int Network3::run_PLA(double& time, double maxTime, double sampleTime,
double& step, double maxStep, double stepInterval,
mu::Parser& stop_condition, bool print_on_stop,
char* prefix,
bool print_cdat, bool print_func, bool print_save_net, bool print_end_net,
bool additional_pla_output,
bool verbose){
// Output files
string outpre(prefix);
bool print_classif = additional_pla_output;
// ...
// Species file (must exist)
FILE* cdat = NULL;
string cFile = outpre + ".cdat";
if ((cdat = fopen(cFile.c_str(),"r"))){
fclose(cdat);
cdat = fopen(cFile.c_str(),"a");
}
else {
cout << "Error in Network3::run_PLA(): Concentrations file \"" << cFile << "\" doesn't exist. Exiting." << endl;
exit(1);
}
// Observables file (optional)
FILE* gdat = NULL;
string gFile = outpre + ".gdat";
if ((gdat = fopen(gFile.c_str(),"r"))){
fclose(gdat);
gdat = fopen(gFile.c_str(),"a");
}
else{
// cout << "Warning: Groups file \"" << gFile << "\" doesn't exist." << endl;
}
// Functions file (optional)
/* FILE* fdat = NULL;
string fFile = outpre + ".fdat";
if ((fdat = fopen(fFile.c_str(),"r"))){
fclose(fdat);
fdat = fopen(fFile.c_str(),"a");
}
else{
// cout << "Warning: Functions file \"" << fFile << "\" doesn't exist." << endl;
}*/
// PLA-specific output files
FILE* classif = NULL;
if (print_classif){
if ((classif = fopen((outpre+"_classif.pla").c_str(),"r"))){
fclose(classif);
classif = fopen((outpre+"_classif.pla").c_str(),"a");
}
else{
cout << "Error in Network3::run_PLA(): 'print_classif' flag set but classifications file \""
<< (outpre+"_classif.pla") << "\" doesn't exist. Exiting." << endl;
exit(1);
}
}
// ...
// Identify observables involved in functions
vector<unsigned int> funcObs;
for (unsigned int i=0;i < FUNCTION.size();i++){
map<string,double*> var = FUNCTION[i]->first->p->GetUsedVar();
for (unsigned int j=0;j < OBSERVABLE.size();j++){
if (var.find(OBSERVABLE[j]->first->name) != var.end()){
bool already = false;
for (unsigned int k=0;k < funcObs.size() && !already;k++){
if (funcObs[k] == j){
already = true;
}
}
if (!already){ // add to the list
funcObs.push_back(j);
}
}
}
}
// Prepare for simulation
double nextOutputTime = time + sampleTime;
double nextOutputStep = stepInterval;
while (nextOutputStep <= step) nextOutputStep += stepInterval;
bool lastOut = true;
// Simulation loop
// PLA_SIM->rc.forceClassifications(RxnClassifier::EXACT_STOCHASTIC);
string print_net_message;
while (time < maxTime && step < maxStep && !stop_condition.Eval())
{
// Next step
step++;
PLA_SIM->nextStep();
if (PLA_SIM->tau < INFINITY && PLA_SIM->tau > -INFINITY){
time += PLA_SIM->tau;
}
else break;
// Error check
if (PLA_SIM->tau <= 0.0){
cout << "Error in Network3::run_PLA(): tau = " << PLA_SIM->tau << ". Shouldn't happen. Exiting." << endl;
exit(1);
}
// Is it time to output?
lastOut = false;
if (time >= nextOutputTime || step >= nextOutputStep) // YES
{
// Update all observables
for (unsigned int i=0;i < OBSERVABLE.size();i++){
OBSERVABLE[i]->second = OBSERVABLE[i]->first->getValue();
}
// Update all functions
for (unsigned int i=0;i < FUNCTION.size();i++){
FUNCTION[i]->second = FUNCTION[i]->first->Eval();
}
// Output to file
if (print_cdat) Network3::print_species_concentrations(cdat,time);
if (gdat) Network3::print_observable_concentrations(gdat,time,print_func);
if (print_func) Network3::print_function_values(gdat,time);
if (print_save_net){ // Write current system state to .net file
// Collect species populations and update network concentrations vector
double* pops = new double[SPECIES.size()];
for (unsigned int j=0;j < SPECIES.size();j++){
pops[j] = SPECIES[j]->population;
}
set_conc_network(pops);
delete pops;
// Print network w/ current species populations using network::print_network()
char buf[1000];
sprintf(buf, "%s_save.net", prefix);
FILE* out = fopen(buf, "w");
print_network(out);
fclose(out);
print_net_message = " Wrote NET file to " + (string)buf;
// fprintf(stdout, " Wrote NET file to %s", buf);
}
if (print_classif){
fprintf(classif,"%19.12e",time);
fprintf(classif," %19.19g",step);
for (unsigned int v=0;v < PLA_SIM->classif.size();v++){
fprintf(classif, " %10d", PLA_SIM->classif[v]);
}
fprintf(classif,"\n");
fflush(classif);
}
// Output to stdout
if (verbose){
cout << "\t" << fixed << setprecision(6) << time << "\t" << setprecision(0) << step;
// for (unsigned int i=0;i < OBSERVABLE.size();i++){
// cout << "\t" << OBSERVABLE[i]->second;
// }
if (print_save_net){
fprintf(stdout, "%s", print_net_message.c_str());
}
cout << endl;
}
// Get next output time and step
if (time >= nextOutputTime) nextOutputTime += sampleTime;
if (step >= nextOutputStep) nextOutputStep += stepInterval;
lastOut = true;
}
else{ // NO
// Only update observables that are involved in functions
for (unsigned int i=0;i < funcObs.size();i++){
OBSERVABLE[funcObs[i]]->second = OBSERVABLE[funcObs[i]]->first->getValue();
}
// Update all functions
for (unsigned int i=0;i < FUNCTION.size();i++){
FUNCTION[i]->second = FUNCTION[i]->first->Eval();
}
}
}
// Final output
if (!lastOut)
{
// Update all observables
for (unsigned int i=0;i < OBSERVABLE.size();i++){
OBSERVABLE[i]->second = OBSERVABLE[i]->first->getValue();
}
// Update all functions
for (unsigned int i=0;i < FUNCTION.size();i++){
FUNCTION[i]->second = FUNCTION[i]->first->Eval();
}
// Output to file
if (print_cdat) Network3::print_species_concentrations(cdat,time);
// Don't print if stopping condition met and !print_on_stop (must print to CDAT)
if (!(stop_condition.Eval() && !print_on_stop)){
if (gdat) Network3::print_observable_concentrations(gdat,time,print_func);
if (print_func) Network3::print_function_values(gdat,time);
string print_net_message;
if (print_save_net){ // Write current system state to .net file
// Collect species populations and update network concentrations vector
double pops[SPECIES.size()];
for (unsigned int j=0;j < SPECIES.size();j++){
pops[j] = SPECIES[j]->population;
}
set_conc_network(pops);
// Print network w/ current species populations using network::print_network()
char buf[1000];
sprintf(buf, "%s_save.net", prefix);
FILE* out = fopen(buf, "w");
print_network(out);
fclose(out);
print_net_message = " Wrote NET file to " + (string)buf;
}
if (print_classif){
fprintf(classif,"%19.12e",time);
for (unsigned int v=0;v < PLA_SIM->classif.size();v++){
fprintf(classif, " %10d", PLA_SIM->classif[v]);
}
fprintf(classif,"\n");
fflush(classif);
}
}
// Output to stdout
if (verbose){
cout << "\t" << fixed << setprecision(6) << time << "\t" << setprecision(0) << step;
// for (unsigned int i=0;i < OBSERVABLE.size();i++) cout << "\t" << OBSERVABLE[i]->second;
if (print_save_net) fprintf(stdout, "%s", print_net_message.c_str());
cout << endl;
}
}
// Messages if stopping conditions met
if (stop_condition.Eval()){ // Stop condition satisfied
cout << "Stopping condition " << stop_condition.GetExpr() << "met in PLA simulation." << endl;
}
// else if (step >= startStep + maxSteps){ // maxSteps limit reached
// cout << "Maximum step limit (" << maxSteps << ") reached in PLA simulation." << endl;
// }
// If print_end_net = true, collect species populations and update network concentrations vector
if (print_end_net){
double pops[SPECIES.size()];
for (unsigned int j=0;j < SPECIES.size();j++){
pops[j] = SPECIES[j]->population;
}
set_conc_network(pops);
}
// Close files
fclose(cdat);
if (gdat) fclose(gdat);
// if (fdat) fclose(fdat);
if (classif) fclose(classif);
// Return value
if (time >= maxTime) return 0;
else if (step >= maxStep) return -1;
else return -2; // stop condition met
}
/*
* Mail a message on standard input to the people indicated
* in the passed header. (Internal interface).
*/
void
mail1(struct header *hp, int use_to, char *orig_to)
{
pid_t p, pid;
int i, s, gotcha;
char **namelist, *deliver;
struct name *to, *np;
FILE *mtf, *fp;
int remote = rflag != NOSTR || rmail;
char **t;
char *deadletter;
char recfile[PATHSIZE];
/*
* Collect user's mail from standard input.
* Get the result as mtf.
*/
pid = (pid_t)-1;
if ((mtf = collect(hp)) == NULL)
return;
hp->h_seq = 1;
if (hp->h_subject == NOSTR)
hp->h_subject = sflag;
if (fsize(mtf) == 0 && hp->h_subject == NOSTR) {
printf(gettext("No message !?!\n"));
goto out;
}
if (intty) {
printf(gettext("EOT\n"));
flush();
}
/*
* If we need to use the To: line to determine the record
* file, save a copy of it before it's sorted below.
*/
if (use_to && orig_to == NOSTR && hp->h_to != NOSTR)
orig_to = strcpy((char *)salloc(strlen(hp->h_to)+1), hp->h_to);
else if (orig_to == NOSTR)
orig_to = "";
/*
* Now, take the user names from the combined
* to and cc lists and do all the alias
* processing.
*/
senderr = 0;
to = cat(extract(hp->h_bcc, GBCC),
cat(extract(hp->h_to, GTO),
extract(hp->h_cc, GCC)));
to = translate(outpre(elide(usermap(to))));
if (!senderr)
mapf(to, myname);
mechk(to);
for (gotcha = 0, np = to; np != NIL; np = np->n_flink)
if ((np->n_type & GDEL) == 0)
gotcha++;
hp->h_to = detract(to, GTO);
hp->h_cc = detract(to, GCC);
hp->h_bcc = detract(to, GBCC);
if ((mtf = infix(hp, mtf)) == NULL) {
fprintf(stderr, gettext(". . . message lost, sorry.\n"));
return;
}
rewind(mtf);
if (askme && isatty(0)) {
char ans[64];
puthead(hp, stdout, GTO|GCC|GBCC, 0);
printf(gettext("Send? "));
printf("[yes] ");
if (fgets(ans, sizeof(ans), stdin) && ans[0] &&
(tolower(ans[0]) != 'y' && ans[0] != '\n'))
goto dead;
}
if (senderr)
goto dead;
/*
* Look through the recipient list for names with /'s
* in them which we write to as files directly.
*/
i = outof(to, mtf);
rewind(mtf);
if (!gotcha && !i) {
printf(gettext("No recipients specified\n"));
goto dead;
}
if (senderr)
goto dead;
getrecf(orig_to, recfile, use_to, sizeof (recfile));
if (recfile != NOSTR && *recfile)
savemail(safeexpand(recfile), hp, mtf);
if (!gotcha)
goto out;
namelist = unpack(to);
if (debug) {
fprintf(stderr, "Recipients of message:\n");
for (t = namelist; *t != NOSTR; t++)
fprintf(stderr, " \"%s\"", *t);
fprintf(stderr, "\n");
return;
}
/*
* Wait, to absorb a potential zombie, then
* fork, set up the temporary mail file as standard
* input for "mail" and exec with the user list we generated
* far above. Return the process id to caller in case he
* wants to await the completion of mail.
*/
#ifdef VMUNIX
while (wait3((int *)0, WNOHANG, (struct rusage *)0) > 0)
;
#else
#ifdef preSVr4
wait((int *)0);
#else
while (waitpid((pid_t)-1, (int *)0, WNOHANG) > 0)
;
#endif
#endif
rewind(mtf);
pid = fork();
if (pid == (pid_t)-1) {
perror("fork");
dead:
deadletter = Getf("DEAD");
if (fp = fopen(deadletter,
value("appenddeadletter") == NOSTR ? "w" : "a")) {
chmod(deadletter, DEADPERM);
puthead(hp, fp, GMASK|GCLEN, fsize(mtf) - textpos);
fseek(mtf, textpos, 0);
lcwrite(deadletter, mtf, fp,
value("appenddeadletter") != NOSTR);
fclose(fp);
} else
perror(deadletter);
goto out;
}
if (pid == 0) {
sigchild();
#ifdef SIGTSTP
if (remote == 0) {
sigset(SIGTSTP, SIG_IGN);
sigset(SIGTTIN, SIG_IGN);
sigset(SIGTTOU, SIG_IGN);
}
#endif
sigset(SIGHUP, SIG_IGN);
sigset(SIGINT, SIG_IGN);
sigset(SIGQUIT, SIG_IGN);
s = fileno(mtf);
(void) fdwalk(closefd_walk, &s);
close(0);
dup(s);
close(s);
#ifdef CC
submit(getpid());
#endif /* CC */
if ((deliver = value("sendmail")) == NOSTR)
#ifdef SENDMAIL
deliver = SENDMAIL;
#else
deliver = MAIL;
#endif
execvp(safeexpand(deliver), namelist);
perror(deliver);
exit(1);
}
if (value("sendwait")!=NOSTR)
remote++;
out:
if (remote) {
while ((p = wait(&s)) != pid && p != (pid_t)-1)
;
if (s != 0)
senderr++;
pid = 0;
}
fclose(mtf);
return;
}
