gmx_stochd_t init_stochd(FILE *fplog,t_inputrec *ir)
{
t_gmx_stochd *sd;
gmx_sd_const_t *sdc;
int ngtc,n;
real y;
snew(sd,1);
/* Initiate random number generator for langevin type dynamics,
* for BD, SD or velocity rescaling temperature coupling.
*/
sd->gaussrand = gmx_rng_init(ir->ld_seed);
ngtc = ir->opts.ngtc;
if (ir->eI == eiBD) {
snew(sd->bd_rf,ngtc);
} else if (EI_SD(ir->eI)) {
snew(sd->sdc,ngtc);
snew(sd->sdsig,ngtc);
sdc = sd->sdc;
for(n=0; n<ngtc; n++) {
sdc[n].gdt = ir->delta_t/ir->opts.tau_t[n];
sdc[n].eph = exp(sdc[n].gdt/2);
sdc[n].emh = exp(-sdc[n].gdt/2);
sdc[n].em = exp(-sdc[n].gdt);
if (sdc[n].gdt >= 0.05) {
sdc[n].b = sdc[n].gdt*(sdc[n].eph*sdc[n].eph - 1)
- 4*(sdc[n].eph - 1)*(sdc[n].eph - 1);
sdc[n].c = sdc[n].gdt - 3 + 4*sdc[n].emh - sdc[n].em;
sdc[n].d = 2 - sdc[n].eph - sdc[n].emh;
} else {
y = sdc[n].gdt/2;
/* Seventh order expansions for small y */
sdc[n].b = y*y*y*y*(1/3.0+y*(1/3.0+y*(17/90.0+y*7/9.0)));
sdc[n].c = y*y*y*(2/3.0+y*(-1/2.0+y*(7/30.0+y*(-1/12.0+y*31/1260.0))));
sdc[n].d = y*y*(-1+y*y*(-1/12.0-y*y/360.0));
}
if(debug)
fprintf(debug,"SD const tc-grp %d: b %g c %g d %g\n",
n,sdc[n].b,sdc[n].c,sdc[n].d);
}
}
return sd;
}
void init_parallel(FILE *log,char *tpxfile,t_commrec *cr,
t_inputrec *inputrec,gmx_mtop_t *mtop,
t_state *state,
int list)
{
int step;
real t;
char buf[256];
if (MASTER(cr)) {
init_inputrec(inputrec);
read_tpx_state(tpxfile,&step,&t,inputrec,state,NULL,mtop);
/* When we will be doing domain decomposition with separate PME nodes
* the rng entries will be too large, we correct for this later.
*/
set_state_entries(state,inputrec,cr->nnodes);
}
bcast_ir_mtop(cr,inputrec,mtop);
if (inputrec->eI == eiBD || EI_SD(inputrec->eI)) {
/* Make sure the random seeds are different on each node */
inputrec->ld_seed += cr->nodeid;
}
/* Printing */
if (list!=0 && log!=NULL)
{
if (list&LIST_INPUTREC)
pr_inputrec(log,0,"parameters of the run",inputrec,FALSE);
if (list&LIST_X)
pr_rvecs(log,0,"box",state->box,DIM);
if (list&LIST_X)
pr_rvecs(log,0,"box_rel",state->box_rel,DIM);
if (list&LIST_V)
pr_rvecs(log,0,"boxv",state->boxv,DIM);
if (list&LIST_X)
pr_rvecs(log,0,int_title("x",0,buf,255),state->x,state->natoms);
if (list&LIST_V)
pr_rvecs(log,0,int_title("v",0,buf,255),state->v,state->natoms);
if (list&LIST_TOP)
pr_mtop(log,0,int_title("topology",cr->nodeid,buf,255),mtop,TRUE);
fflush(log);
}
}
int cmain (int argc, char *argv[])
{
const char *desc[] = {
"tpbconv can edit run input files in four ways.[PAR]",
"[BB]1.[bb] by modifying the number of steps in a run input file",
"with options [TT]-extend[tt], [TT]-until[tt] or [TT]-nsteps[tt]",
"(nsteps=-1 means unlimited number of steps)[PAR]",
"[BB]2.[bb] (OBSOLETE) by creating a run input file",
"for a continuation run when your simulation has crashed due to e.g.",
"a full disk, or by making a continuation run input file.",
"This option is obsolete, since mdrun now writes and reads",
"checkpoint files.",
"[BB]Note[bb] that a frame with coordinates and velocities is needed.",
"When pressure and/or Nose-Hoover temperature coupling is used",
"an energy file can be supplied to get an exact continuation",
"of the original run.[PAR]",
"[BB]3.[bb] by creating a [TT].tpx[tt] file for a subset of your original",
"tpx file, which is useful when you want to remove the solvent from",
"your [TT].tpx[tt] file, or when you want to make e.g. a pure C[GRK]alpha[grk] [TT].tpx[tt] file.",
"Note that you may need to use [TT]-nsteps -1[tt] (or similar) to get",
"this to work.",
"[BB]WARNING: this [TT].tpx[tt] file is not fully functional[bb].[PAR]",
"[BB]4.[bb] by setting the charges of a specified group",
"to zero. This is useful when doing free energy estimates",
"using the LIE (Linear Interaction Energy) method."
};
const char *top_fn, *frame_fn;
t_fileio *fp;
ener_file_t fp_ener = NULL;
t_trnheader head;
int i;
gmx_large_int_t nsteps_req, run_step, frame;
double run_t, state_t;
gmx_bool bOK, bNsteps, bExtend, bUntil, bTime, bTraj;
gmx_bool bFrame, bUse, bSel, bNeedEner, bReadEner, bScanEner, bFepState;
gmx_mtop_t mtop;
t_atoms atoms;
t_inputrec *ir, *irnew = NULL;
t_gromppopts *gopts;
t_state state;
rvec *newx = NULL, *newv = NULL, *tmpx, *tmpv;
matrix newbox;
int gnx;
char *grpname;
atom_id *index = NULL;
int nre;
gmx_enxnm_t *enm = NULL;
t_enxframe *fr_ener = NULL;
char buf[200], buf2[200];
output_env_t oenv;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-f", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efTPX, "-o", "tpxout", ffWRITE }
};
#define NFILE asize(fnm)
/* Command line options */
static int nsteps_req_int = 0;
static real start_t = -1.0, extend_t = 0.0, until_t = 0.0;
static int init_fep_state = 0;
static gmx_bool bContinuation = TRUE, bZeroQ = FALSE, bVel = TRUE;
static t_pargs pa[] = {
{ "-extend", FALSE, etREAL, {&extend_t},
"Extend runtime by this amount (ps)" },
{ "-until", FALSE, etREAL, {&until_t},
"Extend runtime until this ending time (ps)" },
{ "-nsteps", FALSE, etINT, {&nsteps_req_int},
"Change the number of steps" },
{ "-time", FALSE, etREAL, {&start_t},
"Continue from frame at this time (ps) instead of the last frame" },
{ "-zeroq", FALSE, etBOOL, {&bZeroQ},
"Set the charges of a group (from the index) to zero" },
{ "-vel", FALSE, etBOOL, {&bVel},
"Require velocities from trajectory" },
{ "-cont", FALSE, etBOOL, {&bContinuation},
"For exact continuation, the constraints should not be applied before the first step" },
{ "-init_fep_state", FALSE, etINT, {&init_fep_state},
"fep state to initialize from" },
};
int nerror = 0;
CopyRight(stderr, argv[0]);
/* Parse the command line */
parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv);
/* Convert int to gmx_large_int_t */
nsteps_req = nsteps_req_int;
bNsteps = opt2parg_bSet("-nsteps", asize(pa), pa);
bExtend = opt2parg_bSet("-extend", asize(pa), pa);
bUntil = opt2parg_bSet("-until", asize(pa), pa);
bFepState = opt2parg_bSet("-init_fep_state", asize(pa), pa);
bTime = opt2parg_bSet("-time", asize(pa), pa);
bTraj = (opt2bSet("-f", NFILE, fnm) || bTime);
top_fn = ftp2fn(efTPX, NFILE, fnm);
fprintf(stderr, "Reading toplogy and stuff from %s\n", top_fn);
snew(ir, 1);
read_tpx_state(top_fn, ir, &state, NULL, &mtop);
run_step = ir->init_step;
run_t = ir->init_step*ir->delta_t + ir->init_t;
if (!EI_STATE_VELOCITY(ir->eI))
{
bVel = FALSE;
}
if (bTraj)
{
fprintf(stderr, "\n"
"NOTE: Reading the state from trajectory is an obsolete feature of tpbconv.\n"
" Continuation should be done by loading a checkpoint file with mdrun -cpi\n"
" This guarantees that all state variables are transferred.\n"
" tpbconv is now only useful for increasing nsteps,\n"
" but even that can often be avoided by using mdrun -maxh\n"
"\n");
if (ir->bContinuation != bContinuation)
{
fprintf(stderr, "Modifying ir->bContinuation to %s\n",
bool_names[bContinuation]);
}
ir->bContinuation = bContinuation;
bNeedEner = (ir->epc == epcPARRINELLORAHMAN || ir->etc == etcNOSEHOOVER);
bReadEner = (bNeedEner && ftp2bSet(efEDR, NFILE, fnm));
bScanEner = (bReadEner && !bTime);
if (ir->epc != epcNO || EI_SD(ir->eI) || ir->eI == eiBD)
{
fprintf(stderr, "NOTE: The simulation uses pressure coupling and/or stochastic dynamics.\n"
"tpbconv can not provide binary identical continuation.\n"
"If you want that, supply a checkpoint file to mdrun\n\n");
}
if (EI_SD(ir->eI) || ir->eI == eiBD)
{
fprintf(stderr, "\nChanging ld-seed from %d ", ir->ld_seed);
ir->ld_seed = make_seed();
fprintf(stderr, "to %d\n\n", ir->ld_seed);
}
frame_fn = ftp2fn(efTRN, NFILE, fnm);
if (fn2ftp(frame_fn) == efCPT)
{
int sim_part;
fprintf(stderr,
"\nREADING STATE FROM CHECKPOINT %s...\n\n",
frame_fn);
read_checkpoint_state(frame_fn, &sim_part,
&run_step, &run_t, &state);
}
else
{
fprintf(stderr,
"\nREADING COORDS, VELS AND BOX FROM TRAJECTORY %s...\n\n",
frame_fn);
fp = open_trn(frame_fn, "r");
if (bScanEner)
{
fp_ener = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
do_enxnms(fp_ener, &nre, &enm);
snew(fr_ener, 1);
fr_ener->t = -1e-12;
}
/* Now scan until the last set of x and v (step == 0)
* or the ones at step step.
*/
bFrame = TRUE;
frame = 0;
while (bFrame)
{
bFrame = fread_trnheader(fp, &head, &bOK);
if (bOK && frame == 0)
{
if (mtop.natoms != head.natoms)
{
gmx_fatal(FARGS, "Number of atoms in Topology (%d) "
"is not the same as in Trajectory (%d)\n",
mtop.natoms, head.natoms);
}
snew(newx, head.natoms);
snew(newv, head.natoms);
}
bFrame = bFrame && bOK;
if (bFrame)
{
bOK = fread_htrn(fp, &head, newbox, newx, newv, NULL);
}
bFrame = bFrame && bOK;
bUse = FALSE;
if (bFrame &&
(head.x_size) && (head.v_size || !bVel))
{
bUse = TRUE;
if (bScanEner)
{
/* Read until the energy time is >= the trajectory time */
while (fr_ener->t < head.t && do_enx(fp_ener, fr_ener))
{
;
}
bUse = (fr_ener->t == head.t);
}
if (bUse)
{
tmpx = newx;
newx = state.x;
state.x = tmpx;
tmpv = newv;
newv = state.v;
state.v = tmpv;
run_t = head.t;
run_step = head.step;
state.fep_state = head.fep_state;
state.lambda[efptFEP] = head.lambda;
copy_mat(newbox, state.box);
}
}
if (bFrame || !bOK)
{
sprintf(buf, "\r%s %s frame %s%s: step %s%s time %s",
"%s", "%s", "%6", gmx_large_int_fmt, "%6", gmx_large_int_fmt, " %8.3f");
fprintf(stderr, buf,
bUse ? "Read " : "Skipped", ftp2ext(fn2ftp(frame_fn)),
frame, head.step, head.t);
frame++;
if (bTime && (head.t >= start_t))
{
bFrame = FALSE;
}
}
}
if (bScanEner)
{
close_enx(fp_ener);
free_enxframe(fr_ener);
free_enxnms(nre, enm);
}
close_trn(fp);
fprintf(stderr, "\n");
if (!bOK)
{
fprintf(stderr, "%s frame %s (step %s, time %g) is incomplete\n",
ftp2ext(fn2ftp(frame_fn)), gmx_step_str(frame-1, buf2),
gmx_step_str(head.step, buf), head.t);
}
fprintf(stderr, "\nUsing frame of step %s time %g\n",
gmx_step_str(run_step, buf), run_t);
if (bNeedEner)
{
if (bReadEner)
{
get_enx_state(ftp2fn(efEDR, NFILE, fnm), run_t, &mtop.groups, ir, &state);
}
else
{
fprintf(stderr, "\nWARNING: The simulation uses %s temperature and/or %s pressure coupling,\n"
" the continuation will only be exact when an energy file is supplied\n\n",
ETCOUPLTYPE(etcNOSEHOOVER),
EPCOUPLTYPE(epcPARRINELLORAHMAN));
}
}
if (bFepState)
{
ir->fepvals->init_fep_state = init_fep_state;
}
}
}
if (bNsteps)
{
fprintf(stderr, "Setting nsteps to %s\n", gmx_step_str(nsteps_req, buf));
ir->nsteps = nsteps_req;
}
else
{
/* Determine total number of steps remaining */
if (bExtend)
{
ir->nsteps = ir->nsteps - (run_step - ir->init_step) + (gmx_large_int_t)(extend_t/ir->delta_t + 0.5);
printf("Extending remaining runtime of by %g ps (now %s steps)\n",
extend_t, gmx_step_str(ir->nsteps, buf));
}
else if (bUntil)
{
printf("nsteps = %s, run_step = %s, current_t = %g, until = %g\n",
gmx_step_str(ir->nsteps, buf),
gmx_step_str(run_step, buf2),
run_t, until_t);
ir->nsteps = (gmx_large_int_t)((until_t - run_t)/ir->delta_t + 0.5);
printf("Extending remaining runtime until %g ps (now %s steps)\n",
until_t, gmx_step_str(ir->nsteps, buf));
}
else
{
ir->nsteps -= run_step - ir->init_step;
/* Print message */
printf("%s steps (%g ps) remaining from first run.\n",
gmx_step_str(ir->nsteps, buf), ir->nsteps*ir->delta_t);
}
}
if (bNsteps || bZeroQ || (ir->nsteps > 0))
{
ir->init_step = run_step;
if (ftp2bSet(efNDX, NFILE, fnm) ||
!(bNsteps || bExtend || bUntil || bTraj))
{
atoms = gmx_mtop_global_atoms(&mtop);
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1,
&gnx, &index, &grpname);
if (!bZeroQ)
{
bSel = (gnx != state.natoms);
for (i = 0; ((i < gnx) && (!bSel)); i++)
{
bSel = (i != index[i]);
}
}
else
{
bSel = FALSE;
}
if (bSel)
{
fprintf(stderr, "Will write subset %s of original tpx containing %d "
"atoms\n", grpname, gnx);
reduce_topology_x(gnx, index, &mtop, state.x, state.v);
state.natoms = gnx;
}
else if (bZeroQ)
{
zeroq(gnx, index, &mtop);
fprintf(stderr, "Zero-ing charges for group %s\n", grpname);
}
else
{
fprintf(stderr, "Will write full tpx file (no selection)\n");
}
}
state_t = ir->init_t + ir->init_step*ir->delta_t;
sprintf(buf, "Writing statusfile with starting step %s%s and length %s%s steps...\n", "%10", gmx_large_int_fmt, "%10", gmx_large_int_fmt);
fprintf(stderr, buf, ir->init_step, ir->nsteps);
fprintf(stderr, " time %10.3f and length %10.3f ps\n",
state_t, ir->nsteps*ir->delta_t);
write_tpx_state(opt2fn("-o", NFILE, fnm), ir, &state, &mtop);
}
else
{
printf("You've simulated long enough. Not writing tpr file\n");
}
thanx(stderr);
return 0;
}
static void set_state_entries(t_state *state,t_inputrec *ir,int nnodes)
{
/* The entries in the state in the tpx file might not correspond
* with what is needed, so we correct this here.
*/
state->flags = 0;
if (ir->efep != efepNO)
state->flags |= (1<<estLAMBDA);
state->flags |= (1<<estX);
if (state->x == NULL)
snew(state->x,state->nalloc);
if (EI_DYNAMICS(ir->eI)) {
state->flags |= (1<<estV);
if (state->v == NULL)
snew(state->v,state->nalloc);
}
if (ir->eI == eiSD2) {
state->flags |= (1<<estSDX);
if (state->sd_X == NULL) {
/* sd_X is not stored in the tpx file, so we need to allocate it */
snew(state->sd_X,state->nalloc);
}
}
if (ir->eI == eiCG) {
state->flags |= (1<<estCGP);
}
if (EI_SD(ir->eI) || ir->eI == eiBD || ir->etc == etcVRESCALE) {
state->nrng = gmx_rng_n();
state->nrngi = 1;
if (EI_SD(ir->eI) || ir->eI == eiBD) {
/* This will be correct later with DD */
state->nrng *= nnodes;
state->nrngi *= nnodes;
}
state->flags |= ((1<<estLD_RNG) | (1<<estLD_RNGI));
snew(state->ld_rng, state->nrng);
snew(state->ld_rngi,state->nrngi);
} else {
state->nrng = 0;
}
if (ir->ePBC != epbcNONE) {
state->flags |= (1<<estBOX);
if (PRESERVE_SHAPE(*ir)) {
state->flags |= (1<<estBOX_REL);
}
if (ir->epc == epcPARRINELLORAHMAN) {
state->flags |= (1<<estBOXV);
}
if (ir->epc != epcNO) {
state->flags |= (1<<estPRES_PREV);
}
if (ir->etc == etcNOSEHOOVER) {
state->flags |= (1<<estNH_XI);
}
}
if (ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) {
state->flags |= (1<<estTC_INT);
}
init_ekinstate(&state->ekinstate,ir);
init_energyhistory(&state->enerhist);
}
void init_md(FILE *fplog,
t_commrec *cr,t_inputrec *ir,real *t,real *t0,
real *lambda,real *lam0,
t_nrnb *nrnb,gmx_mtop_t *mtop,
gmx_stochd_t *sd,
int nfile,t_filenm fnm[],
int *fp_trn,int *fp_xtc,int *fp_ene,char **fn_cpt,
FILE **fp_dgdl,FILE **fp_field,
t_mdebin **mdebin,
tensor force_vir,tensor shake_vir,rvec mu_tot,
bool *bNEMD,bool *bSimAnn,t_vcm **vcm, unsigned long Flags)
{
int i,j,n;
real tmpt,mod;
char filemode[2];
sprintf(filemode, (Flags & MD_APPENDFILES) ? "a" : "w");
/* Initial values */
*t = *t0 = ir->init_t;
if (ir->efep != efepNO) {
*lam0 = ir->init_lambda;
*lambda = *lam0 + ir->init_step*ir->delta_lambda;
}
else {
*lambda = *lam0 = 0.0;
}
*bSimAnn=FALSE;
for(i=0;i<ir->opts.ngtc;i++) {
/* set bSimAnn if any group is being annealed */
if(ir->opts.annealing[i]!=eannNO)
*bSimAnn = TRUE;
}
if (*bSimAnn) {
update_annealing_target_temp(&(ir->opts),ir->init_t);
}
*bNEMD = (ir->opts.ngacc > 1) || (norm(ir->opts.acc[0]) > 0);
if (sd && (ir->eI == eiBD || EI_SD(ir->eI) || ir->etc == etcVRESCALE)) {
*sd = init_stochd(fplog,ir);
}
if (vcm) {
*vcm = init_vcm(fplog,&mtop->groups,ir);
}
if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES)) {
if (ir->etc == etcBERENDSEN) {
please_cite(fplog,"Berendsen84a");
}
if (ir->etc == etcVRESCALE) {
please_cite(fplog,"Bussi2007a");
}
}
init_nrnb(nrnb);
if (nfile != -1)
{
*fp_trn = -1;
*fp_ene = -1;
*fp_xtc = -1;
if (MASTER(cr))
{
*fp_trn = open_trn(ftp2fn(efTRN,nfile,fnm), filemode);
if (ir->nstxtcout > 0)
{
*fp_xtc = open_xtc(ftp2fn(efXTC,nfile,fnm), filemode);
}
*fp_ene = open_enx(ftp2fn(efENX,nfile,fnm), filemode);
*fn_cpt = opt2fn("-cpo",nfile,fnm);
if ((fp_dgdl != NULL) && ir->efep!=efepNO)
{
if(Flags & MD_APPENDFILES)
{
*fp_dgdl= gmx_fio_fopen(opt2fn("-dgdl",nfile,fnm),filemode);
}
else
{
*fp_dgdl = xvgropen(opt2fn("-dgdl",nfile,fnm),
"dG/d\\8l\\4","Time (ps)",
"dG/d\\8l\\4 (kJ mol\\S-1\\N [\\8l\\4]\\S-1\\N)");
}
}
if ((fp_field != NULL) && (ir->ex[XX].n || ir->ex[YY].n ||ir->ex[ZZ].n))
{
if(Flags & MD_APPENDFILES)
{
*fp_field = gmx_fio_fopen(opt2fn("-field",nfile,fnm),filemode);
}
else
{
*fp_field = xvgropen(opt2fn("-field",nfile,fnm),
"Applied electric field","Time (ps)",
"E (V/nm)");
}
}
}
*mdebin = init_mdebin( (Flags & MD_APPENDFILES) ? -1 : *fp_ene,mtop,ir);
}
/* Initiate variables */
clear_mat(force_vir);
clear_mat(shake_vir);
clear_rvec(mu_tot);
debug_gmx();
}