static void upd_nbfplj(FILE *log,real *nbfp,int atnr,real f6[],real f12[],
int combrule)
{
double *sigma,*epsilon,c6,c12,eps,sig,sig6;
int n,m,k;
/* Update the nonbonded force parameters */
switch (combrule) {
case 1:
for(k=n=0; (n<atnr); n++) {
for(m=0; (m<atnr); m++,k++) {
C6 (nbfp,atnr,n,m) *= f6[k];
C12(nbfp,atnr,n,m) *= f12[k];
}
}
break;
case 2:
case 3:
/* Convert to sigma and epsilon */
snew(sigma,atnr);
snew(epsilon,atnr);
for(n=0; (n<atnr); n++) {
k = n*(atnr+1);
c6 = C6 (nbfp,atnr,n,n) * f6[k];
c12 = C12(nbfp,atnr,n,n) * f12[k];
if ((c6 == 0) || (c12 == 0))
gmx_fatal(FARGS,"You can not use combination rule %d with zero C6 (%f) or C12 (%f)",combrule,c6,c12);
sigma[n] = pow(c12/c6,1.0/6.0);
epsilon[n] = 0.25*(c6*c6/c12);
}
for(k=n=0; (n<atnr); n++) {
for(m=0; (m<atnr); m++,k++) {
eps = sqrt(epsilon[n]*epsilon[m]);
if (combrule == 2)
sig = 0.5*(sigma[n]+sigma[m]);
else
sig = sqrt(sigma[n]*sigma[m]);
sig6 = pow(sig,6.0);
/* nbfp now includes the 6.0/12.0 derivative prefactors */
C6 (nbfp,atnr,n,m) = 4*eps*sig6/6.0;
C12(nbfp,atnr,n,m) = 4*eps*sig6*sig6/12.0;
}
}
sfree(sigma);
sfree(epsilon);
break;
default:
gmx_fatal(FARGS,"Combination rule should be 1,2 or 3 instead of %d",
combrule);
}
}
static real *mk_nbfp(t_idef *idef,bool bBHAM)
{
real *nbfp;
int i,j,k,atnr;
atnr=idef->atnr;
if (bBHAM) {
snew(nbfp,3*atnr*atnr);
for(i=k=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++,k++) {
BHAMA(nbfp,atnr,i,j) = idef->iparams[k].bham.a;
BHAMB(nbfp,atnr,i,j) = idef->iparams[k].bham.b;
BHAMC(nbfp,atnr,i,j) = idef->iparams[k].bham.c;
}
}
}
else {
snew(nbfp,2*atnr*atnr);
for(i=k=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++,k++) {
C6(nbfp,atnr,i,j) = idef->iparams[k].lj.c6;
C12(nbfp,atnr,i,j) = idef->iparams[k].lj.c12;
}
}
}
return nbfp;
}
static double calc_avcsix(FILE *log,real *nbfp,int atnr,
int natoms,int type[],bool bBHAM)
{
int i,j,tpi,tpj;
double csix;
/* Check this code: do we really need a double loop? */
csix = 0;
for(i=0; (i<natoms); i++) {
tpi = type[i];
#ifdef DEBUG
if (tpi >= atnr)
fatal_error(0,"Atomtype[%d] = %d, maximum = %d",i,tpi,atnr);
#endif
for(j=0; (j<natoms); j++) {
tpj = type[j];
#ifdef DEBUG
if (tpj >= atnr)
fatal_error(0,"Atomtype[%d] = %d, maximum = %d",j,tpj,atnr);
#endif
if (bBHAM)
csix += BHAMC(nbfp,atnr,tpi,tpj);
else
csix += C6(nbfp,atnr,tpi,tpj);
}
}
csix /= (natoms*natoms);
if (debug)
fprintf(debug,"Average C6 parameter is: %10g\n",csix);
return csix;
}
static void pr_nbfp(FILE *fp,real *nbfp,bool bBHAM,int atnr)
{
int i,j;
if(fp)
{
for(i=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++) {
fprintf(fp,"%2d - %2d",i,j);
if (bBHAM)
fprintf(fp," a=%10g, b=%10g, c=%10g\n",BHAMA(nbfp,atnr,i,j),
BHAMB(nbfp,atnr,i,j),BHAMC(nbfp,atnr,i,j));
else
fprintf(fp," c6=%10g, c12=%10g\n",C6(nbfp,atnr,i,j),
C12(nbfp,atnr,i,j));
}
}
}
}
void whirlpool_block(WHIRLPOOL_CTX *ctx,const void *inp,size_t n)
{
int r;
const u8 *p=inp;
union { u64 q[8]; u8 c[64]; } S,K,*H=(void *)ctx->H.q;
#ifdef GO_FOR_MMX
GO_FOR_MMX(ctx,inp,n);
#endif
do {
#ifdef OPENSSL_SMALL_FOOTPRINT
u64 L[8];
int i;
for (i=0;i<64;i++) S.c[i] = (K.c[i] = H->c[i]) ^ p[i];
for (r=0;r<ROUNDS;r++)
{
for (i=0;i<8;i++)
{
L[i] = i ? 0 : RC[r];
L[i] ^= C0(K,i) ^ C1(K,(i-1)&7) ^
C2(K,(i-2)&7) ^ C3(K,(i-3)&7) ^
C4(K,(i-4)&7) ^ C5(K,(i-5)&7) ^
C6(K,(i-6)&7) ^ C7(K,(i-7)&7);
}
memcpy (K.q,L,64);
for (i=0;i<8;i++)
{
L[i] ^= C0(S,i) ^ C1(S,(i-1)&7) ^
C2(S,(i-2)&7) ^ C3(S,(i-3)&7) ^
C4(S,(i-4)&7) ^ C5(S,(i-5)&7) ^
C6(S,(i-6)&7) ^ C7(S,(i-7)&7);
}
memcpy (S.q,L,64);
}
for (i=0;i<64;i++) H->c[i] ^= S.c[i] ^ p[i];
#else
u64 L0,L1,L2,L3,L4,L5,L6,L7;
#ifdef __STRICT_ALIGNMENT
if ((size_t)p & 7)
{
memcpy (S.c,p,64);
S.q[0] ^= (K.q[0] = H->q[0]);
S.q[1] ^= (K.q[1] = H->q[1]);
S.q[2] ^= (K.q[2] = H->q[2]);
S.q[3] ^= (K.q[3] = H->q[3]);
S.q[4] ^= (K.q[4] = H->q[4]);
S.q[5] ^= (K.q[5] = H->q[5]);
S.q[6] ^= (K.q[6] = H->q[6]);
S.q[7] ^= (K.q[7] = H->q[7]);
}
else
#endif
{
const u64 *pa = (const u64*)p;
S.q[0] = (K.q[0] = H->q[0]) ^ pa[0];
S.q[1] = (K.q[1] = H->q[1]) ^ pa[1];
S.q[2] = (K.q[2] = H->q[2]) ^ pa[2];
S.q[3] = (K.q[3] = H->q[3]) ^ pa[3];
S.q[4] = (K.q[4] = H->q[4]) ^ pa[4];
S.q[5] = (K.q[5] = H->q[5]) ^ pa[5];
S.q[6] = (K.q[6] = H->q[6]) ^ pa[6];
S.q[7] = (K.q[7] = H->q[7]) ^ pa[7];
}
for(r=0;r<ROUNDS;r++)
{
#ifdef SMALL_REGISTER_BANK
L0 = C0(K,0) ^ C1(K,7) ^ C2(K,6) ^ C3(K,5) ^
C4(K,4) ^ C5(K,3) ^ C6(K,2) ^ C7(K,1) ^ RC[r];
L1 = C0(K,1) ^ C1(K,0) ^ C2(K,7) ^ C3(K,6) ^
C4(K,5) ^ C5(K,4) ^ C6(K,3) ^ C7(K,2);
L2 = C0(K,2) ^ C1(K,1) ^ C2(K,0) ^ C3(K,7) ^
C4(K,6) ^ C5(K,5) ^ C6(K,4) ^ C7(K,3);
L3 = C0(K,3) ^ C1(K,2) ^ C2(K,1) ^ C3(K,0) ^
C4(K,7) ^ C5(K,6) ^ C6(K,5) ^ C7(K,4);
L4 = C0(K,4) ^ C1(K,3) ^ C2(K,2) ^ C3(K,1) ^
C4(K,0) ^ C5(K,7) ^ C6(K,6) ^ C7(K,5);
L5 = C0(K,5) ^ C1(K,4) ^ C2(K,3) ^ C3(K,2) ^
C4(K,1) ^ C5(K,0) ^ C6(K,7) ^ C7(K,6);
L6 = C0(K,6) ^ C1(K,5) ^ C2(K,4) ^ C3(K,3) ^
C4(K,2) ^ C5(K,1) ^ C6(K,0) ^ C7(K,7);
L7 = C0(K,7) ^ C1(K,6) ^ C2(K,5) ^ C3(K,4) ^
C4(K,3) ^ C5(K,2) ^ C6(K,1) ^ C7(K,0);
K.q[0] = L0; K.q[1] = L1; K.q[2] = L2; K.q[3] = L3;
K.q[4] = L4; K.q[5] = L5; K.q[6] = L6; K.q[7] = L7;
L0 ^= C0(S,0) ^ C1(S,7) ^ C2(S,6) ^ C3(S,5) ^
C4(S,4) ^ C5(S,3) ^ C6(S,2) ^ C7(S,1);
L1 ^= C0(S,1) ^ C1(S,0) ^ C2(S,7) ^ C3(S,6) ^
C4(S,5) ^ C5(S,4) ^ C6(S,3) ^ C7(S,2);
L2 ^= C0(S,2) ^ C1(S,1) ^ C2(S,0) ^ C3(S,7) ^
C4(S,6) ^ C5(S,5) ^ C6(S,4) ^ C7(S,3);
L3 ^= C0(S,3) ^ C1(S,2) ^ C2(S,1) ^ C3(S,0) ^
C4(S,7) ^ C5(S,6) ^ C6(S,5) ^ C7(S,4);
L4 ^= C0(S,4) ^ C1(S,3) ^ C2(S,2) ^ C3(S,1) ^
C4(S,0) ^ C5(S,7) ^ C6(S,6) ^ C7(S,5);
L5 ^= C0(S,5) ^ C1(S,4) ^ C2(S,3) ^ C3(S,2) ^
C4(S,1) ^ C5(S,0) ^ C6(S,7) ^ C7(S,6);
L6 ^= C0(S,6) ^ C1(S,5) ^ C2(S,4) ^ C3(S,3) ^
C4(S,2) ^ C5(S,1) ^ C6(S,0) ^ C7(S,7);
L7 ^= C0(S,7) ^ C1(S,6) ^ C2(S,5) ^ C3(S,4) ^
C4(S,3) ^ C5(S,2) ^ C6(S,1) ^ C7(S,0);
S.q[0] = L0; S.q[1] = L1; S.q[2] = L2; S.q[3] = L3;
S.q[4] = L4; S.q[5] = L5; S.q[6] = L6; S.q[7] = L7;
#else
L0 = C0(K,0); L1 = C1(K,0); L2 = C2(K,0); L3 = C3(K,0);
L4 = C4(K,0); L5 = C5(K,0); L6 = C6(K,0); L7 = C7(K,0);
L0 ^= RC[r];
L1 ^= C0(K,1); L2 ^= C1(K,1); L3 ^= C2(K,1); L4 ^= C3(K,1);
L5 ^= C4(K,1); L6 ^= C5(K,1); L7 ^= C6(K,1); L0 ^= C7(K,1);
L2 ^= C0(K,2); L3 ^= C1(K,2); L4 ^= C2(K,2); L5 ^= C3(K,2);
L6 ^= C4(K,2); L7 ^= C5(K,2); L0 ^= C6(K,2); L1 ^= C7(K,2);
L3 ^= C0(K,3); L4 ^= C1(K,3); L5 ^= C2(K,3); L6 ^= C3(K,3);
L7 ^= C4(K,3); L0 ^= C5(K,3); L1 ^= C6(K,3); L2 ^= C7(K,3);
L4 ^= C0(K,4); L5 ^= C1(K,4); L6 ^= C2(K,4); L7 ^= C3(K,4);
L0 ^= C4(K,4); L1 ^= C5(K,4); L2 ^= C6(K,4); L3 ^= C7(K,4);
L5 ^= C0(K,5); L6 ^= C1(K,5); L7 ^= C2(K,5); L0 ^= C3(K,5);
L1 ^= C4(K,5); L2 ^= C5(K,5); L3 ^= C6(K,5); L4 ^= C7(K,5);
L6 ^= C0(K,6); L7 ^= C1(K,6); L0 ^= C2(K,6); L1 ^= C3(K,6);
L2 ^= C4(K,6); L3 ^= C5(K,6); L4 ^= C6(K,6); L5 ^= C7(K,6);
L7 ^= C0(K,7); L0 ^= C1(K,7); L1 ^= C2(K,7); L2 ^= C3(K,7);
L3 ^= C4(K,7); L4 ^= C5(K,7); L5 ^= C6(K,7); L6 ^= C7(K,7);
K.q[0] = L0; K.q[1] = L1; K.q[2] = L2; K.q[3] = L3;
K.q[4] = L4; K.q[5] = L5; K.q[6] = L6; K.q[7] = L7;
L0 ^= C0(S,0); L1 ^= C1(S,0); L2 ^= C2(S,0); L3 ^= C3(S,0);
L4 ^= C4(S,0); L5 ^= C5(S,0); L6 ^= C6(S,0); L7 ^= C7(S,0);
L1 ^= C0(S,1); L2 ^= C1(S,1); L3 ^= C2(S,1); L4 ^= C3(S,1);
L5 ^= C4(S,1); L6 ^= C5(S,1); L7 ^= C6(S,1); L0 ^= C7(S,1);
L2 ^= C0(S,2); L3 ^= C1(S,2); L4 ^= C2(S,2); L5 ^= C3(S,2);
L6 ^= C4(S,2); L7 ^= C5(S,2); L0 ^= C6(S,2); L1 ^= C7(S,2);
L3 ^= C0(S,3); L4 ^= C1(S,3); L5 ^= C2(S,3); L6 ^= C3(S,3);
L7 ^= C4(S,3); L0 ^= C5(S,3); L1 ^= C6(S,3); L2 ^= C7(S,3);
L4 ^= C0(S,4); L5 ^= C1(S,4); L6 ^= C2(S,4); L7 ^= C3(S,4);
L0 ^= C4(S,4); L1 ^= C5(S,4); L2 ^= C6(S,4); L3 ^= C7(S,4);
L5 ^= C0(S,5); L6 ^= C1(S,5); L7 ^= C2(S,5); L0 ^= C3(S,5);
L1 ^= C4(S,5); L2 ^= C5(S,5); L3 ^= C6(S,5); L4 ^= C7(S,5);
L6 ^= C0(S,6); L7 ^= C1(S,6); L0 ^= C2(S,6); L1 ^= C3(S,6);
L2 ^= C4(S,6); L3 ^= C5(S,6); L4 ^= C6(S,6); L5 ^= C7(S,6);
L7 ^= C0(S,7); L0 ^= C1(S,7); L1 ^= C2(S,7); L2 ^= C3(S,7);
L3 ^= C4(S,7); L4 ^= C5(S,7); L5 ^= C6(S,7); L6 ^= C7(S,7);
S.q[0] = L0; S.q[1] = L1; S.q[2] = L2; S.q[3] = L3;
S.q[4] = L4; S.q[5] = L5; S.q[6] = L6; S.q[7] = L7;
#endif
}
#ifdef __STRICT_ALIGNMENT
if ((size_t)p & 7)
{
int i;
for(i=0;i<64;i++) H->c[i] ^= S.c[i] ^ p[i];
}
else
#endif
{
const u64 *pa=(const u64 *)p;
H->q[0] ^= S.q[0] ^ pa[0];
H->q[1] ^= S.q[1] ^ pa[1];
H->q[2] ^= S.q[2] ^ pa[2];
H->q[3] ^= S.q[3] ^ pa[3];
H->q[4] ^= S.q[4] ^ pa[4];
H->q[5] ^= S.q[5] ^ pa[5];
H->q[6] ^= S.q[6] ^ pa[6];
H->q[7] ^= S.q[7] ^ pa[7];
}
#endif
p += 64;
} while(--n);
}
void update_QMMMrec(t_commrec *cr,
t_forcerec *fr,
rvec x[],
t_mdatoms *md,
matrix box,
gmx_localtop_t *top)
{
/* updates the coordinates of both QM atoms and MM atoms and stores
* them in the QMMMrec.
*
* NOTE: is NOT yet working if there are no PBC. Also in ns.c, simple
* ns needs to be fixed!
*/
int
mm_max=0,mm_nr=0,mm_nr_new,i,j,is,k,shift;
t_j_particle
*mm_j_particles=NULL,*qm_i_particles=NULL;
t_QMMMrec
*qr;
t_nblist
QMMMlist;
rvec
dx,crd;
int
*MMatoms;
t_QMrec
*qm;
t_MMrec
*mm;
t_pbc
pbc;
int
*parallelMMarray=NULL;
real
c12au,c6au;
c6au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,6));
c12au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,12));
/* every cpu has this array. On every processor we fill this array
* with 1's and 0's. 1's indicate the atoms is a QM atom on the
* current cpu in a later stage these arrays are all summed. indexes
* > 0 indicate the atom is a QM atom. Every node therefore knows
* whcih atoms are part of the QM subsystem.
*/
/* copy some pointers */
qr = fr->qr;
mm = qr->mm;
QMMMlist = fr->QMMMlist;
/* init_pbc(box); needs to be called first, see pbc.h */
set_pbc_dd(&pbc,fr->ePBC,DOMAINDECOMP(cr) ? cr->dd : NULL,FALSE,box);
/* only in standard (normal) QMMM we need the neighbouring MM
* particles to provide a electric field of point charges for the QM
* atoms.
*/
if(qr->QMMMscheme==eQMMMschemenormal){ /* also implies 1 QM-layer */
/* we NOW create/update a number of QMMMrec entries:
*
* 1) the shiftQM, containing the shifts of the QM atoms
*
* 2) the indexMM array, containing the index of the MM atoms
*
* 3) the shiftMM, containing the shifts of the MM atoms
*
* 4) the shifted coordinates of the MM atoms
*
* the shifts are used for computing virial of the QM/MM particles.
*/
qm = qr->qm[0]; /* in case of normal QMMM, there is only one group */
snew(qm_i_particles,QMMMlist.nri);
if(QMMMlist.nri){
qm_i_particles[0].shift = XYZ2IS(0,0,0);
for(i=0;i<QMMMlist.nri;i++){
qm_i_particles[i].j = QMMMlist.iinr[i];
if(i){
qm_i_particles[i].shift = pbc_dx_aiuc(&pbc,x[QMMMlist.iinr[0]],
x[QMMMlist.iinr[i]],dx);
}
/* However, since nri >= nrQMatoms, we do a quicksort, and throw
* out double, triple, etc. entries later, as we do for the MM
* list too.
*/
/* compute the shift for the MM j-particles with respect to
* the QM i-particle and store them.
*/
crd[0] = IS2X(QMMMlist.shift[i]) + IS2X(qm_i_particles[i].shift);
crd[1] = IS2Y(QMMMlist.shift[i]) + IS2Y(qm_i_particles[i].shift);
crd[2] = IS2Z(QMMMlist.shift[i]) + IS2Z(qm_i_particles[i].shift);
is = XYZ2IS(crd[0],crd[1],crd[2]);
for(j=QMMMlist.jindex[i];
j<QMMMlist.jindex[i+1];
j++){
if(mm_nr >= mm_max){
mm_max += 1000;
srenew(mm_j_particles,mm_max);
}
mm_j_particles[mm_nr].j = QMMMlist.jjnr[j];
mm_j_particles[mm_nr].shift = is;
mm_nr++;
}
}
/* quicksort QM and MM shift arrays and throw away multiple entries */
qsort(qm_i_particles,QMMMlist.nri,
(size_t)sizeof(qm_i_particles[0]),
struct_comp);
qsort(mm_j_particles,mm_nr,
(size_t)sizeof(mm_j_particles[0]),
struct_comp);
/* remove multiples in the QM shift array, since in init_QMMM() we
* went through the atom numbers from 0 to md.nr, the order sorted
* here matches the one of QMindex already.
*/
j=0;
for(i=0;i<QMMMlist.nri;i++){
if (i==0 || qm_i_particles[i].j!=qm_i_particles[i-1].j){
qm_i_particles[j++] = qm_i_particles[i];
}
}
mm_nr_new = 0;
if(qm->bTS||qm->bOPT){
/* only remove double entries for the MM array */
for(i=0;i<mm_nr;i++){
if((i==0 || mm_j_particles[i].j!=mm_j_particles[i-1].j)
&& !md->bQM[mm_j_particles[i].j]){
mm_j_particles[mm_nr_new++] = mm_j_particles[i];
}
}
}
/* we also remove mm atoms that have no charges!
* actually this is already done in the ns.c
*/
else{
for(i=0;i<mm_nr;i++){
if((i==0 || mm_j_particles[i].j!=mm_j_particles[i-1].j)
&& !md->bQM[mm_j_particles[i].j]
&& (md->chargeA[mm_j_particles[i].j]
|| (md->chargeB && md->chargeB[mm_j_particles[i].j]))) {
mm_j_particles[mm_nr_new++] = mm_j_particles[i];
}
}
}
mm_nr = mm_nr_new;
/* store the data retrieved above into the QMMMrec
*/
k=0;
/* Keep the compiler happy,
* shift will always be set in the loop for i=0
*/
shift = 0;
for(i=0;i<qm->nrQMatoms;i++){
/* not all qm particles might have appeared as i
* particles. They might have been part of the same charge
* group for instance.
*/
if (qm->indexQM[i] == qm_i_particles[k].j) {
shift = qm_i_particles[k++].shift;
}
/* use previous shift, assuming they belong the same charge
* group anyway,
*/
qm->shiftQM[i] = shift;
}
}
/* parallel excecution */
if(PAR(cr)){
snew(parallelMMarray,2*(md->nr));
/* only MM particles have a 1 at their atomnumber. The second part
* of the array contains the shifts. Thus:
* p[i]=1/0 depending on wether atomnumber i is a MM particle in the QM
* step or not. p[i+md->nr] is the shift of atomnumber i.
*/
for(i=0;i<2*(md->nr);i++){
parallelMMarray[i]=0;
}
for(i=0;i<mm_nr;i++){
parallelMMarray[mm_j_particles[i].j]=1;
parallelMMarray[mm_j_particles[i].j+(md->nr)]=mm_j_particles[i].shift;
}
gmx_sumi(md->nr,parallelMMarray,cr);
mm_nr=0;
mm_max = 0;
for(i=0;i<md->nr;i++){
if(parallelMMarray[i]){
if(mm_nr >= mm_max){
mm_max += 1000;
srenew(mm->indexMM,mm_max);
srenew(mm->shiftMM,mm_max);
}
mm->indexMM[mm_nr] = i;
mm->shiftMM[mm_nr++]= parallelMMarray[i+md->nr]/parallelMMarray[i];
}
}
mm->nrMMatoms=mm_nr;
free(parallelMMarray);
}
/* serial execution */
else{
mm->nrMMatoms = mm_nr;
srenew(mm->shiftMM,mm_nr);
srenew(mm->indexMM,mm_nr);
for(i=0;i<mm_nr;i++){
mm->indexMM[i]=mm_j_particles[i].j;
mm->shiftMM[i]=mm_j_particles[i].shift;
}
}
/* (re) allocate memory for the MM coordiate array. The QM
* coordinate array was already allocated in init_QMMM, and is
* only (re)filled in the update_QMMM_coordinates routine
*/
srenew(mm->xMM,mm->nrMMatoms);
/* now we (re) fill the array that contains the MM charges with
* the forcefield charges. If requested, these charges will be
* scaled by a factor
*/
srenew(mm->MMcharges,mm->nrMMatoms);
for(i=0;i<mm->nrMMatoms;i++){/* no free energy yet */
mm->MMcharges[i]=md->chargeA[mm->indexMM[i]]*mm->scalefactor;
}
if(qm->bTS||qm->bOPT){
/* store (copy) the c6 and c12 parameters into the MMrec struct
*/
srenew(mm->c6,mm->nrMMatoms);
srenew(mm->c12,mm->nrMMatoms);
for (i=0;i<mm->nrMMatoms;i++){
mm->c6[i] = C6(fr->nbfp,top->idef.atnr,
md->typeA[mm->indexMM[i]],
md->typeA[mm->indexMM[i]])/c6au;
mm->c12[i] =C12(fr->nbfp,top->idef.atnr,
md->typeA[mm->indexMM[i]],
md->typeA[mm->indexMM[i]])/c12au;
}
punch_QMMM_excl(qr->qm[0],mm,&(top->excls));
}
/* the next routine fills the coordinate fields in the QMMM rec of
* both the qunatum atoms and the MM atoms, using the shifts
* calculated above.
*/
update_QMMM_coord(x,fr,qr->qm[0],qr->mm);
free(qm_i_particles);
free(mm_j_particles);
}
else { /* ONIOM */ /* ????? */
mm->nrMMatoms=0;
/* do for each layer */
for (j=0;j<qr->nrQMlayers;j++){
qm = qr->qm[j];
qm->shiftQM[0]=XYZ2IS(0,0,0);
for(i=1;i<qm->nrQMatoms;i++){
qm->shiftQM[i] = pbc_dx_aiuc(&pbc,x[qm->indexQM[0]],x[qm->indexQM[i]],
dx);
}
update_QMMM_coord(x,fr,qm,mm);
}
}
} /* update_QMMM_rec */
void init_QMMMrec(t_commrec *cr,
matrix box,
gmx_mtop_t *mtop,
t_inputrec *ir,
t_forcerec *fr)
{
/* we put the atomsnumbers of atoms that belong to the QMMM group in
* an array that will be copied later to QMMMrec->indexQM[..]. Also
* it will be used to create an QMMMrec->bQMMM index array that
* simply contains true/false for QM and MM (the other) atoms.
*/
gmx_groups_t *groups;
atom_id *qm_arr=NULL,vsite,ai,aj;
int qm_max=0,qm_nr=0,i,j,jmax,k,l,nrvsite2=0;
t_QMMMrec *qr;
t_MMrec *mm;
t_iatom *iatoms;
real c12au,c6au;
gmx_mtop_atomloop_all_t aloop;
t_atom *atom;
gmx_mtop_ilistloop_all_t iloop;
int a_offset;
t_ilist *ilist_mol;
c6au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,6));
c12au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,12));
fprintf(stderr,"there we go!\n");
/* Make a local copy of the QMMMrec */
qr = fr->qr;
/* bQMMM[..] is an array containing TRUE/FALSE for atoms that are
* QM/not QM. We first set all elemenst at false. Afterwards we use
* the qm_arr (=MMrec->indexQM) to changes the elements
* corresponding to the QM atoms at TRUE. */
qr->QMMMscheme = ir->QMMMscheme;
/* we take the possibility into account that a user has
* defined more than one QM group:
*/
/* an ugly work-around in case there is only one group In this case
* the whole system is treated as QM. Otherwise the second group is
* always the rest of the total system and is treated as MM.
*/
/* small problem if there is only QM.... so no MM */
jmax = ir->opts.ngQM;
if(qr->QMMMscheme==eQMMMschemeoniom)
qr->nrQMlayers = jmax;
else
qr->nrQMlayers = 1;
groups = &mtop->groups;
/* there are jmax groups of QM atoms. In case of multiple QM groups
* I assume that the users wants to do ONIOM. However, maybe it
* should also be possible to define more than one QM subsystem with
* independent neighbourlists. I have to think about
* that.. 11-11-2003
*/
snew(qr->qm,jmax);
for(j=0;j<jmax;j++){
/* new layer */
aloop = gmx_mtop_atomloop_all_init(mtop);
while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
if(qm_nr >= qm_max){
qm_max += 1000;
srenew(qm_arr,qm_max);
}
if (ggrpnr(groups,egcQMMM ,i) == j) {
/* hack for tip4p */
qm_arr[qm_nr++] = i;
}
}
if(qr->QMMMscheme==eQMMMschemeoniom){
/* add the atoms to the bQMMM array
*/
/* I assume that users specify the QM groups from small to
* big(ger) in the mdp file
*/
qr->qm[j] = mk_QMrec();
/* we need to throw out link atoms that in the previous layer
* existed to separate this QMlayer from the previous
* QMlayer. We use the iatoms array in the idef for that
* purpose. If all atoms defining the current Link Atom (Dummy2)
* are part of the current QM layer it needs to be removed from
* qm_arr[]. */
iloop = gmx_mtop_ilistloop_all_init(mtop);
while (gmx_mtop_ilistloop_all_next(iloop,&ilist_mol,&a_offset)) {
nrvsite2 = ilist_mol[F_VSITE2].nr;
iatoms = ilist_mol[F_VSITE2].iatoms;
for(k=0; k<nrvsite2; k+=4) {
vsite = a_offset + iatoms[k+1]; /* the vsite */
ai = a_offset + iatoms[k+2]; /* constructing atom */
aj = a_offset + iatoms[k+3]; /* constructing atom */
if (ggrpnr(groups, egcQMMM, vsite) == ggrpnr(groups, egcQMMM, ai)
&&
ggrpnr(groups, egcQMMM, vsite) == ggrpnr(groups, egcQMMM, aj)) {
/* this dummy link atom needs to be removed from the qm_arr
* before making the QMrec of this layer!
*/
for(i=0;i<qm_nr;i++){
if(qm_arr[i]==vsite){
/* drop the element */
for(l=i;l<qm_nr;l++){
qm_arr[l]=qm_arr[l+1];
}
qm_nr--;
}
}
}
}
}
/* store QM atoms in this layer in the QMrec and initialise layer
*/
init_QMrec(j,qr->qm[j],qm_nr,qm_arr,mtop,ir);
/* we now store the LJ C6 and C12 parameters in QM rec in case
* we need to do an optimization
*/
if(qr->qm[j]->bOPT || qr->qm[j]->bTS){
for(i=0;i<qm_nr;i++){
qr->qm[j]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,
atom->type,atom->type)/c6au;
qr->qm[j]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,
atom->type,atom->type)/c12au;
}
}
/* now we check for frontier QM atoms. These occur in pairs that
* construct the vsite
*/
iloop = gmx_mtop_ilistloop_all_init(mtop);
while (gmx_mtop_ilistloop_all_next(iloop,&ilist_mol,&a_offset)) {
nrvsite2 = ilist_mol[F_VSITE2].nr;
iatoms = ilist_mol[F_VSITE2].iatoms;
for(k=0; k<nrvsite2; k+=4){
vsite = a_offset + iatoms[k+1]; /* the vsite */
ai = a_offset + iatoms[k+2]; /* constructing atom */
aj = a_offset + iatoms[k+3]; /* constructing atom */
if(ggrpnr(groups,egcQMMM,ai) < (groups->grps[egcQMMM].nr-1) &&
(ggrpnr(groups,egcQMMM,aj) >= (groups->grps[egcQMMM].nr-1))){
/* mark ai as frontier atom */
for(i=0;i<qm_nr;i++){
if( (qm_arr[i]==ai) || (qm_arr[i]==vsite) ){
qr->qm[j]->frontatoms[i]=TRUE;
}
}
}
else if(ggrpnr(groups,egcQMMM,aj) < (groups->grps[egcQMMM].nr-1) &&
(ggrpnr(groups,egcQMMM,ai) >= (groups->grps[egcQMMM].nr-1))){
/* mark aj as frontier atom */
for(i=0;i<qm_nr;i++){
if( (qm_arr[i]==aj) || (qm_arr[i]==vsite)){
qr->qm[j]->frontatoms[i]=TRUE;
}
}
}
}
}
}
}
if(qr->QMMMscheme!=eQMMMschemeoniom){
/* standard QMMM, all layers are merged together so there is one QM
* subsystem and one MM subsystem.
* Also we set the charges to zero in the md->charge arrays to prevent
* the innerloops from doubly counting the electostatic QM MM interaction
*/
for (k=0;k<qm_nr;k++){
gmx_mtop_atomnr_to_atom(mtop,qm_arr[k],&atom);
atom->q = 0.0;
atom->qB = 0.0;
}
qr->qm[0] = mk_QMrec();
/* store QM atoms in the QMrec and initialise
*/
init_QMrec(0,qr->qm[0],qm_nr,qm_arr,mtop,ir);
if(qr->qm[0]->bOPT || qr->qm[0]->bTS){
for(i=0;i<qm_nr;i++){
gmx_mtop_atomnr_to_atom(mtop,qm_arr[i],&atom);
qr->qm[0]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,
atom->type,atom->type)/c6au;
qr->qm[0]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,
atom->type,atom->type)/c12au;
}
}
/* find frontier atoms and mark them true in the frontieratoms array.
*/
for(i=0;i<qm_nr;i++) {
gmx_mtop_atomnr_to_ilist(mtop,qm_arr[i],&ilist_mol,&a_offset);
nrvsite2 = ilist_mol[F_VSITE2].nr;
iatoms = ilist_mol[F_VSITE2].iatoms;
for(k=0;k<nrvsite2;k+=4){
vsite = a_offset + iatoms[k+1]; /* the vsite */
ai = a_offset + iatoms[k+2]; /* constructing atom */
aj = a_offset + iatoms[k+3]; /* constructing atom */
if(ggrpnr(groups,egcQMMM,ai) < (groups->grps[egcQMMM].nr-1) &&
(ggrpnr(groups,egcQMMM,aj) >= (groups->grps[egcQMMM].nr-1))){
/* mark ai as frontier atom */
if ( (qm_arr[i]==ai) || (qm_arr[i]==vsite) ){
qr->qm[0]->frontatoms[i]=TRUE;
}
}
else if (ggrpnr(groups,egcQMMM,aj) < (groups->grps[egcQMMM].nr-1) &&
(ggrpnr(groups,egcQMMM,ai) >=(groups->grps[egcQMMM].nr-1))) {
/* mark aj as frontier atom */
if ( (qm_arr[i]==aj) || (qm_arr[i]==vsite) ){
qr->qm[0]->frontatoms[i]=TRUE;
}
}
}
}
/* MM rec creation */
mm = mk_MMrec();
mm->scalefactor = ir->scalefactor;
mm->nrMMatoms = (mtop->natoms)-(qr->qm[0]->nrQMatoms); /* rest of the atoms */
qr->mm = mm;
} else {/* ONIOM */
/* MM rec creation */
mm = mk_MMrec();
mm->scalefactor = ir->scalefactor;
mm->nrMMatoms = 0;
qr->mm = mm;
}
/* these variables get updated in the update QMMMrec */
if(qr->nrQMlayers==1){
/* with only one layer there is only one initialisation
* needed. Multilayer is a bit more complicated as it requires
* re-initialisation at every step of the simulation. This is due
* to the use of COMMON blocks in the fortran QM subroutines.
*/
if (qr->qm[0]->QMmethod<eQMmethodRHF)
{
#ifdef GMX_QMMM_MOPAC
/* semi-empiprical 1-layer ONIOM calculation requested (mopac93) */
init_mopac(cr,qr->qm[0],qr->mm);
#else
gmx_fatal(FARGS,"Semi-empirical QM only supported with Mopac.");
#endif
}
else
{
/* ab initio calculation requested (gamess/gaussian/ORCA) */
#ifdef GMX_QMMM_GAMESS
init_gamess(cr,qr->qm[0],qr->mm);
#elif defined GMX_QMMM_GAUSSIAN
init_gaussian(cr,qr->qm[0],qr->mm);
#elif defined GMX_QMMM_ORCA
init_orca(cr,qr->qm[0],qr->mm);
#else
gmx_fatal(FARGS,"Ab-initio calculation only supported with Gamess, Gaussian or ORCA.");
#endif
}
}
} /* init_QMMMrec */
void do_coupling(FILE *log,int nfile,t_filenm fnm[],
t_coupl_rec *tcr,real t,int step,real ener[],
t_forcerec *fr,t_inputrec *ir,bool bMaster,
t_mdatoms *md,t_idef *idef,real mu_aver,int nmols,
t_commrec *cr,matrix box,tensor virial,
tensor pres,rvec mu_tot,
rvec x[],rvec f[],bool bDoIt)
{
#define enm2Debye 48.0321
#define d2e(x) (x)/enm2Debye
#define enm2kjmol(x) (x)*0.0143952 /* = 2.0*4.0*M_PI*EPSILON0 */
static real *f6,*f12,*fa,*fb,*fc,*fq;
static bool bFirst = TRUE;
int i,j,ati,atj,atnr2,type,ftype;
real deviation[eoObsNR],prdev[eoObsNR],epot0,dist,rmsf;
real ff6,ff12,ffa,ffb,ffc,ffq,factor,dt,mu_ind;
real Epol,Eintern,Virial,muabs,xiH=-1,xiS=-1,xi6,xi12;
rvec fmol[2];
bool bTest,bPrint;
t_coupl_LJ *tclj;
t_coupl_BU *tcbu;
t_coupl_Q *tcq;
t_coupl_iparams *tip;
atnr2 = idef->atnr * idef->atnr;
if (bFirst) {
if (PAR(cr))
fprintf(log,"GCT: this is parallel\n");
else
fprintf(log,"GCT: this is not parallel\n");
fflush(log);
snew(f6, atnr2);
snew(f12,atnr2);
snew(fa, atnr2);
snew(fb, atnr2);
snew(fc, atnr2);
snew(fq, idef->atnr);
if (tcr->bVirial) {
int nrdf = 0;
real TTT = 0;
real Vol = det(box);
for(i=0; (i<ir->opts.ngtc); i++) {
nrdf += ir->opts.nrdf[i];
TTT += ir->opts.nrdf[i]*ir->opts.ref_t[i];
}
TTT /= nrdf;
/* Calculate reference virial from reference temperature and pressure */
tcr->ref_value[eoVir] = 0.5*BOLTZ*nrdf*TTT - (3.0/2.0)*
Vol*tcr->ref_value[eoPres];
fprintf(log,"GCT: TTT = %g, nrdf = %d, vir0 = %g, Vol = %g\n",
TTT,nrdf,tcr->ref_value[eoVir],Vol);
fflush(log);
}
bFirst = FALSE;
}
bPrint = MASTER(cr) && do_per_step(step,ir->nstlog);
dt = ir->delta_t;
/* Initiate coupling to the reference pressure and temperature to start
* coupling slowly.
*/
if (step == 0) {
for(i=0; (i<eoObsNR); i++)
tcr->av_value[i] = tcr->ref_value[i];
if ((tcr->ref_value[eoDipole]) != 0.0) {
mu_ind = mu_aver - d2e(tcr->ref_value[eoDipole]); /* in e nm */
Epol = mu_ind*mu_ind/(enm2kjmol(tcr->ref_value[eoPolarizability]));
tcr->av_value[eoEpot] -= Epol;
fprintf(log,"GCT: mu_aver = %g(D), mu_ind = %g(D), Epol = %g (kJ/mol)\n",
mu_aver*enm2Debye,mu_ind*enm2Debye,Epol);
}
}
/* We want to optimize the LJ params, usually to the Vaporization energy
* therefore we only count intermolecular degrees of freedom.
* Note that this is now optional. switch UseEinter to yes in your gct file
* if you want this.
*/
dist = calc_dist(log,x);
muabs = norm(mu_tot);
Eintern = Ecouple(tcr,ener)/nmols;
Virial = virial[XX][XX]+virial[YY][YY]+virial[ZZ][ZZ];
/*calc_force(md->nr,f,fmol);*/
clear_rvec(fmol[0]);
/* Use a memory of tcr->nmemory steps, so we actually couple to the
* average observable over the last tcr->nmemory steps. This may help
* in avoiding local minima in parameter space.
*/
set_act_value(tcr,eoPres, ener[F_PRES],step);
set_act_value(tcr,eoEpot, Eintern, step);
set_act_value(tcr,eoVir, Virial, step);
set_act_value(tcr,eoDist, dist, step);
set_act_value(tcr,eoMu, muabs, step);
set_act_value(tcr,eoFx, fmol[0][XX], step);
set_act_value(tcr,eoFy, fmol[0][YY], step);
set_act_value(tcr,eoFz, fmol[0][ZZ], step);
set_act_value(tcr,eoPx, pres[XX][XX],step);
set_act_value(tcr,eoPy, pres[YY][YY],step);
set_act_value(tcr,eoPz, pres[ZZ][ZZ],step);
epot0 = tcr->ref_value[eoEpot];
/* If dipole != 0.0 assume we want to use polarization corrected coupling */
if ((tcr->ref_value[eoDipole]) != 0.0) {
mu_ind = mu_aver - d2e(tcr->ref_value[eoDipole]); /* in e nm */
Epol = mu_ind*mu_ind/(enm2kjmol(tcr->ref_value[eoPolarizability]));
epot0 -= Epol;
if (debug) {
fprintf(debug,"mu_ind: %g (%g D) mu_aver: %g (%g D)\n",
mu_ind,mu_ind*enm2Debye,mu_aver,mu_aver*enm2Debye);
fprintf(debug,"Eref %g Epol %g Erunav %g Eact %g\n",
tcr->ref_value[eoEpot],Epol,tcr->av_value[eoEpot],
tcr->act_value[eoEpot]);
}
}
if (bPrint) {
pr_ff(tcr,t,idef,cr,nfile,fnm);
}
/* Calculate the deviation of average value from the target value */
for(i=0; (i<eoObsNR); i++) {
deviation[i] = calc_deviation(tcr->av_value[i],tcr->act_value[i],
tcr->ref_value[i]);
prdev[i] = tcr->ref_value[i] - tcr->act_value[i];
}
deviation[eoEpot] = calc_deviation(tcr->av_value[eoEpot],tcr->act_value[eoEpot],
epot0);
prdev[eoEpot] = epot0 - tcr->act_value[eoEpot];
if (bPrint)
pr_dev(tcr,t,prdev,cr,nfile,fnm);
/* First set all factors to 1 */
for(i=0; (i<atnr2); i++) {
f6[i] = f12[i] = fa[i] = fb[i] = fc[i] = 1.0;
}
for(i=0; (i<idef->atnr); i++)
fq[i] = 1.0;
/* Now compute the actual coupling compononents */
if (!fr->bBHAM) {
if (bDoIt) {
for(i=0; (i<tcr->nLJ); i++) {
tclj=&(tcr->tcLJ[i]);
ati=tclj->at_i;
atj=tclj->at_j;
ff6 = ff12 = 1.0;
if (tclj->eObs == eoForce) {
gmx_fatal(FARGS,"Hack code for this to work again ");
if (debug)
fprintf(debug,"Have computed derivatives: xiH = %g, xiS = %g\n",xiH,xiS);
if (ati == 1) {
/* Hydrogen */
ff12 += xiH;
}
else if (ati == 2) {
/* Shell */
ff12 += xiS;
}
else
gmx_fatal(FARGS,"No H, no Shell, edit code at %s, line %d\n",
__FILE__,__LINE__);
if (ff6 > 0)
set_factor_matrix(idef->atnr,f6, sqrt(ff6), ati,atj);
if (ff12 > 0)
set_factor_matrix(idef->atnr,f12,sqrt(ff12),ati,atj);
}
else {
if (debug)
fprintf(debug,"tcr->tcLJ[%d].xi_6 = %g, xi_12 = %g deviation = %g\n",i,
tclj->xi_6,tclj->xi_12,deviation[tclj->eObs]);
factor=deviation[tclj->eObs];
upd_f_value(log,idef->atnr,tclj->xi_6, dt,factor,f6, ati,atj);
upd_f_value(log,idef->atnr,tclj->xi_12,dt,factor,f12,ati,atj);
}
}
}
if (PAR(cr)) {
gprod(cr,atnr2,f6);
gprod(cr,atnr2,f12);
#ifdef DEBUGGCT
dump_fm(log,idef->atnr,f6,"f6");
dump_fm(log,idef->atnr,f12,"f12");
#endif
}
upd_nbfplj(log,fr->nbfp,idef->atnr,f6,f12,tcr->combrule);
/* Copy for printing */
for(i=0; (i<tcr->nLJ); i++) {
tclj=&(tcr->tcLJ[i]);
ati = tclj->at_i;
atj = tclj->at_j;
if (atj == -1)
atj = ati;
tclj->c6 = C6(fr->nbfp,fr->ntype,ati,atj);
tclj->c12 = C12(fr->nbfp,fr->ntype,ati,atj);
}
}
else {
if (bDoIt) {
for(i=0; (i<tcr->nBU); i++) {
tcbu = &(tcr->tcBU[i]);
factor = deviation[tcbu->eObs];
ati = tcbu->at_i;
atj = tcbu->at_j;
upd_f_value(log,idef->atnr,tcbu->xi_a,dt,factor,fa,ati,atj);
upd_f_value(log,idef->atnr,tcbu->xi_b,dt,factor,fb,ati,atj);
upd_f_value(log,idef->atnr,tcbu->xi_c,dt,factor,fc,ati,atj);
}
}
if (PAR(cr)) {
gprod(cr,atnr2,fa);
gprod(cr,atnr2,fb);
gprod(cr,atnr2,fc);
}
upd_nbfpbu(log,fr->nbfp,idef->atnr,fa,fb,fc);
/* Copy for printing */
for(i=0; (i<tcr->nBU); i++) {
tcbu=&(tcr->tcBU[i]);
ati = tcbu->at_i;
atj = tcbu->at_j;
if (atj == -1)
atj = ati;
tcbu->a = BHAMA(fr->nbfp,fr->ntype,ati,atj);
tcbu->b = BHAMB(fr->nbfp,fr->ntype,ati,atj);
tcbu->c = BHAMC(fr->nbfp,fr->ntype,ati,atj);
if (debug)
fprintf(debug,"buck (type=%d) = %e, %e, %e\n",
tcbu->at_i,tcbu->a,tcbu->b,tcbu->c);
}
}
if (bDoIt) {
for(i=0; (i<tcr->nQ); i++) {
tcq=&(tcr->tcQ[i]);
if (tcq->xi_Q)
ffq = 1.0 + (dt/tcq->xi_Q) * deviation[tcq->eObs];
else
ffq = 1.0;
fq[tcq->at_i] *= ffq;
}
}
if (PAR(cr))
gprod(cr,idef->atnr,fq);
for(j=0; (j<md->nr); j++) {
md->chargeA[j] *= fq[md->typeA[j]];
}
for(i=0; (i<tcr->nQ); i++) {
tcq=&(tcr->tcQ[i]);
for(j=0; (j<md->nr); j++) {
if (md->typeA[j] == tcq->at_i) {
tcq->Q = md->chargeA[j];
break;
}
}
if (j == md->nr)
gmx_fatal(FARGS,"Coupling type %d not found",tcq->at_i);
}
for(i=0; (i<tcr->nIP); i++) {
tip = &(tcr->tIP[i]);
type = tip->type;
ftype = idef->functype[type];
factor = dt*deviation[tip->eObs];
switch(ftype) {
case F_BONDS:
if (tip->xi.harmonic.krA) idef->iparams[type].harmonic.krA *= (1+factor/tip->xi.harmonic.krA);
if (tip->xi.harmonic.rA) idef->iparams[type].harmonic.rA *= (1+factor/tip->xi.harmonic.rA);
break;
default:
break;
}
tip->iprint=idef->iparams[type];
}
}
Molecule C6H6()
{
int nAtoms = 12;
// These are in Angstrom
Eigen::Vector3d C1(5.274, 1.999, -8.568);
Eigen::Vector3d C2(6.627, 2.018, -8.209);
Eigen::Vector3d C3(7.366, 0.829, -8.202);
Eigen::Vector3d C4(6.752, -0.379, -8.554);
Eigen::Vector3d C5(5.399, -0.398, -8.912);
Eigen::Vector3d C6(4.660, 0.791, -8.919);
Eigen::Vector3d H1(4.704, 2.916, -8.573);
Eigen::Vector3d H2(7.101, 2.950, -7.938);
Eigen::Vector3d H3(8.410, 0.844, -7.926);
Eigen::Vector3d H4(7.322, -1.296, -8.548);
Eigen::Vector3d H5(4.925, -1.330, -9.183);
Eigen::Vector3d H6(3.616, 0.776, -9.196);
// Scale
C1 /= convertBohrToAngstrom;
C2 /= convertBohrToAngstrom;
C3 /= convertBohrToAngstrom;
C4 /= convertBohrToAngstrom;
C5 /= convertBohrToAngstrom;
C6 /= convertBohrToAngstrom;
H1 /= convertBohrToAngstrom;
H2 /= convertBohrToAngstrom;
H3 /= convertBohrToAngstrom;
H4 /= convertBohrToAngstrom;
H5 /= convertBohrToAngstrom;
H6 /= convertBohrToAngstrom;
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = C2.transpose();
geom.col(2) = C3.transpose();
geom.col(3) = C4.transpose();
geom.col(4) = C5.transpose();
geom.col(5) = C6.transpose();
geom.col(6) = H1.transpose();
geom.col(7) = H2.transpose();
geom.col(8) = H3.transpose();
geom.col(9) = H4.transpose();
geom.col(10) = H5.transpose();
geom.col(11) = H6.transpose();
Eigen::VectorXd charges(12), masses(12);
charges << 6.0, 6.0, 6.0, 6.0, 6.0, 6.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0;
masses << 12.00, 12.0, 12.0, 12.0, 12.0, 12.0, 1.0078250, 1.0078250, 1.0078250,
1.0078250, 1.0078250, 1.0078250;
double radiusC = 1.70 / convertBohrToAngstrom;
double radiusH = 1.20 / convertBohrToAngstrom;
std::vector<Atom> atoms;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(1), masses(1), radiusC, C2, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(2), masses(2), radiusC, C3, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(3), masses(3), radiusC, C4, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(4), masses(4), radiusC, C5, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(5), masses(5), radiusC, C6, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(6), masses(6), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(7), masses(7), radiusH, H2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(8), masses(8), radiusH, H3, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(9), masses(9), radiusH, H4, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(10), masses(10), radiusH, H5, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(11), masses(11), radiusH, H6, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(C2, radiusC);
Sphere sph3(C3, radiusC);
Sphere sph4(C4, radiusC);
Sphere sph5(C5, radiusC);
Sphere sph6(C6, radiusC);
Sphere sph7(H1, radiusH);
Sphere sph8(H2, radiusH);
Sphere sph9(H3, radiusH);
Sphere sph10(H4, radiusH);
Sphere sph11(H5, radiusH);
Sphere sph12(H6, radiusH);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
spheres.push_back(sph5);
spheres.push_back(sph6);
spheres.push_back(sph7);
spheres.push_back(sph8);
spheres.push_back(sph9);
spheres.push_back(sph10);
spheres.push_back(sph11);
spheres.push_back(sph12);
// D2h as generated by Oxy, Oxz, Oyz
Symmetry pGroup = buildGroup(0, 0, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
void do_glas(FILE *log,int start,int homenr,rvec x[],rvec f[],
t_forcerec *fr,t_mdatoms *md,int atnr,t_inputrec *ir,
real ener[])
{
static bool bFirst=TRUE,bGlas;
static real d[2],pi6,pi12,rc9,rc4,rc10,rc3,rc;
static real *c6,*c12;
real wd,wdd,zi,fz,dd,d10,d4,d9,d3,r9,r3,sign,cc6,cc12;
int *type;
int i,j,ti;
type=md->typeA;
if (bFirst) {
pi6 = ir->userreal1;
pi12 = ir->userreal2;
d[0] = ir->userreal3;
d[1] = ir->userreal4;
/* Check whether these constants have been set. */
bGlas = (pi6 != 0) && (pi12 != 0) && (d[0] != 0) && (d[1] != 0);
if (bGlas) {
if (ir->eDispCorr != edispcNO) {
gmx_fatal(FARGS,"Can not have Long Range C6 corrections and GLASMD");
}
rc = max(fr->rvdw,fr->rlist);
rc3 = rc*rc*rc;
rc4 = rc3*rc;
rc9 = rc3*rc3*rc3;
rc10 = rc9*rc;
fprintf(log,
"Constants for GLASMD: pi6 = %10g, pi12 = %10g\n"
" d1 = %10g, d2 = %10g\n"
" rc3 = %10g, rc4 = %10g\n"
" rc9 = %10g, rc10 = %10g\n",
pi6,pi12,d[0],d[1],rc3,rc4,rc9,rc10);
if (d[0] > d[1])
gmx_fatal(FARGS,"d1 > d2 for GLASMD (check log file)");
snew(c6,atnr);
snew(c12,atnr);
for(i=0; (i<atnr); i++) {
c6[i] = C6 (fr->nbfp,atnr,i,i);
c12[i] = C12(fr->nbfp,atnr,i,i);
}
}
else
fprintf(stderr,"No glasmd!\n");
bFirst = FALSE;
}
if (bGlas) {
wd=0;
for(i=start; (i<start+homenr); i++) {
ti = type[i];
if ((c6[ti] != 0) || (c12[ti] != 0)) {
zi = x[i][ZZ];
cc6 = M_PI*sqrt(c6[ti]*pi6);
cc12 = M_PI*sqrt(c12[ti]*pi12);
/* Use a factor for the sign, this saves taking absolute values */
sign = 1;
for(j=0; (j<2); j++) {
dd = sign*(zi-d[j]);
if (dd >= rc) {
d3 = dd*dd*dd;
d9 = d3*d3*d3;
wdd = cc12/(45.0*d9) - cc6/(6.0*d3);
d4 = d3*dd;
d10 = d9*dd;
fz = sign*(cc12/(5.0*d10) - cc6/(2.0*d4));
}
else {
wdd = cc12*(2.0/(9.0*rc9) - dd/(5.0*rc10)) -
cc6*(2.0/(3.0*rc3) - dd/(2.0*rc4));
fz = sign*(cc12/(5.0*rc10)-cc6/(2.0*rc4));
}
wd += wdd;
f[i][ZZ] += fz;
sign = -sign;
}
}
}
ener[F_LJ_LR] = wd;
}
}
static void update_ff(t_forcerec *fr,int nparm,t_range range[],int param_val[])
{
static double *sigma=NULL,*eps=NULL,*c6=NULL,*cn=NULL,*bhama=NULL,*bhamb=NULL,*bhamc=NULL;
real val,*nbfp;
int i,j,atnr;
atnr = fr->ntype;
nbfp = fr->nbfp;
if (fr->bBHAM) {
if (bhama == NULL) {
snew(bhama,atnr);
snew(bhamb,atnr);
snew(bhamc,atnr);
}
}
else {
if (sigma == NULL) {
snew(sigma,atnr);
snew(eps,atnr);
snew(c6,atnr);
snew(cn,atnr);
}
}
/* Get current values for everything */
for(i=0; (i<nparm); i++) {
if (ga)
val = range[i].rval;
else
val = value_range(&range[i],param_val[i]);
if(debug)
fprintf(debug,"val = %g\n",val);
switch (range[i].ptype) {
case eseSIGMA:
sigma[range[i].atype] = val;
break;
case eseEPSILON:
eps[range[i].atype] = val;
break;
case eseBHAMA:
bhama[range[i].atype] = val;
break;
case eseBHAMB:
bhamb[range[i].atype] = val;
break;
case eseBHAMC:
bhamc[range[i].atype] = val;
break;
case eseCELLX:
scale[XX] = val;
break;
case eseCELLY:
scale[YY] = val;
break;
case eseCELLZ:
scale[ZZ] = val;
break;
default:
gmx_fatal(FARGS,"Unknown ptype");
}
}
if (fr->bBHAM) {
for(i=0; (i<atnr); i++) {
for(j=0; (j<=i); j++) {
BHAMA(nbfp,atnr,i,j) = BHAMA(nbfp,atnr,j,i) = sqrt(bhama[i]*bhama[j]);
BHAMB(nbfp,atnr,i,j) = BHAMB(nbfp,atnr,j,i) = sqrt(bhamb[i]*bhamb[j]);
BHAMC(nbfp,atnr,i,j) = BHAMC(nbfp,atnr,j,i) = sqrt(bhamc[i]*bhamc[j]);
}
}
}
else {
/* Now build a new matrix */
for(i=0; (i<atnr); i++) {
c6[i] = 4*eps[i]*pow(sigma[i],6.0);
cn[i] = 4*eps[i]*pow(sigma[i],ff.npow);
}
for(i=0; (i<atnr); i++) {
for(j=0; (j<=i); j++) {
C6(nbfp,atnr,i,j) = C6(nbfp,atnr,j,i) = sqrt(c6[i]*c6[j]);
C12(nbfp,atnr,i,j) = C12(nbfp,atnr,j,i) = sqrt(cn[i]*cn[j]);
}
}
}
if (debug) {
if (!fr->bBHAM)
for(i=0; (i<atnr); i++)
fprintf(debug,"atnr = %2d sigma = %8.4f eps = %8.4f\n",i,sigma[i],eps[i]);
for(i=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++) {
if (fr->bBHAM)
fprintf(debug,"i: %2d j: %2d A: %10.5e B: %10.5e C: %10.5e\n",i,j,
BHAMA(nbfp,atnr,i,j),BHAMB(nbfp,atnr,i,j),BHAMC(nbfp,atnr,i,j));
else
fprintf(debug,"i: %2d j: %2d c6: %10.5e cn: %10.5e\n",i,j,
C6(nbfp,atnr,i,j),C12(nbfp,atnr,i,j));
}
}
}
}
int multiple_detector_fit()
{
std::cout << "Beginning : ... " << std::endl;
Int_t npoints = 1000;
Double_t emin = 0.2;
Double_t emax = 3.0;
bool use100m = true;
bool use470m = true;
bool use600m = true;
std::vector<int> baselines;
std::vector<double> scales;
std::vector<std::string> names;
std::vector<double> volume;
if (use100m) baselines.push_back(100);
if (use470m) baselines.push_back(470);
if (use600m) baselines.push_back(600);
double NULLVec[2][20];
double OscVec[2][1001][7][20];
for(int i = 0; i < 20; i++){
NULLVec[0][i] = 0;
NULLVec[1][i] = 0;
}
for(int u = 0; u < 1000; u++){
for(int s = 0; s < 7; s++){
for(int i = 0; i < 20; i++){
OscVec[0][u][s][i] = 0;
OscVec[1][u][s][i] = 0;
}
}
}
int nbinsE = 0;
if (use100m){
std::string temp_name = /*"../MatrixFiles/combined_ntuple_100m_nu_processed_numu.root";*/"../MatrixFiles/combined_ntuple_100m_nu_processed_CoreyBins_numu.root";
TFile temp_file(temp_name.c_str());
TH1D *NULL_100;
NULL_100 = (TH1D*)(temp_file.Get("NumuCC"));
nbinsE = NULL_100->GetNbinsX();
std::cout << nbinsE << std::endl;
for(int i = 1; i <= nbinsE; i++){
NULLVec[0][i-1] = (NULL_100->GetBinContent(i));
}
for(int u = 0; u < npoints; u++){
for(int s = 0; s < 7; s++){
TH1D *OSC_100;
TString upoint = Form("%d",u);
TString name = "Universe_";
TString name2 = "_MultiSim_";
TString mul = Form("%d",s);
name += upoint;
name += name2;
name += mul;
OSC_100 = (TH1D*)(temp_file.Get(name));
for(int i = 1; i <= nbinsE; i++){
OscVec[0][u][s][i-1] = (OSC_100->GetBinContent(i));
// if(OscVec[0][u][s][i-1] != OscVec[0][u][s][i-1]) std::cout << "erm" <<std::endl;
}
delete OSC_100;
}
}
delete NULL_100;
temp_file.Close();
}
if (use470m){
std::string temp_name = /*"../MatrixFiles/combined_ntuple_600m_onaxis_nu_processed_numu.root";*/"../MatrixFiles/combined_ntuple_600m_onaxis_nu_processed_CoreyBins_numu.root";
TFile temp_file(temp_name.c_str());
TH1D *NULL_470;
NULL_470 = (TH1D*)(temp_file.Get("NumuCC"));
nbinsE = NULL_470->GetNbinsX();
std::cout << nbinsE<< std::endl;
for(int i = 1; i <= nbinsE; i++){
NULLVec[1][i-1] = (NULL_470->GetBinContent(i));
}
for(int u = 0; u < npoints; u++){
for(int s = 0; s < 7; s++){
TH1D *OSC_470;
TString upoint = Form("%d",u);//std::to_string(u);
TString name = "Universe_";
TString name2 = "_MultiSim_";
TString mul = Form("%d",s);// = std::to_string(s);
name += upoint;
name += name2;
name += mul;
OSC_470 = (TH1D*)(temp_file.Get(name));
for(int i = 1; i <= nbinsE; i++){
OscVec[1][u][s][i-1] = (OSC_470->GetBinContent(i));
if(OscVec[1][u][s][i-1] != OscVec[1][u][s][i-1]) OscVec[1][u][s][i-1] = NULLVec[1][i-1];//std::cout << "erm, u :" << u << " s : " << s << " E : " << i <<std::endl;
}
delete OSC_470;
}
}
delete NULL_470;
temp_file.Close();
}
int nL = 2;
int mbins = (nbinsE*nL);
TMatrix M6 (mbins,mbins);
TMatrix M5 (mbins,mbins);
TMatrix M4 (mbins,mbins);
TMatrix M3 (mbins,mbins);
TMatrix M2 (mbins,mbins);
TMatrix M1 (mbins,mbins);
TMatrix M0 (mbins,mbins);
TMatrix C6 (mbins,mbins);
TMatrix C5 (mbins,mbins);
TMatrix C4 (mbins,mbins);
TMatrix C3 (mbins,mbins);
TMatrix C2 (mbins,mbins);
TMatrix C1 (mbins,mbins);
TMatrix C0 (mbins,mbins);
int N = 0;
TH1D *Fig6 = new TH1D("Fig6",";;",mbins,0,mbins);
TH1D *Fig5 = new TH1D("Fig5",";;",mbins,0,mbins);
TH1D *Fig4 = new TH1D("Fig4",";;",mbins,0,mbins);
TH1D *Fig3 = new TH1D("Fig3",";;",mbins,0,mbins);
TH1D *Fig2 = new TH1D("Fig2",";;",mbins,0,mbins);
TH1D *Fig1 = new TH1D("Fig1",";;",mbins,0,mbins);
TH1D *Fig0 = new TH1D("Fig0",";;",mbins,0,mbins);
int Erri = 0, Errj = 0;
std::cout << "Filling Error Matrix..." << std::endl;
for(int Lrow = 0; Lrow < 2; Lrow++){
for(int Erow = 0; Erow < nbinsE; Erow++){
Errj = 0;
for(int Lcol = 0; Lcol < 2; Lcol++){
for(int Ecol = 0; Ecol < nbinsE; Ecol++){
M6 (Erri,Errj) = 0;
M5 (Erri,Errj) = 0;
M4 (Erri,Errj) = 0;
M3 (Erri,Errj) = 0;
M2 (Erri,Errj) = 0;
M1 (Erri,Errj) = 0;
M0 (Erri,Errj) = 0;
N = 0;
for(int u = 0; u < npoints; u++){
M6 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][6][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][6][Ecol]);
M5 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][5][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][5][Ecol]);
M4 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][4][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][4][Ecol]);
M3 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][3][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][3][Ecol]);
M2 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][2][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][2][Ecol]);
M1 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][1][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][1][Ecol]);
M0 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][0][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][0][Ecol]);
N++;
}
M6 (Erri,Errj) /= N;
M5 (Erri,Errj) /= N;
M4 (Erri,Errj) /= N;
M3 (Erri,Errj) /= N;
M2 (Erri,Errj) /= N;
M1 (Erri,Errj) /= N;
M0 (Erri,Errj) /= N;
M6 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M5 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M4 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M3 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M2 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M1 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M0 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
if(Erri == Errj) Fig6->SetBinContent(Erri+1, sqrt(M6 (Erri,Errj)));
if(Erri == Errj) Fig5->SetBinContent(Erri+1, sqrt(M5 (Erri,Errj)));
if(Erri == Errj) Fig4->SetBinContent(Erri+1, sqrt(M4 (Erri,Errj)));
if(Erri == Errj) Fig3->SetBinContent(Erri+1, sqrt(M3 (Erri,Errj)));
if(Erri == Errj) Fig2->SetBinContent(Erri+1, sqrt(M2 (Erri,Errj)));
if(Erri == Errj) Fig1->SetBinContent(Erri+1, sqrt(M1 (Erri,Errj)));
if(Erri == Errj) Fig0->SetBinContent(Erri+1, sqrt(M0 (Erri,Errj)));
std::cout << M6 (Erri,Errj) << "\t";
Errj++;
}}
Erri++;
}}
for(int i = 0; i < Erri; i++){
for(int j = 0; j < Errj; j++){
C6 (i,j) = M6(i,j) / sqrt(M6 (i,i) * M6 (j,j));
C5 (i,j) = M5(i,j) / sqrt(M5 (i,i) * M5 (j,j));
C4 (i,j) = M4(i,j) / sqrt(M4 (i,i) * M4 (j,j));
C3 (i,j) = M3(i,j) / sqrt(M3 (i,i) * M3 (j,j));
C2 (i,j) = M2(i,j) / sqrt(M2 (i,i) * M2 (j,j));
C1 (i,j) = M1(i,j) / sqrt(M1 (i,i) * M1 (j,j));
C0 (i,j) = M0(i,j) / sqrt(M0 (i,i) * M0 (j,j));
}
}
std::cout << "...Error Matrix Filled" << std::endl;
TCanvas* c6 = new TCanvas("c6","",700,700);
c6->SetLeftMargin(.1);
c6->SetBottomMargin(.1);
c6->SetTopMargin(.075);
c6->SetRightMargin(.15);
c6->cd();
M6.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
// TMatrixFBase->GetZaxis()->SetRangeUser(-0.05,0.4);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
// TMatrixFBase->GetZaxis()->SetTitle("Fractional Error Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kBlue);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *ND = new TLatex(.15,.01,"LAr1-ND (100m) ");
ND->SetNDC();
ND->SetTextFont(62);
ND->SetTextSize(0.04);
ND->Draw();
TLatex *MD = new TLatex(.5,.01,"T600 (600m, on axis)");
MD->SetNDC();
MD->SetTextFont(62);
MD->SetTextSize(0.04);
MD->Draw();
TLatex *ND45 = new TLatex(.05,.15,"LAr1-ND (100m) ");
ND45->SetNDC();
ND45->SetTextAngle(90);
ND45->SetTextFont(62);
ND45->SetTextSize(0.04);
ND45->Draw();
TLatex *MD45 = new TLatex(.05,.54,"T600 (600m, on axis)");
MD45->SetNDC();
MD45->SetTextAngle(90);
MD45->SetTextFont(62);
MD45->SetTextSize(0.04);
MD45->Draw();
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} Flux Fractional Error Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
// c6->Print("total_matrix.pdf");
TCanvas* c61 = new TCanvas("c61","",700,700);
c61->SetLeftMargin(.1);
c61->SetBottomMargin(.1);
c61->SetTopMargin(.075);
c61->SetRightMargin(.15);
c61->cd();
C6.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kYellow);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} Flux Correlation Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
// c61->Print("total_correlation_matrix.pdf");
TCanvas* c5 = new TCanvas("c5","",700,700);
c5->SetLeftMargin(.1);
c5->SetBottomMargin(.1);
c5->SetTopMargin(.075);
c5->SetRightMargin(.15);
c5->cd();
M5.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-0.005,0.045);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
// TMatrixFBase->GetZaxis()->SetTitle("K^{+} Covariance Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kBlue);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} K#lower[-0.15]{+} Fractional Error Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c5->Print("mult5_matrix.pdf");
TCanvas* c51 = new TCanvas("c51","",700,700);
c51->SetLeftMargin(.1);
c51->SetBottomMargin(.1);
c51->SetTopMargin(.075);
c51->SetRightMargin(.15);
c51->cd();
C5.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-1,1);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
// TMatrixFBase->GetZaxis()->SetTitle("K#lower[-0.15]{+} Correlation Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kYellow);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} K#lower[-0.15]{+} Correlation Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c51->Print("mult5_correlation_matrix.pdf");
TCanvas* c4 = new TCanvas("c4","",700,700);
c4->SetLeftMargin(.1);
c4->SetBottomMargin(.1);
c4->SetTopMargin(.075);
c4->SetRightMargin(.15);
c4->cd();
M4.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-0.005,0.045);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
//TMatrixFBase->GetZaxis()->SetTitle("K#lower[-0.15]{-} Covariance Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kBlue);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} K#lower[-0.15]{-} Fractional Error Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c4->Print("mult4_matrix.pdf");
TCanvas* c41 = new TCanvas("c41","",700,700);
c41->SetLeftMargin(.1);
c41->SetBottomMargin(.1);
c41->SetTopMargin(.075);
c41->SetRightMargin(.15);
c41->cd();
C4.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-1,1);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
// TMatrixFBase->GetZaxis()->SetTitle("K#lower[-0.15]{-} Correlation Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kYellow);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} K#lower[-0.15]{-} Correlation Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c41->Print("mult4_correlation_matrix.pdf");
TCanvas* c3 = new TCanvas("c3","",700,700);
c3->SetLeftMargin(.1);
c3->SetBottomMargin(.1);
c3->SetTopMargin(.075);
c3->SetRightMargin(.15);
c3->cd();
M3.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-0.005,0.045);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
//TMatrixFBase->GetZaxis()->SetTitle("K#lower[-0.15]{0} Covariance Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kBlue);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} K#lower[-0.15]{0} Fractional Error Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c3->Print("mult3_matrix.pdf");
TCanvas* c31 = new TCanvas("c31","",700,700);
c31->SetLeftMargin(.1);
c31->SetBottomMargin(.1);
c31->SetTopMargin(.075);
c31->SetRightMargin(.15);
c31->cd();
C3.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-1,1);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
//TMatrixFBase->GetZaxis()->SetTitle("K#lower[-0.15]{0} Correlation Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kYellow);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} K#lower[-0.15]{0} Correlation Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c31->Print("mult3_correlation_matrix.pdf");
TCanvas* c2 = new TCanvas("c2","",700,700);
c2->SetLeftMargin(.1);
c2->SetBottomMargin(.1);
c2->SetTopMargin(.075);
c2->SetRightMargin(.15);
c2->cd();
M2.Draw("COLZ");
gStyle->SetPalette(56,0);
//TMatrixFBase->GetZaxis()->SetRangeUser(-0.005,0.045);
TMatrixFBase->SetContour(999);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
//TMatrixFBase->GetZaxis()->SetTitle("#pi#lower[-0.15]{+} Covariance Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kBlue);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} #pi#lower[-0.15]{+} Fractional Error Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c2->Print("mult2_matrix.pdf");
TCanvas* c21 = new TCanvas("c21","",700,700);
c21->SetLeftMargin(.1);
c21->SetBottomMargin(.1);
c21->SetTopMargin(.075);
c21->SetRightMargin(.15);
c21->cd();
C2.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-1,1);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
//TMatrixFBase->GetZaxis()->SetTitle("#pi#lower[-0.15]{+} Correlation Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kYellow);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} #pi#lower[-0.15]{+} Correlation Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c21->Print("mult2_correlation_matrix.pdf");
TCanvas* c1 = new TCanvas("c1","",700,700);
c1->SetLeftMargin(.1);
c1->SetBottomMargin(.1);
c1->SetTopMargin(.075);
c1->SetRightMargin(.15);
c1->cd();
M1.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-0.005,0.045);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
//TMatrixFBase->GetZaxis()->SetTitle("#pi#lower[-0.15]{-} Covariance Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kBlue);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} #pi#lower[-0.15]{-} Fractional Error Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c1->Print("mult1_matrix.pdf");
TCanvas* c11 = new TCanvas("c11","",700,700);
c11->SetLeftMargin(.1);
c11->SetBottomMargin(.1);
c11->SetTopMargin(.075);
c11->SetRightMargin(.15);
c11->cd();
C1.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-1,1);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
// TMatrixFBase->GetZaxis()->SetTitle("#pi#lower[-0.15]{-} Correlation Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kYellow);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} #pi#lower[-0.15]{-} Correlation Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c11->Print("mult1_correlation_matrix.pdf");
TCanvas* c0 = new TCanvas("c0","",700,700);
c0->SetLeftMargin(.1);
c0->SetBottomMargin(.1);
c0->SetTopMargin(.075);
c0->SetRightMargin(.15);
c0->cd();
M0.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-0.005,0.045);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
// TMatrixFBase->GetZaxis()->SetTitle("Beam UniSim Covariance Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kBlue);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} Beam Fractional Error Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c0->Print("mult0_matrix.pdf");
TCanvas* c01 = new TCanvas("c01","",700,700);
c01->SetLeftMargin(.1);
c01->SetBottomMargin(.1);
c01->SetTopMargin(.075);
c01->SetRightMargin(.15);
c01->cd();
C0.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
//TMatrixFBase->GetZaxis()->SetRangeUser(-1,1);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
// TMatrixFBase->GetZaxis()->SetTitle("Beam UniSim Correlation Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
TLine *split = new TLine();
split->SetLineStyle(2);
split->SetLineWidth(5);
split->SetLineColor(kYellow);
split->DrawLineNDC(.1,.51,.849,.51);
split->DrawLineNDC(.475,.101,.475,.930);
add_plot_label("| 0.2 #minus 3.0 GeV | 0.2 #minus 3.0 GeV | ", 0.48,0.08,0.03);
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} Beam Correlation Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
ND->Draw();
MD->Draw();
ND45->Draw();
MD45->Draw();
// c01->Print("mult0_correlation_matrix.pdf");
TCanvas* c86 = new TCanvas("c86","",800,400);
c86->SetLeftMargin(.1);
c86->SetBottomMargin(.1);
c86->SetTopMargin(.05);
c86->SetRightMargin(.05);
c86->cd();
Fig6->GetYaxis()->SetTitle("Fractional Error");
Fig6->GetYaxis()->SetTitleFont(62);
Fig6->GetXaxis()->SetTitleFont(62);
Fig6->GetYaxis()->SetLabelFont(62);
Fig6->GetXaxis()->SetLabelFont(62);
Fig6->GetYaxis()->CenterTitle();
Fig6->GetYaxis()->SetTitleSize(0.06);
Fig6->GetYaxis()->SetTitleOffset(0.8);
Fig6->GetXaxis()->SetLabelSize(0.06);
Fig6->GetYaxis()->SetLabelSize(0.06);
Fig6->GetXaxis()->SetTitleOffset(1.5);
Fig6->SetStats(0);
Fig6->SetMinimum(-0.01);
Fig6->SetMaximum(0.21);
Fig6->SetMarkerStyle(8);
Fig6->GetYaxis()->SetNdivisions(509);
Fig6->GetXaxis()->SetNdivisions(509);
Fig6->Draw("P");
split->SetLineColor(1);
split->SetLineWidth(2);
split->DrawLine(19,-0.01,19,0.21);
TLatex *ND = new TLatex(.23,.85,"LAr1-ND (100m) ");
ND->SetNDC();
ND->SetTextFont(62);
ND->SetTextSize(0.05);
ND->Draw();
TLatex *MD = new TLatex(.65,.85,"T600 (600m, on axis)");
MD->SetNDC();
MD->SetTextFont(62);
MD->SetTextSize(0.05);
MD->Draw();
// c86->Print("FractionalErrors_Total.pdf");
TCanvas* c85 = new TCanvas("c85","",800,400);
c85->SetLeftMargin(.1);
c85->SetBottomMargin(.1);
c85->SetTopMargin(.05);
c85->SetRightMargin(.05);
c85->cd();
Fig5->GetYaxis()->SetTitle("K#lower[-0.2]{+} Fractional Error");
Fig5->GetYaxis()->SetTitleFont(62);
Fig5->GetXaxis()->SetTitleFont(62);
Fig5->GetYaxis()->SetLabelFont(62);
Fig5->GetXaxis()->SetLabelFont(62);
Fig5->GetYaxis()->CenterTitle();
Fig5->GetYaxis()->SetTitleSize(0.06);
Fig5->GetYaxis()->SetTitleOffset(0.8);
Fig5->GetXaxis()->SetLabelSize(0.06);
Fig5->GetYaxis()->SetLabelSize(0.06);
Fig5->GetXaxis()->SetTitleOffset(1.5);
Fig5->SetStats(0);
Fig5->SetMinimum(-0.01);
Fig5->SetMaximum(0.21);
Fig5->SetMarkerStyle(8);
Fig5->GetYaxis()->SetNdivisions(509);
Fig5->GetXaxis()->SetNdivisions(509);
Fig5->Draw("P");
split->SetLineColor(1);
split->SetLineWidth(2);
split->DrawLine(19,-0.01,19,0.21);
ND->Draw();
MD->Draw();
// c85->Print("FractionalErrors_Kplus.pdf");
TCanvas* c84 = new TCanvas("c84","",800,400);
c84->SetLeftMargin(.1);
c84->SetBottomMargin(.1);
c84->SetTopMargin(.05);
c84->SetRightMargin(.05);
c84->cd();
Fig4->GetYaxis()->SetTitle("K#lower[-0.2]{-} Fractional Error");
Fig4->GetYaxis()->SetTitleFont(62);
Fig4->GetXaxis()->SetTitleFont(62);
Fig4->GetYaxis()->SetLabelFont(62);
Fig4->GetXaxis()->SetLabelFont(62);
Fig4->GetYaxis()->CenterTitle();
Fig4->GetYaxis()->SetTitleSize(0.06);
Fig4->GetYaxis()->SetTitleOffset(0.8);
Fig4->GetXaxis()->SetLabelSize(0.06);
Fig4->GetYaxis()->SetLabelSize(0.06);
Fig4->GetXaxis()->SetTitleOffset(1.5);
Fig4->SetStats(0);
Fig4->SetMinimum(-0.01);
Fig4->SetMaximum(0.21);
Fig4->SetMarkerStyle(8);
Fig4->GetYaxis()->SetNdivisions(509);
Fig4->GetXaxis()->SetNdivisions(509);
Fig4->Draw("P");
split->SetLineColor(1);
split->SetLineWidth(2);
split->DrawLine(19,-0.01,19,0.21);
ND->Draw();
MD->Draw();
// c84->Print("FractionalErrors_Kmin.pdf");
TCanvas* c83 = new TCanvas("c83","",800,400);
c83->SetLeftMargin(.1);
c83->SetBottomMargin(.1);
c83->SetTopMargin(.05);
c83->SetRightMargin(.05);
c83->cd();
Fig3->GetYaxis()->SetTitle("K#lower[-0.2]{0} Fractional Error");
Fig3->GetYaxis()->SetTitleFont(62);
Fig3->GetXaxis()->SetTitleFont(62);
Fig3->GetYaxis()->SetLabelFont(62);
Fig3->GetXaxis()->SetLabelFont(62);
Fig3->GetYaxis()->CenterTitle();
Fig3->GetYaxis()->SetTitleSize(0.06);
Fig3->GetYaxis()->SetTitleOffset(0.8);
Fig3->GetXaxis()->SetLabelSize(0.06);
Fig3->GetYaxis()->SetLabelSize(0.06);
Fig3->GetXaxis()->SetTitleOffset(1.5);
Fig3->SetStats(0);
Fig3->SetMinimum(-0.01);
Fig3->SetMaximum(0.21);
Fig3->SetMarkerStyle(8);
Fig3->GetYaxis()->SetNdivisions(509);
Fig3->GetXaxis()->SetNdivisions(509);
Fig3->Draw("P");
split->SetLineColor(1);
split->SetLineWidth(2);
split->DrawLine(19,-0.01,19,0.21);
ND->Draw();
MD->Draw();
// c83->Print("FractionalErrors_K0.pdf");
TCanvas* c82 = new TCanvas("c82","",800,400);
c82->SetLeftMargin(.1);
c82->SetBottomMargin(.1);
c82->SetTopMargin(.05);
c82->SetRightMargin(.05);
c82->cd();
Fig2->GetYaxis()->SetTitle("#pi#lower[-0.2]{+} Fractional Error");
Fig2->GetYaxis()->SetTitleFont(62);
Fig2->GetXaxis()->SetTitleFont(62);
Fig2->GetYaxis()->SetLabelFont(62);
Fig2->GetXaxis()->SetLabelFont(62);
Fig2->GetYaxis()->CenterTitle();
Fig2->GetYaxis()->SetTitleSize(0.06);
Fig2->GetYaxis()->SetTitleOffset(0.8);
Fig2->GetXaxis()->SetLabelSize(0.06);
Fig2->GetYaxis()->SetLabelSize(0.06);
Fig2->GetXaxis()->SetTitleOffset(1.5);
Fig2->SetStats(0);
Fig2->SetMinimum(-0.01);
Fig2->SetMaximum(0.21);
Fig2->SetMarkerStyle(8);
Fig2->GetYaxis()->SetNdivisions(509);
Fig2->GetXaxis()->SetNdivisions(509);
Fig2->Draw("P");
split->SetLineColor(1);
split->SetLineWidth(2);
split->DrawLine(19,-0.01,19,0.21);
ND->Draw();
MD->Draw();
// c82->Print("FractionalErrors_piplus.pdf");
TCanvas* c81 = new TCanvas("c81","",800,400);
c81->SetLeftMargin(.1);
c81->SetBottomMargin(.1);
c81->SetTopMargin(.05);
c81->SetRightMargin(.05);
c81->cd();
Fig1->GetYaxis()->SetTitle("#pi#lower[-0.2]{-} Fractional Error");
Fig1->GetYaxis()->SetTitleFont(62);
Fig1->GetXaxis()->SetTitleFont(62);
Fig1->GetYaxis()->SetLabelFont(62);
Fig1->GetXaxis()->SetLabelFont(62);
Fig1->GetYaxis()->CenterTitle();
Fig1->GetYaxis()->SetTitleSize(0.06);
Fig1->GetYaxis()->SetTitleOffset(0.8);
Fig1->GetXaxis()->SetLabelSize(0.06);
Fig1->GetYaxis()->SetLabelSize(0.06);
Fig1->GetXaxis()->SetTitleOffset(1.5);
Fig1->SetStats(0);
Fig1->SetMinimum(-0.01);
Fig1->SetMaximum(0.21);
Fig1->SetMarkerStyle(8);
Fig1->GetYaxis()->SetNdivisions(509);
Fig1->GetXaxis()->SetNdivisions(509);
Fig1->Draw("P");
split->SetLineColor(1);
split->SetLineWidth(2);
split->DrawLine(19,-0.01,19,0.21);
ND->Draw();
MD->Draw();
// c81->Print("FractionalErrors_pimin.pdf");
TCanvas* c80 = new TCanvas("c80","",800,400);
c80->SetLeftMargin(.1);
c80->SetBottomMargin(.1);
c80->SetTopMargin(.05);
c80->SetRightMargin(.05);
c80->cd();
Fig0->GetYaxis()->SetTitle("Beam Fractional Error");
Fig0->GetYaxis()->SetTitleFont(62);
Fig0->GetXaxis()->SetTitleFont(62);
Fig0->GetYaxis()->SetLabelFont(62);
Fig0->GetXaxis()->SetLabelFont(62);
Fig0->GetYaxis()->CenterTitle();
Fig0->GetYaxis()->SetTitleSize(0.06);
Fig0->GetYaxis()->SetTitleOffset(0.8);
Fig0->GetXaxis()->SetLabelSize(0.06);
Fig0->GetYaxis()->SetLabelSize(0.06);
Fig0->GetXaxis()->SetTitleOffset(1.5);
Fig0->SetStats(0);
Fig0->SetMinimum(-0.01);
Fig0->SetMaximum(0.21);
Fig0->SetMarkerStyle(8);
Fig0->GetYaxis()->SetNdivisions(509);
Fig0->GetXaxis()->SetNdivisions(509);
Fig0->Draw("P");
split->SetLineColor(1);
split->SetLineWidth(2);
split->DrawLine(19,-0.01,19,0.21);
ND->Draw();
MD->Draw();
// c80->Print("FractionalErrors_beam.pdf");
cout<<"\nEnd of routine.\n";
return 0;
}
int main ()
{
return C1 () + C2 () + C3 () + C4 () + C5 () + C6 () + C7 () + C8 ();
}
static void check_solvent(FILE *fp,t_topology *top,t_forcerec *fr,
t_mdatoms *md,t_nsborder *nsb)
{
/* This routine finds out whether a charge group can be used as
* solvent in the innerloops. The routine should be called once
* at the beginning of the MD program.
*/
t_block *cgs,*excl,*mols;
atom_id *cgid;
int i,j,m,j0,j1,nj,k,aj,ak,tjA,tjB,nl_m,nl_n,nl_o;
int warncount;
bool bOneCG;
bool *bAllExcl,bAE,bOrder;
bool *bHaveLJ,*bHaveCoul;
cgs = &(top->blocks[ebCGS]);
excl = &(top->atoms.excl);
mols = &(top->blocks[ebMOLS]);
if (fp)
fprintf(fp,"Going to determine what solvent types we have.\n");
snew(fr->solvent_type,cgs->nr+1);
snew(fr->mno_index,(cgs->nr+1)*3);
/* Generate charge group number for all atoms */
cgid = make_invblock(cgs,cgs->nra);
warncount=0;
/* Loop over molecules */
if (fp)
fprintf(fp,"There are %d molecules, %d charge groups and %d atoms\n",
mols->nr,cgs->nr,cgs->nra);
for(i=0; (i<mols->nr); i++) {
/* Set boolean that determines whether the molecules consists of one CG */
bOneCG = TRUE;
/* Set some counters */
j0 = mols->index[i];
j1 = mols->index[i+1];
nj = j1-j0;
for(j=j0+1; (j<j1); j++) {
bOneCG = bOneCG && (cgid[mols->a[j]] == cgid[mols->a[j-1]]);
}
if (fr->bSolvOpt && bOneCG && nj>1) {
/* Check whether everything is excluded */
snew(bAllExcl,nj);
bAE = TRUE;
/* Loop over all atoms in molecule */
for(j=j0; (j<j1) && bAE; j++) {
/* Set a flag for each atom in the molecule that determines whether
* it is excluded or not
*/
for(k=0; (k<nj); k++)
bAllExcl[k] = FALSE;
/* Now check all the exclusions of this atom */
for(k=excl->index[j]; (k<excl->index[j+1]); k++) {
ak = excl->a[k];
/* Consistency and range check */
if ((ak < j0) || (ak >= j1))
fatal_error(0,"Exclusion outside molecule? ak = %d, j0 = %d, j1 = 5d, mol is %d",ak,j0,j1,i);
bAllExcl[ak-j0] = TRUE;
}
/* Now sum up the booleans */
for(k=0; (k<nj); k++)
bAE = bAE && bAllExcl[k];
}
if (bAE) {
snew(bHaveCoul,nj);
snew(bHaveLJ,nj);
for(j=j0; (j<j1); j++) {
/* Check for coulomb */
aj = mols->a[j];
bHaveCoul[j-j0] = ( (fabs(top->atoms.atom[aj].q ) > GMX_REAL_MIN) ||
(fabs(top->atoms.atom[aj].qB) > GMX_REAL_MIN));
/* Check for LJ. */
tjA = top->atoms.atom[aj].type;
tjB = top->atoms.atom[aj].typeB;
bHaveLJ[j-j0] = FALSE;
for(k=0; (k<fr->ntype); k++) {
if (fr->bBHAM)
bHaveLJ[j-j0] = (bHaveLJ[j-j0] ||
(fabs(BHAMA(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(BHAMB(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(BHAMC(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(BHAMA(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN) ||
(fabs(BHAMB(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN) ||
(fabs(BHAMC(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN));
else
bHaveLJ[j-j0] = (bHaveLJ[j-j0] ||
(fabs(C6(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(C12(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(C6(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN) ||
(fabs(C12(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN));
}
}
/* Now we have determined what particles have which interactions
* In the case of water-like molecules we only check for the number
* of particles and the LJ, not for the Coulomb. Let's just assume
* that the water loops are faster than the MNO loops anyway. DvdS
*/
/* No - there's another problem: To optimize the water
* innerloop assumes the charge of the first i atom is constant
* qO, and charge on atoms 2/3 is constant qH. /EL
*/
/* I won't write any altivec versions of the general solvent inner
* loops. Thus, when USE_PPC_ALTIVEC is defined it is faster
* to use the normal loops instead of the MNO solvent version. /EL
*/
aj=mols->a[j0];
if((nj==3) && bHaveCoul[0] && bHaveLJ[0] &&
!bHaveLJ[1] && !bHaveLJ[2] &&
fabs(top->atoms.atom[aj+1].q - top->atoms.atom[aj+2].q) < GMX_REAL_MIN)
fr->solvent_type[cgid[aj]] = esolWATER;
else {
#ifdef USE_PPC_ALTIVEC
fr->solvent_type[cgid[aj]] = esolNO;
#else
/* Time to compute M & N & O */
for(k=0; (k<nj) && (bHaveLJ[k] && bHaveCoul[k]); k++)
;
nl_n = k;
for(; (k<nj) && (!bHaveLJ[k] && bHaveCoul[k]); k++)
;
nl_o = k;
for(; (k<nj) && (bHaveLJ[k] && !bHaveCoul[k]); k++)
;
nl_m = k;
/* Now check whether we're at the end of the pack */
bOrder = FALSE;
for(; (k<nj); k++)
bOrder = bOrder || (bHaveLJ[k] || bHaveCoul[k]);
if (bOrder) {
/* If we have a solvent molecule with LJC everywhere, then
* we shouldn't issue a warning. Only if we suspect something
* could be better.
*/
if (nl_n != nj) {
warncount++;
if(warncount<11 && fp)
fprintf(fp,"The order in molecule %d could be optimized"
" for better performance\n",i);
if(warncount==10 && fp)
fprintf(fp,"(More than 10 molecules where the order can be optimized)\n");
}
nl_m = nl_n = nl_o = nj;
}
fr->mno_index[cgid[aj]*3] = nl_m;
fr->mno_index[cgid[aj]*3+1] = nl_n;
fr->mno_index[cgid[aj]*3+2] = nl_o;
fr->solvent_type[cgid[aj]] = esolMNO;
#endif /* MNO solvent if not using altivec */
}
/* Last check for perturbed atoms */
for(j=j0; (j<j1); j++)
if (md->bPerturbed[mols->a[j]])
fr->solvent_type[cgid[mols->a[j0]]] = esolNO;
sfree(bHaveLJ);
sfree(bHaveCoul);
}
else {
/* Turn off solvent optimization for all cg's in the molecule,
* here there is only one.
*/
fr->solvent_type[cgid[mols->a[j0]]] = esolNO;
}
sfree(bAllExcl);
}
else {
/* Turn off solvent optimization for all cg's in the molecule */
for(j=mols->index[i]; (j<mols->index[i+1]); j++) {
fr->solvent_type[cgid[mols->a[j]]] = esolNO;
}
}
}
if (debug) {
for(i=0; (i<cgs->nr); i++)
fprintf(debug,"MNO: cg = %5d, m = %2d, n = %2d, o = %2d\n",
i,fr->mno_index[3*i],fr->mno_index[3*i+1],fr->mno_index[3*i+2]);
}
/* Now compute the number of solvent molecules, could be merged with code above */
fr->nMNOMol = 0;
fr->nWatMol = 0;
for(m=0; m<3; m++)
fr->nMNOav[m] = 0;
for(i=0; i<mols->nr; i++) {
j = mols->a[mols->index[i]];
if (j>=START(nsb) && j<START(nsb)+HOMENR(nsb)) {
if (fr->solvent_type[cgid[j]] == esolMNO) {
fr->nMNOMol++;
for(m=0; m<3; m++)
fr->nMNOav[m] += fr->mno_index[3*cgid[j]+m];
}
else if (fr->solvent_type[cgid[j]] == esolWATER)
fr->nWatMol++;
}
}
if (fr->nMNOMol > 0)
for(m=0; (m<3); m++)
fr->nMNOav[m] /= fr->nMNOMol;
sfree(cgid);
if (fp) {
fprintf(fp,"There are %d optimized solvent molecules on node %d\n",
fr->nMNOMol,nsb->nodeid);
if (fr->nMNOMol > 0)
fprintf(fp," aver. nr. of atoms per molecule: vdwc %.1f coul %.1f vdw %.1f\n",
fr->nMNOav[1],fr->nMNOav[2]-fr->nMNOav[1],fr->nMNOav[0]-fr->nMNOav[2]);
fprintf(fp,"There are %d optimized water molecules on node %d\n",
fr->nWatMol,nsb->nodeid);
}
}
int multiple_detector_fit()
{
std::cout << "Beginning : ... " << std::endl;
Int_t npoints = 1000;
Double_t emin = 0.2;
Double_t emax = 3.0;
bool use100m = false;
bool use470m = true;
bool use600m = false;
std::vector<int> baselines;
std::vector<double> scales;
std::vector<std::string> names;
std::vector<double> volume;
if (use100m) baselines.push_back(100);
if (use470m) baselines.push_back(470);
if (use600m) baselines.push_back(600);
int nL = baselines.size();
double NULLVec[3][20];
double OscVec[3][1001][7][20];
for(int i = 0; i < 20; i++){
NULLVec[0][i] = 0;
NULLVec[1][i] = 0;
NULLVec[2][i] = 0;
}
for(int u = 0; u < 1000; u++){
for(int s = 0; s < 7; s++){
for(int i = 0; i < 20; i++){
OscVec[0][u][s][i] = 0;
OscVec[1][u][s][i] = 0;
OscVec[2][u][s][i] = 0;
}
}
}
int nbinsE = 0;
int counter = 0;
if (use100m){
std::string temp_name = "../MatrixFiles/combined_ntuple_100m_nu_processed_numu.root";
TFile temp_file(temp_name.c_str());
TH1D *NULL_100;
NULL_100 = (TH1D*)(temp_file.Get("NumuCC"));
nbinsE = NULL_100->GetNbinsX();
std::cout << nbinsE << std::endl;
for(int i = 1; i <= nbinsE; i++){
NULLVec[counter][i-1] = (NULL_100->GetBinContent(i));
}
for(int u = 0; u < npoints; u++){
for(int s = 0; s < 7; s++){
TH1D *OSC_100;
TString upoint = Form("%d",u);
TString name = "Universe_";
TString name2 = "_MultiSim_";
TString mul = Form("%d",s);
name += upoint;
name += name2;
name += mul;
OSC_100 = (TH1D*)(temp_file.Get(name));
for(int i = 1; i <= nbinsE; i++){
OscVec[counter][u][s][i-1] = (OSC_100->GetBinContent(i));
// if(OscVec[0][u][s][i-1] != OscVec[0][u][s][i-1]) std::cout << "erm" <<std::endl;
}
delete OSC_100;
}
}
counter++;
delete NULL_100;
temp_file.Close();
}
if (use470m){
std::string temp_name = "../MatrixFiles/combined_ntuple_470m_nu_processed_numu.root";
TFile temp_file(temp_name.c_str());
TH1D *NULL_470;
NULL_470 = (TH1D*)(temp_file.Get("NumuCC"));
nbinsE = NULL_470->GetNbinsX();
std::cout << nbinsE<< std::endl;
for(int i = 1; i <= nbinsE; i++){
NULLVec[counter][i-1] = (NULL_470->GetBinContent(i));
}
for(int u = 0; u < npoints; u++){
for(int s = 0; s < 7; s++){
TH1D *OSC_470;
TString upoint = Form("%d",u);//std::to_string(u);
TString name = "Universe_";
TString name2 = "_MultiSim_";
TString mul = Form("%d",s);// = std::to_string(s);
name += upoint;
name += name2;
name += mul;
OSC_470 = (TH1D*)(temp_file.Get(name));
for(int i = 1; i <= nbinsE; i++){
OscVec[counter][u][s][i-1] = (OSC_470->GetBinContent(i));
}
delete OSC_470;
}
}
counter++;
delete NULL_470;
temp_file.Close();
}
if (use600m){
std::string temp_name = "../MatrixFiles/combined_ntuple_600m_onaxis_nu_processed_numu.root";
TFile temp_file(temp_name.c_str());
TH1D *NULL_600;
NULL_600 = (TH1D*)(temp_file.Get("NumuCC"));
nbinsE = NULL_600->GetNbinsX();
std::cout << nbinsE<< std::endl;
for(int i = 1; i <= nbinsE; i++){
NULLVec[counter][i-1] = (NULL_600->GetBinContent(i));
}
for(int u = 0; u < npoints; u++){
for(int s = 0; s < 7; s++){
TH1D *OSC_600;
TString upoint = Form("%d",u);//std::to_string(u);
TString name = "Universe_";
TString name2 = "_MultiSim_";
TString mul = Form("%d",s);// = std::to_string(s);
name += upoint;
name += name2;
name += mul;
OSC_600 = (TH1D*)(temp_file.Get(name));
for(int i = 1; i <= nbinsE; i++){
OscVec[counter][u][s][i-1] = (OSC_600->GetBinContent(i));
}
delete OSC_600;
}
}
counter++;
delete NULL_600;
temp_file.Close();
}
// int nL = 3;
int mbins = (nbinsE*nL);
TMatrix M6 (mbins,mbins);
TMatrix M5 (mbins,mbins);
TMatrix M4 (mbins,mbins);
TMatrix M3 (mbins,mbins);
TMatrix M2 (mbins,mbins);
TMatrix M1 (mbins,mbins);
TMatrix M0 (mbins,mbins);
TMatrix C6 (mbins,mbins);
TMatrix C5 (mbins,mbins);
TMatrix C4 (mbins,mbins);
TMatrix C3 (mbins,mbins);
TMatrix C2 (mbins,mbins);
TMatrix C1 (mbins,mbins);
TMatrix C0 (mbins,mbins);
int N = 0;
TH1D *Fig6 = new TH1D("Fig6",";;",mbins,0,mbins);
TH1D *Fig5 = new TH1D("Fig5",";;",mbins,0,mbins);
TH1D *Fig4 = new TH1D("Fig4",";;",mbins,0,mbins);
TH1D *Fig3 = new TH1D("Fig3",";;",mbins,0,mbins);
TH1D *Fig2 = new TH1D("Fig2",";;",mbins,0,mbins);
TH1D *Fig1 = new TH1D("Fig1",";;",mbins,0,mbins);
TH1D *Fig0 = new TH1D("Fig0",";;",mbins,0,mbins);
int Erri = 0, Errj = 0;
std::cout << "Filling Error Matrix..." << std::endl;
for(int Lrow = 0; Lrow < nL; Lrow++){
for(int Erow = 0; Erow < nbinsE; Erow++){
Errj = 0;
for(int Lcol = 0; Lcol < nL; Lcol++){
for(int Ecol = 0; Ecol < nbinsE; Ecol++){
M6 (Erri,Errj) = 0;
M5 (Erri,Errj) = 0;
M4 (Erri,Errj) = 0;
M3 (Erri,Errj) = 0;
M2 (Erri,Errj) = 0;
M1 (Erri,Errj) = 0;
M0 (Erri,Errj) = 0;
N = 0;
for(int u = 0; u < npoints; u++){
M6 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][6][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][6][Ecol]);
M5 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][5][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][5][Ecol]);
M4 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][4][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][4][Ecol]);
M3 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][3][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][3][Ecol]);
M2 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][2][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][2][Ecol]);
M1 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][1][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][1][Ecol]);
M0 (Erri,Errj) += (NULLVec[Lrow][Erow]-OscVec[Lrow][u][0][Erow])*(NULLVec[Lcol][Ecol]-OscVec[Lcol][u][0][Ecol]);
N++;
}
M6 (Erri,Errj) /= N;
M5 (Erri,Errj) /= N;
M4 (Erri,Errj) /= N;
M3 (Erri,Errj) /= N;
M2 (Erri,Errj) /= N;
M1 (Erri,Errj) /= N;
M0 (Erri,Errj) /= N;
M6 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M5 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M4 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M3 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M2 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M1 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
M0 (Erri,Errj) /= NULLVec[Lrow][Erow]*NULLVec[Lcol][Ecol];
if(Erri == Errj) Fig6->SetBinContent(Erri+1, sqrt(M6 (Erri,Errj)));
if(Erri == Errj) Fig5->SetBinContent(Erri+1, sqrt(M5 (Erri,Errj)));
if(Erri == Errj) Fig4->SetBinContent(Erri+1, sqrt(M4 (Erri,Errj)));
if(Erri == Errj) Fig3->SetBinContent(Erri+1, sqrt(M3 (Erri,Errj)));
if(Erri == Errj) Fig2->SetBinContent(Erri+1, sqrt(M2 (Erri,Errj)));
if(Erri == Errj) Fig1->SetBinContent(Erri+1, sqrt(M1 (Erri,Errj)));
if(Erri == Errj) Fig0->SetBinContent(Erri+1, sqrt(M0 (Erri,Errj)));
Errj++;
}}
Erri++;
}}
for(int i = 0; i < Erri; i++){
for(int j = 0; j < Errj; j++){
C6 (i,j) = M6(i,j) / sqrt(M6 (i,i) * M6 (j,j));
C5 (i,j) = M5(i,j) / sqrt(M5 (i,i) * M5 (j,j));
C4 (i,j) = M4(i,j) / sqrt(M4 (i,i) * M4 (j,j));
C3 (i,j) = M3(i,j) / sqrt(M3 (i,i) * M3 (j,j));
C2 (i,j) = M2(i,j) / sqrt(M2 (i,i) * M2 (j,j));
C1 (i,j) = M1(i,j) / sqrt(M1 (i,i) * M1 (j,j));
C0 (i,j) = M0(i,j) / sqrt(M0 (i,i) * M0 (j,j));
}
}
std::cout << "...Error Matrix Filled" << std::endl;
TCanvas* c6 = new TCanvas("c6","",700,700);
c6->SetLeftMargin(.1);
c6->SetBottomMargin(.1);
c6->SetTopMargin(.075);
c6->SetRightMargin(.15);
c6->cd();
M6.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
// TMatrixFBase->GetZaxis()->SetRangeUser(-0.05,0.4);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
// TMatrixFBase->GetZaxis()->SetTitle("Fractional Error Matrix");
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
add_plot_label(" 0.2 GeV #minus 3.0 GeV ", 0.48,0.07,0.04);
TLatex *MD = new TLatex(.3,.01,"MicroBooNE (470m)");
MD->SetNDC();
MD->SetTextFont(62);
MD->SetTextSize(0.04);
MD->Draw();
TLatex *MD45 = new TLatex(.05,.3,"MicroBooNE (470m)");
MD45->SetNDC();
MD45->SetTextAngle(90);
MD45->SetTextFont(62);
MD45->SetTextSize(0.04);
MD45->Draw();
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} Flux Fractional Error Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
c6->Print("total_1Det_matrix.pdf");
TCanvas* c61 = new TCanvas("c61","",700,700);
c61->SetLeftMargin(.1);
c61->SetBottomMargin(.1);
c61->SetTopMargin(.075);
c61->SetRightMargin(.15);
c61->cd();
C6.Draw("COLZ");
gStyle->SetPalette(56,0);
TMatrixFBase->SetContour(999);
TMatrixFBase->GetZaxis()->SetTitleFont(62);
TMatrixFBase->GetZaxis()->SetLabelFont(62);
TMatrixFBase->GetZaxis()->SetTitleSize(0.045);
TMatrixFBase->GetZaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetXaxis()->SetTitle("");
TMatrixFBase->GetXaxis()->SetLabelSize(0);
TMatrixFBase->GetXaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetTitle("");
TMatrixFBase->GetYaxis()->SetTitleOffset(1.5);
TMatrixFBase->GetYaxis()->SetLabelSize(0);
TMatrixFBase->SetStats(0);
add_plot_label(" 0.2 GeV #minus 3.0 GeV ", 0.48,0.07,0.04);
MD->Draw();
MD45->Draw();
TLatex *Total = new TLatex(.2,.96,"#nu#lower[0.3]{#mu} Flux Correlation Matrix");
Total->SetNDC();
Total->SetTextFont(62);
Total->SetTextSize(0.045);
Total->Draw();
c61->Print("total_1Det_correlation_matrix.pdf");
cout<<"\nEnd of routine.\n";
return 0;
}