void print_orires_log(FILE *log,t_fcdata *fcd)
{
int ex,i,j,nrot;
bool bZero;
matrix S,TMP;
t_oriresdata *od;
static double **M=NULL,*eig,**v;
od = &(fcd->orires);
if (M == NULL) {
snew(M,DIM);
for(i=0; i<DIM; i++)
snew(M[i],DIM);
snew(eig,DIM);
snew(v,DIM);
for(i=0; i<DIM; i++)
snew(v[i],DIM);
}
for(ex=0; ex<od->nex; ex++) {
/* Rotate the S tensor back to the reference frame */
mmul(od->R,od->S[ex],TMP);
mtmul(TMP,od->R,S);
for(i=0; i<DIM; i++)
for(j=0; j<DIM; j++)
M[i][j] = S[i][j];
jacobi(M,DIM,eig,v,&nrot);
j=0;
for(i=1; i<DIM; i++)
if (sqr(eig[i]) > sqr(eig[j]))
j=i;
fprintf(log," Orientation experiment %d:\n",ex+1);
fprintf(log," order parameter: %g\n",eig[j]);
for(i=0; i<DIM; i++)
fprintf(log," eig: %6.3f %6.3f %6.3f %6.3f\n",
(fabs(eig[j])>GMX_REAL_MIN) ? eig[i]/eig[j] : 0,v[XX][i],v[YY][i],v[ZZ][i]);
fprintf(log,"\n");
}
}
void diagonalize_orires_tensors(t_oriresdata *od)
{
int ex,i,j,nrot,ord[DIM],t;
matrix S,TMP;
static double **M=NULL,*eig,**v;
if (M == NULL)
{
snew(M,DIM);
for(i=0; i<DIM; i++)
{
snew(M[i],DIM);
}
snew(eig,DIM);
snew(v,DIM);
for(i=0; i<DIM; i++)
{
snew(v[i],DIM);
}
}
for(ex=0; ex<od->nex; ex++)
{
/* Rotate the S tensor back to the reference frame */
mmul(od->R,od->S[ex],TMP);
mtmul(TMP,od->R,S);
for(i=0; i<DIM; i++)
{
for(j=0; j<DIM; j++)
{
M[i][j] = S[i][j];
}
}
jacobi(M,DIM,eig,v,&nrot);
for(i=0; i<DIM; i++)
{
ord[i] = i;
}
for(i=0; i<DIM; i++)
{
for(j=i+1; j<DIM; j++)
{
if (sqr(eig[ord[j]]) > sqr(eig[ord[i]]))
{
t = ord[i];
ord[i] = ord[j];
ord[j] = t;
}
}
}
for(i=0; i<DIM; i++)
{
od->eig[ex*12 + i] = eig[ord[i]];
}
for(i=0; i<DIM; i++)
{
for(j=0; j<DIM; j++)
{
od->eig[ex*12 + 3 + 3*i + j] = v[j][ord[i]];
}
}
}
}
void parrinellorahman_pcoupl(FILE *fplog,gmx_step_t step,
t_inputrec *ir,real dt,tensor pres,
tensor box,tensor box_rel,tensor boxv,
tensor M,matrix mu,bool bFirstStep)
{
/* This doesn't do any coordinate updating. It just
* integrates the box vector equations from the calculated
* acceleration due to pressure difference. We also compute
* the tensor M which is used in update to couple the particle
* coordinates to the box vectors.
*
* In Nose and Klein (Mol.Phys 50 (1983) no 5., p 1055) this is
* given as
* -1 . . -1
* M_nk = (h') * (h' * h + h' h) * h
*
* with the dots denoting time derivatives and h is the transformation from
* the scaled frame to the real frame, i.e. the TRANSPOSE of the box.
* This also goes for the pressure and M tensors - they are transposed relative
* to ours. Our equation thus becomes:
*
* -1 . . -1
* M_gmx = M_nk' = b * (b * b' + b * b') * b'
*
* where b is the gromacs box matrix.
* Our box accelerations are given by
* .. ..
* b = vol/W inv(box') * (P-ref_P) (=h')
*/
int d,n;
tensor winv;
real vol=box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
real atot,arel,change,maxchange,xy_pressure;
tensor invbox,pdiff,t1,t2;
real maxl;
m_inv_ur0(box,invbox);
if (!bFirstStep) {
/* Note that PRESFAC does not occur here.
* The pressure and compressibility always occur as a product,
* therefore the pressure unit drops out.
*/
maxl=max(box[XX][XX],box[YY][YY]);
maxl=max(maxl,box[ZZ][ZZ]);
for(d=0;d<DIM;d++)
for(n=0;n<DIM;n++)
winv[d][n]=
(4*M_PI*M_PI*ir->compress[d][n])/(3*ir->tau_p*ir->tau_p*maxl);
m_sub(pres,ir->ref_p,pdiff);
if(ir->epct==epctSURFACETENSION) {
/* Unlike Berendsen coupling it might not be trivial to include a z
* pressure correction here? On the other hand we don't scale the
* box momentarily, but change accelerations, so it might not be crucial.
*/
xy_pressure=0.5*(pres[XX][XX]+pres[YY][YY]);
for(d=0;d<ZZ;d++)
pdiff[d][d]=(xy_pressure-(pres[ZZ][ZZ]-ir->ref_p[d][d]/box[d][d]));
}
tmmul(invbox,pdiff,t1);
/* Move the off-diagonal elements of the 'force' to one side to ensure
* that we obey the box constraints.
*/
for(d=0;d<DIM;d++) {
for(n=0;n<d;n++) {
t1[d][n] += t1[n][d];
t1[n][d] = 0;
}
}
switch (ir->epct) {
case epctANISOTROPIC:
for(d=0;d<DIM;d++)
for(n=0;n<=d;n++)
t1[d][n] *= winv[d][n]*vol;
break;
case epctISOTROPIC:
/* calculate total volume acceleration */
atot=box[XX][XX]*box[YY][YY]*t1[ZZ][ZZ]+
box[XX][XX]*t1[YY][YY]*box[ZZ][ZZ]+
t1[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
arel=atot/(3*vol);
/* set all RELATIVE box accelerations equal, and maintain total V
* change speed */
for(d=0;d<DIM;d++)
for(n=0;n<=d;n++)
t1[d][n] = winv[0][0]*vol*arel*box[d][n];
break;
case epctSEMIISOTROPIC:
case epctSURFACETENSION:
/* Note the correction to pdiff above for surftens. coupling */
/* calculate total XY volume acceleration */
atot=box[XX][XX]*t1[YY][YY]+t1[XX][XX]*box[YY][YY];
arel=atot/(2*box[XX][XX]*box[YY][YY]);
/* set RELATIVE XY box accelerations equal, and maintain total V
* change speed. Dont change the third box vector accelerations */
for(d=0;d<ZZ;d++)
for(n=0;n<=d;n++)
t1[d][n] = winv[d][n]*vol*arel*box[d][n];
for(n=0;n<DIM;n++)
t1[ZZ][n] *= winv[d][n]*vol;
break;
default:
gmx_fatal(FARGS,"Parrinello-Rahman pressure coupling type %s "
"not supported yet\n",EPCOUPLTYPETYPE(ir->epct));
break;
}
maxchange=0;
for(d=0;d<DIM;d++)
for(n=0;n<=d;n++) {
boxv[d][n] += dt*t1[d][n];
/* We do NOT update the box vectors themselves here, since
* we need them for shifting later. It is instead done last
* in the update() routine.
*/
/* Calculate the change relative to diagonal elements -
* since it's perfectly ok for the off-diagonal ones to
* be zero it doesn't make sense to check the change relative
* to its current size.
*/
change=fabs(dt*boxv[d][n]/box[d][d]);
if(change>maxchange)
maxchange=change;
}
if (maxchange > 0.01 && fplog) {
char buf[22];
fprintf(fplog,"\nStep %s Warning: Pressure scaling more than 1%%.\n",
gmx_step_str(step,buf));
}
}
preserve_box_shape(ir,box_rel,boxv);
mtmul(boxv,box,t1); /* t1=boxv * b' */
mmul(invbox,t1,t2);
mtmul(t2,invbox,M);
/* Determine the scaling matrix mu for the coordinates */
for(d=0;d<DIM;d++)
for(n=0;n<=d;n++)
t1[d][n] = box[d][n] + dt*boxv[d][n];
preserve_box_shape(ir,box_rel,t1);
/* t1 is the box at t+dt, determine mu as the relative change */
mmul_ur0(invbox,t1,mu);
}
void diagonalize_orires_tensors(t_oriresdata *od)
{
int ex, i, j, nrot, ord[DIM], t;
matrix S, TMP;
if (od->M == NULL)
{
snew(od->M, DIM);
for (i = 0; i < DIM; i++)
{
snew(od->M[i], DIM);
}
snew(od->eig_diag, DIM);
snew(od->v, DIM);
for (i = 0; i < DIM; i++)
{
snew(od->v[i], DIM);
}
}
for (ex = 0; ex < od->nex; ex++)
{
/* Rotate the S tensor back to the reference frame */
mmul(od->R, od->S[ex], TMP);
mtmul(TMP, od->R, S);
for (i = 0; i < DIM; i++)
{
for (j = 0; j < DIM; j++)
{
od->M[i][j] = S[i][j];
}
}
jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);
for (i = 0; i < DIM; i++)
{
ord[i] = i;
}
for (i = 0; i < DIM; i++)
{
for (j = i+1; j < DIM; j++)
{
if (gmx::square(od->eig_diag[ord[j]]) > gmx::square(od->eig_diag[ord[i]]))
{
t = ord[i];
ord[i] = ord[j];
ord[j] = t;
}
}
}
for (i = 0; i < DIM; i++)
{
od->eig[ex*12 + i] = od->eig_diag[ord[i]];
}
for (i = 0; i < DIM; i++)
{
for (j = 0; j < DIM; j++)
{
od->eig[ex*12 + 3 + 3*i + j] = od->v[j][ord[i]];
}
}
}
}
