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calc.c
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calc.c
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/*=================================================================*/
/*= calc.c =*/
/*= main calculation and iteration routines for treekin =*/
/*= --------------------------------------------------------- =*/
/*= Last changed Time-stamp: <2012-01-14 19:04:10 mtw> =*/
/*= $Id: calc.c,v 1.41 2006/11/27 23:01:45 mtw Exp $ =*/
/*= --------------------------------------------------------- =*/
/*= (c) Michael Thomas Wolfinger, W. Andreas Svrcek-Seiler =*/
/*= {mtw,svrci}@tbi.univie.ac.at =*/
/*= treekin =*/
/*=================================================================*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <math.h>
#include <assert.h>
#include <errno.h>
#include "exp_matrix.h" /* functions for matrix-exponent stuff */
#include "mxccm.h" /* functions for eigen-problems stolen from ccmath */
#include "barparser.h" /* functions for input */
#include "calc.h" /* does all matrix stuff for markov process */
#include "globals.h" /* contains getopt-stuff */
#include "calcpp.h"
#define SQ(X) ((X)*(X))
/* private function(s) */
static double *MxMethodeA (BarData *Data);
static double *MxMethodeFULL(double *);
static double *MxMethodeINPUT (BarData *Data, double *);
static double max_saddle(int i, int j, BarData *Data);
static void print_settings(void);
static char *time_stamp(void);
static void MxDoDegeneracyStuff(void);
static void MxBinWrite(double *Mx, char what[], char T);
static int MxBinRead(double** Mx, char what[], char T);
static void MxASCIIWrite(double *Mx, char *asciifile);
static void MxASCIIWriteV(double *Mx, char *asciifile);
static void MxKotzOutMathematica(double *Mx);
static void MxSortEig(double *evals, double *evecs);
static void MxEVLapackSym(double *U);
static void MxEVLapackNonSym(double *U);
static void MxFixevecs(double *, double *);
static void MxDiagHelper(double *P8);
void MxFPrintD(double *mx, char *name, int dim1, int dim2, FILE *out);
/* private vars and arrays */
static int dim = 0;
static double _kT = 1.;
static double *evals = NULL;
static double *evecs = NULL;
static double *_sqrPI = NULL; /* left constant array */
static double *sqrPI_ = NULL; /* right constant array */
static double *D = NULL; /* matrix with degree of degeneracy */
static char Aname[30];
static TypeDegSaddle *saddle = NULL;
/*==*/
void
MxInit (int d)
{
_kT = 0.00198717*(273.15 + opt.T);
if (d > 0 ) dim = d;
else {
fprintf(stderr, "dim <= 0\n");
exit(EXIT_FAILURE);
}
}
/*==*/
double*
MxBar2Matrix ( BarData *Data, double *R)
{
double *U=NULL;
if(opt.want_degenerate) MxDoDegeneracyStuff();
switch (opt.method) {
case 'A':
U = MxMethodeA(Data);
break;
case 'F':
U = MxMethodeFULL(R);
break;
case 'I':
U = MxMethodeINPUT(Data, R);
break;
default:
fprintf (stderr,
"ERROR in MxBar2Matrix(): No handler 4 method %c\n", opt.method);
exit(EXIT_FAILURE);
}
if (opt.dumpU) {
MxASCIIWrite(U, "U.txt");
MxBinWrite(U, "U", 'm');
}
return (U);
}
/*==*/
void
MxGetSpace (double **p8)
{
*p8 = (double *) MxNew (dim*sizeof(double));
evals = (double *) MxNew (dim*sizeof(double));
evecs = (double *) MxNew (dim*dim*sizeof(double));
assert(evals!=NULL);
assert(evecs!=NULL);
assert(p8!=NULL);
if(!opt.absrb) {
_sqrPI = (double *) MxNew (dim*dim*sizeof(double));
sqrPI_ = (double *) MxNew (dim*dim*sizeof(double));
}
}
/*==*/
void
MxStartVec (double **p0)
{
int i;
double *pzero = NULL;
pzero = (double *) MxNew(dim*sizeof(double));
if (opt.pini) {
for (i = 1; i < (int) *opt.pini; i+=2)
pzero[(int)opt.pini[i]-1] = (double)opt.pini[i+1];
/* -1 because our lmins start with 1, not with 0 (as Data does ) */
} else {
// all into first state...
pzero[0]=1.0;
}
if (opt.want_verbose) MxPrint (pzero, "p0", 'v');
*p0=pzero;
}
/*==*/
/* calculate equilibrium distribution */
void
MxEqDistr ( BarData *Data, double **p8 )
{
int i;
double Z = 0.;
if(opt.absrb) {
for(i = 0; i < dim; i++)
(*p8)[i] = 0.;
(*p8)[dim-1] = 1.0; /* last entry is the 'new' absorbing state */
}
else {
for(i = 0; i < dim; i++) Z += exp(-((double)Data[i].energy/_kT));
for(i = 0; i < dim; i++) (*p8)[i] = exp(-((double) Data[i].energy/_kT));
}
/* now normalize the new p8 */
double sumsq=0.0;
for (i=0; i<dim; i++)
sumsq += SQ((*p8)[i]);
if(sumsq > 0.0)
sumsq=1./sqrtl(sumsq);
for (i=0; i<dim; i++)
*(*p8+i) *= sumsq;
if(opt.want_verbose) MxPrint (*p8, "p8", 'v');
return;
}
/*==*/
void
MxEqDistrFULL (SubInfo *E, double *p8 )
{
int i;
double Z = 0.;
if(opt.absrb) {
for(i = 0; i < dim; i++)
p8[i] = 0.;
p8[opt.absrb-1] = 1.;
}
else {
for(i = 0; i < dim; i++) Z += exp(-E[i].energy/_kT);
for(i = 0; i < dim; i++) p8[i] = exp(-E[i].energy/_kT)/Z;
}
if(opt.want_verbose) MxPrint (p8, "p8", 'v');
return;
}
void
MxEqDistrFromLinSys( double *U, double **p8 )
{
extern void dgesv_(int *N,int *NRHS,double *A,int *LDA,int *IPIV,
double *B,int *LDB,int *INFO);
int i,j,n, nrhs, nfo, *ipiv=NULL;
double *A=NULL, *B=NULL;
if(opt.absrb) {
for(i = 0; i < dim; i++)
*(*p8+i) = 0.;
*(*p8+(dim-1)) = 1.0; /* last entry is the 'new' absorbing state */
}
else {
n=dim-1;
A = (double *)malloc(n*n*sizeof(double));
B = (double *)malloc(n*sizeof(double));
ipiv = (int *)malloc(n*sizeof(int));
nrhs=1;
if (opt.want_verbose) MxPrint(U, "U", 'm' );
for(i=1; i<=n; i++) /* all except first row */
for(j=1; j<=n; j++)
A[n*(i-1)+(j-1)]=U[dim*i+j] - (i==j && opt.useplusI ? 1.0 : 0.0); //U-I=Q
for(n=0,i=1; i<dim; i++,n++)
B[n]=-U[dim*i];
dim=n;
trnm(A,n);
if (opt.want_verbose) MxPrint(A, "A in MxEqDistrFromLinSys", 'm' );
if (opt.want_verbose) MxPrint(B, "B in MxEqDistrFromLinSys", 'v' );
//DGESV computes the solution to a real system of linear equations A * X = B
dgesv_(&n, &nrhs, A, &n, ipiv, B, &n, &nfo);
if (nfo != 0) {
fprintf(stderr, "dgesv exited with value %d (Cannot compute the equilibrium distribution) - check if the rates have good dimension(if you, you have probably reached the numerical precision of treekin)\n", nfo);
/// TODO switch to compute from detailed balance
exit(EXIT_FAILURE);
}
if (opt.want_verbose) MxPrint(B, "X in MxEqDistrFromLinSys", 'v' );
dim=n+1;
*p8[0]=1.;
for(i=1; i<dim; i++) *(*p8+i)=B[i-1];
if (opt.want_verbose) MxPrint(*p8, "p8 in MxEqDistrFromLinSys before norm", 'v' );
// now check if all are > 0.0
for (i=dim-1; i!=0; i--) {
if ((*p8)[i]<0.0) {
if (i==0) exit(EXIT_FAILURE);
fprintf(stderr, "Warning: p8[%5d] is negative (%e), setting it to a nearby value (%e)\n", i+1, (*p8)[i], (i==dim-1?(*p8)[i-1]:(*p8)[i+1]));
(*p8)[i] = fabs((i==dim-1?(*p8)[i-1]:(*p8)[i+1]));
}
if ((*p8)[i]==0.0) {
fprintf(stderr, "Warning: p8[%5d] is zero (%e), setting it to a minimum value (%e)\n", i+1, (*p8)[i], 1e-20);
(*p8)[i] = 1e-20;
}
}
/* now make the vector stochastic (sum = 1.0) */
long double sum=0.0;
for (i=0; i<dim; i++) {
sum += (*p8)[i];
}
for (i=0; i<dim; i++) {
(*p8)[i] /= sum;
}
// now normalize the new p8
/*long double sumsq=0.0;
for (i=0; i<dim; i++)
sumsq += SQ((*p8)[i]);
if(sumsq > 0.0)
sumsq=1./sqrtl(sumsq);
for (i=0; i<dim; i++)
*(*p8+i) *= sumsq;
*/
free(A);
free(B);
free(ipiv);
}
if(opt.want_verbose)
MxPrint(*p8, "p8", 'v' );
}
/*==*/
void
MxDiagonalize ( double *U, double **_S, double *P8)
{
int i,j;
double *tmpMx=NULL;
if(opt.dumpMathematica == 1) MxKotzOutMathematica(U);
if(!opt.absrb) {
if (opt.want_verbose) MxPrint (U, "input U", 'm');
tmpMx = (double *) MxNew (dim*dim*sizeof(double));
//if (opt.want_verbose) MxPrint (P8, "P8", 'v');
MxDiagHelper(P8);
mmul(tmpMx, _sqrPI, U, dim);
if (opt.want_verbose) MxPrint (_sqrPI, "_sqrPI", 'm');
if (opt.want_verbose) MxPrint (tmpMx, "tmpMx = _sqrPI*U", 'm');
if (opt.want_verbose) MxPrint (sqrPI_, "sqrPI_", 'm');
memset(U,0,dim*dim*sizeof(double));
mmul(U, tmpMx, sqrPI_, dim);
if (opt.want_verbose) MxPrint (U, "U = _sqrPI*U*sqrPI_ (force symmetrized U - uncorrected)", 'm');
free(tmpMx);
/* correct for numerical errors */
long double err = 0.0; // acumulated error
for (i = 0; i < dim; i++) {
for (j = 0; j < dim; j++) {
long double err_inc = fabs((U[dim*i+j]+U[dim*j+i])/2 - U[dim*i+j]);
/*if (isnan(err_inc)) {
fprintf(stderr, "%d %d\n", i,j);
}*/
err += err_inc;
if (isnan(err_inc)) {
fprintf(stderr, "Weird rates! r(%5d,%5d)=(%e, %e)\n", i, j, U[dim*i+j], U[dim*j+i]);
//exit(-1);
}
U[dim*i+j] = (U[dim*i+j]+U[dim*j+i])/2;
U[dim*j+i] = U[dim*i+j];
}
}
if (isnan(err)) {
fprintf(stderr, "Rates are not good -- check your rates (maybe the equilibrium was not computed correctly? rerun with --equil-file or -v set)!!!... (%Lf)\n", err);
exit(-1);
}
if (!opt.quiet) fprintf(stderr, "Corrected numerical error: %e (%e per number)\n", (double)err, (double)(err/(long double)(dim*dim)));
if (opt.want_verbose) MxPrint (U, "force symmetrized U", 'm');
}
// get eigenv*
if(opt.absrb) {
MxEVLapackNonSym(U);
} else {
MxEVLapackSym(U);
}
MxSortEig(evals, evecs);
/*// ### TEST EIGEN
TestEigen(U, dim, NULL, NULL);
MxPrint(evecs, "Eigenvectors of U (LAPACK)", 'm');
MxPrint(evals, "Eigenvalues of U (LAPACK)", 'v');
/// ### END test*/
if (opt.want_verbose) {
MxPrint(evecs, "Eigenvectors of U (LAPACK)", 'm');
MxPrint(evals, "Eigenvalues of U (LAPACK)", 'v');
}
// check for ergodicity of eigenvectors (if not ergodic, then not all the space can be reached)
int *reachable = MxErgoEigen(evecs, dim);
if (reachable) {
fprintf(stderr, "WARNING: Eigenvector matrix is non-ergodic (unreachable states from 1st state):");
for (i=0; i<dim; i++) if (!reachable[i]) fprintf(stderr, " %4d", i+1);
fprintf(stderr, "\n the overall probability can start to decrease if this state(s) is(are) populated!!!");
free(reachable);
//exit(EXIT_FAILURE);
}
//for (i=0; i< 10; i++) fprintf(stderr, "%30.20g\n", evals[i]);
// fix evals[0] to be 1.0
if (opt.useplusI) evals[0] = 1.0;
else evals[0] = 0.0;
// check if we have only one eval = 0 / eval = 1
i = 0;
if (opt.useplusI) while (evals[i] >= 1.0) evals[i++] = 1.0;
else while (evals[i] >= 0.0) evals[i++] = 0.0;
if (i > 1) {
fprintf(stderr, "WARNING: There are multiple evals=%d.0 (%4d) (multiple population traps -- maybe we compute crap)\n", opt.useplusI?1:0, i);
}
/*
for (i=0; i<dim; i++)
if (evals[i]>(1.0-opt.FEPS)) evals[i]=1.0;
*/
//for (i=0; i< 10; i++) fprintf(stderr, "%30.20g\n", evals[i]);
if(opt.absrb)
MxFixevecs(evecs,evals);
*_S=evecs;
if(opt.wrecover) {
MxBinWrite(evals, "evals", 'v');
MxBinWrite(evecs, "evecs", 'm');
MxASCIIWriteV(evals, "evals.txt");
MxASCIIWrite(evecs, "evecs.txt");
}
// compensate for the +I matrix
if (opt.useplusI) for(i = 0; i < dim; i++) evals[i] -= 1.0; /* compensate 4 translation of matrix U */
}
/*==*/
static void
MxDiagHelper(double *P8)
{
int i,j;
for(i = 0; i < dim; i++)
for(j = 0; j < dim; j++)
if( i == j) {
sqrPI_[dim*i+j] = sqrt(P8[i]); /* pos right */
_sqrPI[dim*i+j] = 1/(sqrPI_[dim*i+j]); /* neg left */
}
}
/*==*/
void
MxRecover (double **_S, double *P8)
{
MxDiagHelper(P8);
free(evecs);
free(evals);
if(MxBinRead(&evecs, "evecs", 'm') != dim ) {
fprintf(stderr, "ERROR: MxBinRead() returns wrong dimension for evecs\n");
exit(EXIT_FAILURE);
}
if(MxBinRead(&evals, "evals", 'v') != dim) {
fprintf(stderr, "ERROR: MxBinRead() returns wrong dimension for evals\n");
exit(EXIT_FAILURE);
}
*_S=evecs;
if(opt.want_verbose) {
MxPrint(evals, "MxRecover: Eigenvalues", 'v');
MxPrint(evecs, "MxRecover: Eigenvectors", 'm');
}
return;
}
/*==*/
/* S which comes into this function contains the (right) eigenvectors
calculated by LAPACK */
void
MxIterate (double *p0, double *p8, double *S)
{
/* solve following equation 4 various times
***** NON-ABSORBING CASE: ******
p(t) = sqrPI_ * S * exp(time * EV) * St * _sqrPI * p(0)
CL = sqrPI_ * S
CR = St * _sqrPI
tmpVec = CR * p(0)
tmpVec2 = exp(time * EV) * tmpVec
p(t) = CL * tmpVec2
******* ABSORBING CASE: *******
p(t) = S * exp(time * EV) * S_inv * p(0)
tmpVec = S_inv * p(0)
tmpVec2 = exp(time * EV) *tmpVec
p(t) = S * tmpVec2
*/
int i, count = 0;
double time, check = 0.;
double *CL = NULL, *CR, *exptL, *tmpVec, *tmpVec2, *pt, *St, *pdiff;
double *ptFULL = NULL; /* prob dist 4 of the effective lmins of the tree at time t */
double *p8FULL = NULL; /* equ dist 4 gradient basins, full process */
tmpVec = (double *) MxNew (dim*sizeof(double));
tmpVec2 = (double *) MxNew (dim*sizeof(double));
pt = (double *) MxNew (dim*sizeof(double));
exptL = (double *) MxNew (dim*dim*sizeof(double));
if(opt.method=='F') {
ptFULL = (double *) MxNew ((lmins+1)*sizeof(double));
p8FULL = (double *) MxNew ((lmins+1)*sizeof(double));
pdiff = (double *) MxNew ((lmins+1)*sizeof(double));
}
else pdiff = (double *) MxNew (dim*sizeof(double));
if(! opt.absrb) { /* NON-absorbing case */
CL = (double *) MxNew (dim*dim*sizeof(double));
CR = (double *) MxNew (dim*dim*sizeof(double));
St = (double *) MxNew (dim*dim*sizeof(double));
mcopy(St, S, dim*dim);
trnm(St, dim); /* transpose S (same as invert(S) ('cause of symmetry) minv(St, dim); )*/
mmul (CL, sqrPI_, S, dim);
mmul (CR, St, _sqrPI, dim);
vmul (tmpVec, CR, p0, dim);
free(St);
free(CR);
//MxPrint(S, "S", 'm');
//MxPrint(CL, "CL", 'm');
//MxPrint(_sqrPI, "sqrPI", 'm');
//MxPrint(CR, "CR", 'm');
//MxPrint(tmpVec, "tmpVec", 'v');
}
else { /* absorbing case */
double *S_inv;
S_inv = (double *) MxNew (dim*dim*sizeof(double));
mcopy(S_inv, S, dim*dim);
minv(S_inv,dim);
if(opt.want_verbose) MxPrint(evals, "evals in MxIterate", 'v');
vmul (tmpVec, S_inv, p0, dim);
free(S_inv);
}
if(opt.method=='F') { /* calculate equilibrium distribution once */
for (i = 0; i < dim; i++) p8FULL[E[i].ag] += p8[i];
for (i = 0; i < lmins; i++) check += fabs(p8FULL[i]);
if ( ((check-1) < -0.1) || ((check-1) > 0.1) ) {
fprintf(stderr, "overall equilibrium probability is %e != 1. !\n", check);
if (opt.num_err == 'H' || check == 0.0) exit(EXIT_FAILURE);
else if (opt.num_err == 'R') {
for (i=0; i<dim; i++) p8[i] /= check;
check = 1.0;
}
}
}
check = 0.;
/* solve fundamental equation */
print_settings();
if (opt.t0 == 0.0) {
if (opt.method=='F') PrintProbFull(p0, dim, 0.0, lmins);
else PrintProb(p0, dim, 0.0);
opt.t0 = TZERO;
}
int underflow[dim];
for (i=0; i<dim; i++) underflow[i] = 0;
// iterate
for (time = opt.t0; time <= opt.t8; time *= opt.tinc) {
for (i = 0; i < dim; i++) {
errno = 0;
exptL[dim*i+i] = exp(time/opt.times*evals[i]);
if ((errno == ERANGE || isnan(exptL[dim*i+i])) && !underflow[i]) {
fprintf(stderr, "WARNING: underflow occured on %dth state at time %g -- exp(%g * %g) = %g\n", i+1, time/opt.times, time/opt.times, evals[i], exptL[dim*i+i]);
// the overall probability can start to decrease if this state is still populated!!!\n p_%d(%g) = %g, so it seems this %s\n", i+1, time/opt.times, time/opt.times, evals[i], exptL[dim*i+i], i+1, time/opt.times, pt[i], pt[i]>0.1?"is DEFINITELLY BAD":(pt[i]>0.001?"is POTENTIALLY BAD":"SHOULD BE OK"));
underflow[i] = 1;
//exit(EXIT_FAILURE);
}
}
vmul(tmpVec2, exptL, tmpVec, dim);
if(!opt.absrb) vmul(pt, CL, tmpVec2, dim);
else vmul(pt, S, tmpVec2, dim);
/*if (count%100 == 0) {
fprintf(stderr, "Time: %g\n", time/opt.times);
MxPrint(tmpVec2, "tmpVec2", 'v');
MxPrint(pt, "pt", 'v');
}*/
count++; /* # of iterations */
if(opt.method=='F') {
memset(ptFULL, 0, (lmins+1)*sizeof(double));
for (i = 0; i < dim; i++) {
ptFULL[E[i].ag] += pt[i];
}
}
// print probabilities with respect to corrected ergodicity
if (opt.method=='F') check = PrintProbFull(pt, dim, time, lmins);
else check = PrintProb(pt, dim, time);
//PrintProbNR(p8FULL, lmins, -1);
int reached;
if (opt.method=='F') reached = ConvergenceReached(p8FULL, ptFULL, lmins, 1);
else reached = ConvergenceReached(p8, pt, dim, 0);
fflush(stdout);
if (reached) break;
}
if (time < opt.t8) {
if (opt.method=='F') PrintProbFull(pt, dim, opt.t8, lmins);
else PrintProb(pt, dim, opt.t8);
}
printf("# of iterations: %d\n", count);
/*** end solve fundamental equation ***/
if(opt.method=='F') {
free(ptFULL);
free(p8FULL);
free(E);
}
free(evals);
free(exptL);
free(CL);
free(tmpVec);
free(tmpVec2);
free(pdiff);
if(pt != NULL) free(pt);
}
/*==*/
static double*
MxMethodeA (BarData *Data)
{
/***************************************/
/* | E_s | */
/* \ ____________ / */
/* \ | /\ | / */
/* \ | / \ | / */
/* \| / \ | / */
/* \/ \ | / */
/* i \ | / */
/* \/ */
/* j */
/* -beta(E_s-E_j) */
/* rate: j->i: prop e */
/* -beta(E_s-E_i) */
/* i->j prop e */
/****************************************/
int i,j,real_abs = 0;
double m_saddle, Zabs, abs_rate, *T, *U;
U = (double *) MxNew (dim*dim*sizeof(double));
for( i = 0; i < dim; i++) {
for( j = i+1; j < dim; j++) {
m_saddle = max_saddle(i, j, Data);
/* rate j -> i */
U[dim*i+j] = 1.0*exp(-(m_saddle-Data[j].energy)/_kT);
/* rate i -> j */
U[dim*j+i] = 1.0*exp(-(m_saddle-Data[i].energy)/_kT);
}
}
if(opt.absrb) { /*==== absorbing states ====*/
dim++;
fprintf(stderr, "dim increased to %i\n", dim);
T = (double *) MxNew(dim*dim*sizeof(double));
real_abs = opt.absrb; /* the original absorbing lmin */
real_abs--;
opt.absrb = dim; /* the 'new' abs state = last row/column of rate matrix */
fprintf(stderr, "new absorbing lmin is: %i\n", opt.absrb);
Zabs = exp((-Data[real_abs].energy)/_kT);
abs_rate = exp((-Data[real_abs].energy)/_kT)/Zabs;
for(i = 0; i < (dim-1); i++) { /* all except the last row */
for(j = 0; j < (dim-1); j++)
T[dim*i+j] = U[(dim-1)*i+j];
T[(dim-1)*j+(dim-1)] = 0.;
}
for(j = 0; j < dim; j++) /* last row */
T[dim*(dim-1)+j] = 0.;
T[dim*(dim-1)+real_abs] = abs_rate;
free(U);
U = T;
if(opt.want_verbose) MxPrint(U, "aufgeblasene Matrix", 'm');
} /*== end absorbing states ==*/
/* set diagonal elements to 0 */
for (i = 0; i < dim; i++) U[dim*i+i] = 0;
for (j = 0; j < dim; j++) {
double tmp = 0.00;
/* calculate column sum */
for(i = 0; i < dim; i++) tmp += U[dim*i+j];
U[dim*j+j] = -tmp; /* make U a stochastic matrix */
if (opt.useplusI) U[dim*j+j] += 1.0;
}
if (opt.want_verbose) MxPrint (U,"U with Methode A", 'm');
return (U);
}
/*==*/
static double*
MxMethodeFULL (double *R)
{
int i, j;
free(D);
if(opt.absrb) { /*==== absorbing states ====*/
for(i = 0; i < dim; i++)
R[dim*i+(opt.absrb-1)] = 0. ;
} /*== end absorbing states ==*/
/* set diagonal elements to 0 */
for (i = 0; i < dim; i++) R[dim*i+i] = 0;
for (j = 0; j < dim; j++) {
double tmp = 0.00;
/* calculate column sum */
for(i = 0; i < dim; i++) tmp += R[dim*i+j];
R[dim*j+j] = -tmp; /* make U a stochastic matrix */
if (opt.useplusI) R[dim*j+j] += 1.0;
}
if (opt.want_verbose) MxPrint (R, "R with Methode F", 'm');
return R;
}
/*==*/
static double*
MxMethodeINPUT (BarData *Data, double *Input)
{
int i, j;
double *U=NULL, Zabs, abs_rate;
if (opt.want_verbose) MxPrint(Input, "Input Matrix", 'm');
if (opt.absrb) { /*==== absorbing states ====*/
dim++;
fprintf(stderr, "dim increased to %i\n", dim);
U = (double *) MxNew(dim*dim*sizeof(double));
opt.real_abs = opt.absrb; /* the original absorbing lmin */
opt.real_abs--;
opt.absrb = dim; /* the 'new' abs state = last row/column of rate matrix */
fprintf(stderr, "new absorbing lmin is: %i\n", opt.absrb);
Zabs = exp((-Data[opt.real_abs].FGr)/_kT);
abs_rate = exp((-Data[opt.real_abs].energy)/_kT)/Zabs;
for(i = 0; i < (dim-1); i++) { /* all except the last row */
for(j = 0; j < (dim-1); j++)
U[dim*i+j] = Input[(dim-1)*i+j];
U[(dim-1)*j+(dim-1)] = 0.;
}
for(j = 0; j < dim; j++) /* last row */
U[dim*(dim-1)+j] = 0.;
U[dim*(dim-1)+opt.real_abs] = abs_rate;
/* if(opt.want_verbose) MxPrint(U, "aufgeblasene Matrix", 'm'); */
} /*== end absorbing states ==*/
else { /*== non-absorbing states ==*/
U = (double *) MxNew(dim*dim*sizeof(double));
memcpy(U, Input, dim*dim*sizeof(double));
} /*== end non-absorbing states ==*/
/* diagonal elements */
for (i = 0; i < dim; i++) U[dim*i+i] = 0;
//fprintf(stderr, "dim is %i\n", dim);
for (i = 0; i < dim; i++) {
double tmp = 0.00;
// calculate column sum
for(j = 0; j < dim; j++) tmp += U[dim*j+i];
U[dim*i+i] = -tmp; // make U a stochastic matrix U = Q+I ??
if (opt.useplusI) U[dim*i+i] += 1.0;
}
/* // normalize each column to sum=1
for (i = 0; i < dim; i++) {
double tmp = 0.00;
for(j = 0; j < dim; j++) tmp += U[dim*j+i];
for(j = 0; j < dim; j++) U[dim*j+i] /= tmp;
}*/
if(opt.want_verbose) MxPrint (U,"U with Methode I" , 'm');
free(Input);
return U;
}
/*==*/
static double
max_saddle(int i, int j, BarData *Data)
{
int tmp;
if(Data[i].number > Data[j].father) { /* exchange i & j */
tmp = i;
i = j;
j = tmp;
}
if(Data[i].number == Data[j].father) return Data[j].energy + Data[j].ediff;
else {
if((Data[j].energy + Data[j].ediff) > max_saddle((Data[j].father - 1), (Data[i].number - 1), Data)) return (Data[j].energy + Data[j].ediff);
else return max_saddle((Data[j].father - 1), (Data[i].number - 1), Data);
}
}
/*==*/
void*
MxNew ( size_t size )
{
void *mx = NULL;
if ( (mx = (void *) calloc (1, size)) == NULL )
fprintf (stderr, "ERROR: new_martix() allocation failed\n");
return mx;
}
void MxFPrintD(double *mx, char *name, int dim1, int dim2, FILE *out)
{
int k, l;
fprintf(out,"%s:{\n", name);
for (k = 0; k < dim1; k++) {
if (k!=0) fprintf(out, ",");
fprintf(out, "{");
for (l=0; l< dim2; l++) {
if (l!=0) fprintf(out, ",");
fprintf(out,"%15.7g (%4d) ", mx[dim2*k+l], dim2*k+l);
}
fprintf(out,"}\n");
}
fprintf(out,"}-----------\n");
}
void MxFPrint(double *mx, char *name, char T, FILE *out, int pure)
{
int k, l;
switch (T) {
case 'm': /* square matrix */
if (!pure) fprintf(out,"%s:\n", name);
for (k = 0; k < dim; k++) {
for (l=0; l< dim; l++) {
fprintf(out,"%15.7g ", mx[dim*k+l]);
}
fprintf(out,"\n");
}
if (!pure) fprintf(out,"---\n");
break;
case 'v':
if (!pure) fprintf(out,"%s:\n", name);
for (k = 0; k < dim; k++) fprintf(out,"%15.7g ", mx[k]);
if (!pure) fprintf(out,"\n---\n");
else fprintf(out, "\n");
break;
default:
fprintf(out,"ERROR MxPrint(): no handler 4 type %c\n", T);
}
}
/*==*/
/* print matrix stored in ccmath-format */
void
MxPrint(double *mx, char *name, char T)
{
MxFPrint(mx, name, T, stderr, 0);
}
void PrintDummy(double *line)
{
print_settings();
PrintProb(line, 1, opt.t0);
PrintProb(line, 1, opt.t8);
}
/*==*/
static void
print_settings(void)
{
printf(
"# Date: %s"
"# Sequence: %s\n"
"# Method: %c Start Time: %.2f Stop Time: %.2f Temperature: %.2f\n",
time_stamp(),
opt.sequence,
opt.method,
opt.t0,
opt.t8,
opt.T
);
if(opt.basename != NULL) printf("# basename: %s\n",opt.basename);
else printf("# basename: <stdin>\n");
if (opt.tinc) printf("# time increment: %.2f\n", opt.tinc);
else printf("# time increment: %.2f \n", opt.tinc);
if(opt.want_degenerate == 1)printf("# degeneracy: on\n");
else printf("# degeneracy: off\n");
if (opt.absrb < 1) printf("# absorbing lmin: none\n");
else printf("# absorbing lmin: %d\n", opt.absrb);
if (opt.n > 0) printf("# nlmins: %d\n", opt.n);
else printf("# nlmins: till EOF\n");
}
/*==*/
static char*
time_stamp(void)
{
time_t cal_time;
cal_time = time(NULL);
return ( ctime(&cal_time) );
}
/*==*/
void
MxMemoryCleanUp (void)
{
if(_sqrPI) free(_sqrPI);
if(sqrPI_) free(sqrPI_);
if(opt.sequence) free(opt.sequence);
if(opt.basename) free(opt.basename);
if(opt.fpt_file) free(opt.fpt_file);
free_gengetopt();
}
/*==*/
static void
MxDoDegeneracyStuff(void)
{
int i, j, b, nr, current, numsad = 1, count = 0;
numsad = ParseSaddleFile(&saddle);
/* loop over all elements of structure-array saddle: */
/* first we fill the upper triangle */
for (count = 0; count < numsad; count++) {
current = 1;
nr = saddle[count].list[0];
/* only for saddles with a cc >= 1 AND those which connect at least 2 lmins */
if(saddle[count].cc >= 1 && nr >= 2 && !(saddle[count].cc == 1 && nr == 2)) {
while(current < nr) {
for(b = current+1; b <= nr; b++) {
/* skip in case a lmin which we don't see is connected by */
/* the saddle (because we can only see --max x lmins) */
if(saddle[count].list[current] > dim || saddle[count].list[b] > dim) {
current++;
continue;
}
/* FIRST: we consider the size of the cc the saddle belongs to */
if(saddle[count].cc > 1) {
D[dim * (saddle[count].list[current]-1) + (saddle[count].list[b]-1)] += (saddle[count].cc - 1);
fprintf(stderr, "transition between %3d - %3d: adding %2d cc\n",
saddle[count].list[current], saddle[count].list[b], saddle[count].cc-1);
/* -1 because if the size of cc == 1 there's nothing special */
/* about it, i.e. there is just one saddle */
}
/* SECOND: we consider that the saddle connects several lmins */
if(nr > 2) {
D[dim * (saddle[count].list[current]-1) + (saddle[count].list[b]-1)]++;
fprintf(stderr, "transition betweed %3d - %3d: adding 1 deg_saddle\n",
saddle[count].list[current], saddle[count].list[b] );
/* -1 because matrix starts with0, NOT with 1 */
}
}
current++;
}
}
}
for(i = 0; i < dim; i++) /* make matrix symmetric */
for(j = 0; j < dim; j++)
if (i != j)
D[dim*j+i] = D[dim*i+j];
if (opt.want_verbose) {
sprintf (Aname, "%s", "D (degeneracies)");
MxPrint (D, Aname, 'm');
}
free(saddle);
}
/*==*/
static void
norm2(double *mx)
{
/* normalize columns of matrix mx */
/* (to euclidean norm 1)*/
int i,j;
long double sumsq;
for (j=0; j<dim; j++) {
sumsq=0.0;
for (i=0; i<dim; i++)
sumsq += SQ(mx[dim*i+j]);
if(sumsq > 0.0)
sumsq=1./sqrtl(sumsq);
for (i=0; i<dim; i++)
mx[dim*i+j] *= sumsq;
}
return;
}
#define abs(x) ((x)>0.0?(x):(-x))
/*==*/
static void
MxFixevecs(double *evecs, double *evals)
/* evecs: eigenvectors columns, dimension N */
/* since the sum over each non-absorbing */
/* column must vanish, replace the */
/* problematic evecs with linear combinations */
/* satisfying that criterion */
/* rationale: with 1^T a row vector of 1s */
/* Q=S*exp(L)*inv(S) */
/* 1^T*Q = 1^T (probabilities sum up to 1) */
/* 1^T*S*exp(L) = 1^T*S */
{
int i,j,maxind,abscount;
double maxent,csum;
/* assume sorted evals */
/* and an absorbing state */
/* im the 1st evec=1st column */
/* take care of possibly more than one abs. state*/
/* all abs. states have been *assigned* eigenvalue one */
/* for each of them, set the largest component of the */
/* eigenvectors to one, all others to zero */
abscount=0;
for (i=0; i<dim; i++) {
if (evals[i]==1.0) {
abscount++;
maxent=0.;
maxind=0;
for (j=0; j<dim; j++) {
if (abs(evecs[dim*j+i]) > maxent) {
maxent=abs(evecs[dim*j+i]);
maxind=j;
}
}
evecs[dim*maxind+i]=1.0;
for (j=0; j<dim; j++) {
if (j==maxind) continue;
evecs[dim*j+i]=0.0;
}
}