static int
serial_open (struct tty_struct* tty, struct file* filp)
{
int line;
NkPort* port;
NkDevVlink* vlink;
line = NKLINE(tty);
port = line + serial_port;
printk("serial_open tty addr = %p, filp = %p, port =%p\n", tty, filp, port);
if (line >= MAX_PORT) {
return -ENODEV;
}
port->count++;
if (port->count > 1) {
return 0;
}
port->id = os_ctx->id;
tty->driver_data = port;
port->stoptx = 0;
port->stoprx = 0;
port->wakeup = 0;
port->sz = 0;
port->poss = 0;
port->tty = tty;
port->vlink = 0;
port->xid = 0;
port->timer.data = 0;
spin_lock_init(&port->lock);
/*
* console specific initialization.
*/
if (line == 1) {
/* history initialization */
return hist_open(port);
} else {
/* use vcons driver if possible */
vlink = vcons_lookup(tty);
if (vlink) {
return vcons_open(port, vlink);
} else {
return cons_open(port);
}
}
}
static hist_t *lj_domc(model_t *m, const double *beta)
{
double emin, emax;
int istep, iT, jT, acc;
double *mctot, *mcacc, *mcamp;
double retot = DBL_MIN, reacc = 0;
lj_t **lj, *ljtmp;
hist_t *hs;
/* round emin and emax to multiples of m->de */
emin = (int) (m->nn * m->emin / m->de) * m->de;
emax = (int) (m->nn * m->emax / m->de) * m->de;
hs = hist_open(m->nT, emin, emax, m->de);
/* randomize the initial state */
mtscramble( time(NULL) );
xnew(lj, m->nT);
for ( iT = 0; iT < m->nT; iT++ ) {
lj[iT] = lj_open(m->nn, m->rho, m->rcdef);
lj[iT]->dof = m->nn * D;
lj_energy( lj[iT] );
}
xnew(mctot, m->nT);
xnew(mcacc, m->nT);
xnew(mcamp, m->nT);
for ( iT = 0; iT < m->nT; iT++ ) {
mctot[iT] = DBL_MIN;
mcacc[iT] = 0;
mcamp[iT] = m->mcamp;
}
/* do simulations */
for ( istep = 1; istep <= m->nequil + m->nsteps; istep++ ) {
for ( iT = 0; iT < m->nT; iT++ ) {
acc = lj_metro(lj[iT], mcamp[iT], beta[iT]);
mcacc[iT] += acc;
mctot[iT] += 1;
}
if ( m->re ) {
/* replica exchange: randomly swap configurations of
* two neighboring temperatures */
double dbdE, r;
iT = (int) (rand01() * (m->nT - 1));
jT = iT + 1;
dbdE = (beta[iT] - beta[jT]) * (lj[iT]->epot - lj[jT]->epot);
acc = 0;
if ( dbdE >= 0 ) {
acc = 1;
} else {
r = rand01();
if ( r < exp(dbdE) ) {
acc = 1;
}
}
if ( acc ) {
/* swap the models */
ljtmp = lj[iT], lj[iT] = lj[jT], lj[jT] = ljtmp;
}
if ( istep > m->nequil ) {
reacc += acc;
retot += 1;
}
}
if ( istep <= m->nequil ) {
/* adjust the MC move amplitude */
if ( istep % m->nstadj == 0 ) {
for ( iT = 0; iT < m->nT; iT++ ) {
fprintf(stderr, "T %g, mcamp %g, mcacc %g%%\n",
1/beta[iT], mcamp[iT], 100*mcacc[iT]/mctot[iT]);
mcamp[iT] *= sqrt( mcacc[iT] / mctot[iT] / 0.5 );
}
}
continue;
}
for ( iT = 0; iT < m->nT; iT++ ) {
hist_add1(hs, iT, lj[iT]->epot, 1.0, HIST_VERBOSE);
}
}
hist_save(hs, m->fnhis, HIST_ADDAHALF | HIST_NOZEROES | HIST_VERBOSE);
fprintf(stderr, "simulation ended, doing WHAM\n");
for ( iT = 0; iT < m->nT; iT++ ) {
lj_close( lj[iT] );
}
free(mctot);
free(mcacc);
free(mcamp);
return hs;
}
int main(void)
{
lj_t *lj;
int t, vtot = 0, vacc = 0, isrun;
real u, k, p, rhoav, bc = 0.f;
static av_t avU, avK, avp, avbc, avrho;
hist_t *hsvol;
lj = lj_open(N, 3, rho, rc);
if (usesw) {
lj_initsw(lj, rs);
printf("rc %g, rs %g, box %g\n", rc, rs, lj->l*.5f);
}
if (initload && 0 != lj_readpos(lj, lj->x, lj->v, fnpos, LJ_LOADBOX)) {
fprintf(stderr, "error loading previous coordinates from %s\n", fnpos);
}
hsvol = hist_open(1, 0, 5.*lj->n/lj->rho, 2.f);
for (t = 1; t <= nequil + nsteps; t++) {
lj_vv(lj, mddt);
lj_shiftcom(lj, lj->v);
lj_vrescalex(lj, tp, thermdt);
isrun = (t > nequil);
if ( t % 5 == 0 ) {
/* different barostats */
if ( barostat == 1 ) {
vacc += lj_mctp(lj, 0.05, tp, pressure, 0, 1e300, 0, 0);
} else if ( barostat == 2 ) {
vacc += lj_mcp(lj, 0.05, tp, pressure, 0, 1e300, 0, 0);
} else if ( barostat == 3 ) {
lj_langtp0(lj, 1e-5, tp, pressure, 0);
} else if ( barostat == 4 ) {
lj_langp0(lj, 1e-5, tp, pressure, 0);
}
vtot++;
if (isrun) {
av_add(&avrho, lj->n / lj->vol);
hist_add1ez(hsvol, lj->vol, HIST_VERBOSE);
}
}
if (isrun) {
av_add(&avU, lj->epot);
av_add(&avK, lj->ekin);
av_add(&avp, lj_calcp(lj, tp)); /* or lj_calcpk(lj) */
if (usesw) {
bc = lj_bconfsw3d(lj, NULL);
av_add(&avbc, bc);
}
}
}
u = av_getave(&avU)/N;
k = av_getave(&avK)/N;
p = av_getave(&avp);
bc = av_getave(&avbc);
rhoav = av_getave(&avrho);
printf("T %g, U/N %6.3f, K/N %6.3f, p %6.3f, bc %6.3f, rho %6.3f, vacc %g%%\n",
tp, u, k, p, bc, rhoav, 100. * vacc / vtot);
u = ljeos3d_getx(rhoav, tp, &p, NULL, NULL, LJEOS_PVEhBHKN);
printf("ref., u %6.3f, p %6.3f\n", u, p);
hist_save(hsvol, "volmd.his", HIST_NOZEROES);
hist_close(hsvol);
lj_writepos(lj, lj->x, lj->v, fnpos);
lj_close(lj);
return 0;
}
static hist_t *lj_domd(model_t *m, const double *beta)
{
double emin, emax;
int istep, iT;
lj_t **lj, *ljtmp;
hist_t *hs;
/* round emin and emax to multiples of m->de */
emin = (int) (m->nn * m->emin / m->de) * m->de;
emax = (int) (m->nn * m->emax / m->de) * m->de;
hs = hist_open(m->nT, emin, emax, m->de);
/* randomize the initial state */
mtscramble( time(NULL) );
xnew(lj, m->nT);
for ( iT = 0; iT < m->nT; iT++ ) {
lj[iT] = lj_open(m->nn, m->rho, m->rcdef);
}
/* do simulations */
for ( istep = 1; istep <= m->nequil + m->nsteps; istep++ ) {
for ( iT = 0; iT < m->nT; iT++ ) {
lj_vv(lj[iT], m->mddt);
lj[iT]->ekin = lj_vrescale(lj[iT], 1/beta[iT], m->thdt);
}
if ( m->re ) {
/* replica exchange: randomly swap configurations of
* two neighboring temperatures */
int jT, acc;
double dbdE, r;
iT = (int) (rand01() * (m->nT - 1));
jT = iT + 1;
dbdE = (beta[iT] - beta[jT]) * (lj[iT]->epot - lj[jT]->epot);
acc = 0;
if ( dbdE >= 0 ) {
acc = 1;
} else {
r = rand01();
if ( r < exp(dbdE) ) {
acc = 1;
}
}
if ( acc ) {
double scl = sqrt( beta[iT]/beta[jT] ); /* sqrt(Tj/Ti) */
int i;
/* scale the velocities */
for ( i = 0; i < m->nn; i++ ) {
vsmul(lj[iT]->v[i], scl);
vsmul(lj[jT]->v[i], 1/scl);
}
/* swap the models */
ljtmp = lj[iT], lj[iT] = lj[jT], lj[jT] = ljtmp;
}
}
if ( istep <= m->nequil ) continue;
for ( iT = 0; iT < m->nT; iT++ ) {
hist_add1(hs, iT, lj[iT]->epot, 1.0, HIST_VERBOSE);
}
}
hist_save(hs, m->fnhis, HIST_ADDAHALF | HIST_NOZEROES | HIST_VERBOSE);
fprintf(stderr, "simulation ended, doing WHAM\n");
for ( iT = 0; iT < m->nT; iT++ ) {
lj_close( lj[iT] );
}
return hs;
}
int main(void)
{
int t, acc = 0, vacc = 0, vtot = 0, isrun = 0;
lj_t *lj;
ljrdf_t *ljrdf;
real u, p, rho1;
hist_t *hsvol;
lj = lj_open(n, d, rho, rcdef);
/* since this is MC, the dof should be n*d
* maybe we can that it were the same dof as MD? */
lj->dof = n * d;
if (usesq) {
lj_initsq(lj, ra, rb);
lj->vir = 0;
}
ljrdf = ljrdf_open(lj, 0.01, 0);
hsvol = hist_open(1, 0, 5.*lj->n/rho, 1.f);
for (t = 1; t <= nsteps; t++) {
acc += lj_metro3d(lj, amp, 1.0f/tp);
isrun = (t > nsteps / 2);
if (nstvmove && t % nstvmove == 0) {
vtot += 1;
vacc += lj_mcp(lj, 0.01, tp, pressure, 0, 1e300, 0, 0);
if (isrun) {
av_add(&avrho, lj->n / lj->vol);
hist_add1ez(hsvol, lj->vol, HIST_VERBOSE);
}
}
if (t % 10000 == 0) { /* refresh energy regularly, just in case */
real epo = lj->epot;
lj_energy(lj);
if (fabs(lj->epot - epo) > 1e-2) {
fprintf(stderr, "energy mismatch %g vs %g\n", epo, lj->epot);
}
}
if (t % 10000 == 0) printf("t %d\n", t);
if (isrun) {
av_add(&avU, lj->epot);
av_add(&avp, lj_calcp(lj, tp));
if (t % nstrdf == 0) ljrdf_add(ljrdf, 0);
}
}
u = av_getave(&avU)/lj->n;
p = av_getave(&avp);
rho1 = av_getave(&avrho);
printf("erg %g, p %g, rho %g, acc %.2f%%, vacc %.2f%%, rdfnfr %d, dof/d %g\n",
u, p, rho1, 100.*acc/nsteps, 100.*vacc/(1e-6 + vtot), ljrdf->nfr,
1.*lj->dof/lj->d);
hist_save(hsvol, "volmc.his", HIST_NOZEROES);
hist_close(hsvol);
ljrdf_save(ljrdf, "rdfmc.dat", HIST_ADDAHALF | HIST_KEEPHIST | HIST_NOZEROES);
ljrdf_close(ljrdf);
lj_close(lj);
return 0;
}
