void CodClassInstCanvas::save(QTextStream & st, bool ref, QString & warning) const {
if (ref)
st << "classinstance_ref " << get_ident() << " // "
<< full_name();
else if (browser_node->get_type() == UmlClass) {
nl_indent(st);
st << "classinstance " << get_ident() << ' ';
browser_node->save(st, TRUE, warning);
nl_indent(st);
ClassInstCanvas::save(st);
st << " name ";
save_string(iname, st);
st << ' ';
save_xyz(st, this, " xyz");
}
else {
nl_indent(st);
st << "classinstancecanvas " << get_ident() << ' ';
browser_node->save(st, TRUE, warning);
indent(+1);
nl_indent(st);
save_xyz(st, this, "xyz");
ClassInstCanvas::save(st);
save_stereotype_property(st, warning);
indent(-1);
nl_indent(st);
st << "end";
}
}
void CodDirsCanvas::save(QTextStream & st, bool ref, QString & warning) const
{
if (ref)
st << "dirscanvas_ref " << get_ident();
else {
nl_indent(st);
st << "dirscanvas " << get_ident() << " z " << zValue() << " ";
link->save(st, TRUE, warning);
indent(+1);
settings.save_msg(st);
if (label != 0) {
nl_indent(st);
st << "forward_label ";
save_string(label->get_name().toLatin1().constData(), st);
save_xyz(st, label, " xyz");
}
if (backward_label != 0) {
nl_indent(st);
st << "backward_label ";
save_string(backward_label->get_name().toLatin1().constData(), st);
save_xyz(st, backward_label, " xyz");
}
indent(-1);
}
}
void IconCanvas::save(Q3TextStream & st, bool, QString & warning) const {
nl_indent(st);
st << "iconcanvas " << get_ident() << ' ';
browser_node->save(st, TRUE, warning);
nl_indent(st);
save_xyz(st, this, " xyz");
}
void PseudoStateCanvas::save(QTextStream & st, bool ref, QString & warning) const {
if (ref) {
st << "pseudostatecanvas_ref " << get_ident() << " // "
<< browser_node->full_name();
}
else {
nl_indent(st);
st << "pseudostatecanvas " << get_ident() << ' ';
browser_node->save(st, TRUE, warning);
indent(+1);
nl_indent(st);
if (horiz)
st << "horizontal ";
if (manual_size)
save_xyzwh(st, this, " xyzwh");
else
save_xyz(st, this, " xyz");
if (label != 0)
save_xy(st, label, " label_xy");
save_stereotype_property(st, warning);
indent(-1);
nl_indent(st);
st << "end";
}
}
void SdObjCanvas::save(QTextStream & st) const {
if (mortal)
st << " mortal";
save_xyz(st, this, " xyz");
if (life_line->is_masked())
st << " life_line_masked";
st << " life_line_z " << life_line->z();
}
void ArrowJunctionCanvas::save(Q3TextStream & st, bool, QString & warning) const {
nl_indent(st);
st << "arrowjunctioncanvas " << get_ident() << ' ';
interface->save(st, TRUE, warning);
nl_indent(st);
save_xyz(st, this, " xyz");
save_xy(st, label, " label_xy");
}
void save_output()
{
if( xyz_file && (step % save_xyz_freq) == 0 ) save_xyz();
if( dcd_file && (step % save_dcd_freq) == 0 ) save_dcd();
if( enr_file && (step % save_enr_freq) == 0 ) save_energy();
if( (step % save_rst_freq) == 0 ) restart_write( rst_filename );/* must be last */
}
void SdLostFoundMsgSupportCanvas::save(QTextStream & st, bool ref, QString &) const {
if (ref)
st << "lostfoundmsgsupport_ref " << get_ident();
else {
nl_indent(st);
st << "lostfoundmsgsupport " << get_ident();
save_xyz(st, this, " xyz");
}
}
void HubCanvas::save(QTextStream & st, bool ref, QString &) const
{
if (ref)
st << "hubcanvas_ref " << get_ident();
else {
nl_indent(st);
st << "hubcanvas " << get_ident();
save_xyz(st, this, " xyz");
}
}
void ImageCanvas::save(QTextStream & st, bool ref, QString &) const {
if (ref) {
st << "image_ref " << get_ident();
}
else {
nl_indent(st);
st << "image " << get_ident() << ' ';
save_string(fromUnicode(path), st);
save_xyz(st, this, " xyz");
st << " end";
}
}
void LabelCanvas::save(QTextStream & st, bool, QString &) const
{
st << "label ";
save_string(text().toLatin1().constData(), st);
if (font().bold())
st << " bold";
if (font().italic())
st << " italic";
if (font().underline())
st << " underlined";
save_xyz(st, this, " xyz");
}
void ParameterSetCanvas::save(QTextStream & st, bool ref, QString & warning) const {
if (ref) {
st << "parametersetcanvas_ref " << get_ident() << " // "
<< browser_node->full_name();
}
else {
nl_indent(st);
st << "parametersetcanvas " << get_ident() << ' ';
browser_node->save(st, TRUE, warning);
nl_indent(st);
if (itscolor != UmlDefaultColor)
st << " color " << stringify(itscolor);
save_xyz(st, this, " xyz");
save_stereotype_property(st, warning);
nl_indent(st);
st << "end";
}
}
void UcClassCanvas::save(Q3TextStream & st, bool ref, QString & warning) const {
if (ref)
st << "classcanvas_ref " << get_ident() << " // " << browser_node->get_name();
else {
nl_indent(st);
st << "classcanvas " << get_ident() << ' ';
browser_node->save(st, TRUE, warning);
indent(+1);
settings.save(st);
nl_indent(st);
if (itscolor != UmlDefaultColor)
st << "color " << stringify(itscolor) << ' ';
save_xyz(st, this, "xyz");
save_stereotype_property(st, warning);
indent(-1);
nl_indent(st);
st << "end";
}
}
void SdMsgBaseCanvas::save(QTextStream & st, QString & warning) const {
nl_indent(st);
st << "to ";
dest->save(st, TRUE, warning);
nl_indent(st);
#ifdef FORCE_INT_COORD
// note : << float bugged in Qt 3.3.3
st << "yz " << (int) y() << ' ' << (int) z();
#else
QString sy, sz;
st << "yz " << sy.setNum(y()) << ' ' << sz.setNum(z());
#endif
if (msg != 0) {
// not a lost, dest is duration
if (msg->deletedp()) {
warning += QString("<b>") + the_canvas()->browser_diagram()->full_name() +
"</b> reference the class <b>" +
((SdDurationCanvas *) dest)->get_line()->get_obj()->get_class()->full_name() +
"</b> deleted operation <b>" + msg->definition(TRUE, FALSE) + "</b><br>\n<br>\n";
if (warning[0] == '!') {
st << " msg ";
msg->save(st, TRUE, warning);
}
else {
st << " explicitmsg ";
save_string(msg->get_browser_node()->get_name(), st);
}
}
else {
st << " msg ";
msg->save(st, TRUE, warning);
}
}
else if (! explicit_msg.isEmpty()) {
st << " explicitmsg ";
save_string(explicit_msg, st);
}
else
st << " unspecifiedmsg";
if (stereotype != 0) {
nl_indent(st);
st << "stereotype ";
save_string(stereotype->get_name(), st);
save_xyz(st, stereotype, " xyz");
}
nl_indent(st);
st << "show_full_operations_definition " << stringify(show_full_oper)
<< " drawing_language " << stringify(drawing_language)
<< " show_context_mode " << stringify(show_context_mode);
if (label != 0) {
if (! args.isEmpty()) {
nl_indent(st);
st << "args ";
save_string(args, st);
}
nl_indent(st);
save_xy(st, label, "label_xy");
}
}
int main(int argc, char **argv) {
#ifdef _OPENMP
printf("ERKALE - Geometry optimization from Hel, OpenMP version, running on %i cores.\n",omp_get_max_threads());
#else
printf("ERKALE - Geometry optimization 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 0;
}
// Initialize libint
init_libint_base();
// Initialize libderiv
init_libderiv_base();
Timer tprog;
tprog.print_time();
// Parse settings
Settings set;
set.add_scf_settings();
set.add_string("SaveChk","File to use as checkpoint","erkale.chk");
set.add_string("LoadChk","File to load old results from","");
set.add_bool("ForcePol","Force polarized calculation",false);
set.add_bool("FreezeCore","Freeze the atomic cores?",false);
set.add_string("Optimizer","Optimizer to use: CGFR, CGPR, BFGS, BFGS2 (default), SD","BFGS2");
set.add_int("MaxSteps","Maximum amount of geometry steps",256);
set.add_string("Criterion","Convergence criterion to use: LOOSE, NORMAL, TIGHT, VERYTIGHT","NORMAL");
set.add_string("OptMovie","xyz movie to store progress in","optimize.xyz");
set.add_string("Result","File to save optimized geometry in","optimized.xyz");
set.set_string("Logfile","erkale_geom.log");
set.parse(std::string(argv[1]),true);
set.print();
bool verbose=set.get_bool("Verbose");
int maxiter=set.get_int("MaxSteps");
std::string optmovie=set.get_string("OptMovie");
std::string result=set.get_string("Result");
// Interpret optimizer
enum minimizer alg;
std::string method=set.get_string("Optimizer");
if(stricmp(method,"CGFR")==0)
alg=gCGFR;
else if(stricmp(method,"CGPR")==0)
alg=gCGPR;
else if(stricmp(method,"BFGS")==0)
alg=gBFGS;
else if(stricmp(method,"BFGS2")==0)
alg=gBFGS2;
else if(stricmp(method,"SD")==0)
alg=gSD;
else {
ERROR_INFO();
throw std::runtime_error("Unknown optimization method.\n");
}
// Interpret optimizer
enum convergence crit;
method=set.get_string("Criterion");
if(stricmp(method,"LOOSE")==0)
crit=LOOSE;
else if(stricmp(method,"NORMAL")==0)
crit=NORMAL;
else if(stricmp(method,"TIGHT")==0)
crit=TIGHT;
else if(stricmp(method,"VERYTIGHT")==0)
crit=VERYTIGHT;
else {
ERROR_INFO();
throw std::runtime_error("Unknown optimization method.\n");
}
// Redirect output?
std::string logfile=set.get_string("Logfile");
if(stricmp(logfile,"stdout")!=0) {
// Redirect stdout to file
FILE *outstream=freopen(logfile.c_str(),"w",stdout);
if(outstream==NULL) {
ERROR_INFO();
throw std::runtime_error("Unable to redirect output!\n");
} else
fprintf(stderr,"\n");
}
// Read in atoms.
std::string atomfile=set.get_string("System");
const std::vector<atom_t> origgeom=load_xyz(atomfile);
std::vector<atom_t> atoms(origgeom);
// Are any atoms fixed?
std::vector<size_t> dofidx;
for(size_t i=0;i<atoms.size();i++) {
bool fixed=false;
if(atoms[i].el.size()>3)
if(stricmp(atoms[i].el.substr(atoms[i].el.size()-3),"-Fx")==0) {
fixed=true;
atoms[i].el=atoms[i].el.substr(0,atoms[i].el.size()-3);
}
// Add to degrees of freedom
if(!fixed)
dofidx.push_back(i);
}
// Read in basis set
BasisSetLibrary baslib;
std::string basfile=set.get_string("Basis");
baslib.load_gaussian94(basfile);
printf("\n");
// Save to output
save_xyz(atoms,"Initial configuration",optmovie,false);
// Minimizer options
opthelper_t pars;
pars.atoms=atoms;
pars.baslib=baslib;
pars.set=set;
pars.dofidx=dofidx;
/* Starting point */
gsl_vector *x = gsl_vector_alloc (3*dofidx.size());
for(size_t i=0;i<dofidx.size();i++) {
gsl_vector_set(x,3*i,atoms[dofidx[i]].x);
gsl_vector_set(x,3*i+1,atoms[dofidx[i]].y);
gsl_vector_set(x,3*i+2,atoms[dofidx[i]].z);
}
// GSL status
int status;
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
gsl_multimin_function_fdf minimizer;
minimizer.n = x->size;
minimizer.f = calc_E;
minimizer.df = calc_f;
minimizer.fdf = calc_Ef;
minimizer.params = (void *) &pars;
if(alg==gCGFR) {
T = gsl_multimin_fdfminimizer_conjugate_fr;
if(verbose) printf("Using Fletcher-Reeves conjugate gradients.\n");
} else if(alg==gCGPR) {
T = gsl_multimin_fdfminimizer_conjugate_pr;
if(verbose) printf("Using Polak-Ribière conjugate gradients.\n");
} else if(alg==gBFGS) {
T = gsl_multimin_fdfminimizer_vector_bfgs;
if(verbose) printf("Using the BFGS minimizer.\n");
} else if(alg==gBFGS2) {
T = gsl_multimin_fdfminimizer_vector_bfgs2;
if(verbose) printf("Using the BFGS2 minimizer.\n");
} else if(alg==gSD) {
T = gsl_multimin_fdfminimizer_steepest_descent;
if(verbose) printf("Using the steepest descent minimizer.\n");
} else {
ERROR_INFO();
throw std::runtime_error("Unsupported minimizer\n");
}
// Run an initial calculation
double oldE=calc_E(x,minimizer.params);
// Turn off verbose setting
pars.set.set_bool("Verbose",false);
// and load from old checkpoint
pars.set.set_string("LoadChk",pars.set.get_string("SaveChk"));
// Initialize minimizer
s = gsl_multimin_fdfminimizer_alloc (T, minimizer.n);
// Use initial step length of 0.02 bohr, and a line search accuracy
// 1e-1 (recommended in the GSL manual for BFGS)
gsl_multimin_fdfminimizer_set (s, &minimizer, x, 0.02, 1e-1);
// Store old force
arma::mat oldf=interpret_force(s->gradient);
fprintf(stderr,"Geometry optimizer initialized in %s.\n",tprog.elapsed().c_str());
fprintf(stderr,"Entering minimization loop with %s optimizer.\n",set.get_string("Optimizer").c_str());
fprintf(stderr,"%4s %16s %10s %10s %9s %9s %9s %9s %s\n","iter","E","dE","dE/dEproj","disp max","disp rms","f max","f rms", "titer");
std::vector<atom_t> oldgeom(atoms);
bool convd=false;
int iter;
for(iter=1;iter<=maxiter;iter++) {
printf("\nGeometry iteration %i\n",(int) iter);
fflush(stdout);
Timer titer;
status = gsl_multimin_fdfminimizer_iterate (s);
if (status) {
fprintf(stderr,"GSL encountered error: \"%s\".\n",gsl_strerror(status));
break;
}
// New geometry is
std::vector<atom_t> geom=get_atoms(s->x,pars);
// Calculate displacements
double dmax, drms;
get_displacement(geom, oldgeom, dmax, drms);
// Calculate projected change of energy
double dEproj=calculate_projection(geom,oldgeom,oldf,pars.dofidx);
// Actual change of energy is
double dE=s->f - oldE;
// Switch geometries
oldgeom=geom;
// Save old force
// Get forces
double fmax, frms;
get_forces(s->gradient, fmax, frms);
// Save geometry step
char comment[80];
sprintf(comment,"Step %i",(int) iter);
save_xyz(get_atoms(s->x,pars),comment,optmovie,true);
// Check convergence
bool fmaxconv=false, frmsconv=false;
bool dmaxconv=false, drmsconv=false;
switch(crit) {
case(LOOSE):
if(fmax < 2.5e-3)
fmaxconv=true;
if(frms < 1.7e-3)
frmsconv=true;
if(dmax < 1.0e-2)
dmaxconv=true;
if(drms < 6.7e-3)
drmsconv=true;
break;
case(NORMAL):
if(fmax < 4.5e-4)
fmaxconv=true;
if(frms < 3.0e-4)
frmsconv=true;
if(dmax < 1.8e-3)
dmaxconv=true;
if(drms < 1.2e-3)
drmsconv=true;
break;
case(TIGHT):
if(fmax < 1.5e-5)
fmaxconv=true;
if(frms < 1.0e-5)
frmsconv=true;
if(dmax < 6.0e-5)
dmaxconv=true;
if(drms < 4.0e-5)
drmsconv=true;
break;
case(VERYTIGHT):
if(fmax < 2.0e-6)
fmaxconv=true;
if(frms < 1.0e-6)
frmsconv=true;
if(dmax < 6.0e-6)
dmaxconv=true;
if(drms < 4.0e-6)
drmsconv=true;
break;
default:
ERROR_INFO();
throw std::runtime_error("Not implemented!\n");
}
// Converged?
const static char cconv[]=" *";
double dEfrac;
if(dEproj!=0.0)
dEfrac=dE/dEproj;
else
dEfrac=0.0;
fprintf(stderr,"%4d % 16.8f % .3e % .3e %.3e%c %.3e%c %.3e%c %.3e%c %s\n", (int) iter, s->f, dE, dEfrac, dmax, cconv[dmaxconv], drms, cconv[drmsconv], fmax, cconv[fmaxconv], frms, cconv[frmsconv], titer.elapsed().c_str());
fflush(stderr);
convd=dmaxconv && drmsconv && fmaxconv && frmsconv;
if(convd) {
fprintf(stderr,"Converged.\n");
break;
}
// Store old energy
oldE=s->f;
// Store old force
oldf=interpret_force(s->gradient);
}
if(convd)
save_xyz(get_atoms(s->x,pars),"Optimized geometry",result);
gsl_multimin_fdfminimizer_free (s);
gsl_vector_free (x);
if(iter==maxiter && !convd) {
printf("Geometry convergence was not achieved!\n");
}
printf("Running program took %s.\n",tprog.elapsed().c_str());
return 0;
}
