void suspend_current(struct list_node *queue)
{
kthread_t *cur;
/* current thread must be on the run queue */
cur = current;
if(list_ismember(&run_list, cur)) {
list_del_obj(current);
list_append_obj(queue, current);
} else {
printk("error: can't suspend thread not on run queue\n");
}
schedule();
}
int NLEnergy_parse_eval(NLEnergy *p, Tcl_Interp *interp,
int objc, Tcl_Obj *const objv[], int evalType) {
enum { KEYWD, ATOM, BOND, ANGLE, DIHED, IMPR, ELEC, VDW, NONB };
const Topology *topo = &(p->topo);
const int32 natoms = Topology_atom_array_length(topo);
const int32 nbonds = Topology_bond_array_length(topo);
const int32 nangles = Topology_angle_array_length(topo);
const int32 ndiheds = Topology_dihed_array_length(topo);
const int32 nimprs = Topology_impr_array_length(topo);
int32 ninvs;
char *atomsel, *nonbsel, *bondsel, *anglesel, *dihedsel, *imprsel, *invsel;
int32 i;
int state = KEYWD, s;
int setnum = 0, mark = FALSE;
boolean invert = FALSE;
TEXT("eval");
if (Array_length(&(p->atomsel)) != natoms
&& (s=Array_resize(&(p->atomsel), natoms)) != OK) return ERROR(s);
atomsel = Array_data(&(p->atomsel));
if (Array_length(&(p->nonbsel)) != natoms
&& (s=Array_resize(&(p->nonbsel), natoms)) != OK) return ERROR(s);
nonbsel = Array_data(&(p->nonbsel));
if (Array_length(&(p->bondsel)) != nbonds
&& (s=Array_resize(&(p->bondsel), nbonds)) != OK) return ERROR(s);
bondsel = Array_data(&(p->bondsel));
if (Array_length(&(p->anglesel)) != nangles
&& (s=Array_resize(&(p->anglesel), nangles)) != OK) return ERROR(s);
anglesel = Array_data(&(p->anglesel));
if (Array_length(&(p->dihedsel)) != ndiheds
&& (s=Array_resize(&(p->dihedsel), ndiheds)) != OK) return ERROR(s);
dihedsel = Array_data(&(p->dihedsel));
if (Array_length(&(p->imprsel)) != nimprs
&& (s=Array_resize(&(p->imprsel), nimprs)) != OK) return ERROR(s);
imprsel = Array_data(&(p->imprsel));
/* find max length for inverse selection array */
ninvs = natoms;
if (ninvs < nbonds) ninvs = nbonds;
if (ninvs < nangles) ninvs = nangles;
if (ninvs < ndiheds) ninvs = ndiheds;
if (ninvs < nimprs) ninvs = nimprs;
if (Array_length(&(p->invsel)) != ninvs
&& (s=Array_resize(&(p->invsel), ninvs)) != OK) return ERROR(s);
invsel = Array_data(&(p->invsel));
if (0 == objc) {
memset(atomsel, 0, natoms);
memset(nonbsel, ASEL_NONB, natoms);
memset(bondsel, TRUE, nbonds);
memset(anglesel, TRUE, nangles);
memset(dihedsel, TRUE, ndiheds);
memset(imprsel, TRUE, nimprs);
}
else {
const char *t = NULL;
state = KEYWD;
memset(atomsel, 0, natoms);
memset(nonbsel, 0, natoms);
memset(bondsel, 0, nbonds);
memset(anglesel, 0, nangles);
memset(dihedsel, 0, ndiheds);
memset(imprsel, 0, nimprs);
i = 0;
INT(objc);
while (i <= objc) {
INT(i);
switch (state) {
case KEYWD:
if (i == objc) { i++; break; }
t = Tcl_GetString(objv[i]);
setnum = 0;
invert = FALSE;
if ('-'==t[0]) { invert = TRUE; t++; }
else if ('+'==t[0]) { t++; }
if (strcmp(t,"atom")==0) state = ATOM;
else if (strcmp(t,"bond")==0) state = BOND;
else if (strcmp(t,"angle")==0) state = ANGLE;
else if (strcmp(t,"dihed")==0) state = DIHED;
else if (strcmp(t,"impr")==0) state = IMPR;
else if (strcmp(t,"elec")==0) state = ELEC;
else if (strcmp(t,"vdw")==0) state = VDW;
else if (strcmp(t,"nonb")==0) state = NONB;
else return ERROR(ERR_EXPECT);
i++;
break;
case BOND:
s = FAIL;
if (i<objc && (s=parse_bondlist(p,interp,objv[i],invert))==OK) i++;
//else if (s < FAIL) return ERROR(s);
else if ( ! invert ) memset(bondsel, TRUE, nbonds);
state = KEYWD;
break;
case ANGLE:
s = FAIL;
if (i<objc && (s=parse_anglelist(p,interp,objv[i],invert))==OK) i++;
//else if (s < FAIL) return ERROR(s);
else if ( ! invert ) memset(anglesel, TRUE, nangles);
state = KEYWD;
break;
case DIHED:
s = FAIL;
if (i<objc && (s=parse_dihedlist(p,interp,objv[i],invert))==OK) i++;
//else if (s < FAIL) return ERROR(s);
else if ( ! invert ) memset(dihedsel, TRUE, ndiheds);
state = KEYWD;
break;
case IMPR:
s = FAIL;
if (i<objc && (s=parse_imprlist(p,interp,objv[i],invert))==OK) i++;
//else if (s < FAIL) return ERROR(s);
else if ( ! invert ) memset(imprsel, TRUE, nimprs);
state = KEYWD;
break;
default: /* ATOM, ELEC, VDW, or NONB */
if (i==objc && setnum > 0) { state = KEYWD; continue; }
if (ATOM==state) mark = (0==setnum ? -ASEL_NONB : -ASEL_NONB_B);
else if (ELEC==state) mark = (0==setnum ? ASEL_ELEC : ASEL_ELEC_B);
else if (VDW==state) mark = (0==setnum ? ASEL_VDW : ASEL_VDW_B);
else mark = (0==setnum ? ASEL_NONB : ASEL_NONB_B);
INT(ASEL_NONB==mark);
INT(ASEL_NONB_B==mark);
s = FAIL;
if (i<objc && (s=parse_atomlist(p,interp,objv[i],invert,mark))==OK) {
i++;
setnum++;
if (invert || 2==setnum) state = KEYWD;
}
#if 0
else if (s < FAIL) {
if (setnum > 0) continue;
else return ERROR(s);
}
#endif
else if (0==setnum && !invert) {
if (mark > 0) {
memset(nonbsel, mark, natoms);
}
else {
memset(atomsel, -mark, natoms);
}
state = KEYWD;
}
else state = KEYWD;
} /* switch */
} /* while */
} /* else */
if ((s=select_from_atomlist(p)) != OK) return ERROR(s);
/* evaluation */
if (EVAL_ENERGY==evalType || EVAL_FORCE==evalType) {
if ((s=NLEnergy_eval_force(p)) != OK) return ERROR(s);
}
else {
/* minimize not yet supported */
return ERROR(ERR_EXPECT);
}
/* output */
if (EVAL_ENERGY==evalType) {
Tcl_Obj *a = NULL;
if ((s=NLEnergy_new_obj_dreal(interp, &a,
p->ener.pe * ENERGY_EXTERNAL)) != OK) {
return ERROR(s);
}
if ((s=NLEnergy_set_obj_result(interp, a)) != OK) return ERROR(s);
}
else if (EVAL_FORCE==evalType || EVAL_MINIMIZE==evalType) {
const dvec *f = Coord_force_const(&(p->coord));
Tcl_Obj *r = NULL; /* return list of lists */
Tcl_Obj *a = NULL; /* list of atom index */
Tcl_Obj *b = NULL; /* list of force or potentials (MINIMIZE) */
if ((s=atomlist_contrib(p)) != OK) return ERROR(s);
if ((s=new_list(interp, &r)) != OK) return ERROR(s);
if ((s=new_list(interp, &a)) != OK) return ERROR(s);
if ((s=new_list(interp, &b)) != OK) return ERROR(s);
for (i = 0; i < natoms; i++) {
if (atomsel[i]) {
if ((s=list_append_atomid(p,interp,a,i)) != OK) return ERROR(s);
if (EVAL_FORCE==evalType) {
dvec fs;
VECMUL(fs, ENERGY_EXTERNAL, f[i]);
if ((s=list_append_dvec(interp,b,&fs)) != OK) return ERROR(s);
}
}
}
if (EVAL_MINIMIZE==evalType) {
return ERROR(ERR_EXPECT);
}
if ((s=list_append_obj(interp, r, a)) != OK) return ERROR(s);
if ((s=list_append_obj(interp, r, b)) != OK) return ERROR(s);
if ((s=set_obj_result(interp, r)) != OK) return ERROR(s);
}
else {
/* nothing else is supported */
return ERROR(ERR_EXPECT);
}
#if 0
if (objc >= 1) {
const char *t = Tcl_GetString(objv[0]);
if (strcmp(t,"bond")==0) {
return NLEnergy_energy_bond(p, interp, objc-1, objv+1);
}
if (strcmp(t,"angle")==0) {
return NLEnergy_energy_angle(p, interp, objc-1, objv+1);
}
if (strcmp(t,"dihed")==0) {
return NLEnergy_energy_dihed(p, interp, objc-1, objv+1);
}
if (strcmp(t,"impr")==0) {
return NLEnergy_energy_impr(p, interp, objc-1, objv+1);
}
if (strcmp(t,"elec")==0) {
return NLEnergy_energy_nonbonded(p, FNBCUT_ELEC, interp, objc-1, objv+1);
}
if (strcmp(t,"vdw")==0) {
return NLEnergy_energy_nonbonded(p, FNBCUT_VDW, interp, objc-1, objv+1);
}
if (strcmp(t,"nonbonded")==0) {
return NLEnergy_energy_nonbonded(p, FNBCUT_ELEC | FNBCUT_VDW,
interp, objc-1, objv+1);
}
}
return ERROR(ERR_EXPECT);
#endif
return OK;
}
void make_runnable(kthread_t *th)
{
/* delete this thread from any other potential list */
list_del_obj(th);
list_append_obj(&run_list, th);
}
