int initialize() {
int i;
if(read_from_file) {
read_popdens(1);
if(noise == 0)flat_constraint(1.);
if(noise == 1)flat_constraint(populationsize);
if(noise == 2)read_constraint(0);
}else{
if(noise == 0)flat_constraint(1.);
if(noise == 1)flat_constraint(populationsize);
if(noise == 2)read_constraint(1);
nn = (double*)calloc(space,sizeof(double));
initialize_with_gaussian_popdens();
}
tmp = (double*)malloc(space*sizeof(double));
gsl_rng_env_setup();
T = gsl_rng_default;
rg = gsl_rng_alloc(T);
gsl_rng_set(rg, randseed);
twoepssqrt = sqrt(2.*epsilon);
speedprefactor = wavespeed/dx*epsilon;
x = (double*)malloc(space*sizeof(double));
for(i=0;i<space;i++)x[i]=(i-space0)*dx;
mutation_2dx = epsilon*mutationrate/(dx*dx);
if(quiet<2) {
printf("#################################################################################\n");
printf("# stochastic simulation of adapting population with exponential mutation kernel #\n");
printf("#################################################################################\n");
printf("# mutationrate = %e\n",mutationrate);
if(noise==0) {
printf("# constraint = deterministic\n");
}
if(noise==1) {
printf("# constraint = fixedN\n");
printf("# populationsize = %e\n",populationsize);
}
if(noise==2) {
printf("# constraint = ustar\n");
printf("# wavespeed = %e\n",wavespeed);
}
printf("# (lattice) space = %d\n",space);
printf("# (lattice) space0 = %d\n",space0);
printf("# (lattice) dx = %e\n",dx);
printf("# randseed = %d\n",randseed);
}
}
bool read_record(Driver* driver, string record){
if (record == CONTINUE)
return true;
if (isallspace(record))
return false;
istringstream is(record, ios::in);
string line;
int i = 0;
do{
++i;
line = line.substr(0, line.find(COMMENT));
if (!line.empty() && !isallspace(line)){
char tag = line[0];
string line2 = line.substr(1);
try{
switch(tag){
case OBJTAG:
if (driver->target.empty())
read_objective(driver, line2);
break;
case ARGTAG:
if (driver->arg.empty())
driver->set_args(line2);
break;
//case EXTTAG:
// driver->set_externals(line2, true);//externalise the list provided in line2
// break;
//case INTTAG:
// driver->set_externals(line2, false);//internalise the list provided in line2
// break;
case EXTTAG://w/ simply set externals with '\'
driver->set_externals_gfa(line2);
break;
case VMAXTAG:
driver->lp->setVMax(str2double(line2));
break;
// case TTAG:
// if (driver->thermo) ((ThermoLP*)driver->lp)->setTemperature(T0 + str2double(line2));
// break;
default:
try{
read_constraint(driver, line, tag);
}
catch(exception &e){;}
}
}
catch(exception &e) {
throw runtime_error(string("error in line ") + num2str(i) + ": " + e.what());
}
}
}
while(getline(is, line, NEWLINE));
return true;
}
/* read state of an individual constraint */
int dom_read_constraint (DOM *dom, PBF *bf, CON *con)
{
/* read iover */
int iover = 2;
if (PBF_Label (bf, "IOVER"))
{
PBF_Int (bf, &iover, 1);
}
/* read constraint */
for (; bf; bf = bf->next)
{
int ncon;
if (PBF_Label (bf, "CONS"))
{
PBF_Int (bf, &ncon, 1);
for (int n = 0; n < ncon; n ++)
{
CON *obj = read_constraint (dom, iover, bf);
if (con->id == obj->id)
{
*con = *obj;
MEM_Free (&dom->conmem, obj); /* not needed */
return 1;
}
else MEM_Free (&dom->conmem, obj); /* skip and continue */
}
}
}
return 0;
}
/* read domain state */
void dom_read_state (DOM *dom, PBF *bf)
{
BODY *bod, *next;
int ncon;
/* clear contacts */
MAP_Free (&dom->mapmem, &dom->idc);
MEM_Release (&dom->conmem);
dom->con = NULL;
dom->ncon = 0;
/* read all bodies if needed */
if (!dom->allbodiesread) read_new_bodies (dom, bf);
/* mark all bodies as absent */
for (bod = dom->bod; bod; bod = bod->next) bod->flags |= BODY_ABSENT;
SET *usedlabel = NULL;
for (; bf; bf = bf->next)
{
if (PBF_Label (bf, "DOM"))
{
/* read iover */
int iover = 2;
if (PBF_Label (bf, "IOVER"))
{
PBF_Int (bf, &iover, 1);
}
/* read time step */
ASSERT (PBF_Label (bf, "STEP"), ERR_FILE_FORMAT);
PBF_Double (bf, &dom->step, 1);
/* read constraints merit */
ASSERT (PBF_Label (bf, "MERIT"), ERR_FILE_FORMAT);
PBF_Double (bf, &dom->merit, 1);
/* read body states */
ASSERT (PBF_Label (bf, "BODS"), ERR_FILE_FORMAT);
int nbod;
PBF_Int (bf, &nbod, 1);
for (int n = 0; n < nbod; n ++)
{
unsigned int id;
PBF_Uint (bf, &id, 1);
bod = MAP_Find (dom->idb, (void*) (long) id, NULL);
if (bod == NULL) /* pick from all bodies set */
{
ASSERT_DEBUG_EXT (bod = MAP_Find (dom->allbodies, (void*) (long) id, NULL), "Body id invalid");
if (bod->label)
{
MAP *node = MAP_Find_Node (dom->lab, bod->label, (MAP_Compare)strcmp);
if (node)
{
node->data = bod; /* body fregments can inherit labels */
SET_Insert (NULL, &usedlabel, bod->label, (SET_Compare)strcmp);
}
else MAP_Insert (&dom->mapmem, &dom->lab, bod->label, bod, (MAP_Compare) strcmp);
}
MAP_Insert (&dom->mapmem, &dom->idb, (void*) (long) bod->id, bod, NULL);
bod->next = dom->bod;
if (dom->bod) dom->bod->prev = bod;
dom->bod = bod;
bod->dom = dom;
dom->nbod ++;
}
BODY_Read_State (bod, bf, iover);
bod->flags &= ~BODY_ABSENT;
}
/* read constraints */
ASSERT (PBF_Label (bf, "CONS"), ERR_FILE_FORMAT);
PBF_Int (bf, &ncon, 1);
for (int n = 0; n < ncon; n ++)
{
CON *con;
con = read_constraint (dom, iover, bf);
MAP_Insert (&dom->mapmem, &dom->idc, (void*) (long) con->id, con, NULL);
con->next = dom->con;
if (dom->con) dom->con->prev = con;
dom->con = con;
}
dom->ncon += ncon;
}
}
/* remove absent bodies */
for (bod = dom->bod; bod; bod = next)
{
next = bod->next;
if (bod->flags & BODY_ABSENT)
{
if (bod->label && !SET_Contains (usedlabel, bod->label, (SET_Compare)strcmp))
MAP_Delete (&dom->mapmem, &dom->lab, bod->label, (MAP_Compare) strcmp);
MAP_Delete (&dom->mapmem, &dom->idb, (void*) (long) bod->id, NULL);
if (bod->next) bod->next->prev = bod->prev;
if (bod->prev) bod->prev->next = bod->next;
else dom->bod = bod->next;
dom->nbod --;
}
}
SET_Free (NULL, &usedlabel);
/* attach constraints to bodies */
dom_attach_constraints (dom);
}
