void bi::ParticleMCMCNetCDFBuffer::create(const long P, const long T) {
int id, i;
VarType type;
Var* var;
Dim* dim;
ncFile->add_att(PACKAGE_TARNAME "_schema", "ParticleMCMC");
ncFile->add_att(PACKAGE_TARNAME "_schema_version", 1);
ncFile->add_att(PACKAGE_TARNAME "_version", PACKAGE_VERSION);
/* dimensions */
nrDim = createDim("nr", T);
for (i = 0; i < m.getNumDims(); ++i) {
dim = m.getDim(i);
nDims.push_back(createDim(dim->getName().c_str(), dim->getSize()));
}
npDim = createDim("np", P);
/* time variable */
tVar = ncFile->add_var("time", netcdf_real, nrDim);
BI_ERROR_MSG(tVar != NULL && tVar->is_valid(), "Could not create time variable");
/* other variables */
for (i = 0; i < NUM_VAR_TYPES; ++i) {
type = static_cast<VarType>(i);
vars[type].resize(m.getNumVars(type), NULL);
if (type == D_VAR || type == R_VAR || type == P_VAR) {
for (id = 0; id < (int)vars[type].size(); ++id) {
var = m.getVar(type, id);
if (var->hasOutput()) {
if (type == P_VAR) {
vars[type][id] = createVar(var, false, true);
} else {
vars[type][id] = createVar(var, !var->getOutputOnce(), true);
}
}
}
}
}
llVar = ncFile->add_var("loglikelihood", netcdf_real, npDim);
BI_ERROR_MSG(llVar != NULL && llVar->is_valid(),
"Could not create loglikelihood variable");
lpVar = ncFile->add_var("logprior", netcdf_real, npDim);
BI_ERROR_MSG(lpVar != NULL && lpVar->is_valid(),
"Could not create logprior variable");
}
B1::B1(const devs::DynamicsInit& model,
const devs::InitEventList& events) :
extension::DifferenceEquation::Simple(model, events)
{
b = createVar("b");
a = createSync("a");
}
//A(t)=B(t-1)+1
A2::A2(const devs::DynamicsInit& model,
const devs::InitEventList& events) :
extension::DifferenceEquation::Simple(model, events)
{
a = createVar("a");
b = createNosync("b");
}
C3(const devs::DynamicsInit& model,
const devs::InitEventList& events) :
vle::extension::DifferenceEquation::Simple(model, events)
{
c = createVar("c");
b = createSync("b");
}
M(
const vd::DynamicsInit& init,
const vd::InitEventList& events)
: ve::DifferentialEquation(init, events)
{
C3 = createVar("C3");
C1 = createVar("C1");
DSAT = createVar("DSAT");
C2 = createVar("C2");
if (events.exist("p1"))
p1 = events.getDouble("p1");
else
throw vle::utils::ModellingError("Parameter p1 not found");
}
varInfo *createString(char *n)
{ varInfo *v;
if ( (v=createVar(n)) )
{ v->T.basicType = T_STRING;
return(v);
}
else
return(NULL);
}
Im(const vle::devs::DynamicsInit& model,
const vle::devs::InitEventList& events) :
ved::DifferentialEquation(model,events)
{
gamma = events.getDouble("gamma"); //= 0.2
sigma = events.getDouble("sigma"); // = 0.5
I = createVar("I");
E = createExt("E");
}
varInfo *createReal(char *n)
{ varInfo *v;
if ( (v=createVar(n)) )
{ v->T.basicType = T_REAL;
return(v);
}
else
return(NULL);
}
Rm(const vle::devs::DynamicsInit& model,
const vle::devs::InitEventList& events) :
ved::DifferentialEquation(model,events)
{
gamma = events.getDouble("gamma"); //= 0.2
nu = events.getDouble("nu");// = 0.0
R = createVar("R");
S = createExt("S");
I = createExt("I");
}
Y(
const vd::DynamicsInit& init,
const vd::InitEventList& events)
: ve::DifferentialEquation(init, events)
{
X = createVar("X");
maturing = createVar("maturing");
masse = createVar("masse");
if (events.exist("KS"))
KS = events.getDouble("KS");
else
throw vle::utils::ModellingError("Parameter KS not found");
if (events.exist("KG"))
KG = events.getDouble("KG");
else
throw vle::utils::ModellingError("Parameter KG not found");
}
LotkaVolterraY(const vle::devs::DynamicsInit& model,
const vle::devs::InitEventList& events) :
ved::DifferentialEquation(model,events)
{
gamma = (events.exist("gamma"))
? events.getDouble("gamma") : 0.5;
delta = (events.exist("delta"))
? events.getDouble("delta") : 0.5;
Y = createVar("Y");
X = createExt("X");
}
Sm(const vle::devs::DynamicsInit& model,
const vle::devs::InitEventList& events) :
ved::DifferentialEquation(model,events)
{
beta = events.getDouble("beta");// = 0.9
nu = events.getDouble("nu");// = 0.0
S = createVar("S");
E = createExt("E");
I = createExt("I");
R = createExt("R");
}
LotkaVolterraX(const vle::devs::DynamicsInit& model,
const vle::devs::InitEventList& events) :
ved::DifferentialEquation(model,events)
{
alpha = (events.exist("alpha"))
? events.getDouble("alpha") : 0.5;
beta = (events.exist("beta"))
? events.getDouble("beta") : 0.5;
X = createVar("X");
Y = createExt("Y");
}
void UserConfig::setValue(const std::string& name, const std::string& value)
{
UserConfigVar *var = findVarByName(name);
if (!var)
{
std::cerr << "Warning: impossible to set value of " <<
"unknown configuration variable " << name <<
"\n Creating new variable" << std::endl;
var = createVar(name, value);
mChangeFlag = true;
return;
}
if (var->Value != value) mChangeFlag = true;
var->Value = value;
}
static void parseAVar(bool diamond){
// it's a valid type
char buf[256];
bool autoRange=false;
float mn=0,mx=0;
int size;
RawDataBuffer *b;
tok.getnextident(buf); // get name
// if diamond, get topic and datum index
char tname[256];
int idx;
#if DIAMOND
if(diamond){
tok.getnextcheck(T_TOPIC);
tok.getnextident(tname);
tok.getnextcheck(T_COMMA);
idx = tok.getnextint();
diamondMap[DiamondTopicKey(tname,idx)]=QString(buf);
diamondapparatus::subscribe(tname);
if(!diamondSet.contains(tname))
diamondSet.insert(tname);
}
#endif
size = tok.getnextint(); // and size
// now get the range
tok.getnextcheck(T_RANGE);
switch(tok.getnext()){
case T_INT:
case T_FLOAT:
mn = tok.getfloat();
tok.getnextcheck(T_TO);
mx = tok.getnextfloat();
break;
case T_AUTO:
autoRange=true;
break;
default:
throw UnexpException(&tok,"number or 'auto'");
break;
}
b=createVar(T_NAMEFLOAT,buf,size,mn,mx);
if(autoRange)
((DataBuffer<float>*)b)->setAutoRange();
}
Photo() {
srand(so.rnd_seed);
// n_names = 12 + (int) floor((double) rand()/RAND_MAX*4);
// n_prefs = 24 + (int) floor((double) rand()/RAND_MAX*12);
n_names = 10 + (int) floor((double) rand()/RAND_MAX*3);
n_prefs = 20 + (int) floor((double) rand()/RAND_MAX*10);
prefs = (int*) malloc(2*n_prefs*sizeof(int));
for (int i = 0; i < 2*n_prefs; i++) prefs[i] = rand()%n_names;
printf("%d preferences\n", n_prefs);
// Create vars
createVars(x, n_names, 1, n_names);
createVars(f, 2*n_prefs);
createVar(sat, 0, n_prefs);
// Post some constraints
// Map preferences to fulfilment
for (int i = 0; i < n_prefs; i++) {
int_rel_reif(x[prefs[2*i+0]], IRT_EQ, x[prefs[2*i+1]], f[2*i], 1);
int_rel_reif(x[prefs[2*i+0]], IRT_EQ, x[prefs[2*i+1]], f[2*i+1], -1);
}
// Sum of fulfilment
bool_linear(f, IRT_GE, sat);
all_different(x);
// Break some symmetries
int_rel(x[0], IRT_LT, x[1]);
// Post some branchings
// branch(x, VAR_INORDER, VAL_MIN);
branch(x, VAR_DEGREE_MAX, VAL_MIN);
// Declare output variables (optional)
optimize(sat, OPT_MAX);
}
bool UserConfig::loadFile(const std::string& filename)
{
PHYSFS_file* fileHandle = PHYSFS_openRead(filename.c_str());
if (!fileHandle)
{
throw FileLoadException(filename);
}
int fileLength = PHYSFS_fileLength(fileHandle);
char* fileBuffer = new char[fileLength + 1];
PHYSFS_read(fileHandle, fileBuffer, 1, fileLength);
fileBuffer[fileLength] = 0;
TiXmlDocument configDoc;
configDoc.Parse(fileBuffer);
delete[] fileBuffer;
PHYSFS_close(fileHandle);
if (configDoc.Error())
{
std::cerr << "Warning: Parse error in " << filename;
std::cerr << "!" << std::endl;
}
TiXmlElement* userConfigElem =
configDoc.FirstChildElement("userconfig");
if (userConfigElem == NULL)
return false;
for (TiXmlElement* varElem =
userConfigElem->FirstChildElement("var");
varElem != NULL;
varElem = varElem->NextSiblingElement("var"))
{
std::string name, value;
const char* c;
c = varElem->Attribute("name");
if (c)
name = c;
c = varElem->Attribute("value");
if (c)
value = c;
createVar(name, value);
}
return true;
}
G1::G1(const devs::DynamicsInit& model,
const devs::InitEventList& events) :
extension::DifferenceEquation::Simple(model, events)
{
g = createVar("g");
}
void parseLinkedVars(bool diamond){
char buf[256];
int size,type;
RawDataBuffer *linkvar,*b;
if(tok.getnext()!=T_OPREN)
throw UnexpException(&tok,"( after linked");
linkedVars.clear();
for(;;){
double mn,mx;
char buf[256];
// get type
type = tok.getnext();
// get name
tok.getnextident(buf);
// if diamond, get topic and datum index
char tname[256];
int idx;
#if DIAMOND
if(diamond){
tok.getnextcheck(T_TOPIC);
tok.getnextident(tname);
tok.getnextcheck(T_COMMA);
idx = tok.getnextint();
diamondMap[DiamondTopicKey(tname,idx)]=QString(buf);
if(!diamondSet.contains(tname))
diamondSet.insert(tname);
diamondapparatus::subscribe(tname);
}
#endif
// now the range
tok.getnextcheck(T_RANGE);
mn = tok.getnextfloat();
tok.getnextcheck(T_TO);
mx = tok.getnextfloat();
// add to a list!
linkedVars.append(LinkedVarEntry(buf,type,mn,mx));
if(tok.getnext()!=T_COMMA){
tok.rewind();
break;
}
}
if(tok.getnext()!=T_CPREN)
throw UnexpException(&tok,") after linked var list");
if(tok.getnext()!=T_INT)
throw UnexpException(&tok,"buffer size after linked var list");
size = tok.getint();
linkvar = NULL;
for(int i=0;i<linkedVars.size();i++){
b = createVar(linkedVars[i].type,
linkedVars[i].name,
size,
linkedVars[i].minVal,
linkedVars[i].maxVal);
if(linkvar)
linkvar->link(b);
else
linkvar = b;
}
}
MOSP(int _n, int _m) : n(_n), m(_m) {
generateInstance();
createVars(s, n, 0, n-1);
createVars(e, n, 0, n-1);
createVars(sb, n, n);
createVars(eb, n, n);
createVars(o, n, n);
createVar(stacks, 0, n);
// create customer graph
bool g[n][n];
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
g[i][j] = false;
for (int k = 0; k < m; k++) {
if (a[i][k] && a[j][k]) {
g[i][j] = true;
break;
}
}
}
}
// AllDiff constraint on e
all_different(e);
// Min constraints on s[i]
for (int i = 0; i < n; i++) {
vec<IntVar*> x;
for (int j = 0; j < n; j++) if (g[i][j]) x.push(e[j]);
minimum(x, s[i]);
}
// open constraints
for (int i = 0; i < n; i++) {
for (int t = 0; t < n; t++) {
int_rel_reif(s[i], IRT_LE, t, sb[i][t]);
int_rel_reif(e[i], IRT_GE, t, eb[i][t]);
vec<BoolView> x;
x.push(sb[i][t]);
x.push(eb[i][t]);
array_bool_and(x, o[t][i]);
}
}
// stack constraints
for (int i = 0; i < n; i++) {
bool_linear(o[i], IRT_LE, stacks);
}
// dominance breaking constraints
vec<vec<BoolView> > r;
createVars(r, n, n);
// Find out which stacks can immediately close
for (int t = 0; t < n; t++) {
for (int i = 0; i < n; i++) {
vec<BoolView> a;
for (int j = 0; j < n; j++) if (g[i][j]) a.push(sb[j][t]);
a.push(eb[i][t]);
array_bool_and(a, r[i][t]);
}
}
// If none of the lex better stacks can instantly close
// and this one can, close it now
for (int t = 0; t < n-1; t++) {
for (int i = 0; i < n; i++) {
vec<BoolView> a, b;
for (int j = 0; j < i; j++) a.push(r[j][t]);
b.push(r[i][t]);
b.push(eb[i][t+1]);
bool_clause(a, b);
}
}
// branch on end times
branch(e, VAR_MIN_MIN, VAL_MIN);
// set optimization target
optimize(stacks, OPT_MIN);
}
void *new_createVar(double lb, double pt, double ub, int count, int index)
{
void *ans = createVar(lb, pt, ub, count, index);
return ans;
}
TValue vm_interpret(AttoVM* vm, AttoBlock* block, int start, int argc)
{
DEBUGF("Interpret block: %d ops\n", block->code->size);
int error = 0;
TValue* max = (TValue*)(block->code->elements + start + block->code->size);
TValue *pc_val = (TValue*)(block->code->elements + start);
Instruction i = TV2INST(*pc_val);
Stack *stack = &block->stack;
const char* opcode_names[] = { OPCODE_NAMES };
const char* op_name = NULL;
int x;
for(x = 0; pc_val < max && !error; ++x) {
op_name = i >= NUM_OPS ? "unknown" : opcode_names[i];
if(i >= NUM_OPS) {
ERROR("bad opcode: %d", i);
}
DEBUGF("[%d]\t%s (%d)\n", x, op_name, i);
switch(i) {
case OP_NOP:
DISPATCH;
case OP_POP:
EXPECT_ON_STACK(1);
TValue v = pop(stack);
valueDestroy(&v);
DISPATCH;
case OP_DUP: {
EXPECT_ON_STACK(1);
TValue v = pop(stack);
push(stack, v);
push(stack, v);
DISPATCH;
}
case OP_SWAP: {
EXPECT_ON_STACK(2);
TValue f = pop(stack);
TValue s = pop(stack);
push(stack, f);
push(stack, s);
DISPATCH;
}
case OP_ADD:
case OP_SUB:
case OP_MUL:
case OP_DIV:
case OP_MOD:
case OP_POW: {
EXPECT_ON_STACK(2);
TValue b = pop(stack);
TValue a = pop(stack);
TValue res = MathOp(i, a, b);
push(stack, res);
DISPATCH;
}
case OP_OR:
case OP_AND:
case OP_XOR: {
EXPECT_ON_STACK(2);
TValue b = pop(stack);
TValue a = pop(stack);
TValue res = BitwiseOp(i, a, b);
push(stack, res);
DISPATCH;
}
case OP_NOT: {
EXPECT_ON_STACK(1);
TValue a = pop(stack);
push(stack, createNumber(~(long)TV2NUM(a)));
DISPATCH;
}
case OP_EQ:
case OP_LT:
case OP_GT:
case OP_LTE:
case OP_GTE:
case OP_CMP: {
EXPECT_ON_STACK(2);
TValue b = pop(stack);
TValue a = pop(stack);
TValue res = ComparisonOp(i, a, b);
push(stack, res);
DISPATCH;
}
case OP_IF: {
EXPECT_ON_STACK(1);
TValue t = pop(stack);
if(boolValue(t)) {
NEXTINST;
}
DISPATCH;
}
case OP_JMP: {
EXPECT_ON_STACK(1);
long jmp = (long)TV2NUM(pop(stack));
if(jmp + pc_val >= max || jmp + (long)pc_val < 0) {
ERROR("Invalid jump: %ld", jmp);
}
pc_val += jmp;
DISPATCH;
}
case OP_PUSHCONST: {
int index = TV2INST(*++pc_val);
if(index >= (int)block->k->size) {
ERROR("Constant index out of bounds: %d", index);
}
TValue k = getIndex(block->k, index);
push(stack, k);
DISPATCH;
}
case OP_PUSHVAR: {
int index = TV2INST(*++pc_val);
if(index < 0 || index >= block->sizev) {
ERROR("Variable index out of bounds: %d", index);
}
DEBUGF("PUSHVAR, index %d, value >> %s\n", index, TValue_to_string(block->vars[index]));
TValue var = block->vars[index];
var.value.var.index = index;
block->vars[index] = var;
push(stack, var);
DISPATCH;
}
case OP_SETVAR: {
EXPECT_ON_STACK(2);
TValue var = pop(stack);
if(var.type != TYPE_VAR) {
ERROR("Expected a var, but got %s", TValue_type_to_string(var));
}
int index = var.value.var.index;
TValue *val = malloc(sizeof(TValue));
*val = pop(stack);
block->vars[index] = createVar(val);
DEBUGF("SETVAR, index %d, value >> %s\n", index, TValue_to_string(block->vars[index]));
DISPATCH;
}
case OP_VALUEVAR: {
EXPECT_ON_STACK(1);
TValue var = pop(stack);
if(var.type != TYPE_VAR) {
ERROR("Expected a var, but got %s", TValue_type_to_string(var));
}
Value val = *var.value.var.value;
AttoType type = var.value.var.type;
TValue t;
t.value = val;
t.type = type;
push(stack, t);
DISPATCH;
}
case OP_BOOLVALUE: {
EXPECT_ON_STACK(1);
TValue tos = pop(stack);
int bool = boolValue(tos);
valueDestroy(&tos);
push(stack, createBool(bool));
DISPATCH;
}
case OP_CONCAT: {
EXPECT_ON_STACK(2);
TValue top = pop(stack);
TValue sec = pop(stack);
if(!(top.type == TYPE_STRING && sec.type == TYPE_STRING)) {
ERROR("Expected two string values, but got %s and %s", TValue_type_to_string(sec),
TValue_type_to_string(top));
}
char *top_s = TV2STR(top);
char *sec_s = TV2STR(sec);
char *str = malloc(strlen(top_s) + strlen(sec_s));
strcpy(str, sec_s);
strcat(str, top_s);
valueDestroy(&top);
valueDestroy(&sec);
push(stack, createString(str, strlen(str), 0));
free(str);
DISPATCH;
}
case OP_PRINT: {
EXPECT_ON_STACK(1);
TValue v = pop(stack);
char *str = TValue_to_string(v);
printf("%s", str);
if(v.type == TYPE_NUMBER) free(str);
valueDestroy(&v);
DISPATCH;
}
case OP_READLINE: {
char *buf = malloc(BUFSIZ);
memset(buf, '\0', BUFSIZ);
if(fgets(buf, BUFSIZ, stdin) ) {
char *nl = strchr(buf, '\n');
if(nl) {
*nl = '\0';
}
}
unsigned len = strlen(buf) + 1;
push(stack, createString(buf, len, 0));
free(buf);
DISPATCH;
}
case OP_DUMPSTACK:
print_stack(*stack);
DISPATCH;
case OP_CLEARSTACK: {
Stack s = StackNew();
StackDestroy(&block->stack);
*stack = s;
DISPATCH;
}
case OP_CALL: {
EXPECT_ON_STACK(2);
TValue fcn = pop(stack);
TValue num = pop(stack);
// FIXME: this explodes when types aren't right :(
if(fcn.type != TYPE_FUNCTION || num.type != TYPE_NUMBER) {
ERROR("Expected function and numeric values, but got %s and %s", TValue_type_to_string(fcn),
TValue_type_to_string(num));
}
int nargs = (int)TV2NUM(num);
EXPECT_ON_STACK(nargs);
int j;
for(j = 0; j < nargs; ++j) {
TValue v = pop(stack);
push(&fcn.value.function.b->stack, v);
}
TValue ret = vm_interpret(vm, fcn.value.function.b, 0, nargs);
if(ret.type != TYPE_NULL) {
push(stack, ret);
}
valueDestroy(&fcn);
valueDestroy(&num);
valueDestroy(&fcn);
DISPATCH;
}
case OP_RETURN: {
EXPECT_ON_STACK(1);
TValue ret = pop(stack);
DEBUGF("Finished block, returning with %s\n", TValue_to_string(ret));
return ret;
DISPATCH;
}
default:
ERROR("Unrecognized opcode: %d", i);
}
}
DEBUGLN("Finished block");
return createNull();
}
PerturbE1(const vd::DynamicsInit& init, const vd::InitEventList& evts)
: ve::DifferenceEquation::Multiple(init,evts)
{
e1 = createVar("e1");
e0 = createSync("e0");
}