela;
chkpt.read("Nel-a",Nela);
// Get orbital coefficients
arma::mat C;
chkpt.read("C",C);
// Do analysis
IAO_analysis(basis,C.cols(0,Nela-1),P,minbas);
} else {
// Get amount of occupied orbitals
int Nela, Nelb;
chkpt.read("Nel-a",Nela);
chkpt.read("Nel-b",Nelb);
// Get orbital coefficients
arma::mat Ca, Cb;
chkpt.read("Ca",Ca);
chkpt.read("Cb",Cb);
// Do analysis
IAO_analysis(basis,Ca.cols(0,Nela-1),Cb.cols(0,Nelb-1),Pa,Pb,minbas);
}
}
if(set.get_bool("Lowdin")) {
if(restr)
lowdin_analysis(basis,P);
else
lowdin_analysis(basis,Pa,Pb);
}
if(set.get_bool("Mulliken")) {
if(restr)
mulliken_analysis(basis,P);
else
mulliken_analysis(basis,Pa,Pb);
}
if(set.get_bool("Stockholder")) {
if(restr)
stockholder_analysis(basis,P,tol);
else
stockholder_analysis(basis,Pa,Pb,tol);
}
if(set.get_bool("Voronoi")) {
if(restr)
voronoi_analysis(basis,P,tol);
else
voronoi_analysis(basis,Pa,Pb,tol);
}
if(set.get_bool("OrbThr")) {
// Calculate orbital density thresholds
// Integration grid
DFTGrid intgrid(&basis,true);
intgrid.construct_becke(set.get_double("OrbThrGrid"));
// Threshold is
double thr=set.get_double("OrbThrVal");
if(restr) {
// Get amount of occupied orbitals
int Nela;
chkpt.read("Nel-a",Nela);
// Get orbital coefficients
arma::mat C;
chkpt.read("C",C);
printf("\n%4s %9s %8s\n","orb","thr","t (s)");
for(int io=0;io<Nela;io++) {
Timer t;
// Orbital density matrix is
arma::mat Po=C.col(io)*arma::trans(C.col(io));
double val=compute_threshold(intgrid,Po,thr,false);
// Print out orbital threshold
printf("%4i %8.3e %8.3f\n", io+1, val, t.get());
fflush(stdout);
}
} else {
// Get amount of occupied orbitals
int Nela, Nelb;
chkpt.read("Nel-a",Nela);
chkpt.read("Nel-b",Nelb);
// Get orbital coefficients
arma::mat Ca, Cb;
chkpt.read("Ca",Ca);
chkpt.read("Cb",Cb);
printf("\n%4s %9s %9s %8s\n","orb","thr-a","thr-b","t (s)");
for(int io=0;io<Nela;io++) {
Timer t;
// Orbital density matrix is
arma::mat Po=Ca.col(io)*arma::trans(Ca.col(io));
double vala=compute_threshold(intgrid,Po,thr,false);
if(io<Nelb) {
Po=Cb.col(io)*arma::trans(Cb.col(io));
double valb=compute_threshold(intgrid,Po,thr,false);
// Print out orbital threshold
printf("%4i %8.3e %8.3e %8.3f\n", io+1, vala, valb, t.get());
fflush(stdout);
} else {
printf("%4i %8.3e %9s %8.3f\n", io+1, vala, "****", t.get());
fflush(stdout);
}
}
}
}
if(set.get_bool("SICThr")) {
// Calculate SIC orbital density thresholds
// Integration grid
DFTGrid intgrid(&basis,true);
intgrid.construct_becke(set.get_double("OrbThrGrid"));
// Threshold is
double thr=set.get_double("OrbThrVal");
if(restr) {
// Get orbital coefficients
arma::cx_mat CW;
chkpt.cread("CW",CW);
printf("\n%4s %9s %8s\n","orb","thr","t (s)");
for(size_t io=0;io<CW.n_cols;io++) {
Timer t;
// Orbital density matrix is
arma::mat Po=arma::real(CW.col(io)*arma::trans(CW.col(io)));
double val=compute_threshold(intgrid,Po,thr,false);
// Print out orbital threshold
printf("%4i %8.3e %8.3f\n", (int) io+1, val, t.get());
fflush(stdout);
}
} else {
// Get orbital coefficients
arma::cx_mat CWa, CWb;
chkpt.cread("CWa",CWa);
chkpt.cread("CWb",CWb);
printf("\n%4s %9s %9s %8s\n","orb","thr-a","thr-b","t (s)");
for(size_t io=0;io<CWa.n_cols;io++) {
Timer t;
// Orbital density matrix is
arma::mat Po=arma::real(CWa.col(io)*arma::trans(CWa.col(io)));
double vala=compute_threshold(intgrid,Po,thr,false);
if(io<CWb.n_cols) {
Po=arma::real(CWb.col(io)*arma::trans(CWb.col(io)));
double valb=compute_threshold(intgrid,Po,thr,false);
// Print out orbital threshold
printf("%4i %8.3e %8.3e %8.3f\n", (int) io+1, vala, valb, t.get());
fflush(stdout);
} else {
printf("%4i %8.3e %9s %8.3f\n", (int) io+1, vala, "****", t.get());
fflush(stdout);
}
}
}
}
if(set.get_bool("DensThr")) {
// Calculate SIC orbital density thresholds
// Integration grid
DFTGrid intgrid(&basis,true);
intgrid.construct_becke(set.get_double("OrbThrGrid"));
// Threshold is
double thr=set.get_double("OrbThrVal");
Timer t;
printf("\n%10s %9s %8s\n","density","thr","t (s)");
if(!restr) {
double aval=compute_threshold(intgrid,Pa,thr*arma::trace(P*basis.overlap()),true);
printf("%10s %8.3e %8.3f\n", "alpha", aval, t.get());
fflush(stdout);
t.set();
double bval=compute_threshold(intgrid,Pb,thr*arma::trace(P*basis.overlap()),true);
printf("%10s %8.3e %8.3f\n", "beta", bval, t.get());
fflush(stdout);
t.set();
}
double val=compute_threshold(intgrid,P,thr*arma::trace(P*basis.overlap()),true);
printf("%10s %8.3e %8.3f\n", "total", val, t.get());
fflush(stdout);
}
return 0;
}
int main(int argc, char **argv) {
#ifdef _OPENMP
printf("ERKALE - Casida from Hel, OpenMP version, running on %i cores.\n",omp_get_max_threads());
#else
printf("ERKALE - Casida from Hel, serial version.\n");
#endif
print_copyright();
print_license();
#ifdef SVNRELEASE
printf("At svn revision %s.\n\n",SVNREVISION);
#endif
print_hostname();
if(argc!=1 && argc!=2) {
printf("Usage: $ %s (runfile)\n",argv[0]);
return 0;
}
// Initialize libint
init_libint_base();
Timer t;
t.print_time();
// Parse settings
Settings set;
set.add_string("FittingBasis","Basis set to use for density fitting (Auto for automatic)","Auto");
set.add_string("CasidaX","Exchange functional for Casida","lda_x");
set.add_string("CasidaC","Correlation functional for Casida","lda_c_vwn");
set.add_bool("CasidaPol","Perform polarized Casida calculation (when using restricted wf)",false);
set.add_int("CasidaCoupling","Coupling mode: 0 for IPA, 1 for RPA and 2 for TDLDA",2);
set.add_double("CasidaTol","Tolerance for Casida grid",1e-4);
set.add_string("CasidaStates","States to include in Casida calculation, eg ""1,3:7,10,13"" ","");
set.add_string("CasidaQval","Values of Q to compute spectrum for","");
set.add_string("LoadChk","Checkpoint to load","erkale.chk");
if(argc==2)
set.parse(std::string(argv[1]));
else
printf("\nDefault settings used.");
// Print settings
set.print();
// Get functional strings
int xfunc=find_func(set.get_string("CasidaX"));
int cfunc=find_func(set.get_string("CasidaC"));
if(is_correlation(xfunc))
throw std::runtime_error("Refusing to use a correlation functional as exchange.\n");
if(is_kinetic(xfunc))
throw std::runtime_error("Refusing to use a kinetic energy functional as exchange.\n");
if(is_exchange(cfunc))
throw std::runtime_error("Refusing to use an exchange functional as correlation.\n");
if(is_kinetic(cfunc))
throw std::runtime_error("Refusing to use a kinetic energy functional as correlation.\n");
set.add_int("CasidaXfunc","Internal variable",xfunc);
set.add_int("CasidaCfunc","Internal variable",cfunc);
// Print information about used functionals
print_info(xfunc,cfunc);
// Get values of q to compute spectrum for
std::vector<double> qvals=parse_range_double(set.get_string("CasidaQval"));
// Load checkpoint
std::string fchk=set.get_string("LoadChk");
Checkpoint chkpt(fchk,false);
// Check that calculation was converged
bool conv;
chkpt.read("Converged",conv);
if(!conv)
throw std::runtime_error("Refusing to run Casida calculation based on a non-converged SCF density!\n");
// Parse input states
std::string states=set.get_string("CasidaStates");
std::string newstates=parse_states(chkpt,states);
set.set_string("CasidaStates",newstates);
if(states.compare(newstates)!=0)
printf("CasidaStates has been parsed to \"%s\".\n",newstates.c_str());
// Load basis set
BasisSet basis;
chkpt.read(basis);
Casida cas;
bool restr;
chkpt.read("Restricted",restr);
if(restr) {
// Load energy and orbitals
arma::mat C, P;
arma::vec E;
std::vector<double> occs;
chkpt.read("P",P);
chkpt.read("C",C);
chkpt.read("E",E);
chkpt.read("occs",occs);
// Check orthonormality
check_orth(C,basis.overlap(),false);
if(set.get_bool("CasidaPol")) {
// Half occupancy (1.0 instead of 2.0)
std::vector<double> hocc(occs);
for(size_t i=0;i<hocc.size();i++)
hocc[i]/=2.0;
cas=Casida(set,basis,E,E,C,C,P/2.0,P/2.0,hocc,hocc);
}
else
cas=Casida(set,basis,E,C,P,occs);
} else {
arma::mat Ca, Cb;
arma::mat Pa, Pb;
arma::vec Ea, Eb;
std::vector<double> occa, occb;
chkpt.read("Pa",Pa);
chkpt.read("Pb",Pb);
chkpt.read("Ca",Ca);
chkpt.read("Cb",Cb);
chkpt.read("Ea",Ea);
chkpt.read("Eb",Eb);
chkpt.read("occa",occa);
chkpt.read("occb",occb);
// Check orthonormality
check_orth(Ca,basis.overlap(),false);
check_orth(Cb,basis.overlap(),false);
cas=Casida(set,basis,Ea,Eb,Ca,Cb,Pa,Pb,occa,occb);
}
// Dipole transition
print_spectrum("casida.dat",cas.dipole_transition(basis));
// Q dependent stuff
for(size_t iq=0;iq<qvals.size();iq++) {
// File to save output
char fname[80];
sprintf(fname,"casida-%.2f.dat",qvals[iq]);
print_spectrum(fname,cas.transition(basis,qvals[iq]));
}
printf("\nRunning program took %s.\n",t.elapsed().c_str());
t.print_time();
return 0;
}
enum calcd run_calc(const BasisSet & basis, Settings & set, bool force) {
// Checkpoint file to load
std::string loadname=set.get_string("LoadChk");
if(stricmp(loadname,"")==0) {
// Nothing to load - run full calculation.
calculate(basis,set,force);
if(force)
return FULLCALC;
else
return ECALC;
}
// Was the calculation converged?
bool convd;
BasisSet oldbas;
{
Checkpoint chkpt(loadname,false);
chkpt.read("Converged",convd);
chkpt.read(oldbas);
}
if(!convd) {
// Old calculation was not converged - run full calculation
set.set_string("LoadName","");
calculate(basis,set,force);
if(force)
return FULLCALC;
else
return ECALC;
}
// Copy the checkpoint if necessary
std::string savename=set.get_string("SaveChk");
if(stricmp(savename,loadname)!=0) {
// Copy the file
std::ostringstream oss;
oss << "cp " << loadname << " " << savename;
int cp=system(oss.str().c_str());
if(cp) {
ERROR_INFO();
throw std::runtime_error("Failed to copy checkpoint file.\n");
}
}
// Strict integrals?
bool strictint(set.get_bool("StrictIntegrals"));
// Check if the basis set is different
if(!(basis==oldbas)) {
// Basis set is different or calculation was not converged - need
// to run calculation. Project Fock matrix to new basis and
// diagonalize to get new orbitals
{
// Open in write mode, don't truncate
Checkpoint chkpt(savename,true,false);
// Save basis
chkpt.write(basis);
// Overlap matrix
arma::mat S=basis.overlap();
chkpt.write("S",S);
arma::mat Sinvh=BasOrth(S,set);
chkpt.write("Sinvh",Sinvh);
// Restricted or unrestricted run?
bool restr;
chkpt.read("Restricted",restr);
chkpt.read(oldbas);
if(restr) {
rscf_t sol;
std::vector<double> occs;
chkpt.read("H",sol.H);
chkpt.read("occs",occs);
// Form new orbitals by diagonalizing H in new geometry
diagonalize(S,Sinvh,sol);
// Form new density
sol.P=form_density(sol.C,occs);
// Write basis set, orbitals and density
chkpt.write("C",sol.C);
chkpt.write("E",sol.E);
chkpt.write("P",sol.P);
} else {
uscf_t sol;
std::vector<double> occa, occb;
chkpt.read("Ha",sol.Ha);
chkpt.read("Hb",sol.Hb);
chkpt.read("occa",occa);
chkpt.read("occb",occb);
// Form new orbitals by diagonalizing H in new geometry
diagonalize(S,Sinvh,sol);
// Form new density
sol.Pa=form_density(sol.Ca,occa);
sol.Pb=form_density(sol.Cb,occb);
sol.P=sol.Pa+sol.Pb;
// Write basis set, orbitals and density
chkpt.write("Ca",sol.Ca);
chkpt.write("Cb",sol.Cb);
chkpt.write("Ea",sol.Ea);
chkpt.write("Eb",sol.Eb);
chkpt.write("Pa",sol.Pa);
chkpt.write("Pb",sol.Pb);
chkpt.write("P",sol.P);
}
// Calculation is now not converged
bool conv=false;
chkpt.write("Converged",conv);
}
// Now we can do the SCF calculation
calculate(basis,set,force);
if(force)
return FULLCALC;
else
return ECALC;
}
// Because we are here, the basis set is the same.
if(!force)
// No force required, can just read energy from file.
return NOCALC;
// Have converged energy, compute force.
// Open the checkpoint in write mode, don't truncate it
Checkpoint chkpt(savename,true,false);
// SCF structure
SCF solver(basis,set,chkpt);
// Do a plain Hartree-Fock calculation?
bool hf= (stricmp(set.get_string("Method"),"HF")==0);
bool rohf=(stricmp(set.get_string("Method"),"ROHF")==0);
dft_t dft;
if(!hf && !rohf) {
// Get exchange and correlation functionals as well as grid settings
dft=parse_dft(set,false);
}
// Force
arma::vec f;
double tol;
chkpt.read("tol",tol);
// Multiplicity
int mult=set.get_int("Multiplicity");
// Amount of electrons
int Nel=basis.Ztot()-set.get_int("Charge");
if(mult==1 && Nel%2==0 && !set.get_bool("ForcePol")) {
rscf_t sol;
chkpt.read("C",sol.C);
chkpt.read("E",sol.E);
chkpt.read("H",sol.H);
chkpt.read("P",sol.P);
std::vector<double> occs;
chkpt.read("occs",occs);
// Restricted case
if(hf) {
f=solver.force_RHF(sol,occs,FINETOL);
} else {
DFTGrid grid(&basis,set.get_bool("Verbose"),dft.lobatto);
DFTGrid nlgrid(&basis,set.get_bool("Verbose"),dft.lobatto);
// Fixed grid?
if(dft.adaptive)
grid.construct(sol.P,dft.gridtol,dft.x_func,dft.c_func);
else {
grid.construct(dft.nrad,dft.lmax,dft.x_func,dft.c_func,strictint);
if(dft.nl)
nlgrid.construct(dft.nlnrad,dft.nllmax,true,false,strictint,true);
}
f=solver.force_RDFT(sol,occs,dft,grid,nlgrid,FINETOL);
}
} else {
uscf_t sol;
chkpt.read("Ca",sol.Ca);
chkpt.read("Ea",sol.Ea);
chkpt.read("Ha",sol.Ha);
chkpt.read("Pa",sol.Pa);
chkpt.read("Cb",sol.Cb);
chkpt.read("Eb",sol.Eb);
chkpt.read("Hb",sol.Hb);
chkpt.read("Pb",sol.Pb);
chkpt.read("P",sol.P);
std::vector<double> occa, occb;
chkpt.read("occa",occa);
chkpt.read("occb",occb);
if(hf) {
f=solver.force_UHF(sol,occa,occb,tol);
} else if(rohf) {
int Nela, Nelb;
chkpt.read("Nel-a",Nela);
chkpt.read("Nel-b",Nelb);
throw std::runtime_error("Not implemented!\n");
// f=solver.force_ROHF(sol,Nela,Nelb,tol);
} else {
DFTGrid grid(&basis,set.get_bool("Verbose"),dft.lobatto);
DFTGrid nlgrid(&basis,set.get_bool("Verbose"),dft.lobatto);
// Fixed grid?
if(dft.adaptive)
grid.construct(sol.P,dft.gridtol,dft.x_func,dft.c_func);
else {
grid.construct(dft.nrad,dft.lmax,dft.x_func,dft.c_func,strictint);
if(dft.nl)
nlgrid.construct(dft.nlnrad,dft.nllmax,true,false,strictint,true);
}
f=solver.force_UDFT(sol,occa,occb,dft,grid,nlgrid,tol);
}
}
chkpt.write("Force",f);
chkpt.close();
return FORCECALC;
}
int main(int argc, char **argv) {
#ifdef _OPENMP
printf("ERKALE - EMD from Hel, OpenMP version, running on %i cores.\n",omp_get_max_threads());
#else
printf("ERKALE - EMD from Hel, serial version.\n");
#endif
print_copyright();
print_license();
#ifdef SVNRELEASE
printf("At svn revision %s.\n\n",SVNREVISION);
#endif
print_hostname();
if(argc!=1 && argc!=2) {
printf("Usage: $ %s (runfile)\n",argv[0]);
return 0;
}
Timer t;
// Parse settings
Settings set;
set.add_string("LoadChk","Checkpoint file to load density from","erkale.chk");
set.add_bool("DoEMD", "Perform calculation of isotropic EMD (moments of EMD, Compton profile)", true);
set.add_double("EMDTol", "Tolerance for the numerical integration of the radial EMD",1e-8);
set.add_string("EMDlm", "Which projection of the radial EMD to compute","");
set.add_bool("EMDAdapt", "Use adaptive grid to compute EMD?", true);
set.add_string("EMDCube", "Calculate EMD on a cube? e.g. -10:.3:10 -5:.2:4 -2:.1:3", "");
set.add_string("EMDOrbitals", "Compute EMD of given orbitals, e.g. 1,2,4:6","");
set.add_string("Similarity", "Compute similarity measure to checkpoint","");
set.add_string("SimilarityGrid", "Grid to use for computing similarity integrals","500 77");
set.add_bool("SimilarityLM", "Seminumerical computation of similarity integrals?", false);
set.add_int("SimilarityLmax", "Maximum angular momentum for seminumerical computation", 6);
if(argc==2)
set.parse(argv[1]);
else
printf("Using default settings.\n");
set.print();
// Get the tolerance
double tol=set.get_double("EMDTol");
// Load checkpoint
Checkpoint chkpt(set.get_string("LoadChk"),false);
// Load basis set
BasisSet basis;
chkpt.read(basis);
// Load density matrix
arma::cx_mat P;
arma::mat Pr, Pi;
chkpt.read("P",Pr);
if(chkpt.exist("P_im")) {
chkpt.read("P_im",Pi);
P=Pr*COMPLEX1 + Pi*COMPLEXI;
} else
P=Pr*COMPLEX1;
// The projection to calculate
int l=0, m=0;
std::string lmstr=set.get_string("EMDlm");
if(lmstr.size()) {
// Get l and m values
std::vector<std::string> lmval=splitline(lmstr);
if(lmval.size()!=2)
throw std::runtime_error("Invalid specification of l and m values.\n");
l=readint(lmval[0]);
m=readint(lmval[1]);
}
bool adaptive=set.get_bool("EMDAdapt");
// Compute orbital EMDs?
if(set.get_string("EMDOrbitals")!="") {
// Get orbitals
std::vector<std::string> orbs=splitline(set.get_string("EMDOrbitals"));
// Polarized calculation?
bool restr;
chkpt.read("Restricted",restr);
if(restr!= (orbs.size()==1))
throw std::runtime_error("Invalid occupancies for spin alpha and beta!\n");
if(l!=0)
printf("\nComputing the (%i %+i) projection of the orbital EMD.\n",l,m);
for(size_t ispin=0;ispin<orbs.size();ispin++) {
// Indices of orbitals to include.
std::vector<size_t> idx=parse_range(orbs[ispin]);
// Change into C++ indexing
for(size_t i=0;i<idx.size();i++)
idx[i]--;
// Read orbitals
arma::mat C;
if(restr)
chkpt.read("C",C);
else {
if(ispin==0)
chkpt.read("Ca",C);
else
chkpt.read("Cb",C);
}
for(size_t i=0;i<idx.size();i++) {
// Names of output files
char emdname[80];
char momname[80];
char Jname[80];
char Jintname[80];
char suffix[80];
if(l==0)
sprintf(suffix,".txt");
else
sprintf(suffix,"_%i_%i.txt",l,m);
if(restr) {
sprintf(emdname,"emd-%i%s",(int) idx[i]+1,suffix);
sprintf(momname,"moments-%i%s",(int) idx[i]+1,suffix);
sprintf(Jname,"compton-%i%s",(int) idx[i]+1,suffix);
sprintf(Jintname,"compton-interp-%i%s",(int) idx[i]+1,suffix);
} else {
if(ispin==0) {
sprintf(emdname,"emd-a-%i%s",(int) idx[i]+1,suffix);
sprintf(momname,"moments-a-%i%s",(int) idx[i]+1,suffix);
sprintf(Jname,"compton-a-%i%s",(int) idx[i]+1,suffix);
sprintf(Jintname,"compton-interp-a-%i%s",(int) idx[i]+1,suffix);
} else {
sprintf(emdname,"emd-b-%i%s",(int) idx[i]+1,suffix);
sprintf(momname,"moments-b-%i%s",(int) idx[i]+1,suffix);
sprintf(Jname,"compton-b-%i%s",(int) idx[i]+1,suffix);
sprintf(Jintname,"compton-interp-b-%i%s",(int) idx[i]+1,suffix);
}
}
// Generate dummy density matrix
arma::cx_mat Pdum=C.col(idx[i])*arma::trans(C.col(idx[i]))*COMPLEX1;
Timer temd;
GaussianEMDEvaluator *poseval=new GaussianEMDEvaluator(basis,Pdum,l,std::abs(m));
GaussianEMDEvaluator *negeval;
if(m!=0)
negeval=new GaussianEMDEvaluator(basis,Pdum,l,-std::abs(m));
else
negeval=NULL;
EMD emd(poseval, negeval, 1, l, m);
if(adaptive) {
emd.initial_fill();
if(l==0 && m==0) emd.find_electrons();
emd.optimize_moments(true,tol);
} else
emd.fixed_fill();
emd.save(emdname);
emd.moments(momname);
if(l==0 && m==0) {
emd.compton_profile(Jname);
emd.compton_profile_interp(Jintname);
}
delete poseval;
if(m!=0) delete negeval;
}
}
}
if(set.get_bool("DoEMD")) {
t.print_time();
printf("\nCalculating EMD properties.\n");
printf("Please read and cite the reference:\n%s\n%s\n%s\n", \
"J. Lehtola, M. Hakala, J. Vaara and K. Hämäläinen", \
"Calculation of isotropic Compton profiles with Gaussian basis sets", \
"Phys. Chem. Chem. Phys. 13 (2011), pp. 5630 - 5641.");
if(l!=0)
printf("\nComputing the (%i %+i) projection of the EMD.\n",l,m);
else
printf("\nComputing the isotropic projection of the EMD.\n");
// Amount of electrons is
int Nel;
chkpt.read("Nel",Nel);
// Construct EMD evaluators
Timer temd;
GaussianEMDEvaluator *poseval=new GaussianEMDEvaluator(basis,P,l,std::abs(m));
GaussianEMDEvaluator *negeval;
if(m!=0)
negeval=new GaussianEMDEvaluator(basis,P,l,-std::abs(m));
else
negeval=NULL;
temd.set();
EMD emd(poseval, negeval, Nel, l, m);
if(adaptive) {
emd.initial_fill();
if(l==0 && m==0) emd.find_electrons();
emd.optimize_moments(true,tol);
} else
emd.fixed_fill();
if(l==0 && m==0) {
emd.save("emd.txt");
emd.moments("moments.txt");
emd.compton_profile("compton.txt");
emd.compton_profile_interp("compton-interp.txt");
} else {
char fname[80];
sprintf(fname,"emd_%i_%i.txt",l,m);
emd.save(fname);
sprintf(fname,"moments_%i_%i.txt",l,m);
emd.moments(fname);
}
if(l==0 && m==0)
printf("Calculating isotropic EMD properties took %s.\n",temd.elapsed().c_str());
else
printf("Calculating projected EMD properties took %s.\n",temd.elapsed().c_str());
delete poseval;
if(m!=0) delete negeval;
}
// Do EMD on a cube?
if(stricmp(set.get_string("EMDCube"),"")!=0) {
t.print_time();
Timer temd;
// Form grid in p space.
std::vector<double> px, py, pz;
parse_cube(set.get_string("EMDCube"),px,py,pz);
// Calculate EMD on cube
emd_cube(basis,P,px,py,pz);
printf("Calculating EMD on a cube took %s.\n",temd.elapsed().c_str());
}
// Compute similarity?
if(stricmp(set.get_string("Similarity"),"")!=0) {
// Load checkpoint
Checkpoint simchk(set.get_string("Similarity"),false);
// Get grid size
std::vector<std::string> gridsize=splitline(set.get_string("SimilarityGrid"));
if(gridsize.size()!=2) {
throw std::runtime_error("Invalid grid size!\n");
}
int nrad=readint(gridsize[0]);
int lmax=readint(gridsize[1]);
int radlmax=set.get_int("SimilarityLmax");
// Load basis set
BasisSet simbas;
simchk.read(simbas);
// Load density matrix
arma::mat simPr, simPi;
arma::cx_mat simP;
simchk.read("P",simPr);
if(simchk.exist("P_im")) {
simchk.read("P_im",simPi);
simP=simPr*COMPLEX1 + simPi*COMPLEXI;
} else
simP=simPr*COMPLEX1;
// Compute momentum density overlap
arma::cube ovl;
if(set.get_bool("SimilarityLM"))
ovl=emd_overlap_semi(basis,P,simbas,simP,nrad,radlmax);
else
ovl=emd_overlap(basis,P,simbas,simP,nrad,lmax);
// Amount of electrons
int Nela, Nelb;
chkpt.read("Nel", Nela);
simchk.read("Nel", Nelb);
// Shape function overlap
arma::cube sh=emd_similarity(ovl,Nela,Nelb);
sh.slice(0).save("similarity.dat",arma::raw_ascii);
sh.slice(1).save("similarity_avg.dat",arma::raw_ascii);
for(int s=0;s<2;s++) {
if(s) {
printf("%2s\t%9s\t%9s\t%9s\t%9s\t%9s\t%9s\t%9s\n","k","S0(AA)","S0(BB)","S0(AB)","I0(AA)","I0(BB)","I0(AB)","D0(AB)");
for(int k=-1;k<3;k++)
// Vandenbussche don't include p^2 in the spherical average
printf("%2i\t%e\t%e\t%e\t%e\t%e\t%e\t%e\n", k+1, sh(k+1,0,s), sh(k+1,1,s), sh(k+1,2,s), sh(k+1,3,s), sh(k+1,4,s), sh(k+1,5,s), sh(k+1,6,s));
} else {
printf("%2s\t%9s\t%9s\t%9s\t%9s\t%9s\t%9s\t%9s\n","k","S(AA)","S(BB)","S(AB)","I(AA)","I(BB)","I(AB)","D(AB)");
for(int k=-1;k<3;k++)
printf("%2i\t%e\t%e\t%e\t%e\t%e\t%e\t%e\n", k, sh(k+1,0,s), sh(k+1,1,s), sh(k+1,2,s), sh(k+1,3,s), sh(k+1,4,s), sh(k+1,5,s), sh(k+1,6,s));
}
printf("\n");
}
}
return 0;
}
