END_TEST
START_TEST (test_L3_Species_boundaryCondition)
{
fail_unless(Species_isSetBoundaryCondition(S) == 0);
Species_setBoundaryCondition(S, 1);
fail_unless(Species_getBoundaryCondition(S) == 1);
fail_unless(Species_isSetBoundaryCondition(S) == 1);
int ret = Species_unsetBoundaryCondition(S);
fail_unless(ret == LIBSBML_OPERATION_SUCCESS);
fail_unless(Species_getBoundaryCondition(S) == 1);
fail_unless(Species_isSetBoundaryCondition(S) == 0);
Species_setBoundaryCondition(S, 0);
fail_unless(Species_getBoundaryCondition(S) == 0);
fail_unless(Species_isSetBoundaryCondition(S) == 1);
ret = Species_unsetBoundaryCondition(S);
fail_unless(ret == LIBSBML_OPERATION_SUCCESS);
fail_unless(Species_getBoundaryCondition(S) == 0);
fail_unless(Species_isSetBoundaryCondition(S) == 0);
}
END_TEST
START_TEST (test_Species_getsetBoundaryCondition)
{
// defaults
fail_unless( Species_getBoundaryCondition(S) == 0);
fail_unless( Species_isSetBoundaryCondition(S) == 1);
Species_setBoundaryCondition(S, 1);
fail_unless( Species_getBoundaryCondition(S) == 1);
fail_unless( Species_isSetBoundaryCondition(S) == 1);
int ret = Species_unsetBoundaryCondition(S);
fail_unless(ret == LIBSBML_UNEXPECTED_ATTRIBUTE);
fail_unless( Species_getBoundaryCondition(S) == 0);
fail_unless( Species_isSetBoundaryCondition(S) == 1);
Species_setBoundaryCondition(S, 0);
fail_unless( Species_getBoundaryCondition(S) == 0);
fail_unless( Species_isSetBoundaryCondition(S) == 1);
ret = Species_unsetBoundaryCondition(S);
fail_unless(ret == LIBSBML_UNEXPECTED_ATTRIBUTE);
fail_unless( Species_getBoundaryCondition(S) == 0);
fail_unless( Species_isSetBoundaryCondition(S) == 1);
}
END_TEST
START_TEST (test_L3_Species_initDefaults)
{
Species_t *s = Species_create(3,1);
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( Species_getSubstanceUnits (s) == NULL );
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( !Species_isSetSubstanceUnits (s) );
fail_unless( !Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( !Species_isSetBoundaryCondition(s) );
fail_unless( !Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_initDefaults(s);
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( !strcmp(Species_getSubstanceUnits (s),"mole" ));
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( Species_isSetSubstanceUnits (s) );
fail_unless( Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( Species_isSetBoundaryCondition(s) );
fail_unless( Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_free(s);
}
END_TEST
START_TEST (test_Species_setBoundaryCondition1)
{
int i = Species_setBoundaryCondition(C, 0);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getBoundaryCondition(C) == 0 );
i = Species_setBoundaryCondition(C, 1);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getBoundaryCondition(C) == 1 );
}
END_TEST
START_TEST (test_L3_Species_boundaryCondition)
{
fail_unless(Species_isSetBoundaryCondition(S) == 0);
Species_setBoundaryCondition(S, 1);
fail_unless(Species_getBoundaryCondition(S) == 1);
fail_unless(Species_isSetBoundaryCondition(S) == 1);
Species_setBoundaryCondition(S, 0);
fail_unless(Species_getBoundaryCondition(S) == 0);
fail_unless(Species_isSetBoundaryCondition(S) == 1);
}
void printSpecies(Model_t *m, FILE *f)
{
int i, j;
Species_t *s;
Compartment_t *c;
fprintf(f, "\n");
fprintf(f, "# Initial Conditions for Species and Compartments:\n");
for ( i=0; i<Model_getNumCompartments(m); i++ ) {
if ( i== 0 ) fprintf(f, "# Compartments:\n");
c = Model_getCompartment(m,i);
if(Compartment_isSetId(c))
fprintf(f, "%s ", Compartment_getId(c));
if(Compartment_isSetName(c))
fprintf(f, "(%s) ", Compartment_getName(c));
if ( Compartment_isSetVolume(c) )
fprintf(f, "= %g; ", Compartment_getSize(c));
fprintf(f, "%s", Compartment_getConstant(c) ? "" : "variable; ");
if(Compartment_isSetOutside(c))
fprintf(f, "outside %s; ", Compartment_getOutside(c));
/* fprintf(f, "\n"); */
fprintf(f, "dimensions %d; ", Compartment_getSpatialDimensions(c));
if(Compartment_isSetUnits(c))
fprintf(f, "[%s]; ", Compartment_getUnits(c));
fprintf(f, "\n");
fprintf(f, "# Species concentrations in `compartment' %s\n",
Compartment_getId(c));
for(j=0;j<Model_getNumSpecies(m);j++){
s = Model_getSpecies(m,j);
if(strcmp(Species_getCompartment(s), Compartment_getId(c))==0){
fprintf(f, "%s ", Species_getId(s));
if(Species_isSetName(s))
fprintf(f, "(%s) ", Species_getName(s));
if ( Species_isSetInitialAmount(s) )
fprintf(f, "= %g/%g; ",
Species_getInitialAmount(s),
Compartment_getSize(c));
else if ( Species_isSetInitialConcentration(s) )
fprintf(f, "= %g; ", Species_getInitialConcentration(s));
else
fprintf(f, "# no initial value;");
fprintf(f, "%s", Species_getBoundaryCondition(s) ? "boundary;" : "");
fprintf(f, "%s", Species_getConstant(s) ? "constant;" : "");
if(Species_isSetCharge(s))
fprintf(f, "charge = %d; ", Species_getCharge(s));
fprintf(f, "\n");
}
}
fprintf(f, "\n");
}
}
END_TEST
START_TEST (test_L3_Species_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Species_t *s =
Species_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) s) == SBML_SPECIES );
fail_unless( SBase_getMetaId ((SBase_t *) s) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) s) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) s) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) s) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) s) == 1 );
fail_unless( Species_getNamespaces (s) != NULL );
fail_unless( XMLNamespaces_getLength(Species_getNamespaces(s)) == 2 );
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( Species_getSubstanceUnits (s) == NULL );
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( !Species_isSetSubstanceUnits (s) );
fail_unless( !Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( !Species_isSetBoundaryCondition(s) );
fail_unless( !Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_free(s);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
myResult* simulate_implicit(Model_t *m, myResult *result, mySpecies *sp[], myParameter *param[], myCompartment *comp[], myReaction *re[], myRule *rule[], myEvent *event[], myInitialAssignment *initAssign[], myAlgebraicEquations *algEq, timeVariantAssignments *timeVarAssign, double sim_time, double dt, int print_interval, double *time, int order, int use_lazy_method, int print_amount, allocated_memory *mem){
unsigned int i, j;
int cycle;
int error;
int end_cycle = get_end_cycle(sim_time, dt);
double reverse_time;
double *value_time_p = result->values_time;
double *value_sp_p = result->values_sp;
double *value_param_p = result->values_param;
double *value_comp_p = result->values_comp;
double **coefficient_matrix = NULL;
double *constant_vector = NULL;
int *alg_pivot = NULL;
double reactants_numerator, products_numerator;
double min_value;
double *init_val;
/* for implicit */
double **jacobian;
int is_convergence = 0;
double *b;
double *pre_b;
int *p; /* for pivot selection */
boolean flag;
double delta = 1.0e-8;
double tolerance = 1.0e-4; /* error tolerance of neuton method */
unsigned int loop;
double *delta_value;
double k_next; /* speculated k value : k(t+1) */
double *k_t; /* k(t) */
/* num of SBase objects */
unsigned int num_of_species = Model_getNumSpecies(m);
unsigned int num_of_parameters = Model_getNumParameters(m);
unsigned int num_of_compartments = Model_getNumCompartments(m);
unsigned int num_of_reactions = Model_getNumReactions(m);
unsigned int num_of_rules = Model_getNumRules(m);
unsigned int num_of_events = Model_getNumEvents(m);
unsigned int num_of_initialAssignments = Model_getNumInitialAssignments(m);
/* num of variables whose quantity is not a constant */
unsigned int num_of_all_var_species = 0;
unsigned int num_of_all_var_parameters = 0;
unsigned int num_of_all_var_compartments = 0;
unsigned int num_of_all_var_species_reference = 0;
/* num of variables (which is NOT changed by assignment nor algebraic rule) */
unsigned int num_of_var_species = 0;
unsigned int num_of_var_parameters = 0;
unsigned int num_of_var_compartments = 0;
unsigned int num_of_var_species_reference = 0;
unsigned int sum_num_of_vars;
/* All variables (whose quantity is not a constant) */
mySpecies **all_var_sp; /* all variable species */
myParameter **all_var_param; /* all variable parameters */
myCompartment **all_var_comp; /* all variable compartments */
mySpeciesReference **all_var_spr; /* all varialbe SpeciesReferences */
/* variables (which is NOT changed by assignment nor algebraic rule) */
mySpecies **var_sp;
myParameter **var_param;
myCompartment **var_comp;
mySpeciesReference **var_spr;
set_seed();
check_num(num_of_species, num_of_parameters, num_of_compartments, num_of_reactions, &num_of_all_var_species, &num_of_all_var_parameters, &num_of_all_var_compartments, &num_of_all_var_species_reference, &num_of_var_species, &num_of_var_parameters, &num_of_var_compartments, &num_of_var_species_reference, sp, param, comp, re);
/* create objects */
all_var_sp = (mySpecies **)malloc(sizeof(mySpecies *) * num_of_all_var_species);
all_var_param = (myParameter **)malloc(sizeof(myParameter *) * num_of_all_var_parameters);
all_var_comp = (myCompartment **)malloc(sizeof(myCompartment *) * num_of_all_var_compartments);
all_var_spr = (mySpeciesReference **)malloc(sizeof(mySpeciesReference *) * num_of_all_var_species_reference);
var_sp = (mySpecies **)malloc(sizeof(mySpecies *) * num_of_var_species);
var_param = (myParameter **)malloc(sizeof(myParameter *) * num_of_var_parameters);
var_comp = (myCompartment **)malloc(sizeof(myCompartment *) * num_of_var_compartments);
var_spr = (mySpeciesReference **)malloc(sizeof(mySpeciesReference *) * num_of_var_species_reference);
/* mySpecies *all_var_sp[num_of_all_var_species]; */
/* myParameter *all_var_param[num_of_all_var_parameters]; */
/* myCompartment *all_var_comp[num_of_all_var_compartments]; */
/* mySpeciesReference *all_var_spr[num_of_all_var_species_reference]; */
/* mySpecies *var_sp[num_of_var_species]; */
/* myParameter *var_param[num_of_var_parameters]; */
/* myCompartment *var_comp[num_of_var_compartments]; */
/* mySpeciesReference *var_spr[num_of_var_species_reference]; */
create_calc_object_list(num_of_species, num_of_parameters, num_of_compartments, num_of_reactions, all_var_sp, all_var_param, all_var_comp, all_var_spr, var_sp, var_param, var_comp, var_spr, sp, param, comp, re);
sum_num_of_vars = num_of_var_species + num_of_var_parameters +
num_of_var_compartments + num_of_var_species_reference;
jacobian = (double**)malloc(sizeof(double*)*(sum_num_of_vars));
for(i=0; i<sum_num_of_vars; i++){
jacobian[i] = (double*)malloc(sizeof(double)*(sum_num_of_vars));
}
b = (double *)malloc(sizeof(double) * (sum_num_of_vars));
pre_b = (double *)malloc(sizeof(double) * (sum_num_of_vars));
p = (int *)malloc(sizeof(int) * (sum_num_of_vars));
delta_value = (double *)malloc(sizeof(double) * (sum_num_of_vars));
k_t = (double *)malloc(sizeof(double) * (sum_num_of_vars));
/*
double b[sum_num_of_vars];
double pre_b[sum_num_of_vars];
int p[sum_num_of_vars];
double delta_value[sum_num_of_vars];
double k_t[sum_num_of_vars];
*/
if(algEq != NULL){
coefficient_matrix = (double**)malloc(sizeof(double*)*(algEq->num_of_algebraic_variables));
for(i=0; i<algEq->num_of_algebraic_variables; i++){
coefficient_matrix[i] = (double*)malloc(sizeof(double)*(algEq->num_of_algebraic_variables));
}
constant_vector = (double*)malloc(sizeof(double)*(algEq->num_of_algebraic_variables));
alg_pivot = (int*)malloc(sizeof(int)*(algEq->num_of_algebraic_variables));
}
PRG_TRACE(("Simulation for [%s] Starts!\n", Model_getId(m)));
cycle = 0;
/* initialize delay_val */
initialize_delay_val(sp, num_of_species, param, num_of_parameters, comp, num_of_compartments, re, num_of_reactions, sim_time, dt, 0);
/* calc temp value by assignment */
for(i=0; i<num_of_all_var_species; i++){
if(all_var_sp[i]->depending_rule != NULL && all_var_sp[i]->depending_rule->is_assignment){
all_var_sp[i]->temp_value = calc(all_var_sp[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<num_of_all_var_parameters; i++){
if(all_var_param[i]->depending_rule != NULL && all_var_param[i]->depending_rule->is_assignment){
all_var_param[i]->temp_value = calc(all_var_param[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<num_of_all_var_compartments; i++){
if(all_var_comp[i]->depending_rule != NULL && all_var_comp[i]->depending_rule->is_assignment){
all_var_comp[i]->temp_value = calc(all_var_comp[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<num_of_all_var_species_reference; i++){
if(all_var_spr[i]->depending_rule != NULL && all_var_spr[i]->depending_rule->is_assignment){
all_var_spr[i]->temp_value = calc(all_var_spr[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
/* forwarding value */
forwarding_value(all_var_sp, num_of_all_var_species, all_var_param, num_of_all_var_parameters, all_var_comp, num_of_all_var_compartments, all_var_spr, num_of_all_var_species_reference);
/* initialize delay_val */
initialize_delay_val(sp, num_of_species, param, num_of_parameters, comp, num_of_compartments, re, num_of_reactions, sim_time, dt, 0);
/* calc InitialAssignment */
calc_initial_assignment(initAssign, num_of_initialAssignments, dt, cycle, &reverse_time);
/* initialize delay_val */
initialize_delay_val(sp, num_of_species, param, num_of_parameters, comp, num_of_compartments, re, num_of_reactions, sim_time, dt, 0);
/* rewriting for explicit delay */
for(i=0; i<num_of_initialAssignments; i++){
for(j=0; j<initAssign[i]->eq->math_length; j++){
if(initAssign[i]->eq->number[j] == time){
TRACE(("time is replaced with reverse time\n"));
initAssign[i]->eq->number[j] = &reverse_time;
}else if(initAssign[i]->eq->number[j] != NULL){
init_val = (double*)malloc(sizeof(double));
*init_val = *initAssign[i]->eq->number[j];
mem->memory[mem->num_of_allocated_memory++] = init_val;
initAssign[i]->eq->number[j] = init_val;
}
}
}
for(i=0; i<timeVarAssign->num_of_time_variant_assignments; i++){
for(j=0; j<timeVarAssign->eq[i]->math_length; j++){
if(timeVarAssign->eq[i]->number[j] == time){
TRACE(("time is replaced with reverse time\n"));
timeVarAssign->eq[i]->number[j] = &reverse_time;
}else if(timeVarAssign->eq[i]->number[j] != NULL){
init_val = (double*)malloc(sizeof(double));
*init_val = *timeVarAssign->eq[i]->number[j];
mem->memory[mem->num_of_allocated_memory++] = init_val;
timeVarAssign->eq[i]->number[j] = init_val;
}
}
}
/* initialize delay_val */
initialize_delay_val(sp, num_of_species, param, num_of_parameters, comp, num_of_compartments, re, num_of_reactions, sim_time, dt, 0);
/* calc temp value by assignment */
for(i=0; i<num_of_all_var_species; i++){
if(all_var_sp[i]->depending_rule != NULL && all_var_sp[i]->depending_rule->is_assignment){
all_var_sp[i]->temp_value = calc(all_var_sp[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<num_of_all_var_parameters; i++){
if(all_var_param[i]->depending_rule != NULL && all_var_param[i]->depending_rule->is_assignment){
all_var_param[i]->temp_value = calc(all_var_param[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<num_of_all_var_compartments; i++){
if(all_var_comp[i]->depending_rule != NULL && all_var_comp[i]->depending_rule->is_assignment){
all_var_comp[i]->temp_value = calc(all_var_comp[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<num_of_all_var_species_reference; i++){
if(all_var_spr[i]->depending_rule != NULL && all_var_spr[i]->depending_rule->is_assignment){
all_var_spr[i]->temp_value = calc(all_var_spr[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
/* forwarding value */
forwarding_value(all_var_sp, num_of_all_var_species, all_var_param, num_of_all_var_parameters, all_var_comp, num_of_all_var_compartments, all_var_spr, num_of_all_var_species_reference);
/* initialize delay_val */
initialize_delay_val(sp, num_of_species, param, num_of_parameters, comp, num_of_compartments, re, num_of_reactions, sim_time, dt, 0);
/* calc temp value algebraic by algebraic */
if(algEq != NULL){
if(algEq->num_of_algebraic_variables > 1){
/* initialize pivot */
for(i=0; i<algEq->num_of_algebraic_variables; i++){
alg_pivot[i] = i;
}
for(i=0; i<algEq->num_of_algebraic_variables; i++){
for(j=0; j<algEq->num_of_algebraic_variables; j++){
coefficient_matrix[i][j] = calc(algEq->coefficient_matrix[i][j], dt, cycle, &reverse_time, 0);
/* TRACE(("coefficient matrix[%d][%d] = %lf\n", i, j, coefficient_matrix[i][j])); */
}
}
for(i=0; i<algEq->num_of_algebraic_variables; i++){
constant_vector[i] = -calc(algEq->constant_vector[i], dt, cycle, &reverse_time, 0);
/* TRACE(("constant vector[%d] = %lf\n", i, constant_vector[i])); */
}
/* LU decompostion */
error = lu_decomposition(coefficient_matrix, alg_pivot, algEq->num_of_algebraic_variables);
if(error == 0){/* failure in LU decomposition */
return NULL;
}
/* forward substitution & backward substitution */
lu_solve(coefficient_matrix, alg_pivot, algEq->num_of_algebraic_variables, constant_vector);
/* for(i=0; i<algEq->num_of_algebraic_variables; i++){ */
/* TRACE(("ans[%d] = %lf\n", i, constant_vector[i])); */
/* } */
for(i=0; i<algEq->num_of_alg_target_sp; i++){
algEq->alg_target_species[i]->target_species->temp_value = constant_vector[algEq->alg_target_species[i]->order];
}
for(i=0; i<algEq->num_of_alg_target_param; i++){
algEq->alg_target_parameter[i]->target_parameter->temp_value = constant_vector[algEq->alg_target_parameter[i]->order];
}
for(i=0; i<algEq->num_of_alg_target_comp; i++){
/* new code */
for(j=0; j<algEq->alg_target_compartment[i]->target_compartment->num_of_including_species; j++){
if(algEq->alg_target_compartment[i]->target_compartment->including_species[j]->is_concentration){
algEq->alg_target_compartment[i]->target_compartment->including_species[j]->temp_value = algEq->alg_target_compartment[i]->target_compartment->including_species[j]->temp_value*algEq->alg_target_compartment[i]->target_compartment->temp_value/constant_vector[algEq->alg_target_compartment[i]->order];
}
}
/* new code end */
algEq->alg_target_compartment[i]->target_compartment->temp_value = constant_vector[algEq->alg_target_compartment[i]->order];
}
}else{
if(algEq->target_species != NULL){
algEq->target_species->temp_value = -calc(algEq->constant, dt, cycle, &reverse_time, 0)/calc(algEq->coefficient, dt, cycle, &reverse_time, 0);
}
if(algEq->target_parameter != NULL){
algEq->target_parameter->temp_value = -calc(algEq->constant, dt, cycle, &reverse_time, 0)/calc(algEq->coefficient, dt, cycle, &reverse_time, 0);
}
if(algEq->target_compartment != NULL){
/* new code */
for(i=0; i<algEq->target_compartment->num_of_including_species; i++){
if(algEq->target_compartment->including_species[i]->is_concentration){
algEq->target_compartment->including_species[i]->temp_value = algEq->target_compartment->including_species[i]->temp_value*algEq->target_compartment->temp_value/(-calc(algEq->constant, dt, cycle, &reverse_time, 0)/calc(algEq->coefficient, dt, cycle, &reverse_time, 0));
}
}
/* new code end */
algEq->target_compartment->temp_value = -calc(algEq->constant, dt, cycle, &reverse_time, 0)/calc(algEq->coefficient, dt, cycle, &reverse_time, 0);
}
}
/* forwarding value */
forwarding_value(all_var_sp, num_of_all_var_species, all_var_param, num_of_all_var_parameters, all_var_comp, num_of_all_var_compartments, all_var_spr, num_of_all_var_species_reference);
}
/* initialize delay_val */
initialize_delay_val(sp, num_of_species, param, num_of_parameters, comp, num_of_compartments, re, num_of_reactions, sim_time, dt, 1);
/* cycle start */
for(cycle=0; cycle<=end_cycle; cycle++){
/* calculate unreversible fast reaction */
for(i=0; i<num_of_reactions; i++){
if(re[i]->is_fast && !re[i]->is_reversible){
if(calc(re[i]->eq, dt, cycle, &reverse_time, 0) > 0){
min_value = DBL_MAX;
for(j=0; j<re[i]->num_of_reactants; j++){
if(min_value > re[i]->reactants[j]->mySp->value/calc(re[i]->reactants[j]->eq, dt, cycle, &reverse_time, 0)){
min_value = re[i]->reactants[j]->mySp->value/calc(re[i]->reactants[j]->eq, dt, cycle, &reverse_time, 0);
}
}
for(j=0; j<re[i]->num_of_products; j++){
if(!Species_getBoundaryCondition(re[i]->products[j]->mySp->origin)){
re[i]->products[j]->mySp->value += calc(re[i]->products[j]->eq, dt, cycle, &reverse_time, 0)*min_value;
re[i]->products[j]->mySp->temp_value = re[i]->products[j]->mySp->value;
}
}
for(j=0; j<re[i]->num_of_reactants; j++){
if(!Species_getBoundaryCondition(re[i]->reactants[j]->mySp->origin)){
re[i]->reactants[j]->mySp->value -= calc(re[i]->reactants[j]->eq, dt, cycle, &reverse_time, 0)*min_value;
re[i]->reactants[j]->mySp->temp_value = re[i]->reactants[j]->mySp->value;
}
}
}
}
}
/* calculate reversible fast reactioin */
for(i=0; i<num_of_reactions; i++){
if(re[i]->is_fast && re[i]->is_reversible){
if(!(Species_getBoundaryCondition(re[i]->products[0]->mySp->origin)
&& Species_getBoundaryCondition(re[i]->reactants[0]->mySp->origin))){
products_numerator = calc(re[i]->products_equili_numerator, dt, cycle, &reverse_time, 0);
reactants_numerator = calc(re[i]->reactants_equili_numerator, dt, cycle, &reverse_time, 0);
if(products_numerator > 0 || reactants_numerator > 0){
if(Species_getBoundaryCondition(re[i]->products[0]->mySp->origin)){
re[i]->reactants[0]->mySp->value = (reactants_numerator/products_numerator)*re[i]->products[0]->mySp->value;
re[i]->reactants[0]->mySp->temp_value = re[i]->reactants[0]->mySp->value;
}else if(Species_getBoundaryCondition(re[i]->reactants[0]->mySp->origin)){
re[i]->products[0]->mySp->value = (products_numerator/reactants_numerator)*re[i]->reactants[0]->mySp->value;
re[i]->products[0]->mySp->temp_value = re[i]->products[0]->mySp->value;
}else{
re[i]->products[0]->mySp->value = (products_numerator/(products_numerator+reactants_numerator))*(re[i]->products[0]->mySp->temp_value+re[i]->reactants[0]->mySp->temp_value);
re[i]->reactants[0]->mySp->value = (reactants_numerator/(products_numerator+reactants_numerator))*(re[i]->products[0]->mySp->temp_value+re[i]->reactants[0]->mySp->temp_value);
re[i]->products[0]->mySp->temp_value = re[i]->products[0]->mySp->value;
re[i]->reactants[0]->mySp->temp_value = re[i]->reactants[0]->mySp->value;
}
}
}
}
}
/* event */
calc_event(event, num_of_events, dt, *time, cycle, &reverse_time);
/* substitute delay val */
substitute_delay_val(sp, num_of_species, param, num_of_parameters, comp, num_of_compartments, re, num_of_reactions, cycle);
/* progress */
if(cycle%(int)(end_cycle/10) == 0){
PRG_TRACE(("%3d %%\n", (int)(100*((double)cycle/(double)end_cycle))));
PRG_TRACE(("\x1b[1A"));
PRG_TRACE(("\x1b[5D"));
}
/* print result */
if(cycle%print_interval == 0){
/* Time */
*value_time_p = *time;
value_time_p++;
/* Species */
for(i=0; i<num_of_species; i++){
/* if(!(Species_getConstant(sp[i]->origin) && Species_getBoundaryCondition(sp[i]->origin))){ // XXX must remove this */
if(print_amount){
if(sp[i]->is_concentration){
*value_sp_p = sp[i]->value*sp[i]->locating_compartment->value;
}else{
*value_sp_p = sp[i]->value;
}
}else{
if(sp[i]->is_amount){
*value_sp_p = sp[i]->value/sp[i]->locating_compartment->value;
}else{
*value_sp_p = sp[i]->value;
}
}
value_sp_p++;
/* } */
}
/* Parameter */
for(i=0; i<num_of_parameters; i++){
/* if(!Parameter_getConstant(param[i]->origin)){ // XXX must remove this */
*value_param_p = param[i]->value;
/* } */
value_param_p++;
}
/* Compartment */
for(i=0; i<num_of_compartments; i++){
/* if(!Compartment_getConstant(comp[i]->origin)){ // XXX must remove this */
*value_comp_p = comp[i]->value;
/* } */
value_comp_p++;
}
}
/* time increase */
*time = (cycle+1)*dt;
/* implicit method */
/* define init value by Euler start */
calc_k(all_var_sp, num_of_all_var_species, all_var_param, num_of_all_var_parameters, all_var_comp, num_of_all_var_compartments, all_var_spr, num_of_all_var_species_reference, re, num_of_reactions, rule, num_of_rules, cycle, dt, &reverse_time, 0, 1);
/* preserve k(t) value */
for(i=0; i<sum_num_of_vars; i++){
if(i < num_of_var_species){
k_t[i] = var_sp[i]->k[0];
}else if(i < num_of_var_species+num_of_var_parameters){
k_t[i] = var_param[i-num_of_var_species]->k[0];
}else if(i < num_of_var_species+num_of_var_parameters+num_of_var_compartments){
k_t[i] = var_comp[i-num_of_var_species-num_of_var_parameters]->k[0];
}else{
k_t[i] = var_spr[i-num_of_var_species-num_of_var_parameters-num_of_var_compartments]->k[0];
}
}
calc_temp_value(all_var_sp, num_of_all_var_species, all_var_param, num_of_all_var_parameters, all_var_comp, num_of_all_var_compartments, all_var_spr, num_of_all_var_species_reference, dt, 0);
/* define init value by Euler end */
/* newton method */
if(use_lazy_method){
is_convergence = 0;
for(i=0; i<sum_num_of_vars; i++){
pre_b[i] = 0;
}
}
flag = 1;
while(flag){
/* calc b */
calc_k(var_sp, num_of_var_species, var_param, num_of_var_parameters, var_comp, num_of_var_compartments, var_spr, num_of_var_species_reference, re, num_of_reactions, rule, num_of_rules, cycle, dt, &reverse_time, 0, 0);
for(i=0; i<num_of_var_species; i++){
k_next = var_sp[i]->k[0];
b[i] = calc_implicit_formula(order, var_sp[i]->temp_value, var_sp[i]->value, var_sp[i]->prev_val[0], var_sp[i]->prev_val[1], var_sp[i]->prev_val[2], k_next, k_t[i], var_sp[i]->prev_k[0], var_sp[i]->prev_k[1], dt);
}
for(i=0; i<num_of_var_parameters; i++){
b[num_of_var_species+i] = calc_implicit_formula(order, var_param[i]->temp_value, var_param[i]->value, var_param[i]->prev_val[0], var_param[i]->prev_val[1], var_param[i]->prev_val[2], var_param[i]->k[0], k_t[num_of_var_species+i], var_param[i]->prev_k[0], var_param[i]->prev_k[1], dt);
}
for(i=0; i<num_of_var_compartments; i++){
b[num_of_var_species+num_of_var_parameters+i] = calc_implicit_formula(order, var_comp[i]->temp_value, var_comp[i]->value, var_comp[i]->prev_val[0], var_comp[i]->prev_val[1], var_comp[i]->prev_val[2], var_comp[i]->k[0], k_t[num_of_var_species+num_of_var_parameters+i], var_comp[i]->prev_k[0], var_comp[i]->prev_k[1], dt);
}
for(i=0; i<num_of_var_species_reference; i++){
b[num_of_var_species+num_of_var_parameters+num_of_var_compartments+i] = calc_implicit_formula(order, var_spr[i]->temp_value, var_spr[i]->value, var_spr[i]->prev_val[0], var_spr[i]->prev_val[1], var_spr[i]->prev_val[2], var_spr[i]->k[0], k_t[num_of_var_species+num_of_var_parameters+num_of_var_compartments+i], var_spr[i]->prev_k[0], var_spr[i]->prev_k[1], dt);
}
if(!use_lazy_method || !is_convergence){
/* calc jacobian by numerical differentiation */
for(loop=0; loop<sum_num_of_vars; loop++){
if(loop < num_of_var_species){
var_sp[loop]->temp_value += delta;
}else if(loop < num_of_var_species+num_of_var_parameters){
var_param[loop-num_of_var_species]->temp_value += delta;
}else if(loop < num_of_var_species+num_of_var_parameters+num_of_var_compartments){
var_comp[loop-num_of_var_species-num_of_var_parameters]->temp_value += delta;
}else{
var_spr[loop-num_of_var_species-num_of_var_parameters-num_of_var_compartments]->temp_value += delta;
}
calc_k(var_sp, num_of_var_species, var_param, num_of_var_parameters, var_comp, num_of_var_compartments, var_spr, num_of_var_species_reference, re, num_of_reactions, rule, num_of_rules, cycle, dt, &reverse_time, 0, 0);
for(i=0; i<num_of_var_species; i++){
k_next = var_sp[i]->k[0];
delta_value[i] = calc_implicit_formula(order, var_sp[i]->temp_value, var_sp[i]->value, var_sp[i]->prev_val[0], var_sp[i]->prev_val[1], var_sp[i]->prev_val[2], k_next, k_t[i], var_sp[i]->prev_k[0], var_sp[i]->prev_k[1], dt);
/* numerical differentiation */
jacobian[i][loop] = (delta_value[i]-b[i])/delta;
}
for(i=0; i<num_of_var_parameters; i++){
delta_value[num_of_var_species+i] = calc_implicit_formula(order, var_param[i]->temp_value, var_param[i]->value, var_param[i]->prev_val[0], var_param[i]->prev_val[1], var_param[i]->prev_val[2], var_param[i]->k[0], k_t[num_of_var_species+i], var_param[i]->prev_k[0], var_param[i]->prev_k[1], dt);
/* numerical differentiation */
jacobian[num_of_var_species+i][loop] = (delta_value[num_of_var_species+i]-b[num_of_var_species+i])/delta;
}
for(i=0; i<num_of_var_compartments; i++){
delta_value[num_of_var_species+num_of_var_parameters+i] = calc_implicit_formula(order, var_comp[i]->temp_value, var_comp[i]->value, var_comp[i]->prev_val[0], var_comp[i]->prev_val[1], var_comp[i]->prev_val[2], var_comp[i]->k[0], k_t[num_of_var_species+num_of_var_parameters+i], var_comp[i]->prev_k[0], var_comp[i]->prev_k[1], dt);
/* numerical differentiation */
jacobian[num_of_var_species+num_of_var_parameters+i][loop] = (delta_value[num_of_var_species+num_of_var_parameters+i]-b[num_of_var_species+num_of_var_parameters+i])/delta;
}
for(i=0; i<num_of_var_species_reference; i++){
delta_value[num_of_var_species+num_of_var_parameters+num_of_var_compartments+i] = calc_implicit_formula(order, var_spr[i]->temp_value, var_spr[i]->value, var_spr[i]->prev_val[0], var_spr[i]->prev_val[1], var_spr[i]->prev_val[2], var_spr[i]->k[0], k_t[num_of_var_species+num_of_var_parameters+num_of_var_compartments+i], var_spr[i]->prev_k[0], var_spr[i]->prev_k[1], dt);
/* numerical differentiation */
jacobian[num_of_var_species+num_of_var_parameters+num_of_var_compartments+i][loop] = (delta_value[num_of_var_species+num_of_var_parameters+num_of_var_compartments+i]-b[num_of_var_species+num_of_var_parameters+num_of_var_compartments+i])/delta;
}
if(loop < num_of_var_species){
var_sp[loop]->temp_value -= delta;
}else if(loop < num_of_var_species+num_of_var_parameters){
var_param[loop-num_of_var_species]->temp_value -= delta;
}else if(loop < num_of_var_species+num_of_var_parameters+num_of_var_compartments){
var_comp[loop-num_of_var_species-num_of_var_parameters]->temp_value -= delta;
}else{
var_spr[loop-num_of_var_species-num_of_var_parameters-num_of_var_compartments]->temp_value -= delta;
}
}
}
/* initialize p */
for(i=0; i<sum_num_of_vars; i++){
p[i] = i;
}
/* LU decomposition */
error = lu_decomposition(jacobian, p, sum_num_of_vars);
if(error == 0){/* failure in LU decomposition */
return NULL;
}
/* forward substitution & backward substitution */
lu_solve(jacobian, p, sum_num_of_vars, b);
/* calculate next temp value */
for(i=0; i<sum_num_of_vars; i++){
if(i < num_of_var_species){
var_sp[i]->temp_value -= b[i];
}else if(i < num_of_var_species+num_of_var_parameters){
var_param[i-num_of_var_species]->temp_value -= b[i];
}else if(i < num_of_var_species+num_of_var_parameters+num_of_var_compartments){
var_comp[i-num_of_var_species-num_of_var_parameters]->temp_value -= b[i];
}else{
var_spr[i-num_of_var_species-num_of_var_parameters-num_of_var_compartments]->temp_value -= b[i];
}
}
/* convergence judgement */
if(use_lazy_method){
is_convergence = 1;
for(i=0; i<sum_num_of_vars; i++){
if(fabs(b[i]) > fabs(pre_b[i])){
is_convergence = 0;
}
}
for(i=0; i<sum_num_of_vars; i++){
pre_b[i] = b[i];
}
}
/* error judgement */
flag = 0;
for(i=0; i<sum_num_of_vars; i++){
if(fabs(b[i]) > tolerance){
flag = 1;
}
}
}
/* calc temp value by assignment */
for(i=0; i<num_of_all_var_species; i++){
if(all_var_sp[i]->depending_rule != NULL && all_var_sp[i]->depending_rule->is_assignment){
all_var_sp[i]->temp_value = calc(all_var_sp[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<num_of_all_var_parameters; i++){
if(all_var_param[i]->depending_rule != NULL && all_var_param[i]->depending_rule->is_assignment){
all_var_param[i]->temp_value = calc(all_var_param[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<num_of_all_var_compartments; i++){
if(all_var_comp[i]->depending_rule != NULL && all_var_comp[i]->depending_rule->is_assignment){
all_var_comp[i]->temp_value = calc(all_var_comp[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<num_of_all_var_species_reference; i++){
if(all_var_spr[i]->depending_rule != NULL && all_var_spr[i]->depending_rule->is_assignment){
all_var_spr[i]->temp_value = calc(all_var_spr[i]->depending_rule->eq, dt, cycle, &reverse_time, 0);
}
}
/* calc temp value algebraic by algebraic */
if(algEq != NULL){
if(algEq->num_of_algebraic_variables > 1){
/* initialize pivot */
for(i=0; i<algEq->num_of_algebraic_variables; i++){
alg_pivot[i] = i;
}
for(i=0; i<algEq->num_of_algebraic_variables; i++){
for(j=0; j<algEq->num_of_algebraic_variables; j++){
coefficient_matrix[i][j] = calc(algEq->coefficient_matrix[i][j], dt, cycle, &reverse_time, 0);
}
}
for(i=0; i<algEq->num_of_algebraic_variables; i++){
constant_vector[i] = -calc(algEq->constant_vector[i], dt, cycle, &reverse_time, 0);
}
/* LU decompostion */
error = lu_decomposition(coefficient_matrix, alg_pivot, algEq->num_of_algebraic_variables);
if(error == 0){/* failure in LU decomposition */
return NULL;
}
/* forward substitution & backward substitution */
lu_solve(coefficient_matrix, alg_pivot, algEq->num_of_algebraic_variables, constant_vector);
for(i=0; i<algEq->num_of_alg_target_sp; i++){
algEq->alg_target_species[i]->target_species->temp_value = constant_vector[algEq->alg_target_species[i]->order];
}
for(i=0; i<algEq->num_of_alg_target_param; i++){
algEq->alg_target_parameter[i]->target_parameter->temp_value = constant_vector[algEq->alg_target_parameter[i]->order];
}
for(i=0; i<algEq->num_of_alg_target_comp; i++){
/* new code */
for(j=0; j<algEq->alg_target_compartment[i]->target_compartment->num_of_including_species; j++){
if(algEq->alg_target_compartment[i]->target_compartment->including_species[j]->is_concentration){
algEq->alg_target_compartment[i]->target_compartment->including_species[j]->temp_value = algEq->alg_target_compartment[i]->target_compartment->including_species[j]->temp_value*algEq->alg_target_compartment[i]->target_compartment->temp_value/constant_vector[algEq->alg_target_compartment[i]->order];
}
}
/* new code end */
algEq->alg_target_compartment[i]->target_compartment->temp_value = constant_vector[algEq->alg_target_compartment[i]->order];
}
}else{
if(algEq->target_species != NULL){
algEq->target_species->temp_value = -calc(algEq->constant, dt, cycle, &reverse_time, 0)/calc(algEq->coefficient, dt, cycle, &reverse_time, 0);
}
if(algEq->target_parameter != NULL){
algEq->target_parameter->temp_value = -calc(algEq->constant, dt, cycle, &reverse_time, 0)/calc(algEq->coefficient, dt, cycle, &reverse_time, 0);
}
if(algEq->target_compartment != NULL){
/* new code */
for(i=0; i<algEq->target_compartment->num_of_including_species; i++){
if(algEq->target_compartment->including_species[i]->is_concentration){
algEq->target_compartment->including_species[i]->temp_value = algEq->target_compartment->including_species[i]->temp_value*algEq->target_compartment->temp_value/(-calc(algEq->constant, dt, cycle, &reverse_time, 0)/calc(algEq->coefficient, dt, cycle, &reverse_time, 0));
}
}
/* new code end */
algEq->target_compartment->temp_value = -calc(algEq->constant, dt, cycle, &reverse_time, 0)/calc(algEq->coefficient, dt, cycle, &reverse_time, 0);
}
}
}
/* preserve prev_value and prev_k for multistep solution */
for(i=0; i<num_of_var_species; i++){
var_sp[i]->prev_val[2] = var_sp[i]->prev_val[1];
var_sp[i]->prev_val[1] = var_sp[i]->prev_val[0];
var_sp[i]->prev_val[0] = var_sp[i]->value;
var_sp[i]->prev_k[2] = var_sp[i]->prev_k[1];
var_sp[i]->prev_k[1] = var_sp[i]->prev_k[0];
var_sp[i]->prev_k[0] = k_t[i];
}
for(i=0; i<num_of_var_parameters; i++){
var_param[i]->prev_val[2] = var_param[i]->prev_val[1];
var_param[i]->prev_val[1] = var_param[i]->prev_val[0];
var_param[i]->prev_val[0] = var_param[i]->value;
var_param[i]->prev_k[2] = var_param[i]->prev_k[1];
var_param[i]->prev_k[1] = var_param[i]->prev_k[0];
var_param[i]->prev_k[0] = k_t[num_of_var_species+i];
}
for(i=0; i<num_of_var_compartments; i++){
var_comp[i]->prev_val[2] = var_comp[i]->prev_val[1];
var_comp[i]->prev_val[1] = var_comp[i]->prev_val[0];
var_comp[i]->prev_val[0] = var_comp[i]->value;
var_comp[i]->prev_k[2] = var_comp[i]->prev_k[1];
var_comp[i]->prev_k[1] = var_comp[i]->prev_k[0];
var_comp[i]->prev_k[0] = k_t[num_of_var_species+num_of_var_parameters+i];
}
for(i=0; i<num_of_var_species_reference; i++){
var_spr[i]->prev_val[2] = var_spr[i]->prev_val[1];
var_spr[i]->prev_val[1] = var_spr[i]->prev_val[0];
var_spr[i]->prev_val[0] = var_spr[i]->value;
var_spr[i]->prev_k[2] = var_spr[i]->prev_k[1];
var_spr[i]->prev_k[1] = var_spr[i]->prev_k[0];
var_spr[i]->prev_k[0] = k_t[num_of_var_species+num_of_var_parameters+i];
}
/* forwarding value */
forwarding_value(all_var_sp, num_of_all_var_species, all_var_param, num_of_all_var_parameters, all_var_comp, num_of_all_var_compartments, all_var_spr, num_of_all_var_species_reference);
}
PRG_TRACE(("Simulation for [%s] Ends!\n", Model_getId(m)));
if(algEq != NULL){
for(i=0; i<algEq->num_of_algebraic_variables; i++){
free(coefficient_matrix[i]);
}
free(coefficient_matrix);
free(constant_vector);
free(alg_pivot);
}
for(i=0; i<sum_num_of_vars; i++){
free(jacobian[i]);
}
free(all_var_sp);
free(all_var_param);
free(all_var_comp);
free(all_var_spr);
free(var_sp);
free(var_param);
free(var_comp);
free(var_spr);
/* for implicit */
free(jacobian);
return result;
}
/*
setValues: the user can enter a species name and
change its initial condition (amount or concentration)
*/
static void setValues(Model_t *m) {
char *species;
char *newIA;
char *newIC;
Species_t *s;
printf("Please enter the id of the species to change: ");
species = get_line(stdin);
species = util_trim(species);
if ( (s = Model_getSpeciesById(m,species) ) ) {
printf("\n");
printf("Id: %s\n", Species_getId(s));
if ( Species_isSetName(s) ) {
printf("Name: %s\n", Species_getName(s));
}
if ( Species_isSetInitialAmount(s) ) {
printf("Initial Amount: %g", Species_getInitialAmount(s));
}
else if (Species_isSetInitialConcentration(s) ) {
printf("Initial Concentration: %g", Species_getInitialConcentration(s));
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
} else {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
if ( Species_isSetSpatialSizeUnits(s) ) {
printf("%s%s", "/", Species_getSpatialSizeUnits(s));
}
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
printf(" (has only substance units)");
}
printf("\n");
if ( Species_isSetCharge(s) ) {
printf("Charge: %-10d", Species_getCharge(s));
}
printf("\n");
printf("%s ", Species_getBoundaryCondition(s) ?
"Species is a Boundary\n" : "\n");
printf("%s ", Species_getConstant(s) ?
"Species is set constant" : "\n");
printf("\n");
if ( Species_isSetInitialAmount(s) ) {
printf("Please enter new initial Amount: ");
newIA = get_line(stdin);
newIA = util_trim(newIA);
Species_setInitialAmount(s, (float) atof(newIA));
}
else if ( Species_isSetInitialConcentration(s) ) {
printf("Please enter new initial Concentration: ");
newIC = get_line(stdin);
newIC = util_trim(newIC);
Species_setInitialConcentration(s, (float) atof(newIC));
}
}
else {
printf("%s not found.\n", species);
}
}
SBML_ODESOLVER_API int drawModel(Model_t *m, char* file, char *format) {
#if !USE_GRAPHVIZ
SolverError_error(
WARNING_ERROR_TYPE,
SOLVER_ERROR_NO_GRAPHVIZ,
"odeSolver has been compiled without GRAPHIZ functionality. ",
"Graphs are printed to stdout in the graphviz' .dot format.");
drawModelTxt(m, file);
#else
GVC_t *gvc;
Agraph_t *g;
Agnode_t *r;
Agnode_t *s;
Agedge_t *e;
Agsym_t *a;
Species_t *sp;
Reaction_t *re;
const ASTNode_t *math;
SpeciesReference_t *sref;
ModifierSpeciesReference_t *mref;
char *output[4];
char *command = "dot";
char *formatopt;
char *outfile;
int i,j;
int reversible;
char name[WORDSIZE];
char label[WORDSIZE];
/* setting name of outfile */
ASSIGN_NEW_MEMORY_BLOCK(outfile, strlen(file)+ strlen(format)+7, char, 0);
sprintf(outfile, "-o%s_rn.%s", file, format);
/* setting output format */
ASSIGN_NEW_MEMORY_BLOCK(formatopt, strlen(format)+3, char, 0);
sprintf(formatopt, "-T%s", format);
/* construct command-line */
output[0] = command;
output[1] = formatopt;
output[2] = outfile;
output[3] = NULL;
/* set up renderer context */
gvc = (GVC_t *) gvContext();
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION < 4
dotneato_initialize(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
parse_args(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvParseArgs(gvc, 3, output);
#endif
g = agopen("G", AGDIGRAPH);
/* avoid overlapping nodes, for graph embedding by neato */
a = agraphattr(g, "overlap", "");
agxset(g, a->index, "scale");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
re = Model_getReaction(m,i);
reversible = Reaction_getReversible(re);
sprintf(name, "%s", Reaction_getId(re));
r = agnode(g,name);
a = agnodeattr(g, "shape", "ellipse");
agxset(r, a->index, "box");
sprintf(label, "%s", Reaction_isSetName(re) ?
Reaction_getName(re) : Reaction_getId(re));
agset(r, "label", label);
sprintf(label, "%s.htm", Reaction_getId(re));
a = agnodeattr(g, "URL", "");
agxset(r, a->index, label);
for ( j=0; j<Reaction_getNumModifiers(re); j++ ) {
mref = Reaction_getModifier(re,j);
sp = Model_getSpeciesById(m, ModifierSpeciesReference_getSpecies(mref));
sprintf(name,"%s", Species_getId(sp));
s = agnode(g,name);
sprintf(label, "%s", Species_isSetName(sp) ?
Species_getName(sp) : Species_getId(sp));
agset(s, "label", label);
if ( Species_getBoundaryCondition(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "blue");
}
if ( Species_getConstant(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "green4");
}
sprintf(label, "%s.htm", Species_getId(sp));
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,s,r);
a = agedgeattr(g, "style", "");
agxset(e, a->index, "dashed");
a = agedgeattr(g, "arrowhead", "");
agxset(e, a->index, "odot");
}
for ( j=0; j<Reaction_getNumReactants(re); j++ ) {
sref = Reaction_getReactant(re,j);
sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref));
sprintf(name,"%s", Species_getId(sp));
s = agnode(g, name);
sprintf(label, "%s", Species_isSetName(sp) ?
Species_getName(sp) : Species_getId(sp));
agset(s, "label", label);
if ( Species_getBoundaryCondition(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "blue");
}
if ( Species_getConstant(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "green4");
}
sprintf(label, "%s.htm", Species_getId(sp));
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,s,r);
a = agedgeattr(g, "label", "");
if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
agxset (e, a->index, SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1 ) {
sprintf(name, "%g", SpeciesReference_getStoichiometry(sref));
agxset (e, a->index, name);
}
}
if ( reversible == 1 ) {
a = agedgeattr(g, "arrowtail", "");
agxset(e, a->index, "onormal");
}
}
for ( j=0; j<Reaction_getNumProducts(re); j++ ) {
sref = Reaction_getProduct(re,j);
sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref));
sprintf(name,"%s", Species_getId(sp));
s = agnode(g,name);
sprintf(label, "%s", Species_isSetName(sp) ?
Species_getName(sp) : Species_getId(sp));
agset(s, "label", label);
if ( Species_getBoundaryCondition(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "blue");
}
if ( Species_getConstant(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "green4");
}
sprintf(label, "%s.htm", Species_getId(sp));
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,r,s);
a = agedgeattr(g, "label", "");
if ( SpeciesReference_isSetStoichiometryMath(sref) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
agxset (e, a->index, SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1 ) {
sprintf(name, "%g",SpeciesReference_getStoichiometry(sref));
agxset (e, a->index,name);
}
}
if ( reversible == 1 ) {
a = agedgeattr(g, "arrowtail", "");
agxset(e, a->index, "onormal");
}
}
}
/* Compute a layout */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvBindContext(gvc, g);
dot_layout(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_layout(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvLayoutJobs(gvc, g);
#endif
/* Write the graph according to -T and -o options */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dotneato_write(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
emit_jobs(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvRenderJobs(gvc, g);
#endif
/* Clean out layout data */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_cleanup(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeLayout(gvc, g);
#endif
/* Free graph structures */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#else
agclose(g);
#endif
/* Clean up output file and errors */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvFREEcontext(gvc);
dotneato_eof(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
dotneato_terminate(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeContext(gvc);
#endif
xfree(formatopt);
xfree(outfile);
#endif
return 1;
}
