void SingleStar::read_from_file(const char* str, int* i1, int* i2) {
if (MPI_rank() == 0) {
printf("Reading checkpoint file\n");
}
PhysicalConstants::set_cgs();
char* fname;
Real omega;
FILE* fp;
_3Vec O;
asprintf(&fname, "checkpoint.%s.%i.bin", str, MPI_rank());
fp = fopen(fname, "rb");
if (fp == NULL) {
printf("Error - Checkpoint file not found!");
abort();
}
free(fname);
// fread(&refine_floor, sizeof(Real), 1, fp);
fread(&State::ei_floor, sizeof(Real), 1, fp);
fread(&State::rho_floor, sizeof(Real), 1, fp);
// fread(&com_vel_correction, sizeof(_3Vec), 1, fp);
fread(&O, sizeof(_3Vec), 1, fp);
fread(&omega, sizeof(Real), 1, fp);
// set_origin(O);
fread(&last_dt, sizeof(Real), 1, fp);
fread(i1, sizeof(int), 1, fp);
fread(i2, sizeof(int), 1, fp);
get_root()->read_checkpoint(fp);
fclose(fp);
State::set_omega(omega);
int count = OctNode::get_local_node_cnt();
for (int i = 0; i < count; i++) {
dynamic_cast<MultiGrid*>(OctNode::get_local_node(i))->phi_calc_amr_bounds();
}
#ifdef USE_FMM
FMM_solve();
#else
solve_poisson();
#endif
}
real do_optimize_poisson(FILE *log, bool bVerbose,
t_inputrec *ir, int natoms,
rvec x[], rvec f[],
real charge[], rvec box,
real phi[], t_commrec *cr,
t_nrnb *nrnb, rvec f_ref[],
real phi_ref[], rvec beta,
bool bOld)
{
#define BMIN 1.6
#define DB 0.025
#define NB (1+(int)((2.1-BMIN)/DB))
static bool bFirst = TRUE;
static bool bSecond = TRUE;
static t_PSgrid *pot,*rho;
static int maxnit;
static real r1,rc;
real rmsf[NB][NB][NB],rmsf_min,rrmsf;
ivec minimum;
const real tol = 1e-2;
int i,m,bx,by,bz;
char buf[128];
real ener;
ener = 0.0;
if (bFirst) {
maxnit = ir->userint1;
fprintf(log,"Will use Poisson Solver for long-range electrostatics\n");
fprintf(log,"Grid size is %d x %d x %d\n",ir->nkx,ir->nky,ir->nkz);
if ((ir->nkx < 4) || (ir->nky < 4) || (ir->nkz < 4))
fatal_error(0,"Grid must be at least 4 points in all directions");
pot = mk_PSgrid(ir->nkx,ir->nky,ir->nkz);
rho = mk_PSgrid(ir->nkx,ir->nky,ir->nkz);
r1 = ir->rcoulomb_switch;
rc = ir->rcoulomb;
for(m=0; (m<DIM); m++)
beta[m] = 4.0/3.0;
bFirst = FALSE;
}
/* Make the grid empty */
clear_PSgrid(rho);
spread_q_poisson(log,bVerbose,TRUE,natoms,x,charge,box,rc,rho,nrnb,
bOld,r1);
symmetrize_PSgrid(log,rho,0.0);
if (bSecond)
copy_PSgrid(pot,rho);
/* Second step: solving the poisson equation in real space */
(void) solve_poisson(log,pot,rho,bVerbose,nrnb,maxnit,tol,box);
symmetrize_PSgrid(log,pot,0.0);
/* Third and last step: gather the forces, energies and potential
* from the grid.
*/
#define BETA(n) (BMIN+n*DB)
/* Optimization of beta in progress */
for(bx=0; (bx<NB); bx++) {
beta[XX] = BETA(bx);
for(by=0; (by<NB); by++) {
beta[YY] = BETA(by);
for(bz=0; (bz<NB); bz++) {
beta[ZZ] = BETA(bz);
for(i=0; (i<natoms); i++) {
phi[i] = 0.0;
clear_rvec(f[i]);
}
ener = ps_gather_f(log,bVerbose,natoms,x,f,charge,box,
phi,pot,beta,nrnb);
sprintf(buf,"Poisson, beta = %g\n",beta[XX]);
rmsf[bx][by][bz] =
analyse_diff(log,buf,natoms,f_ref,f,phi_ref,phi,NULL,
/*"fcorr.xvg","pcorr.xvg"*/NULL,NULL,NULL,NULL);
}
}
}
rmsf_min = rmsf[0][0][0];
minimum[XX] = minimum[YY] = minimum[ZZ] = 0;
for(bx=0; (bx<NB); bx++) {
beta[XX] = BETA(bx);
for(by=0; (by<NB); by++) {
beta[YY] = BETA(by);
for(bz=0; (bz<NB); bz++) {
beta[ZZ] = BETA(bz);
rrmsf = rmsf[bx][by][bz];
fprintf(log,"Beta: %6.3f %6.3f %6.3f RMSF: %8.3f\n",
beta[XX],beta[YY],beta[ZZ],rrmsf);
if (rrmsf < rmsf_min) {
rmsf_min = rrmsf;
minimum[XX] = bx;
minimum[YY] = by;
minimum[ZZ] = bz;
}
}
}
}
beta[XX] = BETA(minimum[XX]);
beta[YY] = BETA(minimum[YY]);
beta[ZZ] = BETA(minimum[ZZ]);
fprintf(log,"Minimum RMSF %8.3f at Beta = %6.3f %6.3f %6.3f\n",
rmsf_min,beta[XX],beta[YY],beta[ZZ]);
/* Computing optimum once more... */
for(i=0; (i<natoms); i++) {
phi[i] = 0.0;
clear_rvec(f[i]);
}
ener = ps_gather_f(log,bVerbose,natoms,x,f,charge,box,phi,pot,beta,nrnb);
return ener;
}
real do_poisson(FILE *log, bool bVerbose,
t_inputrec *ir, int natoms,
rvec x[], rvec f[],
real charge[], rvec box,
real phi[], t_commrec *cr,
t_nrnb *nrnb, int *nit,
bool bOld)
{
static bool bFirst = TRUE;
static t_PSgrid *pot,*rho;
static int maxnit;
static real r1,rc;
static rvec beta;
const real tol = 1e-2;
int m;
real ener;
ener = 0.0;
if (bFirst) {
maxnit = ir->userint1;
fprintf(log,"Will use Poisson Solver for long-range electrostatics\n");
fprintf(log,"Grid size is %d x %d x %d\n",ir->nkx,ir->nky,ir->nkz);
if ((ir->nkx < 4) || (ir->nky < 4) || (ir->nkz < 4))
fatal_error(0,"Grid must be at least 4 points in all directions");
pot = mk_PSgrid(ir->nkx,ir->nky,ir->nkz);
rho = mk_PSgrid(ir->nkx,ir->nky,ir->nkz);
r1 = ir->rcoulomb_switch;
rc = ir->rcoulomb;
for(m=0; (m<DIM); m++)
beta[m] = 1.85;
}
/* Make the grid empty and spread the charges */
clear_PSgrid(rho);
spread_q_poisson(log,bVerbose,TRUE,natoms,x,charge,box,rc,rho,nrnb,bOld,r1);
/* Subtract average charge distribution from each grid point. This does not
* influence the forces, but it may influence the potential and the energy.
* On the other hand the charge distribution should sum up to zero if the
* system is neutral!
*/
symmetrize_PSgrid(debug,rho,0.0);
/* For the first time we solve the potential we copy the charge distribution to
* the potential as a start for the solver. Later we use the previous step's
* solution.
*/
if (bFirst)
copy_PSgrid(pot,rho);
/* Second step: solving the poisson equation in real space */
*nit = solve_poisson(log,pot,rho,bVerbose,nrnb,maxnit,tol,box);
symmetrize_PSgrid(debug,pot,0.0);
/* Third and last step: gather the forces, energies and potential
* from the grid.
*/
ener = ps_gather_f(log,bVerbose,natoms,x,f,charge,box,phi,pot,beta,nrnb);
bFirst = FALSE;
return ener;
}