void berendsen_pscale(t_inputrec *ir,matrix mu,
matrix box,matrix box_rel,
int start,int nr_atoms,
rvec x[],unsigned short cFREEZE[],
t_nrnb *nrnb)
{
ivec *nFreeze=ir->opts.nFreeze;
int n,d,g=0;
/* Scale the positions */
for (n=start; n<start+nr_atoms; n++) {
if (cFREEZE)
g = cFREEZE[n];
if (!nFreeze[g][XX])
x[n][XX] = mu[XX][XX]*x[n][XX]+mu[YY][XX]*x[n][YY]+mu[ZZ][XX]*x[n][ZZ];
if (!nFreeze[g][YY])
x[n][YY] = mu[YY][YY]*x[n][YY]+mu[ZZ][YY]*x[n][ZZ];
if (!nFreeze[g][ZZ])
x[n][ZZ] = mu[ZZ][ZZ]*x[n][ZZ];
}
/* compute final boxlengths */
for (d=0; d<DIM; d++) {
box[d][XX] = mu[XX][XX]*box[d][XX]+mu[YY][XX]*box[d][YY]+mu[ZZ][XX]*box[d][ZZ];
box[d][YY] = mu[YY][YY]*box[d][YY]+mu[ZZ][YY]*box[d][ZZ];
box[d][ZZ] = mu[ZZ][ZZ]*box[d][ZZ];
}
preserve_box_shape(ir,box_rel,box);
/* (un)shifting should NOT be done after this,
* since the box vectors might have changed
*/
inc_nrnb(nrnb,eNR_PCOUPL,nr_atoms);
}
static void cont_status(char *slog,char *ener,
bool bNeedVel,bool bGenVel, real fr_time,
t_inputrec *ir,t_state *state,
gmx_mtop_t *sys)
/* If fr_time == -1 read the last frame available which is complete */
{
t_trxframe fr;
int fp;
fprintf(stderr,
"Reading Coordinates%s and Box size from old trajectory\n",
(!bNeedVel || bGenVel) ? "" : ", Velocities");
if (fr_time == -1)
fprintf(stderr,"Will read whole trajectory\n");
else
fprintf(stderr,"Will read till time %g\n",fr_time);
if (!bNeedVel || bGenVel) {
if (bGenVel)
fprintf(stderr,"Velocities generated: "
"ignoring velocities in input trajectory\n");
read_first_frame(&fp,slog,&fr,TRX_NEED_X);
} else
read_first_frame(&fp,slog,&fr,TRX_NEED_X | TRX_NEED_V);
state->natoms = fr.natoms;
if (sys->natoms != state->natoms)
gmx_fatal(FARGS,"Number of atoms in Topology "
"is not the same as in Trajectory");
/* Find the appropriate frame */
while ((fr_time == -1 || fr.time < fr_time) && read_next_frame(fp,&fr));
close_trj(fp);
if (fr.not_ok & FRAME_NOT_OK)
gmx_fatal(FARGS,"Can not start from an incomplete frame");
state->x = fr.x;
if (bNeedVel && !bGenVel)
state->v = fr.v;
copy_mat(fr.box,state->box);
/* Set the relative box lengths for preserving the box shape.
* Note that this call can lead to differences in the last bit
* with respect to using tpbconv to create a tpx file.
*/
set_box_rel(ir,state);
fprintf(stderr,"Using frame at t = %g ps\n",fr.time);
fprintf(stderr,"Starting time for run is %g ps\n",ir->init_t);
if ((ir->epc != epcNO || ir->etc ==etcNOSEHOOVER) && ener) {
get_enx_state(ener,fr.time,&sys->groups,ir,state);
preserve_box_shape(ir,state->box_rel,state->boxv);
}
}
void mc_pscale(t_inputrec *ir,matrix mu,
matrix box,matrix box_rel,
int start,int nr_atoms,
rvec x[],unsigned short cFREEZE[],
t_nrnb *nrnb,t_block *mols,rvec *xcm,t_graph *graph)
{
ivec *nFreeze=ir->opts.nFreeze;
int n,m,d,g=0,natoms;
real dv;
rvec dxcm,dx,*xs;
snew(xs,nr_atoms);
for(n=start;n<nr_atoms;n++)
{
copy_rvec(x[n],xs[n]);
}
shift_self(graph,box,xs);
for (d=0; d<DIM; d++) {
box[d][XX] = mu[XX][XX]*box[d][XX]+mu[YY][XX]*box[d][YY]+mu[ZZ][XX]*box[d][ZZ];
box[d][YY] = mu[YY][YY]*box[d][YY]+mu[ZZ][YY]*box[d][ZZ];
box[d][ZZ] = mu[ZZ][ZZ]*box[d][ZZ];
}
preserve_box_shape(ir,box_rel,box);
/* Scale the positions */
shift_self(graph,box,x);
for (n=0; n<mols->nr; n++) {
clear_rvec(dxcm);
natoms = mols->index[n+1]-mols->index[n];
dxcm[XX] = mu[XX][XX]*xcm[n][XX]+mu[YY][XX]*xcm[n][YY]+mu[ZZ][XX]*xcm[n][ZZ];
dxcm[YY] = mu[YY][YY]*xcm[n][YY]+mu[ZZ][YY]*xcm[n][ZZ];
dxcm[ZZ] = mu[ZZ][ZZ]*xcm[n][ZZ];
for(m=mols->index[n];m<mols->index[n+1];m++) {
//rvec_sub(x[m],xcm[n],dx);
rvec_sub(dxcm,xcm[n],dx);
rvec_add(xs[m],dx,x[m]);
}
}
unshift_self(graph,box,x);
/*for (n=start; n<start+nr_atoms; n++) {
x[n][XX] = mu[XX][XX]*x[n][XX]+mu[YY][XX]*x[n][YY]+mu[ZZ][XX]*x[n][ZZ];
x[n][YY] = mu[YY][YY]*x[n][YY]+mu[ZZ][YY]*x[n][ZZ];
x[n][ZZ] = mu[ZZ][ZZ]*x[n][ZZ];
}*/
/* (un)shifting should NOT be done after this,
* since the box vectors might have changed
*/
inc_nrnb(nrnb,eNR_PCOUPL,nr_atoms);
sfree(xs);
}
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);
}
