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readsys.c
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readsys.c
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/*
Reading and setup of the spinsystem
Copyright (C) 1999 Mads Bak, Jimmy T. Rasmussen
2009 ZT modification with new matrix types
This file is part of the SIMPSON General NMR Simulation Package
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Reads the spin system from the 'spinsys' section in the input
file and creates the Hamiltonian for the spin system.
Called from sim.c the setup and performs the simulation
*/
#include <stdio.h>
#include <errno.h>
#include <stdlib.h>
#include <string.h>
#include <tcl.h>c
#include <assert.h>
#include "matrix.h"
#include "spinsys.h"
#include "wigner.h"
#include "sim.h"
#include "defs.h"
#include "cm.h"
#include "blockdiag.h"
#include "ham.h"
/* based on NRC QuickSort algorithm */
void sort_mzmap(int Nmz, int row, int c_ini, int n_c, int *mzmap, int *permvec)
{
long i, indxt, ir, itemp, j, k, l, *indx;
int jstack = 0, *istack, *idum;
int a;
const int nstack = 64;
// printf("sort_mzmap: row %d, from column %d, %d elements ... \n",row,c_ini,n_c);
istack = malloc(nstack*sizeof(int));
indx = malloc((n_c)*sizeof(unsigned long));
for (i=0; i<n_c; i++) indx[i] = i;
l = 0;
ir = n_c-1;
for (;;) {
if (ir-l < 10) {
/* insertion sort when subarray small */
for (j=l+1; j<=ir; j++) {
indxt = indx[j];
a = mzmap[row+(indxt+c_ini)*Nmz];
for (i=j-1; i>=l; i--) {
if (mzmap[row+(indx[i]+c_ini)*Nmz] <= a) break;
indx[i+1] = indx[i];
}
indx[i+1] = indxt;
}
if (jstack == 0) break;
ir = istack[jstack--];
l = istack[jstack--];
} else {
k = (l +ir) >> 1;
itemp = indx[k]; indx[k] = indx[l+1]; indx[l+1] = itemp;
if (mzmap[row+(indx[l]+c_ini)*Nmz] > mzmap[row+(indx[ir]+c_ini)*Nmz]) {
itemp = indx[l]; indx[l] = indx[ir]; indx[ir] = itemp;
}
if (mzmap[row+(indx[l+1]+c_ini)*Nmz] > mzmap[row+(indx[ir]+c_ini)*Nmz]) {
itemp = indx[l+1]; indx[l+1] = indx[ir]; indx[ir] = itemp;
}
if (mzmap[row+(indx[l]+c_ini)*Nmz] > mzmap[row+(indx[l+1]+c_ini)*Nmz]) {
itemp = indx[l]; indx[l] = indx[l+1]; indx[l+1] = itemp;
}
i = l+1;
j = ir;
indxt = indx[l+1];
a = mzmap[row+(indxt+c_ini)*Nmz];
for (;;) {
do i++; while (mzmap[row+(indx[i]+c_ini)*Nmz] < a);
do j--; while (mzmap[row+(indx[j]+c_ini)*Nmz] > a);
if (j < i) break;
itemp = indx[i]; indx[i] = indx[j]; indx[j] = itemp;
}
indx[l+1] = indx[j];
indx[j] = indxt;
jstack += 2;
if (jstack > nstack) {
fprintf(stderr,"Error in sort_mzmap: nstack too small\n");
exit(1);
}
if (ir-i+1 >= j-l) {
istack[jstack] = ir;
istack[jstack-1] = i;
ir = j-1;
} else {
istack[jstack] = j-1;
istack[jstack-1] = l;
l = i;
}
}
}
idum = malloc(n_c*sizeof(int));
for (i=0; i<n_c; i++) idum[i] = permvec[i+c_ini+1];
for (i=0; i<n_c; i++) permvec[i+c_ini+1] = idum[indx[i]];
for (j=0; j< Nmz; j++) {
for (i=0; i<n_c; i++) idum[i] = mzmap[j +(i+c_ini)*Nmz];
for (i=0; i<n_c; i++) mzmap[j +(i+c_ini)*Nmz] = idum[indx[i]];
}
free(idum);
free(indx);
free(istack);
}
void readsys(Tcl_Interp* interp,Sim_info* s)
{
SpinSys* ss;
int ver, Nnuc, Nchan, Nelm, NN, i, j, n1, n2, Jiso, Jani;
int Nshift=0, Nj=0, Ndip=0, Nquad=0, Nmix=0, Ngten=0, Nhf=0, Naniso;
char *buf, **names, **spins;
Tcl_Obj **vals;
Shift *csptr;
Dipole *ddptr;
Quadrupole *qptr;
Jcoupling *jptr;
Mixing *mptr;
Gtensor *gptr;
Hyperfine *hfptr;
double data[8];
int *spin_code, *mzmap=NULL, *permvec, Nmz, reps, mzpos, Ival, Icur, c_ini, n_c, Nblk, *blk_dims=NULL;
int Hiso_isdiag, HQ_isdiag, Nbasis;
ss=s->ss;
ss_initialize(ss);
ver = (verbose & VERBOSE_SPINSYS);
if (ver) printf("Reading spinsystem:\n");
/* get number of nuclei and their names */
buf=Tcl_GetVar2(interp,"spinsysres","nuclei",TCL_GLOBAL_ONLY);
if (!buf) {
fprintf(stderr,"Error: the spinsystem must contain 'nuclei' field\n");
exit(1);
}
if (Tcl_SplitList(interp, buf, &Nnuc, &spins) != TCL_OK) {
fprintf(stderr,"Error: readsys cannot decompose list spinsysres(nuclei)\n");
exit(1);
}
if (ver) printf( "Number of spins : %d\n",Nnuc);
for (i=0; i<Nnuc; i++) {
if (ver) {
if (!strncmp(spins[i],"e",1)) {
printf(" electron %3d : '%s'\n",i+1,spins[i]);
} else {
printf(" nucleus %3d : '%s'\n",i+1,spins[i]);
}
}
ss_addspin(ss,spins[i]);
}
/* read in channels info */
buf=Tcl_GetVar2(interp,"spinsysres","channels",TCL_GLOBAL_ONLY);
if (!buf) {
fprintf(stderr,"Error: the spinsystem must contain 'channels' field\n");
exit(1);
}
if (Tcl_SplitList(interp, buf, &Nchan, &names) != TCL_OK) {
fprintf(stderr,"Error: readsys cannot decompose list spinsysres(channels)\n");
exit(1);
}
if (Nchan > MAXCHAN) {
fprintf(stderr,"Error: maximal number of channels exceeded (MAXCHAN=%d)\n",MAXCHAN);
exit(1);
}
ss->nchan = Nchan;
NN = 0;
spin_code = int_vector(Nnuc);
iv_zero(spin_code);
for (i=1; i<=Nchan; i++) {
strcpy(ss->channames[i],names[i-1]);
ss->nchanelem[i] = 0;
for (j=1; j<=Nnuc; j++) {
//DEBUGPRINT("readsys: comparing (%d)-'%s' with (%d)-'%s'\n",i,ss->channames[i],j,spins[j-1]);
if (!strcmp(spins[j-1],ss->channames[i])) {
ss->nchanelem[i]++;
ss->chan[i][ss->nchanelem[i]] = j;
NN++;
spin_code[j] = i;
}
}
if (ss->nchanelem[i] == 0) {
fprintf(stderr,"Error: empty channel '%s'\n",names[i-1]);
exit(1);
}
}
/* gather info for Hamiltonian block diagonalization */
//s->permvec = NULL;
//s->blk_dims = NULL;
//s->Nmz = 0;
if (s->block_diag) {
Nmz = Nchan;
if (Nnuc != NN) {
/* some spins do not have assigned channel but I want to use them */
for (i=1; i<= Nnuc; i++) {
if (spin_code[i] != 0) continue;
Nmz++;
spin_code[i] = Nmz;
ss->nchanelem[Nmz] = 1;
ss->chan[Nmz][ss->nchanelem[Nmz]] = i;
for (j=i+1; j<=Nnuc; j++) {
if (!strcmp(spins[j-1],spins[i-1])) {
spin_code[j] = Nmz;
ss->nchanelem[Nmz]++;
ss->chan[Nmz][ss->nchanelem[Nmz]] = j;
}
}
}
}
/* test output BEGIN
printf("readsys block_diag info:\n");
for (i=1; i<=Nmz; i++) {
printf("channel %d:",i);
for (j=1; j<=ss->nchanelem[i]; j++) {
printf(" %d",ss->chan[i][j]);
}
printf("\n");
}
test output END */
/* fill map of quantum numbers mz*2 on each channel */
mzmap = calloc(Nmz*ss->matdim,sizeof(int));
if (mzmap == NULL) {
fprintf(stderr,"Error: readsys can not allocate mzmap\n");
exit(1);
}
reps = 1;
for (i=Nnuc; i>0; i--) {
Icur = (int)round(2*ss->iso[i]->spin);
//printf("nucleus %d has spin %d\n",i,Icur);
mzpos = 0;
while (mzpos < ss->matdim) {
for (Ival=Icur; Ival>=-Icur; Ival-=2) {
for (j=0; j<reps; j++) {
assert(mzpos < ss->matdim);
mzmap[spin_code[i]-1 + mzpos*Nmz] += Ival;
//printf("mzmap[%d][%d] += %d\n",spin_code[i]-1,mzpos,Ival);
mzpos++;
}
}
}
reps *= Icur+1;
}
/* test output BEGIN
printf("readsys block_diag info:\n\tmz map\n\t======\n");
for (i=0; i<Nmz; i++) {
for (j=0; j<ss->matdim; j++) {
printf("%3d ",mzmap[i+j*Nmz]);
}
printf("\n");
}
test output END */
/* sort mz map and get product basis permutation vector */
permvec = int_vector(ss->matdim);
for (i=1; i<=ss->matdim; i++) permvec[i] = i;
sort_mzmap(Nmz,0,0,ss->matdim,mzmap,permvec);
for (i=1; i<Nmz; i++) {
c_ini = 0;
n_c = 0;
while (c_ini<ss->matdim) {
do n_c++; while ((c_ini+n_c)<ss->matdim && mzmap[i-1+(c_ini+n_c)*Nmz] == mzmap[i-1+(c_ini+n_c-1)*Nmz]);
if (n_c != 1 ) sort_mzmap(Nmz,i,c_ini,n_c,mzmap,permvec);
c_ini += n_c;
n_c = 0;
}
}
/* test output BEGIN
printf("readsys block_diag info:\n\tSORTED mz map\n\t======\n");
for (i=0; i<Nmz; i++) {
for (j=0; j<ss->matdim; j++) {
printf("%3d ",mzmap[i+j*Nmz]);
}
printf("\n");
}
printf("permutation vector\n");
for (i=1;i<=ss->matdim; i++) printf("%d ",permvec[i]);
printf("\n\n");
test output END */
/* prepare information vector about block structure */
Nblk = 1;
for (i=1; i<=Nmz; i++) Nblk *= ((int)round(2*ss->iso[ss->chan[i][1]]->spin))*ss->nchanelem[i]+1;
blk_dims = int_vector(Nblk);
Nblk = 0;
c_ini = 0;
n_c = 0;
while (c_ini<ss->matdim) {
do n_c++; while ((c_ini+n_c)<ss->matdim && mzmap[Nmz-1+(c_ini+n_c)*Nmz] == mzmap[Nmz-1+(c_ini+n_c-1)*Nmz]);
c_ini += n_c;
Nblk++;
assert(Nblk <= LEN(blk_dims));
blk_dims[Nblk] = n_c;
n_c = 0;
}
/* test output BEGIN
printf("Number of blocks = %d\ndims =",LEN(blk_dims));
for (i=1; i<=LEN(blk_dims);i++) printf(" %d",blk_dims[i]);
printf("\n\n");
text output END */
//s->permvec = permvec;
//s->blk_dims = blk_dims;
s->Nmz = Nmz;
s->Nbasis = Nbasis = 1<<Nmz;
/* generation of permutation table */
s->perm_table = (int**)malloc(Nbasis*Nbasis*sizeof(int*));
s->dims_table = (int**)malloc(Nbasis*sizeof(int*));
if (s->perm_table == NULL) {
fprintf(stderr,"Error: readsys can not allocate perm_table\n");
exit(1);
}
if (s->dims_table == NULL) {
fprintf(stderr,"Error: readsys can not allocate dims_table\n");
exit(1);
}
int *mzmap_tmp = malloc(Nmz*ss->matdim*sizeof(int));
int *Pvec, *blkdm;
for (i=1; i<Nbasis-1; i++) {
//printf("\n\n basis index %d\n=======================\n",i);
memcpy(mzmap_tmp,mzmap,Nmz*ss->matdim*sizeof(int));
int code = i;
s->perm_table[(Nbasis-1) + i*Nbasis] = Pvec = int_vector(ss->matdim);
for (j=1; j<=ss->matdim; j++) Pvec[j] = j;
int r1 = 0, r2 = 0;
while ( !(code & (1<<0)) ) {
r1++;
code >>= 1;
}
//printf("\t\tr1 = %d\n",r1);
sort_mzmap(Nmz,r1,0,ss->matdim,mzmap_tmp,Pvec);
Nblk = ((int)round(2*ss->iso[ss->chan[r1+1][1]]->spin))*ss->nchanelem[r1+1]+1;
r2 = r1 + 1;
code >>= 1;
while (code != 0) {
while ( !(code & (1<<0)) ) {
r2++;
code >>= 1;
}
//printf("\t\tr2 = %d",r2);
c_ini = 0;
n_c = 0;
while (c_ini<ss->matdim) {
do n_c++; while ((c_ini+n_c)<ss->matdim && mzmap_tmp[r1+(c_ini+n_c)*Nmz] == mzmap_tmp[r1+(c_ini+n_c-1)*Nmz]);
if (n_c != 1 ) sort_mzmap(Nmz,r2,c_ini,n_c,mzmap_tmp,Pvec);
c_ini += n_c;
n_c = 0;
}
r1 = r2;
code >>= 1;
r2++;
Nblk *= ((int)round(2*ss->iso[ss->chan[r2][1]]->spin))*ss->nchanelem[r2]+1;
}
/* prepare information vector about block structure */
//printf("\tNumber of blocks = %d\n",Nblk);
s->dims_table[i] = blkdm = int_vector(Nblk);
Nblk = 0;
c_ini = 0;
n_c = 0;
while (c_ini<ss->matdim) {
do n_c++; while ((c_ini+n_c)<ss->matdim && mzmap_tmp[r2-1+(c_ini+n_c)*Nmz] == mzmap_tmp[r2-1+(c_ini+n_c-1)*Nmz]);
c_ini += n_c;
Nblk++;
assert(Nblk <= LEN(blkdm));
blkdm[Nblk] = n_c;
n_c = 0;
}
//printf("\tpermvec = "); for (j=1;j<=ss->matdim; j++) printf("%d ",Pvec[j]);
//printf("\n\tdims = "); for (j=1;j<=Nblk; j++) printf("%d ",blkdm[j]);
/* inverse permutation */
int *permvec_inv;
s->perm_table[i + (Nbasis-1)*Nbasis] = permvec_inv = int_vector(ss->matdim);
for (j=1; j<=ss->matdim; j++) permvec_inv[Pvec[j]] = j;
}
free(mzmap_tmp);
free(mzmap);
/* all other permutations */
int k;
int *permv1, *permv2;
for (i=1; i<Nbasis-1; i++) {
permv1 = s->perm_table[i + (Nbasis-1)*Nbasis];
assert(LEN(permv1) == ss->matdim);
for (j=i+1; j<Nbasis-1; j++) {
permv2 = s->perm_table[(Nbasis-1) + j*Nbasis];
assert(LEN(permv2) == ss->matdim);
s->perm_table[i + j*Nbasis] = Pvec = int_vector(ss->matdim);
for (k=1; k<=ss->matdim; k++) Pvec[k] = permv1[permv2[k]];
s->perm_table[j + i*Nbasis] = permv2 = int_vector(ss->matdim);
for (k=1; k<=ss->matdim; k++) permv2[Pvec[k]] = k;
/* check inverse perm with combined perm
printf("\npermutation %d->%d\n",j,i);
for (k=1; k<=ss->matdim; k++) printf("%d ",permv2[k]);
permvec = s->perm_table[j+(Nbasis-1)*Nbasis];
permv2 = s->perm_table[(Nbasis-1)+i*Nbasis];
printf("\npermutation %d->%d->%d\n",j,Nbasis-1,i);
for (k=1; k<=ss->matdim; k++) printf("%d ",permvec[permv2[k]]);
printf("\n");
**********************/
}
}
/* permutations from and to basis 0 should also be included */
s->perm_table[0 + (Nbasis-1)*Nbasis] = permv1 = permvec;
//memcpy(permv1+1,s->permvec+1,LEN(permv1)*sizeof(int));
s->perm_table[(Nbasis-1) + 0*Nbasis] = permv2 = int_vector(ss->matdim);
for (k=1; k<=ss->matdim; k++) permv2[permv1[k]] = k;
//permv1 = s->permvec;
for (i=1; i<Nbasis-1; i++) {
permv2 = s->perm_table[(Nbasis-1) + i*Nbasis];
assert(LEN(permv2) == ss->matdim);
s->perm_table[0 + i*Nbasis] = Pvec = int_vector(ss->matdim);
for (k=1; k<=ss->matdim; k++) Pvec[k] = permv1[permv2[k]];
s->perm_table[i + 0*Nbasis] = permv2 = int_vector(ss->matdim);
for (k=1; k<=ss->matdim; k++) permv2[Pvec[k]] = k;
}
for (i=0; i<Nbasis; i++) s->perm_table[i+i*Nbasis] = NULL;
s->dims_table[Nbasis-1] = blk_dims;
//memcpy(s->dims_table[0]+1,s->blk_dims+1,LEN(s->blk_dims)*sizeof(int));
s->dims_table[0] = blkdm = int_vector(1);
blkdm[1] = ss->matdim;
} else {
s->Nmz = 0;
s->Nbasis = 0;
s->perm_table = NULL;
s->dims_table = NULL;
}
Tcl_Free((char*)names);
Tcl_Free((char*)spins);
free_int_vector(spin_code);
if (ver) {
printf("Number of channels : %d\n",ss->nchan);
for (i=1;i<=ss->nchan;i++) {
printf( " channel %3d : '%s' contain",i,ss->channames[i]);
for (j=1;j<=ss->nchanelem[i];j++) {
printf(" nucleus(%d,%s)",ss->chan[i][j],ss->iso[ss->chan[i][j]]->name);
}
printf("\n");
}
}
if (Tcl_EvalEx(interp,"array names spinsysres",-1,TCL_EVAL_GLOBAL) != TCL_OK) {
fprintf(stderr,"Error: readsys can not get spinsysres fields:\n %s\n",Tcl_GetStringResult(interp));
exit(1);
}
buf = Tcl_GetStringResult(interp);
if (Tcl_SplitList(interp, buf, &Nelm, &names) != TCL_OK) {
fprintf(stderr,"Error: readsys cannot decompose spinsysres array names from a list\n");
exit(1);
}
for (i=0; i<Nelm; i++) {
if (!strncmp(names[i],"nuclei",6)) continue;
if (!strncmp(names[i],"channels",8)) continue;
if (!strncmp(names[i],"shift",5)) {
Nshift++;
continue;
}
if (!strncmp(names[i],"jcoupling",9)) {
Nj++;
continue;
}
if (!strncmp(names[i],"dipole",6)) {
Ndip++;
continue;
}
if (!strncmp(names[i],"quadrupole",10)) {
Nquad++;
continue;
}
if (!strncmp(names[i],"mixing",6)) {
Nmix++;
continue;
}
if (!strncmp(names[i],"gtensor",7)) {
Ngten++;
continue;
}
if (!strncmp(names[i],"hyperfine",9)) {
Nhf++;
continue;
}
}
s->CS = (Shift**)malloc(Nshift*sizeof(Shift*));
s->nCS = 0;
s->J = (Jcoupling**)malloc(Nj*sizeof(Jcoupling*));
s->nJ = 0;
s->DD = (Dipole**)malloc(Ndip*sizeof(Dipole*));
s->nDD = 0;
s->Q = (Quadrupole**)malloc(Nquad*sizeof(Quadrupole*));
s->nQ = 0;
s->MIX = (Mixing**)malloc(Nmix*sizeof(Mixing*));
s->nMIX = 0;
s->G = (Gtensor**)malloc(Ngten*sizeof(Gtensor*));
s->nG = 0;
s->HF = (Hyperfine**)malloc(Nhf*sizeof(Hyperfine*));
s->nHF = 0;
s->matdim = ss->matdim;
s->Hint_isdiag = 1;
Hiso_isdiag = 1;
HQ_isdiag = 1;
Naniso = 0;
for (i=0; i<Nelm; i++) {
if (!strncmp(names[i],"nuclei",6)) continue;
if (!strncmp(names[i],"channels",8)) continue;
if (Tcl_ListObjGetElements(interp,Tcl_GetVar2Ex(interp,"spinsysres",names[i],TCL_GLOBAL_ONLY), &NN, &vals) != TCL_OK) {
fprintf(stderr,"Error: readsys cannot decompose list of parameters for spinsysres(%s)\n",names[i]);
exit(1);
}
if (!strncmp(names[i],"shift",5)) {
if (NN != 7) {
fprintf(stderr,"Error: reading shift - parameter count mismatch\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[0],&n1) != TCL_OK) {
fprintf(stderr,"Error: readsys - shift - int conversion failure\n");
exit(1);
}
if (n1 < 1 || n1 > ss->nspins) {
fprintf(stderr,"Error: spinsys: shift %d out of defined range\n",n1);
exit(1);
}
if (shift_exist(s,n1) >= 0) {
fprintf(stderr,"Error: spinsys: shift already exists for nucleus %d\n",n1);
exit(1);
}
for (j=1; j<NN; j++) {
if (Tcl_GetDoubleFromObj(interp,vals[j],&(data[j-1])) != TCL_OK) {
fprintf(stderr,"Error: readsys - shift - double conversion failure\n");
exit(1);
}
}
/* when zero amplitudes, do nothing */
if ( (fabs(data[0]) < TINY) && (fabs(data[1]) < TINY) ) continue;
s->CS[(s->nCS)++] = csptr = (Shift*)malloc(sizeof(Shift));
csptr->nuc = n1; csptr->eta = data[2]; csptr->pas[0] = data[3]; csptr->pas[1] = data[4]; csptr->pas[2] = data[5];
if (ss_gamma(ss,n1) > 0) {
csptr->iso = -data[0]*2.0*M_PI; csptr->delta = -data[1]*2.0*M_PI;
} else {
csptr->iso = data[0]*2.0*M_PI; csptr->delta = data[1]*2.0*M_PI;
}
if (fabs(csptr->delta) > TINY) {
Naniso++;
csptr->Rmol = Dtensor2(SQRT2BY3*csptr->delta, csptr->eta);
csptr->Rmol = wig2roti(csptr->Rmol, csptr->pas[0], csptr->pas[1], csptr->pas[2]);
} else {
csptr->Rmol = NULL;
}
csptr->T = NULL;
if ( ver ) {
printf( "Chemical shift on nucleus %d\n",n1);
printf( " isotropic shift : %g Hz\n",csptr->iso/2.0/M_PI);
printf( " anisotropic shift : %g Hz\n",csptr->delta/2.0/M_PI);
printf( " asymmetry parameter : %g\n",csptr->eta);
printf( " euler angles of tensor : (%g,%g,%g) degrees\n",csptr->pas[0],csptr->pas[1],csptr->pas[2]);
//dm_print(csptr->T,"Operator matrix");
}
continue;
}
if (!strncmp(names[i],"jcoupling",9)) {
if (NN != 8) {
fprintf(stderr,"Error: reading jcoupling - parameter count mismatch\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[0],&n1) != TCL_OK) {
fprintf(stderr,"Error: readsys - jcoupling - int conversion failure\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[1],&n2) != TCL_OK) {
fprintf(stderr,"Error: readsys - jcoupling - int conversion failure\n");
exit(1);
}
if (n1 < 1 || n1 > ss->nspins || n2 < 1 || n2 > ss->nspins) {
fprintf(stderr,"Error: spinsys: jcoupling %d %d out of defined nuclei range\n",n1,n2);
exit(1);
}
if (jcoupling_exist(s,n1,n2) >= 0) {
fprintf(stderr,"Error: spinsys: jcoupling already exists for nuclei (%d, %d)\n",n1, n2);
exit(1);
}
for (j=2; j<NN; j++) {
if (Tcl_GetDoubleFromObj(interp,vals[j],&(data[j-2])) != TCL_OK) {
fprintf(stderr,"Error: readsys - jcoupling - double conversion failure\n");
exit(1);
}
}
if (fabs(data[0]) > TINY) Jiso = 1; else Jiso = 0;
if (fabs(data[1]) > TINY) Jani = 1; else Jani = 0;
if ( Jani + Jiso == 0) continue;
s->J[(s->nJ)++] = jptr = (Jcoupling*)malloc(sizeof(Jcoupling));
if (n1 < n2) {
jptr->nuc[0] = n1; jptr->nuc[1] = n2;
} else {
jptr->nuc[0] = n2; jptr->nuc[1] = n1;
}
jptr->iso = data[0]*2.0*M_PI; jptr->delta = data[1]*2.0*M_PI; jptr->eta = data[2];
jptr->pas[0] = data[3]; jptr->pas[1] = data[4]; jptr->pas[2] = data[5];
jptr->blk_Tiso = NULL; jptr->blk_T = NULL;
if (ss_issame(ss,n1,n2)) {
if (ver) printf( "Homonuclear ");
if (Jiso) Hiso_isdiag = 0;
if (Jani) {
Naniso++;
HQ_isdiag = 0;
}
s->Hint_isdiag = 0;
} else {
if (ver) printf( "Heteronuclear ");
if (Jani) {
Naniso++;
}
}
if (Jani) {
jptr->Rmol = Dtensor2(jptr->delta*2.0, jptr->eta);
jptr->Rmol = wig2roti(jptr->Rmol,jptr->pas[0],jptr->pas[1],jptr->pas[2]);
} else {
jptr->Rmol = NULL;
}
if (ver) {
printf( "J-coupling between nucleus %d and %d\n",n1,n2);
printf( " isotropic value : %g Hz\n",jptr->iso/2.0/M_PI);
printf( " anisotropic value : %g Hz\n",jptr->delta/2.0/M_PI);
printf( " asymmetry : %g \n",jptr->eta);
printf( " euler angles of tensor : (%g,%g,%g) degrees\n",jptr->pas[0],jptr->pas[1],jptr->pas[2]);
}
continue;
}
if (!strncmp(names[i],"dipole",6)) {
if (NN != 6 && NN != 7) {
fprintf(stderr,"Error: reading dipole - parameter count mismatch\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[0],&n1) != TCL_OK) {
fprintf(stderr,"Error: readsys - dipole - int conversion failure\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[1],&n2) != TCL_OK) {
fprintf(stderr,"Error: readsys - dipole - int conversion failure\n");
exit(1);
}
if (n1 < 1 || n1 > ss->nspins || n2 < 1 || n2 > ss->nspins) {
fprintf(stderr,"Error: spinsys: dipole %d %d out of defined nuclei range\n",n1,n2);
exit(1);
}
if (dipole_exist(s,n1,n2) >=0 ) {
fprintf(stderr,"Error: spinsys: dipole already exists for nuclei (%d, %d)\n",n1, n2);
exit(1);
}
for (j=2; j<NN; j++) {
if (Tcl_GetDoubleFromObj(interp,vals[j],&(data[j-2])) != TCL_OK) {
fprintf(stderr,"Error: readsys - dipole - double conversion failure\n");
exit(1);
}
}
if (fabs(data[0]) < TINY) continue;
s->DD[(s->nDD)++] = ddptr = (Dipole*)malloc(sizeof(Dipole));
if (n1 < n2) {
ddptr->nuc[0] = n1; ddptr->nuc[1] = n2;
} else {
ddptr->nuc[0] = n2; ddptr->nuc[1] = n1;
}
ddptr->delta = data[0];
if (NN == 6) {
ddptr->eta = 0.0; ddptr->pas[0] = data[1]; ddptr->pas[1] = data[2]; ddptr->pas[2] = data[3];
} else {
assert(NN==7);
ddptr->eta = data[1]; ddptr->pas[0] = data[2]; ddptr->pas[1] = data[3]; ddptr->pas[2] = data[4];
}
if (ss_issame(ss,n1,n2)) {
if (ver) printf( "Homonuclear ");
HQ_isdiag = 0;
s->Hint_isdiag = 0;
} else {
if (ver) printf( "Heteronuclear ");
}
ddptr->blk_T = NULL;
Naniso++;
if (ver) {
printf( "dipolar coupling between nucleus %d and %d\n",n1,n2);
printf( " dipolar coupling : %g Hz\n",ddptr->delta);
if (NN==7) printf(" effective asymmetry : %g Hz\n",ddptr->eta);
printf( " euler angles of tensor : (%g,%g,%g) degrees\n",ddptr->pas[0],ddptr->pas[1],ddptr->pas[2]);
}
if (s->dipole_check) {
int bsign = ( -ss_gamma(ss,n1)*ss_gamma(ss,n2) > 0 ? 1 : -1);
if (ddptr->delta > 0.0 && bsign < 0) {
fprintf(stderr,"error: the dipolar coupling between nucleus %d and %d must be negative to comply\n"
" to the conventions used in this program. Set 'dipole_check' to 'false' to\n"
" override this sign check.\n",n1,n2);
exit(1);
} else if (ddptr->delta < 0.0 && bsign > 0) {
fprintf(stderr,"error: the dipolar coupling between nucleus %d and %d must be positive to comply\n"
" to the conventions used in this program. Set 'dipole_check' to 'false' to\n"
" override this sign check.\n",n1,n2);
exit(1);
}
}
ddptr->Rmol = Dtensor2(4.0*M_PI*ddptr->delta, ddptr->eta);
ddptr->Rmol = wig2roti(ddptr->Rmol, ddptr->pas[0], ddptr->pas[1], ddptr->pas[2]);
continue;
}
if (!strncmp(names[i],"quadrupole",10)) {
if (NN != 7) {
fprintf(stderr,"Error: reading quadrupole - parameter count mismatch\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[0],&n1) != TCL_OK) {
fprintf(stderr,"Error: readsys - quadrupole - int conversion failure\n");
exit(1);
}
if (n1 < 1 || n1 > ss->nspins) {
fprintf(stderr,"Error: spinsys: quadrupole %d out of defined nuclei range\n",n1);
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[1],&n2) != TCL_OK) {
fprintf(stderr,"Error: readsys - quadrupole - int conversion failure\n");
exit(1);
}
if (fabs(ss_qn(ss,n1)) < 0.99) {
fprintf(stderr,"Error: spinsys: quadrupole defined for nuclear spin %d/2\n",(int)(ss_qn(ss,n1)*2));
exit(1);
}
if (quadrupole_exist(s,n1) >= 0) {
fprintf(stderr,"Error: spinsys: quadrupole already exists for nucleus %d\n",n1);
exit(1);
}
for (j=2; j<NN; j++) {
if (Tcl_GetDoubleFromObj(interp,vals[j],&(data[j-2])) != TCL_OK) {
fprintf(stderr,"Error: readsys - quadrupole - double conversion failure\n");
exit(1);
}
}
if (fabs(data[0]) < TINY) continue;
s->Q[(s->nQ)++] = qptr = (Quadrupole*)malloc(sizeof(Quadrupole));
qptr->nuc = n1; qptr->order = n2; qptr->pas[0] = data[2]; qptr->pas[1] = data[3]; qptr->pas[2] = data[4];
qptr->eta = data[1];
qptr->wq = data[0]*2*M_PI/(4.0*ss_qn(ss,n1)*(2.0*ss_qn(ss,n1)-1));
//DEBUGPRINT("%f; %f\n",data[0],ss_qn(ss,n1));
qptr->w0 = ss_gamma(ss,n1)*s->specfreq/ss_gamma1H()*2*M_PI;
//DEBUGPRINT("%f * %f / %f * 2pi/n",ss_gamma(ss,n1),s->specfreq,ss_gamma1H());
qptr->Rmol = Dtensor2(2.0*qptr->wq,qptr->eta);
qptr->Rmol = wig2roti(qptr->Rmol,qptr->pas[0],qptr->pas[1],qptr->pas[2]);
Naniso++;
qptr->T = qptr->Ta = qptr->Tb = qptr->T3a = qptr->T3b = qptr->T3c = NULL;
if (n2 > 3) {
fprintf(stderr,"Error: order '%d' of quadrupolar interaction not supported, just up to the third.\n",n2);
exit(1);
}
if (ver) {
printf( "Quadrupolar coupling on nucleus %d up to order %d\n",n1,n2);
printf( " quadrupolar constant : %g Hz\n",data[0]);
printf( " quadrupolar assymetry : %g\n",qptr->eta);
printf( " euler angles of tensor : (%g,%g,%g) degrees\n",qptr->pas[0],qptr->pas[1],qptr->pas[2]);
printf(" perturbation treatment validity report: %3.2f << 1 is%s fulfilled\n",fabs(qptr->wq/qptr->w0), fabs(10*qptr->wq/qptr->w0) < 1 ? "" : " not");
}
continue;
}
if (!strncmp(names[i],"mixing",6)) {
//fprintf(stderr,"Error: mixing not implemented\n");
//exit(1);
if (NN == 1) {
/* syntax "mixing N" */
// if (Tcl_GetIntFromObj(interp,vals[0],&n1) != TCL_OK) {
// fprintf(stderr,"Error: readsys - mixing - Q/CSA int conversion failure\n");
// exit(1);
// }
// s->MIX[(s->nMIX)++] = mptr = (Mixing*)malloc(sizeof(Mixing));
// mptr->type = 1;
// mptr->couple[0] = n1;
// mptr->couple[1] = n1;
// mptr->qidx = mptr->idx = -1;
// mptr->T = NULL;
// mptr->Ta = mptr->Tb = NULL;
fprintf(stderr,"Error: reading mixing - syntax mixing N not supported\n");
exit(1);
} else if (NN == 2) {
/* syntax "mixing Nq Nd" */
if (Tcl_GetIntFromObj(interp,vals[0],&n1) != TCL_OK) {
fprintf(stderr,"Error: readsys - mixing - int conversion failure\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[1],&n2) != TCL_OK) {
fprintf(stderr,"Error: readsys - mixing - int conversion failure\n");
exit(1);
}
s->MIX[(s->nMIX)++] = mptr = (Mixing*)malloc(sizeof(Mixing));
if (n1 == n2) {
mptr->type = 1; // Q-CSA
} else {
mptr->type = 2; // Q-DD
}
mptr->couple[0] = n1;
mptr->couple[1] = n2;
mptr->qidx = mptr->idx = -1;
mptr->T = NULL;
mptr->Ta = mptr->Tb = NULL;
if (ver) {
if (mptr->type == 1) {
printf( "Second order mixing quadrupole-CSA\n" );
printf( " quadrupole and shift nucleus : %d \n",n1);
} else {
printf( "Second order mixing quadrupole-dipole\n" );
printf( " quadrupole nucleus : %d \n",n1);
printf( " dipole nuclei : %d and %d\n",n1,n2);
}
}
} else {
fprintf(stderr,"Error: reading mixing - parameter count mismatch\n");
exit(1);
}
continue;
}
if (!strncmp(names[i],"gtensor",7)) {
if (NN != 7) {
fprintf(stderr,"Error: reading gtensor - parameter count mismatch\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[0],&n1) != TCL_OK) {
fprintf(stderr,"Error: readsys - gtensor - int conversion failure\n");
exit(1);
}
if (n1 < 1 || n1 > ss->nspins) {
fprintf(stderr,"Error: spinsys: gtensor %d out of defined range\n",n1);
exit(1);
}
if (gtensor_exist(s,n1) >= 0) {
fprintf(stderr,"Error: spinsys: gtensor already exists for electron %d\n",n1);
exit(1);
}
// test if it is electron
if (ss->iso[n1]->number != 0) {
fprintf(stderr,"Error: spinsys: gtensor : element %d is not electron\n",n1);
exit(1);
}
for (j=1; j<NN; j++) {
if (Tcl_GetDoubleFromObj(interp,vals[j],&(data[j-1])) != TCL_OK) {
fprintf(stderr,"Error: readsys - gtensor - double conversion failure\n");
exit(1);
}
}
/* when zero amplitudes, do nothing */
if ( (fabs(data[0]) < TINY) && (fabs(data[1]) < TINY) ) continue;
s->G[(s->nG)++] = gptr = (Gtensor*)malloc(sizeof(Gtensor));
gptr->nuc = n1; gptr->eta = data[2]; gptr->pas[0] = data[3]; gptr->pas[1] = data[4]; gptr->pas[2] = data[5];
gptr->iso = -data[0]*2.0*M_PI; gptr->delta = -data[1]*2.0*M_PI;
if (fabs(gptr->delta) > TINY) {
Naniso++;
gptr->Rmol = Dtensor2(SQRT2BY3*gptr->delta, gptr->eta);
gptr->Rmol = wig2roti(gptr->Rmol, gptr->pas[0], gptr->pas[1], gptr->pas[2]);
} else {
gptr->Rmol = NULL;
}
gptr->T = NULL;
gptr->T2q[0] = gptr->T2q[1] = gptr->T2q[2] = gptr->T2q[3] = gptr->T2q[4] = NULL;
if ( ver ) {
printf( "G-tensor for electron %d\n",n1);
printf( " isotropic value : %g Hz\n",gptr->iso/2.0/M_PI);
printf( " anisotropic value : %g Hz\n",gptr->delta/2.0/M_PI);
printf( " asymmetry parameter : %g\n",gptr->eta);
printf( " euler angles of tensor : (%g,%g,%g) degrees\n",gptr->pas[0],gptr->pas[1],gptr->pas[2]);
}
continue;
}
if (!strncmp(names[i],"hyperfine",9)) {
if (NN != 8) {
fprintf(stderr,"Error: reading hyperfine - parameter count mismatch\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[0],&n1) != TCL_OK) {
fprintf(stderr,"Error: readsys - hyperfine - int conversion failure\n");
exit(1);
}
if (Tcl_GetIntFromObj(interp,vals[1],&n2) != TCL_OK) {
fprintf(stderr,"Error: readsys - hyperfine - int conversion failure\n");
exit(1);
}
if (n1 < 1 || n1 > ss->nspins || n2 < 1 || n2 > ss->nspins) {
fprintf(stderr,"Error: spinsys: hyperfine %d %d out of defined elements range\n",n1,n2);
exit(1);
}
if (hyperfine_exist(s,n1,n2) >= 0) {
fprintf(stderr,"Error: readsys: hyperfine already exists for elements (%d, %d)\n",n1, n2);
exit(1);
}
if ( (ss->iso[n1]->number != 0) && (ss->iso[n2]->number != 0) ) {
fprintf(stderr,"Error: readsys: none of hyperfine elements %d and %d are electron\n", n1, n2);
exit(1);
}
if ( (ss->iso[n1]->number == 0) && (ss->iso[n2]->number == 0) ) {
fprintf(stderr,"Error: readsys: both hyperfine elements %d and %d are electrons\n", n1, n2);
exit(1);
}
for (j=2; j<NN; j++) {
if (Tcl_GetDoubleFromObj(interp,vals[j],&(data[j-2])) != TCL_OK) {
fprintf(stderr,"Error: readsys - hyperfine - double conversion failure\n");
exit(1);
}
}
if (fabs(data[0]) > TINY) Jiso = 1; else Jiso = 0;
if (fabs(data[1]) > TINY) {
Jani = 1;
Naniso++;
HQ_isdiag = 0;
s->Hint_isdiag = 0;
if (s->frame != LABFRAME) s->frame = DNPFRAME;
} else {
Jani = 0;
}
if ( Jani + Jiso == 0) continue;
s->HF[(s->nHF)++] = hfptr = (Hyperfine*)malloc(sizeof(Hyperfine));
if (ss->iso[n1]->number == 0) { // n1 is electron
hfptr->nuc[0] = n1; hfptr->nuc[1] = n2;
} else { // n2 is electron
hfptr->nuc[0] = n2; hfptr->nuc[1] = n1;
}
hfptr->iso = data[0]*2.0*M_PI; hfptr->delta = data[1]*2.0*M_PI; hfptr->eta = data[2];
hfptr->pas[0] = data[3]; hfptr->pas[1] = data[4]; hfptr->pas[2] = data[5];
hfptr->blk_Tiso = NULL; hfptr->blk_T = NULL; hfptr->blk_Ta = NULL; hfptr->blk_Tb = NULL;
hfptr->T2q[0] = hfptr->T2q[1] = hfptr->T2q[2] = hfptr->T2q[3] = hfptr->T2q[4] = NULL;
if (Jani) {
hfptr->Rmol = Dtensor2(hfptr->delta*2.0, hfptr->eta);
hfptr->Rmol = wig2roti(hfptr->Rmol,hfptr->pas[0],hfptr->pas[1],hfptr->pas[2]);
} else {
hfptr->Rmol = NULL;
}
if (ver) {
printf( "Hyperfine coupling between electron %d and nucleus %d\n",hfptr->nuc[0],hfptr->nuc[1]);
printf( " isotropic value : %g Hz\n",hfptr->iso/2.0/M_PI);
printf( " anisotropic value : %g Hz\n",hfptr->delta/2.0/M_PI);
printf( " asymmetry : %g \n",hfptr->eta);
printf( " euler angles of tensor : (%g,%g,%g) degrees\n",hfptr->pas[0],hfptr->pas[1],hfptr->pas[2]);
}
continue;
}
fprintf(stderr,"Error: unknown identifier '%s' in spinsys, must be one of\n",names[i]);
fprintf(stderr," channels, nuclei, shift, dipole, jcoupling, quadrupole,\n");
fprintf(stderr," or mixing.\n");
exit(1);
}
// in labframe we do not use H assembly and block_diag
if (s->frame == LABFRAME) {
s->Hassembly = 0;
s->block_diag = 0;
s->Hint_isdiag = 0;
Naniso = -Naniso;
}
if (s->block_diag && !(s->Hint_isdiag)) {
Nblk = LEN(blk_dims);
s->basis = (1 << s->Nmz) - 1;
} else {
Nblk = 1;
s->basis = 0;
}
if ( (Naniso > 4) || ( (Naniso != 0) && (s->block_diag) ) ) {
s->Hassembly = 1;
} else {
s->Hassembly = 0;
}
/****************************
printf("Hamiltonian block structure will");
if (s->block_diag != 0) {
printf(" be based on %d nuclei types\n",Nmz);
printf("\t number of blocks: %d\n",LEN(blk_dims));
printf("\t dims:");
for (i=1; i<=LEN(blk_dims); i++) printf(" %d",blk_dims[i]);