END_TEST
START_TEST(test_parseModel_basic)
{
doc = parseModel(EXAMPLES_FILENAME("basic.xml"), 0, 1);
ck_assert(doc != NULL);
model = SBMLDocument_getModel(doc);
ck_assert(model != NULL);
ck_assert(Model_getNumFunctionDefinitions(model) == 0);
ck_assert(Model_getNumUnitDefinitions(model) == 0);
ck_assert(Model_getNumCompartmentTypes(model) == 0);
ck_assert(Model_getNumSpeciesTypes(model) == 0);
ck_assert(Model_getNumCompartments(model) == 1);
ck_assert(Model_getNumSpecies(model) == 2);
ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
ck_assert(Model_getNumParameters(model) == 1);
ck_assert(Model_getNumInitialAssignments(model) == 0);
ck_assert(Model_getNumRules(model) == 0);
ck_assert(Model_getNumConstraints(model) == 0);
ck_assert(Model_getNumReactions(model) == 2);
ck_assert(Model_getNumEvents(model) == 0);
CHECK_PARAMETER(model, 0, "k_1");
CHECK_REACTION(model, 0, "R1", "k_1 * S1");
CHECK_REACTION(model, 1, "R2", "k_2 * S2");
}
/* create contents of myResult object */
myResult *create_myResult(Model_t *m, mySpecies *mySp[], myParameter *myParam[], myCompartment *myComp[], double sim_time, double dt, int print_interval) {
int i;
myResult *result;
int num_of_species = Model_getNumSpecies(m);
int num_of_parameters = Model_getNumParameters(m);
int num_of_compartments = Model_getNumCompartments(m);
int end_cycle = get_end_cycle(sim_time, dt);
result = (myResult *)malloc(sizeof(myResult));
result->error_code = NoError;
result->error_message = NULL;
result->num_of_columns_sp = num_of_species;
result->num_of_columns_param = num_of_parameters;
result->num_of_columns_comp = num_of_compartments;
result->num_of_rows = end_cycle / print_interval + 1;
result->column_name_time = dupstr("time");
result->column_name_sp = (const char **)malloc(sizeof(char *) * num_of_species);
result->column_name_param = (const char **)malloc(sizeof(char *) * num_of_parameters);
result->column_name_comp = (const char **)malloc(sizeof(char *) * num_of_compartments);
result->values_time = (double *)malloc(sizeof(double) * result->num_of_rows);
result->values_sp = (double *)malloc(sizeof(double) * num_of_species * result->num_of_rows);
result->values_param = (double *)malloc(sizeof(double) * num_of_parameters * result->num_of_rows);
result->values_comp = (double *)malloc(sizeof(double) * num_of_compartments * result->num_of_rows);
for(i=0; i<num_of_species; i++){
result->column_name_sp[i] = dupstr(Species_getId(mySp[i]->origin));
}
for(i=0; i<num_of_parameters; i++){
result->column_name_param[i] = dupstr(Parameter_getId(myParam[i]->origin));
}
for(i=0; i<num_of_compartments; i++){
result->column_name_comp[i] = dupstr(Compartment_getId(myComp[i]->origin));
}
return result;
}
END_TEST
START_TEST(test_parseModel_repressilator)
{
doc = parseModel(EXAMPLES_FILENAME("repressilator.xml"), 0, 1);
ck_assert(doc != NULL);
model = SBMLDocument_getModel(doc);
ck_assert(model != NULL);
ck_assert(Model_getNumFunctionDefinitions(model) == 0);
ck_assert(Model_getNumUnitDefinitions(model) == 0);
ck_assert(Model_getNumCompartmentTypes(model) == 0);
ck_assert(Model_getNumSpeciesTypes(model) == 0);
ck_assert(Model_getNumCompartments(model) == 1);
ck_assert(Model_getNumSpecies(model) == 6);
ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
ck_assert(Model_getNumParameters(model) == 3);
ck_assert(Model_getNumInitialAssignments(model) == 0);
ck_assert(Model_getNumRules(model) == 6);
ck_assert(Model_getNumConstraints(model) == 0);
ck_assert(Model_getNumReactions(model) == 0);
ck_assert(Model_getNumEvents(model) == 0);
CHECK_PARAMETER(model, 0, "alpha");
CHECK_PARAMETER(model, 1, "beta");
CHECK_PARAMETER(model, 2, "rho");
CHECK_RULE(model, 0, "beta * (y1 - x1)");
CHECK_RULE(model, 1, "beta * (y2 - x2)");
CHECK_RULE(model, 2, "beta * (y3 - x3)");
CHECK_RULE(model, 3, "alpha * x1 / (1 + x1 + rho * x3) - y1");
CHECK_RULE(model, 4, "alpha * x2 / (1 + x2 + rho * x1) - y2");
CHECK_RULE(model, 5, "alpha * x3 / (1 + x3 + rho * x2) - y3");
}
int
main (int argc, char *argv[])
{
const char *filename;
SBMLDocument_t *d;
Model_t *m;
unsigned int level, version;
if (argc != 2)
{
printf("Usage: printSBML filename\n");
return 2;
}
filename = argv[1];
d = readSBML(filename);
SBMLDocument_printErrors(d, stdout);
m = SBMLDocument_getModel(d);
level = SBMLDocument_getLevel (d);
version = SBMLDocument_getVersion(d);
printf("\n");
printf("File: %s (Level %u, version %u)\n", filename, level, version);
if (m == NULL)
{
printf("No model present.");
return 1;
}
printf(" ");
printf(" model id: %s\n", Model_isSetId(m) ? Model_getId(m) : "(empty)");
printf( "functionDefinitions: %d\n", Model_getNumFunctionDefinitions(m) );
printf( " unitDefinitions: %d\n", Model_getNumUnitDefinitions (m) );
printf( " compartmentTypes: %d\n", Model_getNumCompartmentTypes (m) );
printf( " specieTypes: %d\n", Model_getNumSpeciesTypes (m) );
printf( " compartments: %d\n", Model_getNumCompartments (m) );
printf( " species: %d\n", Model_getNumSpecies (m) );
printf( " parameters: %d\n", Model_getNumParameters (m) );
printf( " initialAssignments: %d\n", Model_getNumInitialAssignments (m) );
printf( " rules: %d\n", Model_getNumRules (m) );
printf( " constraints: %d\n", Model_getNumConstraints (m) );
printf( " reactions: %d\n", Model_getNumReactions (m) );
printf( " events: %d\n", Model_getNumEvents (m) );
printf( "\n" );
SBMLDocument_free(d);
return 0;
}
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");
}
}
void printModel(Model_t *m, FILE *f)
{
fprintf(f, "\n");
fprintf(f, "Model Statistics:\n");
fprintf(f, " Model id: %s\n",
Model_isSetId(m) ? Model_getId(m) : "(not set)");
fprintf(f, " Model name: %s\n",
Model_isSetName(m) ? Model_getName(m) : "(not set)");
fprintf(f, "\n");
fprintf(f, " Compartments: %d\n", Model_getNumCompartments(m));
fprintf(f, " Species: %d\n", Model_getNumSpecies(m));
fprintf(f, " Reactions: %d\n", Model_getNumReactions(m));
fprintf(f, " Rules: %d\n", Model_getNumRules(m));
fprintf(f, " Events: %d\n", Model_getNumEvents(m));
fprintf(f, " Functions: %d\n", Model_getNumFunctionDefinitions(m) );
fprintf(f, "\n");
}
END_TEST
START_TEST(test_parseModel_huang96)
{
doc = parseModel(EXAMPLES_FILENAME("huang96.xml"), 0, 1);
ck_assert(doc != NULL);
model = SBMLDocument_getModel(doc);
ck_assert(model != NULL);
ck_assert(Model_getNumFunctionDefinitions(model) == 0);
ck_assert(Model_getNumUnitDefinitions(model) == 0);
ck_assert(Model_getNumCompartmentTypes(model) == 0);
ck_assert(Model_getNumSpeciesTypes(model) == 0);
ck_assert(Model_getNumCompartments(model) == 1);
ck_assert(Model_getNumSpecies(model) == 22);
ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
ck_assert(Model_getNumParameters(model) == 0);
ck_assert(Model_getNumInitialAssignments(model) == 0);
ck_assert(Model_getNumRules(model) == 0);
ck_assert(Model_getNumConstraints(model) == 0);
ck_assert(Model_getNumReactions(model) == 20);
ck_assert(Model_getNumEvents(model) == 0);
CHECK_REACTION(model, 0, "r1a", "a1 * E1 * KKK - d1 * E1_KKK");
CHECK_REACTION(model, 1, "r1b", "k2 * E1_KKK");
CHECK_REACTION(model, 2, "r2a", "a2 * E2 * P_KKK - d2 * E2_P_KKK");
CHECK_REACTION(model, 3, "r2b", "k2 * E2_P_KKK");
CHECK_REACTION(model, 4, "r3a", "a3 * KK * P_KKK - d3 * P_KKK_KK");
CHECK_REACTION(model, 5, "r3b", "k3 * P_KKK_KK");
CHECK_REACTION(model, 6, "r4a", "a4 * P_KK * KKPase - d4 * KKPase_P_KK");
CHECK_REACTION(model, 7, "r4b", "k4 * KKPase_P_KK");
CHECK_REACTION(model, 8, "r5a", "a5 * P_KK * P_KKK - d5 * P_KKK_P_KK");
CHECK_REACTION(model, 9, "r5b", "k5 * P_KKK_P_KK");
CHECK_REACTION(model, 10, "r6a", "a6 * PP_KK * KKPase - d6 * KKPase_PP_KK");
CHECK_REACTION(model, 11, "r6b", "k6 * KKPase_PP_KK");
CHECK_REACTION(model, 12, "r7a", "a7 * K * PP_KK - d7 * PP_KK_K");
CHECK_REACTION(model, 13, "r7b", "k7 * PP_KK_K");
CHECK_REACTION(model, 14, "r8a", "a8 * P_K * KPase - d8 * KPase_P_K");
CHECK_REACTION(model, 15, "r8b", "k8 * KPase_P_K");
CHECK_REACTION(model, 16, "r9a", "a9 * P_K * PP_KK - d9 * PP_KK_P_K");
CHECK_REACTION(model, 17, "r9b", "k9 * PP_KK_P_K");
CHECK_REACTION(model, 18, "r10a", "a10 * PP_K * KPase - d10 * KPase_PP_K");
CHECK_REACTION(model, 19, "r10b", "k10 * KPase_PP_K");
/* TODO */
}
void print_result_list(Model_t *m, mySpecies *mySp[], myParameter *myParam[], myCompartment *myComp[]){
FILE *fp = NULL;
unsigned int i;
int column = 2;
if ((fp = my_fopen(fp, "./simulation_results/result_list.dat", "w")) == NULL) {
return;
}
TRACE(("Result : Species List\n"));
fprintf(fp, "Result : Species List\n");
for(i=0; i<Model_getNumSpecies(m); i++){
/* if(!(Species_getConstant(mySp[i]->origin) && Species_getBoundaryCondition(mySp[i]->origin))){ //XXX must remove this */
fprintf(fp, "column %d : ID=%s Name=%s\n", column, Species_getId(mySp[i]->origin), Species_getName(mySp[i]->origin));
column++;
/* } */
}
TRACE(("\n"));
fprintf(fp, "\n");
fprintf(fp, "Result : Parameter List\n");
column = 2;
for(i=0; i<Model_getNumParameters(m); i++){
/* if(!Parameter_getConstant(myParam[i]->origin)){ //XXX must remove this */
TRACE(("column %d : ID=%s Name=%s\n", column, Parameter_getId(myParam[i]->origin), Parameter_getName(myParam[i]->origin)));
fprintf(fp, "column %d : ID=%s Name=%s\n", column, Parameter_getId(myParam[i]->origin), Parameter_getName(myParam[i]->origin));
column++;
/* } */
}
TRACE(("Result : Compartment List\n"));
fprintf(fp, "Result : Compartment List\n");
column = 2;
for(i=0; i<Model_getNumCompartments(m); i++){
/* if(!Compartment_getConstant(myComp[i]->origin)){ //XXX must remove this */
TRACE(("column %d : ID=%s Name=%s\n", column, Compartment_getId(myComp[i]->origin), Compartment_getName(myComp[i]->origin)));
fprintf(fp, "column %d : ID=%s Name=%s\n", column, Compartment_getId(myComp[i]->origin), Compartment_getName(myComp[i]->origin));
column++;
/* } */
}
fclose(fp);
}
END_TEST
START_TEST(test_parseModel_events_1_event_1_assignment_l2)
{
doc = parseModel(EXAMPLES_FILENAME("events-1-event-1-assignment-l2.xml"), 0, 1);
ck_assert(doc != NULL);
model = SBMLDocument_getModel(doc);
ck_assert(model != NULL);
ck_assert(Model_getNumFunctionDefinitions(model) == 0);
ck_assert(Model_getNumUnitDefinitions(model) == 0);
ck_assert(Model_getNumCompartmentTypes(model) == 0);
ck_assert(Model_getNumSpeciesTypes(model) == 0);
ck_assert(Model_getNumCompartments(model) == 1);
ck_assert(Model_getNumSpecies(model) == 2);
ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
ck_assert(Model_getNumParameters(model) == 0);
ck_assert(Model_getNumInitialAssignments(model) == 0);
ck_assert(Model_getNumRules(model) == 0);
ck_assert(Model_getNumConstraints(model) == 0);
ck_assert(Model_getNumReactions(model) == 1);
ck_assert(Model_getNumEvents(model) == 1);
CHECK_REACTION(model, 0, "R", "S1");
/* TODO */
}
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;
}
int
main (int argc, char* argv[])
{
unsigned int i,j,errors;
const char* filename = argv[1];
SBMLDocument_t* document;
Model_t* m;
if (argc != 3)
{
printf("\nUsage: unsetNotes <input-filename> <output-filename>\n");
return 1;
}
filename = argv[1];
document = readSBML(filename);
errors = SBMLDocument_getNumErrors(document);
if(errors > 0)
{
SBMLDocument_printErrors(document, stderr);
SBMLDocument_free(document);
return errors;
}
m = SBMLDocument_getModel( document );
SBase_unsetNotes((SBase_t*)m);
for(i=0; i < Model_getNumReactions(m); i++)
{
Reaction_t* re = Model_getReaction(m, i);
SBase_unsetNotes((SBase_t*)re);
for(j=0; j < Reaction_getNumReactants(re); j++)
{
SpeciesReference_t* rt = Reaction_getReactant(re,j);
SBase_unsetNotes((SBase_t*)rt);
}
for(j=0; j < Reaction_getNumProducts(re); j++)
{
SpeciesReference_t* rt = Reaction_getProduct(re,j);
SBase_unsetNotes((SBase_t*)rt);
}
for(j=0; j < Reaction_getNumModifiers(re); j++)
{
SpeciesReference_t* md = Reaction_getModifier(re,j);
SBase_unsetNotes((SBase_t*)md);
}
if(Reaction_isSetKineticLaw(re))
{
KineticLaw_t* kl = Reaction_getKineticLaw(re);
SBase_unsetNotes((SBase_t*)kl);
for(j=0; j < KineticLaw_getNumParameters(kl); j++)
{
Parameter_t* pa = KineticLaw_getParameter(kl, j);
SBase_unsetNotes((SBase_t*)pa);
}
}
}
for(i=0; i < Model_getNumSpecies(m); i++)
{
Species_t* sp = Model_getSpecies(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumCompartments(m); i++)
{
Compartment_t* sp = Model_getCompartment(m,i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
{
FunctionDefinition_t* sp = Model_getFunctionDefinition(m,i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumUnitDefinitions(m); i++)
{
UnitDefinition_t* sp = Model_getUnitDefinition(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumParameters(m); i++)
{
Parameter_t* sp = Model_getParameter(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumRules(m); i++)
{
Rule_t* sp = Model_getRule(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumInitialAssignments(m); i++)
{
InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumEvents(m); i++)
{
Event_t* sp = Model_getEvent(m, i);
SBase_unsetNotes((SBase_t*)sp);
for(j=0; j < Event_getNumEventAssignments(sp); j++)
{
EventAssignment_t* ea = Event_getEventAssignment(sp, j);
SBase_unsetNotes((SBase_t*)ea);
}
}
for(i=0; i < Model_getNumSpeciesTypes(m); i++)
{
SpeciesType_t* sp = Model_getSpeciesType(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumConstraints(m); i++)
{
Constraint_t* sp = Model_getConstraint(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
writeSBML(document, argv[2]);
SBMLDocument_free(document);
return errors;
}
/* allocates memory for substructures of a new odeModel, writes
variable and parameter names and returns a pointer to the
the newly created odeModel. */
static odeModel_t *
ODEModel_fillStructures(Model_t *ode)
{
int i, j, found, neq, nalg, nconst, nass, nevents, nvalues;
Compartment_t *c;
Parameter_t *p;
Species_t *s;
Rule_t *rl;
AssignmentRule_t *ar;
AlgebraicRule_t *alr;
RateRule_t *rr;
SBMLTypeCode_t type;
ASTNode_t *math;
odeModel_t *om;
neq = 0;
nalg = 0;
nconst = 0;
nass = 0;
nvalues = 0;
found = 0;
/*
counting number of equations (ODEs/rateRules and assignment Rules)
to initialize CvodeData structure. Any other occuring values are
stored as parameters.
*/
for ( j=0; j<Model_getNumRules(ode); j++ ) {
rl = Model_getRule(ode,j);
type = SBase_getTypeCode((SBase_t *)rl);
if ( type == SBML_RATE_RULE )
neq++;
if ( type == SBML_ASSIGNMENT_RULE )
nass++;
if ( type == SBML_ALGEBRAIC_RULE ) {
nalg++;
}
}
nvalues = Model_getNumCompartments(ode) + Model_getNumSpecies(ode) +
Model_getNumParameters(ode);
nconst = nvalues - nass - neq - nalg;
nevents = Model_getNumEvents(ode);
om = ODEModel_allocate(neq, nconst, nass, nevents, nalg);
RETURN_ON_FATALS_WITH(NULL);
om->neq = neq;
om->nalg = nalg; /* this causes crash at the moment, because
ODEs have been constructed for that
should be defined by alg. rules */
om->nconst = nconst;
om->nass = nass;
om->nsens = 0; /* sensitivity parameters can be chosen later */
/*
filling the Ids of all rate rules (ODEs) and assignment rules
the ODE model
*/
neq = 0;
nass = 0;
nalg = 0;
for ( j=0; j<Model_getNumRules(ode); j++ ) {
rl = Model_getRule(ode,j);
type = SBase_getTypeCode((SBase_t *)rl);
if ( type == SBML_RATE_RULE ) {
rr = (RateRule_t *)rl;
ASSIGN_NEW_MEMORY_BLOCK(om->names[neq],
strlen(RateRule_getVariable(rr))+1, char, NULL)
sprintf(om->names[neq],RateRule_getVariable(rr));
neq++;
}
else if ( type == SBML_ASSIGNMENT_RULE ) {
int
main (int argc, char* argv[])
{
unsigned int i,j,errors;
const char* filename;
SBMLDocument_t* document;
Model_t* m;
if (argc != 2)
{
printf("\nUsage: printNotes filename\n\n");
return 1;
}
filename = argv[1];
document = readSBML(filename);
errors = SBMLDocument_getNumErrors( document);
printf("\n%s\n\n", filename);
if(errors > 0)
{
SBMLDocument_printErrors(document, stderr);
SBMLDocument_free(document);
return errors;
}
/* Model */
m = SBMLDocument_getModel(document);
printNotes((SBase_t*)m, Model_getId(m));
for(i=0; i < Model_getNumReactions(m); i++)
{
Reaction_t* re = Model_getReaction( m, i);
printNotes((SBase_t*)re, Reaction_getId(re));
/* SpeciesReference (Reactant) */
for(j=0; j < Reaction_getNumReactants( re); j++)
{
SpeciesReference_t* rt = Reaction_getReactant(re, j);
if (SBase_isSetNotes((SBase_t*) rt)) printf(" ");
printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
}
/* SpeciesReference (Product) */
for(j=0; j < Reaction_getNumProducts( re ); j++)
{
SpeciesReference_t* rt = Reaction_getProduct( re, j);
if (SBase_isSetNotes((SBase_t*) rt)) printf(" ");
printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
}
/* ModifierSpeciesReference (Modifiers) */
for(j=0; j < Reaction_getNumModifiers( re ); j++)
{
SpeciesReference_t* md = Reaction_getModifier(re, j);
if (SBase_isSetNotes((SBase_t*) md)) printf(" ");
printNotes((SBase_t*)md, SpeciesReference_getSpecies( md ) );
}
/* KineticLaw */
if(Reaction_isSetKineticLaw( re ))
{
KineticLaw_t* kl = Reaction_getKineticLaw( re );
if (SBase_isSetNotes((SBase_t*) kl)) printf(" ");
printNotes((SBase_t*)kl, "");
/* Parameter */
for(j=0; j < KineticLaw_getNumParameters( kl ); j++)
{
Parameter_t* pa = KineticLaw_getParameter( kl, j);
if (SBase_isSetNotes((SBase_t*) pa)) printf(" ");
printNotes((SBase_t*)pa, Parameter_getId(pa));
}
}
}
/* Species */
for(i=0; i < Model_getNumSpecies(m); i++)
{
Species_t* sp = Model_getSpecies(m, i);
printNotes((SBase_t*)sp, Species_getId(sp));
}
/* Compartments */
for(i=0; i < Model_getNumCompartments( m ); i++)
{
Compartment_t* sp = Model_getCompartment(m, i);
printNotes((SBase_t*)sp, Compartment_getId(sp));
}
/* FunctionDefinition */
for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
{
FunctionDefinition_t* sp = Model_getFunctionDefinition(m, i);
printNotes((SBase_t*)sp, FunctionDefinition_getId(sp));
}
/* UnitDefinition */
for(i=0; i < Model_getNumUnitDefinitions(m); i++)
{
UnitDefinition_t* sp = Model_getUnitDefinition( m, i);
printNotes((SBase_t*)sp, UnitDefinition_getId(sp));
}
/* Parameter */
for(i=0; i < Model_getNumParameters( m ); i++)
{
Parameter_t* sp = Model_getParameter( m, i);
printNotes((SBase_t*)sp, Parameter_getId(sp));
}
/* Rule */
for(i=0; i < Model_getNumReactions( m ); i++)
{
Rule_t* sp = Model_getRule(m, i);
printNotes((SBase_t*)sp, "");
}
/* InitialAssignment */
for(i=0; i < Model_getNumInitialAssignments(m); i++)
{
InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
printNotes((SBase_t*)sp, "");
}
/* Event */
for(i=0; i < Model_getNumEvents(m); i++)
{
Event_t* sp = Model_getEvent(m, i);
printNotes((SBase_t*)sp, Event_getId(sp));
/* Trigger */
if(Event_isSetTrigger( sp ))
{
Trigger_t* tg = Event_getTrigger(sp);
if (SBase_isSetNotes( (SBase_t*) tg)) printf( " " );
printNotes((SBase_t*)tg, "");
}
/* Delay */
if(Event_isSetDelay(sp))
{
Delay_t* dl = Event_getDelay(sp);
if (SBase_isSetNotes( (SBase_t*) dl)) printf( " " );
printNotes((SBase_t*) dl, "");
}
/* EventAssignment */
for(j=0; j < Event_getNumEventAssignments(sp); j++)
{
EventAssignment_t* ea = Event_getEventAssignment(sp, j);
if (SBase_isSetNotes( (SBase_t*) ea)) printf( " " );
printNotes((SBase_t*)ea, "");
}
}
/* SpeciesType */
for(i=0; i < Model_getNumSpeciesTypes(m); i++)
{
SpeciesType_t* sp = Model_getSpeciesType(m, i);
printNotes((SBase_t*)sp, SpeciesType_getId(sp));
}
/* Constraints */
for(i=0; i < Model_getNumConstraints(m); i++)
{
Constraint_t* sp = Model_getConstraint(m, i);
printNotes((SBase_t*)sp, "");
}
SBMLDocument_free( document );
return errors;
}
