// Cleanup allocations done during evolve.
void gsl_gradient::cleanup(gsl_vector *x, gsl_multimin_fdfminimizer *s)
{
if (x) {
gsl_vector_free(x);
}
if (s) {
gsl_multimin_fdfminimizer_free(s);
}
}
GSLFDFSolver::~GSLFDFSolver()
{
if(gslSolver_ != NULL)
{
free(gslSolver_->x->block);
free(gslSolver_->gradient->block);
gsl_multimin_fdfminimizer_free(gslSolver_);
}
}
void GSLFDFSolver::doSetup_(const Function &objFunc,
const vector< double > &x0,
const Solver::Setup &solverSetup,
const Constraints &C)
{
const int n = objFunc.getN();
double stepSize, tol;
NativeGradientSolver::doSetup_(objFunc, x0, solverSetup, C);
if(typeid(solverSetup) == typeid(Solver::DefaultSetup))
{
stepSize = 1.0;
tol = 0.1;
}
else
{
stepSize = dynamic_cast< const GSLFDFSolver::Setup & >(solverSetup).stepSize;
tol = dynamic_cast< const GSLFDFSolver::Setup & >(solverSetup).tol;
}
if(gslSolver_ != NULL)
{
free(gslSolver_->x->block);
free(gslSolver_->gradient->block);
gsl_multimin_fdfminimizer_free(gslSolver_);
}
gslSolver_ = gsl_multimin_fdfminimizer_alloc(type_, n);
// THIS IS A HACK!
free(gslSolver_->x->block->data);
gslSolver_->x->data = gslSolver_->x->block->data = &state_.x[0];
gslSolver_->x->owner = 0;
gslSolver_->x->size = n;
gslSolver_->x->stride = 1;
free(gslSolver_->gradient->block->data);
gslSolver_->gradient->data = gslSolver_->gradient->block->data = &state_.g[0];
gslSolver_->gradient->owner = 0;
gslSolver_->gradient->size = n;
gslSolver_->gradient->stride = 1;
// !!!!!!!!!!!!!!!
gslFunction_.n = n;
gslFunction_.params = NULL;
gslFunction_.f = &gslutils::f;
// by using a pointer-to-member it would be something like this:
// (double (*)(const gsl_vector *, void *))(gslWrapper_.*(&GSLWrapper::f));
gslFunction_.df = &gslutils::df;
gslFunction_.fdf = &gslutils::fdf;
gslutils::setFunction(setup_->f);
gsl_vector *x0_ = gsl_vector_alloc(n);
gslutils::BoostToGSLVector(x0, x0_);
gsl_multimin_fdfminimizer_set(gslSolver_, &gslFunction_, x0_, stepSize, tol);
gsl_vector_free(x0_);
}
int
test_fdf(const char * desc,
gsl_multimin_function_fdf *f,
initpt_function initpt,
const gsl_multimin_fdfminimizer_type *T)
{
int status;
size_t iter = 0;
double step_size;
gsl_vector *x = gsl_vector_alloc (f->n);
gsl_multimin_fdfminimizer *s;
fcount = 0; gcount = 0;
(*initpt) (x);
step_size = 0.1 * gsl_blas_dnrm2 (x);
s = gsl_multimin_fdfminimizer_alloc(T, f->n);
gsl_multimin_fdfminimizer_set (s, f, x, step_size, 0.1);
#ifdef DEBUG
printf("x "); gsl_vector_fprintf (stdout, s->x, "%g");
printf("g "); gsl_vector_fprintf (stdout, s->gradient, "%g");
#endif
do
{
iter++;
status = gsl_multimin_fdfminimizer_iterate(s);
#ifdef DEBUG
printf("%i: \n",iter);
printf("x "); gsl_vector_fprintf (stdout, s->x, "%g");
printf("g "); gsl_vector_fprintf (stdout, s->gradient, "%g");
printf("f(x) %g\n",s->f);
printf("dx %g\n",gsl_blas_dnrm2(s->dx));
printf("\n");
#endif
status = gsl_multimin_test_gradient(s->gradient,1e-3);
}
while (iter < 5000 && status == GSL_CONTINUE);
status |= (fabs(s->f) > 1e-5);
gsl_test(status, "%s, on %s: %i iters (fn+g=%d+%d), f(x)=%g",
gsl_multimin_fdfminimizer_name(s),desc, iter, fcount, gcount, s->f);
gsl_multimin_fdfminimizer_free(s);
gsl_vector_free(x);
return status;
}
int
main (void)
{
size_t iter = 0;
int status;
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
/* Position of the minimum (1,2). */
double par[2] = { 1.0, 2.0 };
gsl_vector *x;
gsl_multimin_function_fdf my_func;
my_func.f = &my_f;
my_func.df = &my_df;
my_func.fdf = &my_fdf;
my_func.n = 2;
my_func.params = ∥
/* Starting point, x = (5,7) */
x = gsl_vector_alloc (2);
gsl_vector_set (x, 0, 5.0);
gsl_vector_set (x, 1, 7.0);
T = gsl_multimin_fdfminimizer_conjugate_fr;
s = gsl_multimin_fdfminimizer_alloc (T, 2);
gsl_multimin_fdfminimizer_set (s, &my_func, x, 0.01, 1e-4);
do
{
iter++;
status = gsl_multimin_fdfminimizer_iterate (s);
if (status)
break;
status = gsl_multimin_test_gradient (s->gradient, 1e-3);
if (status == GSL_SUCCESS)
printf ("Minimum found at:\n");
printf ("%5d %.5f %.5f %10.5f\n", iter,
gsl_vector_get (s->x, 0), gsl_vector_get (s->x, 1), s->f);
}
while (status == GSL_CONTINUE && iter < 100);
gsl_multimin_fdfminimizer_free (s);
gsl_vector_free (x);
return 0;
}
void MStep (Dataset *data)
{
double lastF;
int iter, status;
int numParams = data->num_labelers + data->num_beta;
gsl_vector *x;
gsl_multimin_fdfminimizer *s;
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_function_fdf obj_func;
gsl_set_error_handler_off();
// Pack parameters into a gsl_vector
x = gsl_vector_alloc(numParams);
packX(x, data);
std::cerr << "Packed" << std::endl;
// Initialize objective function
obj_func.n = numParams;
obj_func.f = &objective_function;
obj_func.df = &get_gradients;
obj_func.fdf = &set_functions;
obj_func.params = data;
// Initialize a minimizer
T = gsl_multimin_fdfminimizer_conjugate_pr;
s = gsl_multimin_fdfminimizer_alloc(T, numParams);
gsl_multimin_fdfminimizer_set(s, &obj_func, x, 0.01, 0.01);
iter = 0;
std::cerr << "Start optimization" << std::endl;
do {
lastF = s->f;
iter++;
printf("[MStep:%d] f=%f\n", iter, s->f);
status = gsl_multimin_fdfminimizer_iterate(s);
if (status) {
printf("Error occurred [MStep]\n");
break;
}
status = gsl_multimin_test_gradient(s->gradient, 1e-2);
if (status == GSL_SUCCESS) {
printf ("Minimum found");
}
} while (lastF - s->f > 1e-5 && status == GSL_CONTINUE && iter < 25);
/* Unpack alpha and beta from gsl_vector */
unpackX(s->x, data);
gsl_multimin_fdfminimizer_free(s);
gsl_vector_free(x);
}
double Fitting(FittinfPar *Par)
{
size_t iter = 0;
int status;
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
/* Starting point */
//adding on 2011.8.27
Par->Initial();
//////////////////
double a0=Error_std(Par)*0.6;
double b0=a0*0.4;
gsl_vector *v;
v=gsl_vector_alloc(2);
gsl_vector_set(v,0,a0);
gsl_vector_set(v,1,b0);
Par->a=a0;
Par->b=b0;
gsl_multimin_function_fdf my_func;
my_func.f = &IntR_Res_f;
my_func.df = &IntR_Res_df;
my_func.fdf = &IntR_Res_fdf;
my_func.n = 2;
my_func.params =(void *)Par;
T = gsl_multimin_fdfminimizer_vector_bfgs;
s = gsl_multimin_fdfminimizer_alloc(T,2);//3 是未知数个数
gsl_multimin_fdfminimizer_set(s,&my_func,v,0.01,1e-5);
do
{
iter++;
status = gsl_multimin_fdfminimizer_iterate(s);
if(status==GSL_ENOPROG)
{
Par->a=gsl_vector_get(s->x,0);
Par->b=gsl_vector_get(s->x,1);
break;
}
status = gsl_multimin_test_gradient(s->gradient,1e-6);
if(status == GSL_SUCCESS)
{
Par->a=gsl_vector_get(s->x,0);
Par->b=gsl_vector_get(s->x,1);
}
}while(status==GSL_CONTINUE&&iter<100);
//printf("Iter=%d\n",iter);
double breturn=IntR_Res_f(s->x,(void *)Par);
gsl_multimin_fdfminimizer_free(s);
gsl_vector_free(v);
//cal the goodness of fitting
return -breturn;
}
double GSLOptimizer::optimize(unsigned int iter,
const gsl_multimin_fdfminimizer_type*t,
double step, double param,
double min_gradient) {
fis_= get_optimized_attributes();
best_score_=std::numeric_limits<double>::max();
unsigned int n= get_dimension();
if (n ==0) {
IMP_LOG(TERSE, "Nothing to optimize" << std::endl);
return get_scoring_function()->evaluate(false);
}
gsl_multimin_fdfminimizer *s=gsl_multimin_fdfminimizer_alloc (t, n);
gsl_vector *x= gsl_vector_alloc(get_dimension());
gsl_multimin_function_fdf f= internal::create_function_data(this);
update_state(x);
gsl_multimin_fdfminimizer_set (s, &f, x, step, param);
try {
int status;
do {
--iter;
//update_state(x);
status = gsl_multimin_fdfminimizer_iterate(s);
update_states();
if (status) {
IMP_LOG(TERSE, "Ending optimization because of status "
<< status << std::endl);
break;
}
status = gsl_multimin_test_gradient (s->gradient, min_gradient);
if (status == GSL_SUCCESS) {
IMP_LOG(TERSE, "Ending optimization because of small gradient "
<< s->gradient << std::endl);
break;
}
} while (status == GSL_CONTINUE && iter >0);
} catch (AllDone){
}
gsl_vector *ret=gsl_multimin_fdfminimizer_x (s);
write_state(ret);
gsl_multimin_fdfminimizer_free (s);
gsl_vector_free (x);
return best_score_;
}
void optimize_alpha(gsl_vector * x, void * data, int n, gsl_vector * x2){
size_t iter = 0;
int status, j;
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
gsl_multimin_function_fdf my_func;
my_func.n = n;
my_func.f = my_f;
my_func.df = my_df;
my_func.fdf = my_fdf;
my_func.params = data;
T = gsl_multimin_fdfminimizer_conjugate_fr;
s = gsl_multimin_fdfminimizer_alloc (T, n);
gsl_multimin_fdfminimizer_set (s, &my_func, x, 0.01, 1e-3);
do{
iter++;
status = gsl_multimin_fdfminimizer_iterate (s);
//printf ("status = %s\n", gsl_strerror (status));
if (status){
if (iter == 1){
for (j = 0; j < n; j++){
gsl_vector_set(x2, j, gsl_vector_get(x, j));
}
}
break;
}
status = gsl_multimin_test_gradient (s->gradient, 1e-3);
if ((isnan(s->f)) || (isinf(s->f)))
break;
for (j = 0; j < n; j++){
gsl_vector_set(x2, j, gsl_vector_get(s->x, j));
}
}while (status == GSL_CONTINUE && iter < 100);
gsl_multimin_fdfminimizer_free (s);
}
static void optimise_lambda_k(double *adLambdaK, struct data_t *data,
double *adZ)
{
const int S = data->S;
int i, status;
size_t iter = 0;
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
gsl_multimin_function_fdf fdf;
gsl_vector *ptLambda;
/*initialise vector*/
ptLambda = gsl_vector_alloc(S);
for (i = 0; i < S; i++)
gsl_vector_set(ptLambda, i, adLambdaK[i]);
/*initialise function to be solved*/
data->adPi = adZ;
fdf.n = S;
fdf.f = neg_log_evidence_lambda_pi;
fdf.df = neg_log_derive_evidence_lambda_pi;
fdf.fdf = neg_log_FDF_lamba_pi;
fdf.params = data;
T = gsl_multimin_fdfminimizer_vector_bfgs2;
s = gsl_multimin_fdfminimizer_alloc(T, S);
gsl_multimin_fdfminimizer_set(s, &fdf, ptLambda, 1.0e-6, 0.1);
do {
iter++;
status = gsl_multimin_fdfminimizer_iterate(s);
if (status)
break;
status = gsl_multimin_test_gradient(s->gradient, 1e-3);
} while (status == GSL_CONTINUE && iter < MAX_GRAD_ITER);
for (i = 0; i < S; i++)
adLambdaK[i] = gsl_vector_get(s->x, i);
gsl_vector_free(ptLambda);
gsl_multimin_fdfminimizer_free(s);
}
void optimize_fdf(int dim,
gsl_vector* x,
void* params,
void (*fdf)(const gsl_vector*, void*, double*, gsl_vector*),
void (*df)(const gsl_vector*, void*, gsl_vector*),
double (*f)(const gsl_vector*, void*),
double* f_val,
double* conv_val,
int* niter) {
gsl_multimin_function_fdf obj;
obj.f = f;
obj.df = df;
obj.fdf = fdf;
obj.n = dim;
obj.params = params;
// const gsl_multimin_fdfminimizer_type * method =
// gsl_multimin_fdfminimizer_vector_bfgs;
const gsl_multimin_fdfminimizer_type * method =
gsl_multimin_fdfminimizer_conjugate_fr;
gsl_multimin_fdfminimizer * opt =
gsl_multimin_fdfminimizer_alloc(method, dim);
gsl_multimin_fdfminimizer_set(opt, &obj, x, 0.01, 1e-3);
int iter = 0, status;
double converged, f_old = 0;
do {
iter++;
status = gsl_multimin_fdfminimizer_iterate(opt);
// assert(status==0);
converged = fabs((f_old - opt->f) / (dim * f_old));
// status = gsl_multimin_test_gradient(opt->gradient, 1e-3);
// printf("f = %1.15e; conv = %5.3e; norm = %5.3e; niter = %03d\n",
// opt->f, converged, norm(opt->gradient), iter);
f_old = opt->f;
} while (converged > 1e-8 && iter < MAX_ITER);
// while (status == GSL_CONTINUE);
*f_val = opt->f;
*conv_val = converged;
*niter = iter;
gsl_multimin_fdfminimizer_free(opt);
}
void multidim_minimization_steepest_descent()
{
// Position of the minimum (1,2)
double par[2] = { 1.0, 2.0 };
gsl_multimin_function_fdf my_func;
my_func.f = &local::my_f;
my_func.df = &local::my_df;
my_func.fdf = &local::my_fdf;
my_func.n = 2; // the dimension of the system, i.e. the number of components of the vectors x
my_func.params = (void*)∥
// Starting point, x = (5,7)
gsl_vector *x = gsl_vector_alloc(2);
gsl_vector_set(x, 0, 5.0);
gsl_vector_set(x, 1, 7.0);
const gsl_multimin_fdfminimizer_type *T = gsl_multimin_fdfminimizer_steepest_descent;
gsl_multimin_fdfminimizer *s = gsl_multimin_fdfminimizer_alloc(T, 2);
gsl_multimin_fdfminimizer_set(s, &my_func, x, 0.01, 1e-4);
size_t iter = 0;
int status;
do
{
++iter;
status = gsl_multimin_fdfminimizer_iterate(s);
if (status)
break;
status = gsl_multimin_test_gradient(s->gradient, 1e-7);
if (status == GSL_SUCCESS)
printf("Minimum found at:\n");
printf("%5d %.5f %.5f %10.5f\n", iter,
gsl_vector_get(s->x, 0),
gsl_vector_get(s->x, 1),
s->f);
} while (status == GSL_CONTINUE && iter < 1000);
//
gsl_multimin_fdfminimizer_free(s);
gsl_vector_free(x);
}
/*
internal function used by get_theta_matrix(). Minimizes
the function func():
e0*cos(th0) + e1*cos(th1) + e2*cos(th0+th1+phi) for th0, th1
*/
void
minimize_for_thetas(gsl_vector *th, struct func_params *f_params)
{
const int niter = 10000;
const double eps = 1.e-5;
const gsl_multimin_fdfminimizer_type *minimizer_type;
gsl_multimin_fdfminimizer *minimizer;
int status;
size_t iter = 0;
const size_t n = 2;
gsl_multimin_function_fdf fdf =
{
&func,
&dfunc,
&funcdfunc,
n,
(void *)f_params
};
minimizer_type = gsl_multimin_fdfminimizer_conjugate_fr;
minimizer = gsl_multimin_fdfminimizer_alloc (minimizer_type, 2);
gsl_multimin_fdfminimizer_set (minimizer, &fdf, th, 0.1, eps);
do{
iter++;
status = gsl_multimin_fdfminimizer_iterate (minimizer);
if(status)
break;
status = gsl_multimin_test_gradient (minimizer->gradient, eps);
}while(status == GSL_CONTINUE && iter < niter);
if(status == GSL_CONTINUE){
fprintf(stderr," failed to find minimum in %s(), quitting\n", __func__);
exit(-3);
}
gsl_vector_set (th, 0, gsl_vector_get (minimizer->x, 0));
gsl_vector_set (th, 1, gsl_vector_get (minimizer->x, 1));
gsl_multimin_fdfminimizer_free (minimizer);
return;
}
~RatesEM()
{
//gsl_root_fdfsolver_free(sol_gene_rate);
gsl_root_fsolver_free(sol_gene_rate);
gsl_multimin_fdfminimizer_free(sol_sp_rate);
}
int
main (int argc, char *argv[])
{
int i;
int outp;
int n = atoi (argv[1]);
double x, y, z;
gsl_vector *r = gsl_vector_alloc (3 * n);
gsl_vector *dr = gsl_vector_alloc (3 * n);
double uu = 0;
double est;
double tmp1, tmp2;
FILE *in, *out;
//Reading input
in = fopen (argv[2], "r");
if (in != NULL)
{
out = fopen (argv[3], "w");
for (i = 0; i < n; i++)
{
outp = fscanf (in, "%lf %lf %lf", &x, &y, &z);
gsl_vector_set (r, 3 * i, x);
gsl_vector_set (r, 3 * i + 1, y);
gsl_vector_set (r, 3 * i + 2, z);
}
fclose (in);
//Initial energies and forces before optimization
gupta_fdf (r, &n, &uu, dr);
tmp1 = tmp2 = 0.0;
for (i = 0; i < 3 * n; i++)
{
tmp1 = gsl_vector_get (dr, i);
tmp2 += tmp1 * tmp1;
}
tmp2 = sqrt (tmp2);
fprintf (stdout,
"\n \nInitial Energy in file %s was E=%lf and the value of the norm of the gradient was |df|=%lf\n ",
argv[2], uu, tmp2);
//Setting the optimizer
size_t iter = 0;
int status;
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
gsl_multimin_function_fdf my_func;
my_func.n = 3 * n;
my_func.f = gupta_f;
my_func.df = gupta_df;
my_func.fdf = gupta_fdf;
my_func.params = &n;
T = gsl_multimin_fdfminimizer_vector_bfgs2;
s = gsl_multimin_fdfminimizer_alloc (T, 3 * n);
gsl_multimin_fdfminimizer_set (s, &my_func, r, 0.01, 1e-4);
//The actual optimization
do
{
iter++;
status = gsl_multimin_fdfminimizer_iterate (s);
if (status)
break;
status = gsl_multimin_test_gradient (s->gradient, 1e-6);
}
while (status == GSL_CONTINUE && iter < 10000);
est = gsl_multimin_fdfminimizer_minimum (s);
gsl_vector_memcpy (r, gsl_multimin_fdfminimizer_x (s));
//The values of the energies and forces after the optimization
gupta_fdf (r, &n, &uu, dr);
tmp1 = tmp2 = 0.0;
for (i = 0; i < 3 * n; i++)
{
tmp1 = gsl_vector_get (dr, i);
tmp2 += tmp1 * tmp1;
}
tmp2 = sqrt (tmp2);
fprintf (stdout,
"\n \nFinal Energy in file %s was E=%lf and the value of the norm of the gradient was |df|=%lf\n ",
argv[3], uu, tmp2);
for (i = 0; i < n; i++)
{
fprintf (out, "%.16e %.16e %.16e\n", gsl_vector_get (r, 3 * i),
gsl_vector_get (r, 3 * i + 1), gsl_vector_get (r,
3 * i + 2));
}
gsl_multimin_fdfminimizer_free (s);
gsl_vector_free (r);
}
else
{
fprintf (stdout, "The file %s was not found\n", argv[2]);
}
return 0;
}
int main(int argc, char *argv[]) {
struct RNAfold_args_info args_info;
char *string, *input_string, *structure=NULL, *cstruc=NULL;
char fname[80], ffname[80], gfname[80], *ParamFile=NULL;
char *ns_bases=NULL, *c;
int i, j, ii, jj, mu, length, l, sym, r, pf=0, noconv=0;
unsigned int input_type;
double energy, min_en, kT, sfact=1.07;
int doMEA=0, circular = 0, N;
char *pf_struc;
double dist;
plist *pl;
FILE * filehandle;
FILE * statsfile;
char* line;
double tau = 0.01; /* Variance of energy parameters */
double sigma = 0.01; /* Variance of experimental constraints */
double *gradient; /* Gradient for steepest descent search
epsilon[i+1]= epsilon[i] - gradient *
step_size */
double initial_step_size = 0.5; /* Initial step size for steepest
descent search */
double step_size;
double D; /* Discrepancy (i.e. value of objective
function) for the current
prediction */
int iteration, max_iteration = 2000; /* Current and maximum number of
iterations after which
algorithm stops */
double precision = 0.1; /* cutoff used for stop conditions */
double tolerance = 0.1; /* Parameter used by various GSL minimizers */
int method_id = 1; /* Method to use for minimization, 0 and 1
are custom steepest descent, the rest
are GSL implementations (see below)*/
int initial_guess_method = 0;
int sample_N = 1000;
double *prev_epsilon;
double *prev_gradient;
double DD, prev_D, sum, norm;
int status;
double* gradient_numeric;
double* gradient_numeric_gsl;
/* Minimizer vars */
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *minimizer;
gsl_vector *minimizer_x;
gsl_vector *minimizer_g;
gsl_multimin_function_fdf minimizer_func;
minimizer_pars_struct minimizer_pars;
char *constraints;
char outfile[256];
char constraints_file[256];
char epsilon_file[256];
FILE* fh;
double last_non_nan_lnQ;
pf_overflow = 0;
pf_underflow = 0;
dangles=2;
do_backtrack = 1;
string = NULL;
noPS = 0;
outfile[0]='\0';
epsilon_file[0]='\0';
strcpy(psDir, "dotplots");
if(RNAfold_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* RNAbpfold specific options */
if (args_info.tau_given) tau = args_info.tau_arg;
if (args_info.sigma_given) sigma = args_info.sigma_arg;
if (args_info.precision_given) precision = args_info.precision_arg;
if (args_info.step_given) initial_step_size = args_info.step_arg;
if (args_info.maxN_given) max_iteration = args_info.maxN_arg;
if (args_info.minimization_given) method_id = args_info.minimization_arg;
if (args_info.init_given) initial_guess_method = args_info.init_arg;
if (args_info.tolerance_given) tolerance = args_info.tolerance_arg;
if (args_info.outfile_given) strcpy(outfile, args_info.outfile_arg);
if (args_info.constraints_given) strcpy(constraints_file, args_info.constraints_arg);
if (args_info.epsilon_given) strcpy(epsilon_file, args_info.epsilon_arg);
if (args_info.sampleGradient_given) sample_conditionals=1;
if (args_info.hybridGradient_given) {
sample_conditionals=1;
hybrid_conditionals=1;
}
if (args_info.numericalGradient_given) numerical=1;
if (args_info.sampleStructure_given) sample_structure=1;
if (args_info.psDir_given) strcpy(psDir, args_info.psDir_arg);
if (args_info.sparsePS_given) sparsePS=args_info.sparsePS_arg;
if (args_info.gridSearch_given) grid_search = 1;
/* Generic RNAfold options */
if (args_info.temp_given) temperature = args_info.temp_arg;
if (args_info.reference_given) fold_constrained=1;
if (args_info.noTetra_given) tetra_loop=0;
if (args_info.dangles_given) dangles = args_info.dangles_arg;
if (args_info.noLP_given) noLonelyPairs = 1;
if (args_info.noGU_given) noGU = 1;
if (args_info.noClosingGU_given) no_closingGU = 1;
if (args_info.noconv_given) noconv = 1;
if (args_info.energyModel_given) energy_set = args_info.energyModel_arg;
if (args_info.paramFile_given) ParamFile = strdup(args_info.paramFile_arg);
if (args_info.nsp_given) ns_bases = strdup(args_info.nsp_arg);
if (args_info.pfScale_given) sfact = args_info.pfScale_arg;
if (args_info.noPS_given) noPS=1;
/* Create postscript directory */
if (!noPS) {
struct stat stat_p;
if (stat (psDir, &stat_p) != 0) {
if (mkdir(psDir, S_IRWXU|S_IROTH|S_IRGRP ) !=0) {
fprintf(stderr, "WARNING: Could not create directory: %s", psDir);
}
}
}
if (ParamFile != NULL) {
read_parameter_file(ParamFile);
}
if (ns_bases != NULL) {
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-') {
sym=1;
c++;
}
while (*c!='\0') {
if (*c!=',') {
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1))) {
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
/*Read sequence*/
fname[0] = '\0';
while((input_type = get_input_line(&input_string, 0)) & VRNA_INPUT_FASTA_HEADER) {
(void) sscanf(input_string, "%42s", fname);
free(input_string);
}
length = (int) strlen(input_string);
string = strdup(input_string);
free(input_string);
structure = (char *) space((unsigned) length+1);
/* For testing purpose pass dot bracket structure of reference structure via -C */
if (fold_constrained) {
input_type = get_input_line(&input_string, VRNA_INPUT_NOSKIP_COMMENTS);
if(input_type & VRNA_INPUT_QUIT) {
exit(1);
}
else if((input_type & VRNA_INPUT_MISC) && (strlen(input_string) > 0)) {
cstruc = strdup(input_string);
free(input_string);
}
else warn_user("-C was given but reference structure is missing");
}
if(noconv) {
str_RNA2RNA(string);
} else {
str_DNA2RNA(string);
}
/* Allocating space */
epsilon = (double *) space(sizeof(double)*(length+1));
exp_pert = (double **)space(sizeof(double *)*(length+1));
perturbations = (double **)space(sizeof(double *)*(length+1));
prev_epsilon = (double *) space(sizeof(double)*(length+1));
gradient = (double *) space(sizeof(double)*(length+1));
gradient_numeric = (double *) space(sizeof(double)*(length+1));
gradient_numeric_gsl = (double *) space(sizeof(double)*(length+1));
prev_gradient = (double *) space(sizeof(double)*(length+1));
q_unpaired = (double *) space(sizeof(double)*(length+1));
p_unpaired_cond = (double **)space(sizeof(double *)*(length+1));
p_unpaired_cond_sampled = (double **)space(sizeof(double *)*(length+1));
p_pp = (double **)space(sizeof(double *)*(length+1));
p_unpaired = (double *) space(sizeof(double)*(length+1));
p_unpaired_tmp = (double *) space(sizeof(double)*(length+1));
for (i=0; i <= length; i++) {
epsilon[i] = gradient[i] = q_unpaired[i] = 0.0;
p_unpaired_cond[i] = (double *) space(sizeof(double)*(length+1));
p_unpaired_cond_sampled[i] = (double *) space(sizeof(double)*(length+1));
p_pp[i] = (double *) space(sizeof(double)*(length+1));
exp_pert[i] = (double *) space(sizeof(double)*(length+1));
perturbations[i] = (double *) space(sizeof(double)*(length+1));
for (j=0; j <= length; j++) {
p_pp[i][j]=p_unpaired_cond[i][j] = 0.0;
p_unpaired_cond_sampled[i][j] = 0.0;
}
}
/*** If file with perturbation vector epsilon is given we fold using
this epsilon and are done ***/
if (args_info.epsilon_given) {
plist *pl, *pl1,*pl2;
filehandle = fopen (epsilon_file,"r");
if (filehandle == NULL) {
nrerror("Could not open file with perturbation vector.");
}
i=1;
while (1) {
double t;
line = get_line(filehandle);
if (line == NULL) break;
if (i>length) nrerror("Too many values in perturbation vector file.");
if (sscanf(line, "%lf", &epsilon[i]) !=1) {
nrerror("Error while reading perturbation vector file.");
}
i++;
}
if (i-1 != length) {
nrerror("Too few values in perturbation vector file.");
}
init_pf_fold(length);
pf_fold_pb(string, NULL);
sprintf(fname,"%s/dot.ps", psDir);
pl1 = make_plist(length, 1e-5);
(void) PS_dot_plot_list_epsilon(string, fname, NULL, pl1, epsilon, "");
exit(0);
}
/*** Get constraints from reference structure or from external file ***/
/* Structure was given by -C */
if (fold_constrained) {
for (i=0; i<length; i++) {
if (cstruc[i] == '(' || cstruc[i] == ')') {
q_unpaired[i+1] = 0.0;
} else {
q_unpaired[i+1] = 1.0;
}
}
/*Read constraints from file*/
} else {
filehandle = fopen (constraints_file,"r");
if (filehandle == NULL) {
nrerror("No constraints given as dot bracket or wrong file name");
}
i=1;
while (1) {
double t;
line = get_line(filehandle);
if (line == NULL) break;
if (i>length) nrerror("Too many values in constraints.dat");
if (sscanf(line, "%lf", &q_unpaired[i]) !=1) {
nrerror("Error while reading constraints.dat");
}
i++;
}
if (i-1 != length) {
nrerror("Too few values in constraints.dat");
}
}
/* Create file handle */
if (outfile[0] !='\0') {
statsfile = fopen (outfile,"w");
} else {
statsfile = fopen ("stats.dat","w");
}
setvbuf(statsfile, NULL, _IONBF, 0);
if (!grid_search) {
fprintf(statsfile, "Iteration\tDiscrepancy\tNorm\tdfCount\tMEA\tSampled_structure\tSampled_energy\tSampled_distance\tEpsilon\ttimestamp\n");
} else {
/* If we do a grid search we have a different output. */
fprintf(statsfile, "Dummy\tm\tb\tdummy\tMEA\tepsilon\n");
}
if (statsfile == NULL) {
nrerror("Could not open stats.dat for writing.");
}
fprintf(stderr, "tau^2 = %.4f; sigma^2 = %.4f; precision = %.4f; tolerance = %.4f; step-size: %.4f\n\n",
tau, sigma, precision, tolerance, initial_step_size);
st_back=1;
min_en = fold(string, structure);
(void) fflush(stdout);
if (length>2000) free_arrays();
pf_struc = (char *) space((unsigned) length+1);
kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
/* Set up minimizer */
minimizer_x = gsl_vector_alloc (length+1);
minimizer_g = gsl_vector_alloc (length+1);
for (i=0; i <= length; i++) {
epsilon[i] = 0.0;
gsl_vector_set (minimizer_g, i, 0.0);
gsl_vector_set (minimizer_x, i, epsilon[i]);
}
minimizer_pars.length=length;
minimizer_pars.seq = string;
minimizer_pars.tau=tau;
minimizer_pars.sigma=sigma;
minimizer_pars.kT=kT;
minimizer_func.n = length+1;
minimizer_func.f = calculate_f;
minimizer_func.df = numerical ? calculate_df_numerically: calculate_df;
minimizer_func.fdf = calculate_fdf;
minimizer_func.params = &minimizer_pars;
//min_en = fold_pb(string, structure);
//fprintf(stderr, "%f", min_en);
//exit(0);
/* Calling test functions for debugging */
for (i=1; i <= length; i++) {
if (i%2==0) {
epsilon[i] = +0.2*i;
} else {
epsilon[i] = -0.2*i;
}
}
//test_folding(string, length);
/* //test_stochastic_backtracking(string, length); */
/* //test_gradient(minimizer_func, minimizer_pars); */
/* //test_gradient_sampling(minimizer_func, minimizer_pars); */
//exit(1);
count_df_evaluations=0;
/* Initial guess for epsilon */
if (initial_guess_method !=0 && initial_guess_method !=3) {
/* Vars for inital guess methods */
double m,b;
double* curr_epsilon;
double* best_epsilon;
double best_m, best_b, best_scale;
double curr_D;
double min_D = 999999999.0;
double inc = +0.25;
double cut;
if (initial_guess_method == 1) fprintf(stderr, "Mathew's constant perturbations\n");
if (initial_guess_method == 2) fprintf(stderr, "Perturbations proportional to q-p\n");
curr_epsilon = (double *) space(sizeof(double)*(length+1));
best_epsilon = (double *) space(sizeof(double)*(length+1));
last_non_nan_lnQ = min_en;
// Calculate p_unpaired for unperturbed state which we need later
// for the proportinal method
if (initial_guess_method == 2) {
init_pf_fold(length);
for (i=0; i <= length; i++) {
epsilon[i] = 0.0;
}
pf_fold_pb(string, NULL);
for (i = 1; i < length; i++) {
for (j = i+1; j<= length; j++) {
p_pp[i][j]=p_pp[j][i]=pr[iindx[i]-j];
}
}
get_pair_prob_vector(p_pp, p_unpaired_tmp, length, 1);
free_pf_arrays();
}
/* We do the same grid search as in the Mathews paper Fig. 4*/
for (m=0.25; m <=7.0; m+=0.25) {
// Weird way of writing this inner loop for the grid search. We
// traverse the grid without big jumps in the parameters to make
// sure that the updated scaling factor is accurate all the time.
inc*=-1;
for (b = inc < 0.0 ? 0.0 : -3.0; inc < 0.0 ? b >= -3.0 : b<= 0.0 ; b+=inc) {
// calculate cut point with x-axis and skip parameter pairs
// which give a cut point outside the range of
// q_unpaired (0 to 1). They gave frequently overflows and the
// idea is that we both want positive and negative perturbations
cut = exp( (-1) * b / m ) - 1;
fprintf(stderr, "\nm = %.2f, b = %.2f, cut=%.2f\n", m, b, cut);
if (cut > 1.0 || cut < 0.01) {
fprintf(stderr, "\nSkipping m = %.2f, b = %.2f\n", m, b);
continue;
}
/* Mathew's constant perturbations */
if (initial_guess_method == 1) {
for (i=0; i <= length; i++) {
/* We add epsilon to unpaired regions (as opposed to
paired regions as in the Mathews paper) so we multiply
by -1; if missing data we set it to 0.0 */
if (q_unpaired[i] < -0.5) {
curr_epsilon[i] = 0.0;
} else {
curr_epsilon[i] = (m *(log(q_unpaired[i]+1))+b) *(-1);
}
gsl_vector_set (minimizer_x, i, curr_epsilon[i]);
}
/* Perturbations proportional to q-p */
} else {
for (i=0; i <= length; i++) {
curr_epsilon[i] = (m *(log(q_unpaired[i]+1)-log(p_unpaired_tmp[i]+1))+ b ) * (-1);
gsl_vector_set (minimizer_x, i, curr_epsilon[i]);
}
}
// Repeat and adjust scaling factor until we get result without over-/underflows
do {
// First we use default scaling factor
if (pf_underflow == 0 && pf_overflow == 0) {
sfact = 1.070;
}
if (pf_underflow) {
sfact *= 0.8;
fprintf(stderr,"Underflow, adjusting sfact to %.4f\n", sfact );
}
if (pf_overflow) {
sfact *= 1.2;
fprintf(stderr,"Overflow, adjusting sfact to %.4f\n", sfact );
}
pf_scale = exp(-(sfact*last_non_nan_lnQ)/kT/length);
//fprintf(stderr,"Scaling factor is now: %.4e\n", pf_scale);
curr_D = calculate_f(minimizer_x, (void*)&minimizer_pars);
if (!isnan(last_lnQ)) last_non_nan_lnQ = last_lnQ;
// Give up when even extreme scaling does not give results
// (for some reason I could not get rid of overflows even with high scaling factors)
if (sfact < 0.1 || sfact > 2.0) break;
} while (pf_underflow == 1 || pf_overflow == 1);
// We have not given up so everything is ok now
if (!(sfact < 0.1 || sfact > 2.0)) {
if (curr_D < min_D) {
min_D = curr_D;
for (i=0; i <= length; i++) {
best_epsilon[i] = curr_epsilon[i];
}
best_m = m;
best_b = b;
best_scale = pf_scale;
}
/*If we are interested in the grid search we misuse the
print_stats function and report m and b together with MEA*/
if (grid_search) {
for (i=0; i <= length; i++) {
epsilon[i] = curr_epsilon[i];
}
print_stats(statsfile, string, cstruc, length, 0, 0, m, 0.0, b, 0);
}
fprintf(stderr, "curr D: %.2f, minimum D: %.2f\n", curr_D, min_D);
// Adjust pf_scale with default scaling factor but lnQ from
// previous step
sfact = 1.070;
pf_scale = exp(-(sfact*last_lnQ)/kT/length);
} else {
sfact = 1.070;
fprintf(stderr, "Skipping m = %.2f, b = %.2f; did not get stable result.\n", m, b);
}
} // for b
} // for m
fprintf(stderr, "Minimum found: m=%.2f, b=%.2f: %.2f\n", best_m, best_b, min_D);
for (i=0; i <= length; i++) {
epsilon[i] = best_epsilon[i];
gsl_vector_set (minimizer_x, i, best_epsilon[i]);
}
pf_scale = best_scale;
}
if (initial_guess_method == 3) {
srand((unsigned)time(0));
for (i=0; i <= length; i++) {
double r = (double)rand()/(double)RAND_MAX * 4 - 2;
epsilon[i] = r;
gsl_vector_set (minimizer_x, i, epsilon[i]);
}
}
/* If we just wanted a grid search we are done now. */
if (grid_search) {
exit(0);
}
prev_D = calculate_f(minimizer_x, (void*)&minimizer_pars);
print_stats(statsfile, string, cstruc, length, 0 , count_df_evaluations , prev_D, -1.0, 0.0,1);
/* GSL minimization */
if (method_id !=0) {
if (method_id > 2) {
char name[100];
// Available algorithms
// 3 gsl_multimin_fdfminimizer_conjugate_fr
// 4 gsl_multimin_fdfminimizer_conjugate_pr
// 5 gsl_multimin_fdfminimizer_vector_bfgs
// 6 gsl_multimin_fdfminimizer_vector_bfgs2
// 7 gsl_multimin_fdfminimizer_steepest_descent
// http://www.gnu.org/software/gsl/manual/html_node/Multimin-Algorithms-with-Derivatives.html
switch (method_id) {
case 2:
minimizer = gsl_multimin_fdfminimizer_alloc (gsl_multimin_fdfminimizer_conjugate_fr, length+1);
strcpy(name, "Fletcher-Reeves conjugate gradient");
break;
case 3:
minimizer = gsl_multimin_fdfminimizer_alloc (gsl_multimin_fdfminimizer_conjugate_pr, length+1);
strcpy(name, "Polak-Ribiere conjugate gradient");
break;
case 4:
minimizer = gsl_multimin_fdfminimizer_alloc ( gsl_multimin_fdfminimizer_vector_bfgs, length+1);
strcpy(name, "Broyden-Fletcher-Goldfarb-Shanno");
break;
case 5:
minimizer = gsl_multimin_fdfminimizer_alloc ( gsl_multimin_fdfminimizer_vector_bfgs2, length+1);
strcpy(name, "Broyden-Fletcher-Goldfarb-Shanno (improved version)");
break;
case 6:
minimizer = gsl_multimin_fdfminimizer_alloc (gsl_multimin_fdfminimizer_steepest_descent, length+1);
strcpy(name, "Gradient descent (GSL implmementation)");
break;
}
fprintf(stderr, "Starting minimization via GSL implementation of %s...\n\n", name);
// The last two parmeters are step size and tolerance (with
// different meaning for different algorithms
gsl_multimin_fdfminimizer_set (minimizer, &minimizer_func, minimizer_x, initial_step_size, tolerance);
iteration = 1;
do {
status = gsl_multimin_fdfminimizer_iterate (minimizer);
D = minimizer->f;
norm = gsl_blas_dnrm2(minimizer->gradient);
print_stats(statsfile, string, cstruc, length,iteration, count_df_evaluations, D, prev_D, norm, iteration%sparsePS == 0);
prev_D = D;
if (status) {
fprintf(stderr, "An unexpected error has occured in the iteration (status:%i)\n", status);
break;
}
status = gsl_multimin_test_gradient (minimizer->gradient, precision);
if (status == GSL_SUCCESS) fprintf(stderr, "Minimum found stopping.\n");
iteration++;
} while (status == GSL_CONTINUE && iteration < max_iteration);
gsl_multimin_fdfminimizer_free (minimizer);
gsl_vector_free (minimizer_x);
/* Custom implementation of steepest descent */
} else {
if (method_id == 1) {
fprintf(stderr, "Starting custom implemented steepest descent search...\n\n");
} else {
fprintf(stderr, "Starting custom implemented steepest descent search with Barzilai Borwein step size...\n\n");
}
iteration = 0;
D = 0.0;
while (iteration++ < max_iteration) {
for (i=1; i <= length; i++) {
gsl_vector_set (minimizer_x, i, epsilon[i]);
}
D = calculate_f(minimizer_x, (void*)&minimizer_pars);
if (numerical) {
calculate_df_numerically(minimizer_x, (void*)&minimizer_pars, minimizer_g);
} else {
calculate_df(minimizer_x, (void*)&minimizer_pars, minimizer_g);
}
for (i=1; i <= length; i++) {
gradient[i] = gsl_vector_get (minimizer_g, i);
}
// Do line search
fprintf(stderr, "\nLine search:\n");
// After the first iteration, use Barzilai-Borwain (1988) step size (currently turned off)
if (iteration>1 && method_id==2) {
double denominator=0.0;
double numerator=0.0;
for (i=1; i <= length; i++) {
numerator += (epsilon[i]-prev_epsilon[i]) * (gradient[i]-prev_gradient[i]);
denominator+=(gradient[i]-prev_gradient[i]) * (gradient[i]-prev_gradient[i]);
}
step_size = numerator / denominator;
norm =1.0;
} else {
// Use step sized given by the user (normalize it first)
step_size = initial_step_size / calculate_norm(gradient, length);
}
for (i=1; i <= length; i++) {
prev_epsilon[i] = epsilon[i];
prev_gradient[i] = gradient[i];
}
do {
for (mu=1; mu <= length; mu++) {
epsilon[mu] = prev_epsilon[mu] - step_size * gradient[mu];
}
for (i=1; i <= length; i++) {
gsl_vector_set (minimizer_x, i, epsilon[i]);
}
DD = calculate_f(minimizer_x, (void*)&minimizer_pars);
if (step_size > 0.0001) {
fprintf(stderr, "Old D: %.4f; New D: %.4f; Step size: %.4f\n", D, DD, step_size);
} else {
fprintf(stderr, "Old D: %.4f; New D: %.4f; Step size: %.4e\n", D, DD, step_size);
}
step_size /= 2;
} while (step_size > 1e-12 && DD > D);
norm = calculate_norm(gradient,length);
if (DD > D) {
fprintf(stderr, "Line search did not improve D in iteration %i. Stop.\n", iteration);
if (hybrid_conditionals) {
sample_conditionals=0;
} else {
break;
}
}
print_stats(statsfile, string, cstruc, length,iteration, count_df_evaluations, DD, prev_D, norm, iteration%sparsePS == 0);
if (norm<precision && iteration>1) {
fprintf(stderr, "Minimum found stopping.\n");
break;
}
prev_D = DD;
}
}
/* Force last dotplot to be printed */
print_stats(statsfile, string, cstruc, length,iteration, count_df_evaluations, DD, prev_D, norm, 1);
}
free(pf_struc);
if (cstruc!=NULL) free(cstruc);
(void) fflush(stdout);
free(string);
free(structure);
RNAfold_cmdline_parser_free (&args_info);
return 0;
}
void
multimin(size_t n,double *x,double *fun,
const unsigned *type, const double *xmin,const double *xmax,
void (*f) (const size_t,const double *,void *,double *),
void (* df) (const size_t,const double *, void *,double *),
void (* fdf) (const size_t,const double *, void *,double *,double *),
void *fparams,
const struct multimin_params oparams)
{
unsigned iter=0;
int status;
size_t i;
double dtmp1;
const gsl_multimin_fdfminimizer_type *Tfdf;
const gsl_multimin_fminimizer_type *Tf;
const char *Tname;
gsl_vector * y = gsl_vector_alloc (n);
/* set the algorithm */
switch(oparams.method){
case 0:/* Fletcher-Reeves conjugate gradient */
Tfdf = gsl_multimin_fdfminimizer_conjugate_fr;
Tname = Tfdf->name;
break;
case 1:/* Polak-Ribiere conjugate gradient */
Tfdf = gsl_multimin_fdfminimizer_conjugate_pr;
Tname = Tfdf->name;
break;
case 2:/* Vector Broyden-Fletcher-Goldfarb-Shanno method */
Tfdf = gsl_multimin_fdfminimizer_vector_bfgs;
Tname = Tfdf->name;
break;
case 3:/* Steepest descent algorithm */
Tfdf =gsl_multimin_fdfminimizer_steepest_descent;
Tname = Tfdf->name;
break;
case 4:/* Simplex */
Tf = gsl_multimin_fminimizer_nmsimplex2;
Tname = Tf->name;
break;
case 5:/* Vector Broyden-Fletcher-Goldfarb-Shanno2 method */
Tfdf = gsl_multimin_fdfminimizer_vector_bfgs2;
Tname = Tfdf->name;
break;
default:
fprintf(stderr,"Optimization method not recognized. Try -h\n");
exit(EXIT_FAILURE);
}
/* --- OUPUT ---------------------------------- */
if(oparams.verbosity>0){
fprintf(stderr,"#--- MULTIMIN START\n");
fprintf(stderr,"# method %s\n",Tname);
if(oparams.method<4 || oparams.method==5){
fprintf(stderr,"# initial step size %g\n", oparams.step_size);
fprintf(stderr,"# line minimization tolerance %g\n",oparams.tol);
fprintf(stderr,"# maximum number of iterations %u\n",oparams.maxiter);
fprintf(stderr,"# precision %g\n",oparams.epsabs);
}
else{
fprintf(stderr,"# maximum number of iterations %u\n",oparams.maxiter);
fprintf(stderr,"# maximum simplex size %g\n",oparams.maxsize);
}
}
/* -------------------------------------------- */
/* compute values of y for initial condition */
for(i=0;i<n;i++){
if(type==NULL)
SET(y,i,x[i]);
else
switch(type[i]){
case 0:/* (-inf,+inf) */
SET(y,i,x[i]);
break;
case 1:/* [a,+inf) */
SET(y,i,sqrt( x[i]-xmin[i] ));
break;
case 2:/* (-inf,a] */
SET(y,i,sqrt( xmax[i]-x[i] ));
break;
case 3:/* [a,b] */
dtmp1 = (xmax[i]>xmin[i]?
(2.*x[i]-xmax[i]-xmin[i])/(xmax[i]-xmin[i]) : 0);
/* dtmp1 = (2.*x[i]-xmax[i]-xmin[i])/(xmax[i]-xmin[i]); */
SET(y,i,asin( dtmp1 ));
break;
case 4:/* (a,+inf) */
SET(y,i,log( x[i]-xmin[i] ));
break;
case 5:/* (-inf,a) */
SET(y,i,log( xmax[i]-x[i] ));
break;
case 6:/* (a,b) */
dtmp1 = (2.*x[i]-xmax[i]-xmin[i])/(xmax[i]-xmin[i]);
SET(y,i,gsl_atanh ( dtmp1 ));
break;
case 7:/* (a,b) second approach */
dtmp1 = (2.*x[i]-xmax[i]-xmin[i])/(xmax[i]-xmin[i]);
SET(y,i, dtmp1/sqrt(1-dtmp1*dtmp1));
break;
case 8:/* (a,+inf) second approach */
dtmp1 = x[i]-xmin[i];
SET(y,i, dtmp1-1./(4.*dtmp1));
break;
}
}
/* --- OUPUT ---------------------------------- */
if(oparams.verbosity>1){
fprintf(stderr,"# - variables initial value and boundaries\n");
for(i=0;i<n;i++){
if(type==NULL)
fprintf(stderr,"# x[%d]=%e (-inf,+inf) -> %e\n",(int) i,x[i],GET(y,i));
else
switch(type[i]){
case 0:/* (-inf,+inf) */
fprintf(stderr,"# x[%d]=%e (-inf,+inf) -> %e\n",(int) i,x[i],GET(y,i));
break;
case 1:/* [a,+inf) */
fprintf(stderr,"# x[%d]=%e [%g,+inf) -> %e\n",(int) i,x[i],xmin[i],GET(y,i));
break;
case 2:/* (-inf,a] */
fprintf(stderr,"# x[%d]=%e (-inf,%g] -> %e\n",(int) i,x[i],xmax[i],GET(y,i));
break;
case 3:/* [a,b] */
fprintf(stderr,"# x[%d]=%e [%g,%g] -> %e\n",(int) i,x[i],xmin[i],xmax[i],GET(y,i));
break;
case 4:/* (a,+inf) */
fprintf(stderr,"# x[%d]=%e (%g,+inf) -> %e\n",(int) i,x[i],xmin[i],GET(y,i));
break;
case 5:/* (-inf,a) */
fprintf(stderr,"# x[%d]=%e (-inf,%g) -> %e\n",(int) i,x[i],xmax[i],GET(y,i));
break;
case 6:/* (a,b) */
case 7:
fprintf(stderr,"# x[%d]=%e (%g,%g) -> %e\n",(int) i,x[i],xmin[i],xmax[i],GET(y,i));
break;
case 8:/* [a,+inf) */
fprintf(stderr,"# x[%d]=%e (%g,+inf) -> %e\n",(int) i,x[i],xmin[i],GET(y,i));
break;
}
}
{
double res;
fprintf(stderr,"# - function initial value\n");
f(n,x,fparams,&res);
fprintf(stderr,"# f=%e\n",res);
}
}
/* -------------------------------------------- */
if(oparams.method<4 || oparams.method==5){/* methods with derivatives */
struct g_params gparams;
gsl_multimin_function_fdf GdG;
gsl_multimin_fdfminimizer *s = gsl_multimin_fdfminimizer_alloc (Tfdf,n);
/* set the parameters of the new function */
gparams.n = n;
gparams.type = type;
gparams.xmin = xmin;
gparams.xmax = xmax;
gparams.f = f;
gparams.df = df;
gparams.fdf = fdf;
gparams.fparams = fparams;
/* set the function to solve */
GdG.f=g;
GdG.df=dg;
GdG.fdf=gdg;
GdG.n=n;
GdG.params=(void *) &gparams;
/* initialize minimizer */
status=gsl_multimin_fdfminimizer_set(s,&GdG,y,oparams.step_size,oparams.tol);
if(status)
{
fprintf(stderr,"#ERROR: %s\n",gsl_strerror (status));
exit(EXIT_FAILURE);
}
/* +++++++++++++++++++++++++++++++++++++++++++++++ */
if(oparams.verbosity>2)
fprintf(stderr,"# - start minimization \n");
/* +++++++++++++++++++++++++++++++++++++++++++++++ */
do
{
iter++;
status = gsl_multimin_fdfminimizer_iterate (s);
/* +++++++++++++++++++++++++++++++++++++++++++++++ */
if(oparams.verbosity>2){
fprintf(stderr,"# [%d]",iter);
fprintf(stderr," g=%+12.6e y=( ",s->f);
for(i=0;i<n;i++)
fprintf(stderr,"%+12.6e ",GET(s->x,i));
fprintf(stderr,") dg=( ");
for(i=0;i<n;i++)
fprintf(stderr,"%+12.6e ",GET(s->gradient,i));
fprintf(stderr,") |dg|=%12.6e ",gsl_blas_dnrm2 (s->gradient));
fprintf(stderr,"|dx|=%12.6e\n",gsl_blas_dnrm2 (s->dx));
}
/* +++++++++++++++++++++++++++++++++++++++++++++++ */
if(status == GSL_ENOPROG){
fprintf(stderr,"# status: %s\n",gsl_strerror (status));
break;
}
if(status){
fprintf(stderr,"#WARNING: %s\n", gsl_strerror (status));
break;
}
/* { */
/* const double eps = oparams.epsabs; */
/* const double norm_x = gsl_blas_dnrm2 (s->x); */
/* const double norm_dx = gsl_blas_dnrm2 (s->dx); */
/* const double norm_g = gsl_blas_dnrm2 (s->gradient); */
/* if( norm_dx < eps && norm_dx < norm_x*eps && norm_g < eps ) */
/* status = GSL_SUCCESS; */
/* else */
/* status = GSL_CONTINUE; */
/* fprintf(stderr,"|x|=%f |dx|=%f |dg|=%f\n",norm_x,norm_dx,norm_g); */
/* } */
status = gsl_multimin_test_gradient (s->gradient,oparams.epsabs);
}
while (status == GSL_CONTINUE && iter < oparams.maxiter);
gsl_vector_memcpy (y,s->x);
*fun=s->f;
gsl_multimin_fdfminimizer_free (s);
}
else{ /* methods without derivatives */
gsl_vector *ss = gsl_vector_alloc (n);
struct g_params gparams;
gsl_multimin_function G;
gsl_multimin_fminimizer *s=gsl_multimin_fminimizer_alloc (Tf,n);
/* set the parameters of the new function */
gparams.n = n;
gparams.type = type;
gparams.xmin = xmin;
gparams.xmax = xmax;
gparams.f = f;
gparams.fparams = fparams;
/* set the function to solve */
G.f=g;
G.n=n;
G.params=(void *) &gparams;
/* Initial vertex size vector */
{
/* size_t i; */
/* dg(y,&gparams,ss); */
/* gsl_vector_set_all (ss,1); */
/* for(i=0;i<n;i++) */
/* SET(ss,i,fabs(GET(ss,i))); */
/* gsl_vector_add_constant (ss,oparams.maxsize); */
gsl_vector_set_all (ss,oparams.step_size+oparams.maxsize);
}
/* --- OUPUT ---------------------------------- */
if(oparams.verbosity>0){
size_t i;
fprintf(stderr,"# initial simplex sizes\n");
fprintf(stderr,"# ");
for(i=0;i<n;i++)
fprintf(stderr," %g", GET(ss,i));
fprintf(stderr,"\n");
}
/* -------------------------------------------- */
/* Initialize minimizer */
status=gsl_multimin_fminimizer_set(s,&G,y,ss);
do
{
status = gsl_multimin_fminimizer_iterate(s);
const double size = gsl_multimin_fminimizer_size (s);
iter++;
/* +++++++++++++++++++++++++++++++++++++++++++++++ */
if(oparams.verbosity>2){
fprintf(stderr,"# g=%g y=( ",s->fval);
for(i=0;i<n;i++)
fprintf(stderr,"%g ",GET(s->x,i));
fprintf(stderr,") ");
fprintf(stderr," simplex size=%g ",size);
fprintf(stderr,"\n");
}
/* +++++++++++++++++++++++++++++++++++++++++++++++ */
status=gsl_multimin_test_size (size,oparams.maxsize);
}
while (status == GSL_CONTINUE && iter < oparams.maxiter);
gsl_vector_memcpy (y, s->x);
*fun=s->fval;
gsl_multimin_fminimizer_free (s);
gsl_vector_free(ss);
}
/* compute values of x */
for(i=0;i<n;i++){
if(type==NULL) /* (-inf,+inf) */
x[i]=GET(y,i);
else
switch(type[i]){
case 0:/* (-inf,+inf) */
x[i]=GET(y,i);
break;
case 1:/* [a,+inf) */
x[i]=xmin[i]+GET(y,i)*GET(y,i);
break;
case 2:/* (-inf,a] */
x[i]=xmax[i]-GET(y,i)*GET(y,i);
break;
case 3:/* [a,b] */
dtmp1 = sin( GET(y,i) );
x[i]=.5*(xmin[i]*(1-dtmp1) +xmax[i]*(1+dtmp1));
break;
case 4:/* (a,+inf) */
dtmp1 = exp( GET(y,i) );
x[i]=xmin[i]+dtmp1;
break;
case 5:/* (-inf,a) */
dtmp1 = -exp( GET(y,i) );
x[i]=xmax[i]+dtmp1;
break;
case 6:/* (a,b) */
dtmp1 = tanh( GET(y,i) );
x[i]=.5*(xmin[i]*(1-dtmp1) +xmax[i]*(1+dtmp1));
break;
case 7:/* (a,b) second approach */
dtmp1 = GET(y,i) ;
dtmp1 = dtmp1/sqrt(1.+dtmp1*dtmp1);
x[i]=.5*(xmin[i]*(1-dtmp1) +xmax[i]*(1+dtmp1));
break;
case 8:/* (a,+inf) second approach */
dtmp1 = sqrt(1.+GET(y,i)*GET(y,i));
x[i]= xmin[i] + .5*(dtmp1+GET(y,i));
break;
}
}
/* --- OUPUT ---------------------------------- */
if(oparams.verbosity>0){
fprintf(stderr,"# - end minimization\n");
fprintf(stderr,"# iterations %u\n",iter);
for(i=0;i<n;i++)
fprintf(stderr,"# %e -> x[%zd]=%e\n",GET(y,i),i,x[i]);
fprintf(stderr,"#--- MULTIMIN END --- \n");
}
/* -------------------------------------------- */
gsl_vector_free (y);
}
GslMinimizerHolder::Instance::~Instance () {
gsl_multimin_fdfminimizer* &gslMinimizer( *this );
gsl_multimin_fdfminimizer_free( gslMinimizer );
gslMinimizer = NULL;
}
arma::vec DIIS::get_w_adiis() const {
// Number of parameters
size_t N=PiF.n_elem;
if(N==1) {
// Trivial case.
arma::vec ret(1);
ret.ones();
return ret;
}
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
gsl_vector *x;
gsl_multimin_function_fdf minfunc;
minfunc.f = adiis::min_f;
minfunc.df = adiis::min_df;
minfunc.fdf = adiis::min_fdf;
minfunc.n = N;
minfunc.params = (void *) this;
T=gsl_multimin_fdfminimizer_vector_bfgs2;
s=gsl_multimin_fdfminimizer_alloc(T,N);
// Starting point: equal weights on all matrices
x=gsl_vector_alloc(N);
gsl_vector_set_all(x,1.0/N);
// Initial energy estimate
// double E_initial=get_E(x);
// Initialize the optimizer. Use initial step size 0.02, and an
// orthogonality tolerance of 0.1 in the line searches (recommended
// by GSL manual for bfgs).
gsl_multimin_fdfminimizer_set(s, &minfunc, x, 0.02, 0.1);
size_t iter=0;
int status;
do {
iter++;
// printf("iteration %lu\n",iter);
status = gsl_multimin_fdfminimizer_iterate (s);
if (status) {
// printf("Error %i in minimization\n",status);
break;
}
status = gsl_multimin_test_gradient (s->gradient, 1e-7);
/*
if (status == GSL_SUCCESS)
printf ("Minimum found at:\n");
printf("%5lu ", iter);
for(size_t i=0;i<N;i++)
printf("%.5g ",gsl_vector_get(s->x,i));
printf("%10.5g\n",s->f);
*/
}
while (status == GSL_CONTINUE && iter < 1000);
// Final estimate
// double E_final=get_E(s->x);
// Form minimum
arma::vec c=adiis::compute_c(s->x);
gsl_multimin_fdfminimizer_free (s);
gsl_vector_free (x);
// printf("Minimized estimate of %lu matrices by %e from %e to %e in %lu iterations.\n",D.size(),E_final-E_initial,E_initial,E_final,iter);
return c;
}
void GslOptimizer::minimize_with_gradient( unsigned int dim, OptimizerMonitor* monitor )
{
// Set initial point
gsl_vector * x = gsl_vector_alloc(dim);
for (unsigned int i = 0; i < dim; i++) {
gsl_vector_set(x, i, (*m_initialPoint)[i]);
}
// Tell GSL which solver we're using
const gsl_multimin_fdfminimizer_type* type = NULL;
// We use m_solver_type here because we need the enum
switch(m_solver_type)
{
case(FLETCHER_REEVES_CG):
type = gsl_multimin_fdfminimizer_conjugate_fr;
break;
case(POLAK_RIBIERE_CG):
type = gsl_multimin_fdfminimizer_conjugate_pr;
break;
case(BFGS):
type = gsl_multimin_fdfminimizer_vector_bfgs;
break;
case(BFGS2):
type = gsl_multimin_fdfminimizer_vector_bfgs2;
break;
case(STEEPEST_DESCENT):
type = gsl_multimin_fdfminimizer_steepest_descent;
break;
case(NELDER_MEAD):
case(NELDER_MEAD2):
case(NELDER_MEAD2_RAND):
default:
// Wat?!
queso_error();
}
// Init solver
gsl_multimin_fdfminimizer * solver =
gsl_multimin_fdfminimizer_alloc(type, dim);
// Point GSL to the right functions
gsl_multimin_function_fdf minusLogPosterior;
minusLogPosterior.n = dim;
minusLogPosterior.f = &c_evaluate;
minusLogPosterior.df = &c_evaluate_derivative;
minusLogPosterior.fdf = &c_evaluate_with_derivative;
minusLogPosterior.params = (void *)(this);
gsl_multimin_fdfminimizer_set(solver, &minusLogPosterior, x, getFdfstepSize(), getLineTolerance());
int status;
size_t iter = 0;
do {
iter++;
status = gsl_multimin_fdfminimizer_iterate(solver);
if (status) {
if( m_objectiveFunction.domainSet().env().fullRank() == 0 )
{
std::cerr << "Error while GSL does optimisation. "
<< "See below for GSL error type." << std::endl;
std::cerr << "Gsl error: " << gsl_strerror(status) << std::endl;
}
break;
}
status = gsl_multimin_test_gradient(solver->gradient, this->getTolerance());
if(monitor)
{
gsl_vector* x = gsl_multimin_fdfminimizer_x(solver);
std::vector<double> x_min(dim);
for( unsigned int i = 0; i < dim; i++)
x_min[i] = gsl_vector_get(x,i);
double f = gsl_multimin_fdfminimizer_minimum(solver);
gsl_vector* grad = gsl_multimin_fdfminimizer_gradient(solver);
double grad_norm = gsl_blas_dnrm2(grad);
monitor->append( x_min, f, grad_norm );
}
} while ((status == GSL_CONTINUE) && (iter < this->getMaxIterations()));
for (unsigned int i = 0; i < dim; i++) {
(*m_minimizer)[i] = gsl_vector_get(solver->x, i);
}
// We're being good human beings and cleaning up the memory we allocated
gsl_multimin_fdfminimizer_free(solver);
gsl_vector_free(x);
return;
}
void minim(density_t * ndft){
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
gsl_multimin_function_fdf my_func;
gsl_vector * grad_initial;
size_t iter;
ipf_t ipf_previous;
int status;
double minimum, g_initial, norm_initial;
char * output_string;
int i;
params_gsl_multimin_function_t params;
output_string = (char *) malloc(25*sizeof(char));
params.nDFT = density_get_val(ndft);
my_func.n = ipf.npar;
my_func.f = my_f;
my_func.df = my_df;
my_func.fdf = my_fdf;
my_func.params = (void *) (¶ms);
/* We use the BFGS algorithm from thee GNU Scientific Library (GSL)
in its optimized version bfgs2 */
T = gsl_multimin_fdfminimizer_vector_bfgs2;
messages_basic("\n\nStarting the optimization.\n\n\n");
grad_initial = gsl_vector_alloc(ipf.npar);
my_fdf (ipf.gamma, ¶ms, &g_initial, grad_initial);
norm_initial = gsl_blas_dnrm2(grad_initial);
if(g_initial < epsilon_gvalue){
if(myid == 0) printf("The value of G for the starting gamma is %.12lg,\n", g_initial);
if(myid == 0) printf("which is already below the requested threshold of %.12lg\n", epsilon_gvalue);
parallel_end(EXIT_SUCCESS);
}
if(norm_initial < epsilon_grad){
if(myid == 0) printf("The value of the normm of the gradient of G for the starting gamma is %.12lg,\n", norm_initial);
if(myid == 0) printf("which is already below the requested threshold of %.12lg\n", epsilon_grad);
parallel_end(EXIT_SUCCESS);
}
if(myid == 0) printf(" Starting from gamma = ");
if(myid == 0) {for(i = 0; i < ipf.npar; i++) printf ("%.5f ", gsl_vector_get (ipf.gamma, i));}
if(myid == 0) printf("\n G(gamma) = %.12lg\n", g_initial);
if(myid == 0) printf(" ||Grad G(gamma)|| = %.12lg\n\n", norm_initial);
/* Initialization of the minimizer s for the function
my_func starting at the x point
The step for the first try is 0.1
and the convergence criteria is 0.1 */
messages_basic("\n\nInitialization of the minimizer.\n\n\n");
s = gsl_multimin_fdfminimizer_alloc (T, ipf.npar);
gsl_multimin_fdfminimizer_set (s, &my_func, ipf.gamma, 0.1, 0.1);
minimum = g_initial;
iter = 0;
do{
iter++;
ipf_copy(&ipf_previous, &ipf);
if(myid == 0) printf(" Iter = %d\n", (int)iter);
if(myid == 0) printf(" starting gamma = ");
if(myid == 0) {for(i = 0; i < ipf.npar; i++) printf ("%.5f ", gsl_vector_get (gsl_multimin_fdfminimizer_x(s), i));}
if(myid == 0) printf("\n starting G(gamma) = %15.10f\n", minimum);
/* We make an iteration of the minimizer s */
status = gsl_multimin_fdfminimizer_iterate (s);
minimum = gsl_multimin_fdfminimizer_minimum(s);
if (status){
if(myid == 0) printf(" Breaking. Reason: %s\n", gsl_strerror(status));
break;
}
if(myid == 0) printf(" ||Grad G(gamma)|| = %15.10f\n", gsl_blas_dnrm2(gsl_multimin_fdfminimizer_gradient(s)));
if(myid == 0) printf(" G(gamma) = %15.10f\n", minimum);
/* Checks convergence */
if(minimum < epsilon_gvalue){
status = GSL_SUCCESS;
}else{
status = gsl_multimin_test_gradient (gsl_multimin_fdfminimizer_gradient(s), epsilon_grad);
}
gsl_vector_memcpy(ipf.gamma, gsl_multimin_fdfminimizer_x(s));
ipf_write(ipf, ipf_ref, "intermediate-pot");
/* Print the diff between initial and reference IPFs */
if(myid == 0) printf(" Diff[ IPF(previous), IPF(new) ] = %.12lg\n", ipf_diff(&ipf_previous, &ipf));
ipf_end(&ipf_previous);
}
while (status == GSL_CONTINUE && iter < minim_maxiter);
if(myid == 0) printf("\n\nFinished optimization. status = %d (%s)\n", status, gsl_strerror(status));
if(myid == 0) printf(" Final gamma = ");
if(myid == 0) {for(i = 0; i < ipf.npar; i++) printf ("%.5f ", gsl_vector_get (gsl_multimin_fdfminimizer_x(s), i));}
if(myid == 0) printf("\n With value: G(gamma) = %.12lg\n\n", gsl_multimin_fdfminimizer_minimum(s));
gsl_vector_memcpy(ipf.gamma, gsl_multimin_fdfminimizer_x(s));
sprintf(output_string, "pot");
ipf_write(ipf, ipf_ref, output_string);
gsl_multimin_fdfminimizer_free (s);
fflush(stdout);
}
int main (int argc, char *argv[])
{
printf("Number of haplotypes: %d\n", atoi(argv[1]) );
int temp =0;
temp = atoi(argv[1]);
printf("Number of time intervals: %d\n", atoi(argv[2]) );
printf("File name: %s\n", argv[3] );
int num_haps = atoi(argv[1]);
int num_times = atoi(argv[2]);
//make_bins(num_haps);
//readfile(argv[3]);
read_binned_file(argv[3]);
//make_custom_bins(num_haps); // one bin per match length
// printf("num_loci = %d\n", num_loci);
// printf("marker %f\n", 1.7);
// printf("a;lskdjf %d\n", 3);
make_times(num_haps, num_times);
read_quant_file(argv[4]);
precompute(num_haps, num_times);
/*
struct scenario the_scenario;
the_scenario.num_haps = argv[1];
the_scenario.num_times = argv[2];*/
size_t iter = 0;
// size_t i; // commented out to fix the problem labelled XYRQ below
// there was a comparison between signed/unsiged int
int status;
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
/* Position of the minimum (1,2). */
int j=0;
double par[2];
par[0] = num_haps;
par[1] = num_times;
gsl_vector *x;
gsl_multimin_function_fdf my_func;
my_func.f = &my_f;
my_func.df = &my_df;
my_func.fdf = &my_fdf;
my_func.n = num_times;
my_func.params = ∥
/* Starting point, x = (5,7) */
x = gsl_vector_alloc (num_times);
for (j=0; j<num_times; j++)
{
if(j<=50){gsl_vector_set (x, j, 30000 );}
else {gsl_vector_set (x, j, 20000 );}
}
T = gsl_multimin_fdfminimizer_conjugate_fr;
// T = gsl_multimin_fdfminimizer_vector_bfgs2;
s = gsl_multimin_fdfminimizer_alloc (T, num_times);
// likelihood setting
gsl_multimin_fdfminimizer_set (s, &my_func, x, 10000, .000001);
// quantile setting
//gsl_multimin_fdfminimizer_set (s, &my_func, x, 3000.0, .100);
do
{
iter++;
status = gsl_multimin_fdfminimizer_iterate (s);
//printf("help %d\n", 3);
if (status){
printf ("Iteration terminated at:\nSTART HERE\n");
//printf ("%5zu ", iter); // using %zu instead of %d b/c iter is type size_t not type int
int k=0;
for (k = 0; k < num_times; k++)
{
printf ("%f\t%10.3f\n", time[k], gsl_vector_get (s->x, k)); // problem XYRQ
// using k here renders size_t i above unused
}
printf ("f() = %7.3f \n", s->f);
// q
break;}
//printf("help %d\n", 4);
//.likelihood setting
status = gsl_multimin_test_gradient (s->gradient, 1e-10 );
// quantile setting
// status = gsl_multimin_test_gradient (s->gradient, .010 );
if (status == GSL_SUCCESS)
{ printf ("Minimum found at:\nSTART HERE\n");}
int k=0;
for (k = 0; k < num_times; k++)
{
printf ("%f\t%10.3f\n", time[k], gsl_vector_get (s->x, k)); // problem XYRQ
// using k here renders size_t i above unused
}
//printf ("f() = %7.3f \n", s->f);
// printf ("Minimum found at:\n");
//
// printf ("%5zu ", iter); // using %zu instead of %d b/c iter is type size_t not type int
// int k=0;
// for (k = 0; k < num_times; k++)
// {
// printf ("%10.3e ", gsl_vector_get (s->x, k)); // problem XYRQ
// using k here renders size_t i above unused
// }
// printf ("%5d %.5f %.5f %10.5f\n", iter,
// gsl_vector_get (s->x, 0),
// gsl_vector_get (s->x, 1),
// s->f);
}
while (status == GSL_CONTINUE && iter < 1000);
gsl_multimin_fdfminimizer_free (s);
gsl_vector_free (x);
return 0;
}
int FC_FUNC_(oct_minimize, OCT_MINIMIZE)
(const int *method, const int *dim, double *point, const double *step, const double *line_tol,
const double *tolgrad, const double *toldr, const int *maxiter, func_d f,
const print_f_ptr write_info, double *minimum)
{
int iter = 0;
int status;
double maxgrad, maxdr;
int i;
double * oldpoint;
double * grad;
const gsl_multimin_fdfminimizer_type *T = NULL;
gsl_multimin_fdfminimizer *s;
gsl_vector *x;
gsl_vector *absgrad, *absdr;
gsl_multimin_function_fdf my_func;
param_fdf_t p;
p.func = f;
oldpoint = (double *) malloc(*dim * sizeof(double));
grad = (double *) malloc(*dim * sizeof(double));
my_func.f = &my_f;
my_func.df = &my_df;
my_func.fdf = &my_fdf;
my_func.n = *dim;
my_func.params = (void *) &p;
/* Starting point */
x = gsl_vector_alloc (*dim);
for(i=0; i<*dim; i++) gsl_vector_set (x, i, point[i]);
/* Allocate space for the gradient */
absgrad = gsl_vector_alloc (*dim);
absdr = gsl_vector_alloc (*dim);
//GSL recommends line_tol = 0.1;
switch(*method){
case 1:
T = gsl_multimin_fdfminimizer_steepest_descent;
break;
case 2:
T = gsl_multimin_fdfminimizer_conjugate_fr;
break;
case 3:
T = gsl_multimin_fdfminimizer_conjugate_pr;
break;
case 4:
T = gsl_multimin_fdfminimizer_vector_bfgs;
break;
case 5:
T = gsl_multimin_fdfminimizer_vector_bfgs2;
break;
}
s = gsl_multimin_fdfminimizer_alloc (T, *dim);
gsl_multimin_fdfminimizer_set (s, &my_func, x, *step, *line_tol);
do
{
iter++;
for(i=0; i<*dim; i++) oldpoint[i] = point[i];
/* Iterate */
status = gsl_multimin_fdfminimizer_iterate (s);
/* Get current minimum, point and gradient */
*minimum = gsl_multimin_fdfminimizer_minimum(s);
for(i=0; i<*dim; i++) point[i] = gsl_vector_get(gsl_multimin_fdfminimizer_x(s), i);
for(i=0; i<*dim; i++) grad[i] = gsl_vector_get(gsl_multimin_fdfminimizer_gradient(s), i);
/* Compute convergence criteria */
for(i=0; i<*dim; i++) gsl_vector_set(absdr, i, fabs(point[i]-oldpoint[i]));
maxdr = gsl_vector_max(absdr);
for(i=0; i<*dim; i++) gsl_vector_set(absgrad, i, fabs(grad[i]));
maxgrad = gsl_vector_max(absgrad);
/* Print information */
write_info(&iter, dim, minimum, &maxdr, &maxgrad, point);
/* Store infomation for next iteration */
for(i=0; i<*dim; i++) oldpoint[i] = point[i];
if (status)
break;
if ( (maxgrad <= *tolgrad) || (maxdr <= *toldr) ) status = GSL_SUCCESS;
else status = GSL_CONTINUE;
}
while (status == GSL_CONTINUE && iter <= *maxiter);
if(status == GSL_CONTINUE) status = 1025;
gsl_multimin_fdfminimizer_free (s);
gsl_vector_free (x); gsl_vector_free(absgrad); gsl_vector_free(absdr);
free(oldpoint);
free(grad);
return status;
}
std::vector<contr_t> slater_fit(double zeta, int am, int nf, bool verbose, int method) {
sto_params_t par;
par.zeta=zeta;
par.l=am;
par.Nf=nf;
par.method=method;
int maxiter=1000;
// Degrees of freedom
int dof;
if(par.method==0 && nf>=2)
dof=2;
else
// Full optimization
par.method=2;
if(par.method==1 && nf>=4)
dof=4;
else
// Full optimization
par.method=2;
// Full optimization
if(par.method==2)
dof=par.Nf;
gsl_multimin_function_fdf minfunc;
minfunc.n=dof;
minfunc.f=eval_difference;
minfunc.df=eval_difference_df;
minfunc.fdf=eval_difference_fdf;
minfunc.params=(void *) ∥
gsl_multimin_fdfminimizer *min;
// Allocate minimizer
// min=gsl_multimin_fdfminimizer_alloc(gsl_multimin_fdfminimizer_vector_bfgs2,dof);
min=gsl_multimin_fdfminimizer_alloc(gsl_multimin_fdfminimizer_conjugate_pr,dof);
gsl_vector *x;
x=gsl_vector_alloc(dof);
// Initialize vector
gsl_vector_set_all(x,0.0);
// Set starting point
switch(par.method) {
case(2):
// Legendre - same as for even tempered
case(1):
// Well tempered - same initialization as for even-tempered
case(0):
// Even tempered, set alpha=1.0 and beta=2.0
gsl_vector_set(x,0,1.0);
if(dof>1)
gsl_vector_set(x,1,2.0);
break;
/*
case(2):
// Free minimization, set exponents to i
for(int i=0;i<nf;i++)
gsl_vector_set(x,i,i);
break;
*/
default:
ERROR_INFO();
throw std::runtime_error("Unknown Slater fitting method.\n");
}
// Set minimizer
gsl_multimin_fdfminimizer_set(min, &minfunc, x, 0.01, 1e-4);
// Iterate
int iter=0;
int iterdelta=0;
int status;
double cost=0;
if(verbose) printf("Iteration\tDelta\n");
do {
iter++;
iterdelta++;
// Simplex
status = gsl_multimin_fdfminimizer_iterate(min);
if (status) {
// printf("Encountered GSL error \"%s\"\n",gsl_strerror(status));
break;
}
// Are we converged?
status = gsl_multimin_test_gradient (min->gradient, 1e-12);
if (verbose && status == GSL_SUCCESS)
{
printf ("converged to minimum at\n");
}
if(min->f!=cost) {
if(verbose) printf("%i\t%e\t%e\t%e\n",iter,min->f,min->f-cost,gsl_blas_dnrm2(min->gradient));
cost=min->f;
iterdelta=0;
}
} while (status == GSL_CONTINUE && iterdelta < maxiter);
// Get best exponents and coefficients
std::vector<double> optexp=get_exps(min->x,&par);
arma::vec optc=solve_coefficients(optexp,par.zeta,par.l);
// Free memory
gsl_vector_free(x);
gsl_multimin_fdfminimizer_free(min);
// Return
std::vector<contr_t> ret(nf);
for(int i=0;i<nf;i++) {
ret[i].z=optexp[i];
ret[i].c=optc[i];
}
return ret;
}
int lua_multimin_minimize(lua_State * L) {
bool ssdel=false;
double eps=0.00001;
double tol=0.0001;
double step_size=0.01;
int maxiter=1000;
bool print=false;
array<double> * x=0;
array<double> * ss=0;
const gsl_multimin_fminimizer_type *Tf = 0;
const gsl_multimin_fdfminimizer_type *Tdf = 0;
multi_param mp;
mp.L=L;
mp.fdf_index=-1;
lua_pushstring(L,"f");
lua_gettable(L,-2);
if(lua_isfunction(L,-1)) {
mp.f_index=luaL_ref(L, LUA_REGISTRYINDEX);
} else {
luaL_error(L,"%s\n","missing function");
}
lua_pushstring(L,"df");
lua_gettable(L,-2);
if(lua_isfunction(L,-1)) {
mp.df_index=luaL_ref(L, LUA_REGISTRYINDEX);
Tdf= gsl_multimin_fdfminimizer_conjugate_fr;
} else {
lua_pop(L,1);
Tf= gsl_multimin_fminimizer_nmsimplex2;
}
lua_pushstring(L,"fdf");
lua_gettable(L,-2);
if(lua_isfunction(L,-1)) {
mp.fdf_index=luaL_ref(L, LUA_REGISTRYINDEX);
} else {
lua_pop(L,1);
mp.fdf_index=-1;
}
lua_pushstring(L,"algorithm");
lua_gettable(L,-2);
if(lua_isstring(L,-1)) {
if(Tf!=0) {
if(!strcmp(lua_tostring(L,-1),"nmsimplex")) {
Tf = gsl_multimin_fminimizer_nmsimplex;
} else if(!strcmp(lua_tostring(L,-1),"nmsimplex2rand")) {
Tf = gsl_multimin_fminimizer_nmsimplex2rand;
} else if(!strcmp(lua_tostring(L,-1),"nmsimplex2")) {
Tf = gsl_multimin_fminimizer_nmsimplex2;
} else {
luaL_error(L,"%s\n","invalid algorithm");
}
} else {
if(!strcmp(lua_tostring(L,-1),"conjugate_pr")) {
Tdf = gsl_multimin_fdfminimizer_conjugate_pr;
} else if(!strcmp(lua_tostring(L,-1),"steepest_descent")) {
Tdf = gsl_multimin_fdfminimizer_steepest_descent;
} else if(!strcmp(lua_tostring(L,-1),"vector_bfgs")) {
Tdf = gsl_multimin_fdfminimizer_vector_bfgs;
} else if(!strcmp(lua_tostring(L,-1),"vector_bfgs2")) {
Tdf = gsl_multimin_fdfminimizer_vector_bfgs2;
} else if(!strcmp(lua_tostring(L,-1),"conjugate_fr")) {
Tdf = gsl_multimin_fdfminimizer_conjugate_fr;
} else {
luaL_error(L,"%s\n","invalid algorithm");
}
}
}
lua_pop(L,1);
lua_pushstring(L,"show_iterations");
lua_gettable(L,-2);
if(lua_isboolean(L,-1)) {
print=(lua_toboolean(L,-1)==1);
}
lua_pop(L,1);
lua_pushstring(L,"eps");
lua_gettable(L,-2);
if(lua_isnumber(L,-1)) {
eps=lua_tonumber(L,-1);
}
lua_pop(L,1);
lua_pushstring(L,"step_size");
lua_gettable(L,-2);
if(lua_isnumber(L,-1)) {
step_size=lua_tonumber(L,-1);
}
lua_pop(L,1);
lua_pushstring(L,"tol");
lua_gettable(L,-2);
if(lua_isnumber(L,-1)) {
tol=lua_tonumber(L,-1);
}
lua_pop(L,1);
lua_pushstring(L,"maxiter");
lua_gettable(L,-2);
if(lua_isnumber(L,-1)) {
maxiter=(int)lua_tonumber(L,-1);
}
lua_pop(L,1);
lua_pushstring(L,"starting_point");
lua_gettable(L,-2);
if(!lua_isuserdata(L,-1)) lua_error(L);
if (!SWIG_IsOK(SWIG_ConvertPtr(L,-1,(void**)&x,SWIGTYPE_p_arrayT_double_t,0))){
luaL_error(L,"%s\n","missing starting point");
}
lua_pop(L,1);
if(Tf) {
lua_pushstring(L,"step_sizes");
lua_gettable(L,-2);
if(lua_isuserdata(L,-1)) {
if (!SWIG_IsOK(SWIG_ConvertPtr(L,-1,(void**)&ss,SWIGTYPE_p_arrayT_double_t,0))){
lua_error(L);
}
} else {
ssdel=true;
ss=new array<double>(x->size());
ss->set_all(1.0);
if(lua_isnumber(L,-1)) {
double v=lua_tonumber(L,-1);
ss->set_all(v);
}
}
lua_pop(L,1);
}
lua_pop(L,1);
if(Tf) {
gsl_multimin_fminimizer *s = NULL;
gsl_vector SS, X;
gsl_multimin_function minex_func;
int iter = 0;
int status;
double size;
int N=x->size();
/* Starting point */
X.size=x->size();
X.stride=1;
X.data=x->data();
X.owner=0;
/* Set initial step sizes */
SS.size=ss->size();
SS.stride=1;
SS.data=ss->data();
SS.owner=0;
/* Initialize method and iterate */
minex_func.n = N;
minex_func.f = multimin_f_cb;
minex_func.params = ∓
s = gsl_multimin_fminimizer_alloc (Tf, N);
gsl_multimin_fminimizer_set (s, &minex_func, &X, &SS);
if(print) printf ("running algorithm '%s'\n",
gsl_multimin_fminimizer_name (s));
do
{
iter++;
status = gsl_multimin_fminimizer_iterate(s);
if (status)
break;
size = gsl_multimin_fminimizer_size (s);
status = gsl_multimin_test_size (size, eps);
if (status == GSL_SUCCESS)
{
if(print) printf ("converged to minimum at\n");
}
if(print) printf ("%5d f() = %12.3f size = %.9f\n",
iter,
s->fval, size);
} while (status == GSL_CONTINUE && iter < maxiter);
for(int i=0;i<N;++i) x->set(i,gsl_vector_get(s->x,i));
luaL_unref(L, LUA_REGISTRYINDEX, mp.f_index);
gsl_multimin_fminimizer_free (s);
} else {
gsl_multimin_fdfminimizer *s = NULL;
gsl_vector X;
gsl_multimin_function_fdf minex_func;
int iter = 0;
int status;
double size;
int N=x->size();
/* Starting point */
X.size=x->size();
X.stride=1;
X.data=x->data();
X.owner=0;
/* Initialize method and iterate */
minex_func.n = N;
minex_func.f = multimin_f_cb;
minex_func.df = multimin_df_cb;
minex_func.fdf = multimin_fdf_cb;
minex_func.params = ∓
s = gsl_multimin_fdfminimizer_alloc (Tdf, N);
gsl_multimin_fdfminimizer_set (s, &minex_func, &X, step_size, tol);
if(print) printf ("running algorithm '%s'\n",
gsl_multimin_fdfminimizer_name (s));
do
{
iter++;
status = gsl_multimin_fdfminimizer_iterate(s);
if (status)
break;
status = gsl_multimin_test_gradient (s->gradient, eps);
if (status == GSL_SUCCESS)
{
if(print) printf ("converged to minimum at\n");
}
if(print) printf ("%5d f() = %12.3f\n",
iter,
s->f);
} while (status == GSL_CONTINUE && iter < maxiter);
for(int i=0;i<N;++i) x->set(i,gsl_vector_get(s->x,i));
luaL_unref(L, LUA_REGISTRYINDEX, mp.f_index);
luaL_unref(L, LUA_REGISTRYINDEX, mp.df_index);
gsl_multimin_fdfminimizer_free (s);
}
if(mp.fdf_index>=0) {
luaL_unref(L, LUA_REGISTRYINDEX, mp.fdf_index);
}
if(ssdel) {
delete ss;
}
return 0;
}
/**
* Destructor.
*/
DerivMinimizer::~DerivMinimizer() {
if (m_gslSolver != nullptr) {
gsl_multimin_fdfminimizer_free(m_gslSolver);
gsl_vector_free(m_x);
}
}
int OptimizationOptions::gslOptimize( NLSFunction *F, gsl_vector* x_vec,
gsl_matrix *v, IterationLogger *itLog ) {
const gsl_multifit_fdfsolver_type *Tlm[] =
{ gsl_multifit_fdfsolver_lmder, gsl_multifit_fdfsolver_lmsder };
const gsl_multimin_fdfminimizer_type *Tqn[] =
{ gsl_multimin_fdfminimizer_vector_bfgs,
gsl_multimin_fdfminimizer_vector_bfgs2,
gsl_multimin_fdfminimizer_conjugate_fr,
gsl_multimin_fdfminimizer_conjugate_pr };
const gsl_multimin_fminimizer_type *Tnm[] =
{ gsl_multimin_fminimizer_nmsimplex, gsl_multimin_fminimizer_nmsimplex2,
gsl_multimin_fminimizer_nmsimplex2rand };
int gsl_submethod_max[] = { sizeof(Tlm) / sizeof(Tlm[0]),
sizeof(Tqn) / sizeof(Tqn[0]),
sizeof(Tnm) / sizeof(Tnm[0]) };
int status, status_dx, status_grad, k;
double g_norm, x_norm;
/* vectorize x row-wise */
size_t max_ind, min_ind;
double max_val, min_val, abs_max_val = 0, abs_min_val;
if (this->method < 0 ||
this->method > sizeof(gsl_submethod_max)/sizeof(gsl_submethod_max[0]) ||
this->submethod < 0 ||
this->submethod > gsl_submethod_max[this->method]) {
throw new Exception("Unknown optimization method.\n");
}
if (this->maxiter < 0 || this->maxiter > 5000) {
throw new Exception("opt.maxiter should be in [0;5000].\n");
}
/* LM */
gsl_multifit_fdfsolver* solverlm;
gsl_multifit_function_fdf fdflm = { &(F->_f_ls), &(F->_df_ls), &(F->_fdf_ls),
F->getNsq(), F->getNvar(), F };
gsl_vector *g;
/* QN */
double stepqn = this->step;
gsl_multimin_fdfminimizer* solverqn;
gsl_multimin_function_fdf fdfqn = {
&(F->_f), &(F->_df), &(F->_fdf), F->getNvar(), F };
/* NM */
double size;
gsl_vector *stepnm;
gsl_multimin_fminimizer* solvernm;
gsl_multimin_function fnm = { &(F->_f), F->getNvar(), F };
/* initialize the optimization method */
switch (this->method) {
case SLRA_OPT_METHOD_LM: /* LM */
solverlm = gsl_multifit_fdfsolver_alloc(Tlm[this->submethod],
F->getNsq(), F->getNvar());
gsl_multifit_fdfsolver_set(solverlm, &fdflm, x_vec);
g = gsl_vector_alloc(F->getNvar());
break;
case SLRA_OPT_METHOD_QN: /* QN */
solverqn = gsl_multimin_fdfminimizer_alloc(Tqn[this->submethod],
F->getNvar() );
gsl_multimin_fdfminimizer_set(solverqn, &fdfqn, x_vec,
stepqn, this->tol);
status_dx = GSL_CONTINUE;
break;
case SLRA_OPT_METHOD_NM: /* NM */
solvernm = gsl_multimin_fminimizer_alloc(Tnm[this->submethod], F->getNvar());
stepnm = gsl_vector_alloc(F->getNvar());
gsl_vector_set_all(stepnm, this->step);
gsl_multimin_fminimizer_set( solvernm, &fnm, x_vec, stepnm );
break;
}
/* optimization loop */
Log::lprintf(Log::LOG_LEVEL_FINAL, "SLRA optimization:\n");
status = GSL_SUCCESS;
status_dx = GSL_CONTINUE;
status_grad = GSL_CONTINUE;
this->iter = 0;
switch (this->method) {
case SLRA_OPT_METHOD_LM:
gsl_blas_ddot(solverlm->f, solverlm->f, &this->fmin);
gsl_multifit_gradient(solverlm->J, solverlm->f, g);
gsl_vector_scale(g, 2);
{
gsl_vector *g2 = gsl_vector_alloc(g->size);
F->computeFuncAndGrad(x_vec, NULL, g2);
gsl_vector_sub(g2, g);
if (gsl_vector_max(g2) > 1e-10 || gsl_vector_min(g2) < -1e-10) {
Log::lprintf(Log::LOG_LEVEL_NOTIFY,
"Gradient error, max = %14.10f, min = %14.10f ...",
gsl_vector_max(g2), gsl_vector_min(g2));
print_vec(g2);
}
gsl_vector_free(g2);
}
if (itLog != NULL) {
itLog->reportIteration(0, solverlm->x, this->fmin, g);
}
break;
case SLRA_OPT_METHOD_QN:
this->fmin = gsl_multimin_fdfminimizer_minimum(solverqn);
if (itLog != NULL) {
itLog->reportIteration(0, solverqn->x, this->fmin, solverqn->gradient);
}
break;
case SLRA_OPT_METHOD_NM:
this->fmin = gsl_multimin_fminimizer_minimum( solvernm );
if (itLog != NULL) {
itLog->reportIteration(this->iter, solvernm->x, this->fmin, NULL);
}
break;
}
while (status_dx == GSL_CONTINUE &&
status_grad == GSL_CONTINUE &&
status == GSL_SUCCESS &&
this->iter < this->maxiter) {
if (this->method == SLRA_OPT_METHOD_LM && this->maxx > 0) {
if (gsl_vector_max(solverlm->x) > this->maxx ||
gsl_vector_min(solverlm->x) < -this->maxx ){
break;
}
}
this->iter++;
switch (this->method) {
case SLRA_OPT_METHOD_LM: /* Levenberg-Marquardt */
status = gsl_multifit_fdfsolver_iterate(solverlm);
gsl_multifit_gradient(solverlm->J, solverlm->f, g);
gsl_vector_scale(g, 2);
/* check the convergence criteria */
if (this->epsabs != 0 || this->epsrel != 0) {
status_dx = gsl_multifit_test_delta(solverlm->dx, solverlm->x,
this->epsabs, this->epsrel);
} else {
status_dx = GSL_CONTINUE;
}
status_grad = gsl_multifit_test_gradient(g, this->epsgrad);
gsl_blas_ddot(solverlm->f, solverlm->f, &this->fmin);
if (itLog != NULL) {
itLog->reportIteration(this->iter, solverlm->x, this->fmin, g);
}
break;
case SLRA_OPT_METHOD_QN:
status = gsl_multimin_fdfminimizer_iterate( solverqn );
/* check the convergence criteria */
status_grad = gsl_multimin_test_gradient(
gsl_multimin_fdfminimizer_gradient(solverqn), this->epsgrad);
status_dx = gsl_multifit_test_delta(solverqn->dx, solverqn->x,
this->epsabs, this->epsrel);
this->fmin = gsl_multimin_fdfminimizer_minimum(solverqn);
if (itLog != NULL) {
itLog->reportIteration(this->iter, solverqn->x, this->fmin, solverqn->gradient);
}
break;
case SLRA_OPT_METHOD_NM:
status = gsl_multimin_fminimizer_iterate( solvernm );
/* check the convergence criteria */
size = gsl_multimin_fminimizer_size( solvernm );
status_dx = gsl_multimin_test_size( size, this->epsx );
this->fmin = gsl_multimin_fminimizer_minimum( solvernm );
if (itLog != NULL) {
itLog->reportIteration(this->iter, solvernm->x, this->fmin, NULL);
}
break;
}
}
if (this->iter >= this->maxiter) {
status = EITER;
}
switch (this->method) {
case SLRA_OPT_METHOD_LM:
gsl_vector_memcpy(x_vec, solverlm->x);
if (v != NULL) {
gsl_multifit_covar(solverlm->J, this->epscov, v); /* ??? Different eps */
}
gsl_blas_ddot(solverlm->f, solverlm->f, &this->fmin);
break;
case SLRA_OPT_METHOD_QN:
gsl_vector_memcpy(x_vec, solverqn->x);
this->fmin = solverqn->f;
break;
case SLRA_OPT_METHOD_NM:
gsl_vector_memcpy(x_vec, solvernm->x);
this->fmin = solvernm->fval;
break;
}
/* print exit information */
if (Log::getMaxLevel() >= Log::LOG_LEVEL_FINAL) { /* unless "off" */
switch (status) {
case EITER:
Log::lprintf("SLRA optimization terminated by reaching "
"the maximum number of iterations.\n"
"The result could be far from optimal.\n");
break;
case GSL_ETOLF:
Log::lprintf("Lack of convergence: "
"progress in function value < machine EPS.\n");
break;
case GSL_ETOLX:
Log::lprintf("Lack of convergence: "
"change in parameters < machine EPS.\n");
break;
case GSL_ETOLG:
Log::lprintf("Lack of convergence: "
"change in gradient < machine EPS.\n");
break;
case GSL_ENOPROG:
Log::lprintf("Possible lack of convergence: no progress.\n");
break;
}
if (status_grad != GSL_CONTINUE && status_dx != GSL_CONTINUE) {
Log::lprintf("Optimization terminated by reaching the convergence "
"tolerance for both X and the gradient.\n");
} else {
if (status_grad != GSL_CONTINUE) {
Log::lprintf("Optimization terminated by reaching the convergence "
"tolerance for the gradient.\n");
} else {
Log::lprintf("Optimization terminated by reaching the convergence "
"tolerance for X.\n");
}
}
}
/* Cleanup */
switch (this->method) {
case SLRA_OPT_METHOD_LM: /* LM */
gsl_multifit_fdfsolver_free(solverlm);
gsl_vector_free(g);
break;
case SLRA_OPT_METHOD_QN: /* QN */
gsl_multimin_fdfminimizer_free(solverqn);
break;
case SLRA_OPT_METHOD_NM: /* NM */
gsl_multimin_fminimizer_free(solvernm);
gsl_vector_free(stepnm);
break;
}
return GSL_SUCCESS; /* <- correct with status */
}
// Relax the map
void rmap_relax(rmap_t *self, int num_cycles)
{
int i, n;
gsl_vector *x, *y;
gsl_multimin_function_fdf fdf;
gsl_multimin_fdfminimizer *s;
double step_size, tol;
rmap_scan_t *scan;
// HACK
step_size = 0.01;
tol = 0.001;
// Compute number of free variables
n = 3 * self->num_key_scans;
// Set the initial vector
x = gsl_vector_alloc(n);
for (i = 0; i < self->num_scans; i++)
{
scan = self->scans + i;
if (scan->index >= 0)
{
gsl_vector_set(x, 3 * scan->index + 0, scan->pose.pos.x);
gsl_vector_set(x, 3 * scan->index + 1, scan->pose.pos.y);
gsl_vector_set(x, 3 * scan->index + 2, scan->pose.rot);
}
}
// Allocate minimizer
fdf.f = (double (*) (const gsl_vector*, void*)) rmap_fit_f;
fdf.df = (void (*) (const gsl_vector*, void*, gsl_vector*)) rmap_fit_df;
fdf.fdf = (void (*) (const gsl_vector*, void*, double*, gsl_vector*)) rmap_fit_fdf;
fdf.n = n;
fdf.params = self;
s = gsl_multimin_fdfminimizer_alloc(gsl_multimin_fdfminimizer_vector_bfgs, n);
// Initialize minimizer
gsl_multimin_fdfminimizer_set(s, &fdf, x, step_size, tol);
// Optimize
for (i = 0; i < num_cycles; i++)
{
if (gsl_multimin_fdfminimizer_iterate(s) != GSL_SUCCESS)
break;
}
self->relax_err = gsl_multimin_fdfminimizer_minimum(s);
// Copy corrections back to data structures
y = gsl_multimin_fdfminimizer_x(s);
for (i = 0; i < self->num_scans; i++)
{
scan = self->scans + i;
if (scan->index >= 0)
{
scan->delta.pos.x = gsl_vector_get(y, 3 * scan->index + 0) - scan->pose.pos.x;
scan->delta.pos.y = gsl_vector_get(y, 3 * scan->index + 1) - scan->pose.pos.y;
scan->delta.rot = gsl_vector_get(y, 3 * scan->index + 2) - scan->pose.rot;
}
}
// Clean up
gsl_multimin_fdfminimizer_free(s);
gsl_vector_free(x);
return;
}
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;
}
