END_TEST
START_TEST (test_L3_Model_id)
{
const char *id = "mitochondria";
fail_unless( !Model_isSetId(M) );
Model_setId(M, id);
fail_unless( !strcmp(Model_getId(M), id) );
fail_unless( Model_isSetId(M) );
if (Model_getId(M) == id)
{
fail("Model_setId(...) did not make a copy of string.");
}
Model_unsetId(M);
fail_unless( !Model_isSetId(M) );
if (Model_getId(M) != NULL)
{
fail("Model_unsetId(M) did not clear string.");
}
}
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
printMath (Model_t *m)
{
unsigned int n;
/* a digraph must have a name thus
* need to check that Model_getId does not return NULL
* and provide a name if it does
*/
if (Model_getId(m) != NULL) {
fprintf(fout, "digraph %s {\n", Model_getId(m));
}
else {
fprintf(fout, "digraph example {\n");
}
fprintf(fout, "compound=true;\n");
for (n = 0; n < Model_getNumFunctionDefinitions(m); ++n)
{
printFunctionDefinition(n + 1, Model_getFunctionDefinition(m, n));
}
for (n = 0; n < Model_getNumRules(m); ++n)
{
printRuleMath(n + 1, Model_getRule(m, n));
}
printf("\n");
for (n = 0; n < Model_getNumReactions(m); ++n)
{
printReactionMath(n + 1, Model_getReaction(m, n));
}
printf("\n");
for (n = 0; n < Model_getNumEvents(m); ++n)
{
printEventMath(n + 1, Model_getEvent(m, n));
}
fprintf(fout, "}\n");
}
static int drawJacobyTxt(cvodeData_t *data, char *file)
{
int i, j;
char filename[WORDSIZE];
FILE *f;
sprintf(filename, "%s.dot", file);
f = fopen(filename, "w");
fprintf(f ,"digraph jacoby {\n");
fprintf(f ,"overlap=scale;\n");
if ( Model_isSetName(data->model->m) )
fprintf(f ,"label=\"%s at time %g\";\n", Model_getName(data->model->m),
data->currenttime);
else if ( Model_isSetId(data->model->m) )
fprintf(f ,"label=\"%s at time %g\";\n", Model_getId(data->model->m),
data->currenttime);
else
fprintf(f ,"label=\"at time %g\";\n", data->currenttime);
/*
Set edges from species A to species B if the
corresponding entry in the jacobian ((d[B]/dt)/d[A])
is not '0'. Set edge color 'red' and arrowhead 'tee'
if negative.
*/
for ( i=0; i<data->model->neq; i++ )
{
for ( j=0; j<data->model->neq; j++ )
{
if ( evaluateAST(data->model->jacob[i][j], data) != 0 )
{
fprintf(f ,"%s->%s [label=\"%g\" ",
data->model->names[j],
data->model->names[i],
evaluateAST(data->model->jacob[i][j],
data));
if ( evaluateAST(data->model->jacob[i][j], data) < 0 )
fprintf(f ,"arrowhead=tee color=red];\n");
else
fprintf(f ,"];\n");
}
}
}
for ( i=0; i<data->model->neq; i++ )
{
fprintf(f ,"%s [label=\"%s\"];", data->model->names[i],
data->model->names[i]);
}
fprintf(f, "}\n");
return 1;
}
END_TEST
START_TEST (test_L3_Model_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);
Model_t *m =
Model_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) m) == SBML_MODEL );
fail_unless( SBase_getMetaId ((SBase_t *) m) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) m) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) m) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) m) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) m) == 1 );
fail_unless( Model_getNamespaces (m) != NULL );
fail_unless( XMLNamespaces_getLength(Model_getNamespaces(m)) == 2 );
fail_unless( Model_getId (m) == NULL );
fail_unless( Model_getName (m) == NULL );
fail_unless( Model_getSubstanceUnits(m) == NULL );
fail_unless( Model_getTimeUnits(m) == NULL );
fail_unless( Model_getVolumeUnits(m) == NULL );
fail_unless( Model_getAreaUnits(m) == NULL );
fail_unless( Model_getLengthUnits(m) == NULL );
fail_unless( Model_getConversionFactor(m) == NULL );
fail_unless( !Model_isSetId (m) );
fail_unless( !Model_isSetName (m) );
fail_unless( !Model_isSetSubstanceUnits(m) );
fail_unless( !Model_isSetTimeUnits(m) );
fail_unless( !Model_isSetVolumeUnits(m) );
fail_unless( !Model_isSetAreaUnits(m) );
fail_unless( !Model_isSetLengthUnits(m) );
fail_unless( !Model_isSetConversionFactor(m) );
Model_free(m);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
static int openXMGrace(cvodeData_t *data)
{
double maxY;
/* Open XMGrace */
if ( !GraceIsOpen() ) {
GraceRegisterErrorFunction(grace_error);
/* Start Grace with a buffer size of 2048 and open the pipe */
if ( GraceOpen(2048) == -1 ) {
fprintf(stderr, "Can't run Grace. \n");
return 1;
}
else if ( GraceIsOpen() ) {
maxY = 1.0;
/*
"with g%d" might become useful, when printing multiple
graphs into one XMGrace subprocess.
*/
/* GracePrintf("with g%d", data->results->xmgrace); */
GracePrintf("world xmax %g", data->currenttime);
GracePrintf("world ymax %g", 1.25*maxY);
GracePrintf("xaxis tick major %g", data->currenttime/10);
/* GracePrintf("xaxis tick minor %d", (int) data->currenttime/100); */
GracePrintf("yaxis tick major %g", (1.25*maxY)/12.5 );
GracePrintf("xaxis label font 4");
GracePrintf("xaxis label \"time\"");
GracePrintf("xaxis ticklabel font 4");
GracePrintf("xaxis ticklabel char size 0.7");
GracePrintf("yaxis label font 4");
GracePrintf("yaxis label \"concentration\"");
GracePrintf("yaxis ticklabel font 4");
GracePrintf("yaxis ticklabel char size 0.7");
if ( Model_isSetName(data->model->simple) )
GracePrintf("subtitle \"%s\"", Model_getName(data->model->simple));
else if ( Model_isSetId(data->model->simple) )
GracePrintf("subtitle \"%s\"", Model_getId(data->model->simple));
else
GracePrintf("subtitle \"model has no name/id\"");
GracePrintf("subtitle font 8");
}
}
else {
fprintf(stderr, "Please close XMGrace first.\n");
return 1;
}
return 0;
}
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");
}
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;
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;
}
static int
drawModelTxt(Model_t *m, char *file) {
Species_t *s;
Reaction_t *re;
const ASTNode_t *math;
SpeciesReference_t *sref;
ModifierSpeciesReference_t *mref;
int i,j;
int reversible;
char filename[WORDSIZE];
FILE *f;
sprintf(filename, "%s.dot", file);
f = fopen(filename, "w");
fprintf(f ,"digraph reactionnetwork {\n");
fprintf(f ,"label=\"%s\";\n",
Model_isSetName(m) ?
Model_getName(m) : (Model_isSetId(m) ? Model_getId(m) : "noId") );
fprintf(f ,"overlap=scale;\n");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
re = Model_getReaction(m,i);
reversible = Reaction_getReversible(re);
for ( j=0; j<Reaction_getNumModifiers(re); j++ ) {
mref = Reaction_getModifier(re,j);
fprintf(f ,"%s->%s [style=dashed arrowhead=odot];\n",
ModifierSpeciesReference_getSpecies(mref), Reaction_getId(re));
}
for ( j=0; j<Reaction_getNumReactants(re); j++ ) {
sref = Reaction_getReactant(re,j);
fprintf(f ,"%s->%s [label=\"",
SpeciesReference_getSpecies(sref), Reaction_getId(re));
if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
fprintf(f ,"%s", SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1) {
fprintf(f ,"%g",SpeciesReference_getStoichiometry(sref));
}
}
if ( reversible == 1 ) {
fprintf(f ,"\" arrowtail=onormal];\n");
}
else {
fprintf(f ,"\" ];\n");
}
}
for ( j=0; j<Reaction_getNumProducts(re); j++ ) {
sref = Reaction_getProduct(re,j);
fprintf(f ,"%s->%s [label=\"",
Reaction_getId(re), SpeciesReference_getSpecies(sref));
if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
fprintf(f ,"%s ", SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1) {
fprintf(f ,"%g ",SpeciesReference_getStoichiometry(sref));
}
}
if ( reversible == 1 ) {
fprintf(f ,"\" arrowtail=onormal];\n");
}
else {
fprintf(f ,"\" ];\n");
}
}
}
for ( i=0; i<Model_getNumReactions(m); i++ ) {
re = Model_getReaction(m,i);
fprintf(f ,"%s [label=\"%s\" shape=box];\n",
Reaction_getId(re),
Reaction_isSetName(re) ?
Reaction_getName(re) : Reaction_getId(re));
}
for ( i=0; i<Model_getNumSpecies(m); i++) {
s = Model_getSpecies(m, i);
fprintf(f ,"%s [label=\"%s\"];",
Species_getId(s),
Species_isSetName(s) ? Species_getName(s) : Species_getId(s));
}
fprintf(f ,"}\n");
return 1;
}
SBML_ODESOLVER_API int drawJacoby(cvodeData_t *data, 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.");
drawJacobyTxt(data, file);
#else
int i, j;
GVC_t *gvc;
Agraph_t *g;
Agnode_t *r;
Agnode_t *s;
Agedge_t *e;
Agsym_t *a;
char name[WORDSIZE];
char label[WORDSIZE];
char *output[3];
char *command = "dot";
char *formatopt;
char *outfile;
/* setting name of outfile */
ASSIGN_NEW_MEMORY_BLOCK(outfile, strlen(file)+ strlen(format)+7, char, 0);
sprintf(outfile, "-o%s_jm.%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");
/* set graph label */
if ( Model_isSetName(data->model->m) )
sprintf(label, "%s at time %g", Model_getName(data->model->m),
data->currenttime);
else if ( Model_isSetId(data->model->m) )
sprintf(label, "%s at time %g", Model_getId(data->model->m),
data->currenttime);
else
sprintf(label, "label=\"at time %g\";\n", data->currenttime);
a = agraphattr(g, "label", "");
agxset(g, a->index, label);
/*
Set edges from species A to species B if the
corresponding entry in the jacobian ((d[B]/dt)/d[A])
is not '0'. Set edge color 'red' and arrowhead 'tee'
if negative.
*/
for ( i=0; i<data->model->neq; i++ ) {
for ( j=0; j<data->model->neq; j++ ) {
if ( evaluateAST(data->model->jacob[i][j], data) != 0 ) {
sprintf(name, "%s", data->model->names[j]);
r = agnode(g,name);
agset(r, "label", data->model->names[j]);
sprintf(label, "%s.htm", data->model->names[j]);
a = agnodeattr(g, "URL", "");
agxset(r, a->index, label);
sprintf(name,"%s", data->model->names[i]);
s = agnode(g,name);
agset(s, "label", data->model->names[i]);
sprintf(label, "%s.htm", data->model->names[i]);
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,r,s);
a = agedgeattr(g, "label", "");
sprintf(name, "%g", evaluateAST(data->model->jacob[i][j], data));
agxset (e, a->index, name);
if ( evaluateAST(data->model->jacob[i][j], data) < 0 ) {
a = agedgeattr(g, "arrowhead", "");
agxset(e, a->index, "tee");
a = agedgeattr(g, "color", "");
agxset(e, a->index, "red");
}
}
}
}
/* 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);
#endif
agclose(g);
/* 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;
}
static int
drawSensitivityTxt(cvodeData_t *data, char *file, double threshold) {
int i, j;
char filename[WORDSIZE];
FILE *f;
odeModel_t *om;
double *highest;
double *lowest;
om = data->model;
sprintf(filename, "%s.dot", file);
f = fopen(filename, "w");
fprintf(f ,"digraph jacoby {\n");
fprintf(f ,"overlap=scale;\n");
if ( Model_isSetName(om->m) )
fprintf(f ,"label=\"%s at time %g\";\n", Model_getName(om->m),
data->currenttime);
else if ( Model_isSetId(om->m) )
fprintf(f ,"label=\"%s at time %g\";\n", Model_getId(om->m),
data->currenttime);
else
fprintf(f ,"label=\"at time %g\";\n", data->currenttime);
/*
Set edges from species A to species B if the
corresponding entry in the jacobian ((d[B]/dt)/d[A])
is not '0'. Set edge color 'red' and arrowhead 'tee'
if negative.
*/
ASSIGN_NEW_MEMORY_BLOCK(highest, data->nsens, double, 0);
ASSIGN_NEW_MEMORY_BLOCK(lowest, data->nsens, double, 0);
for ( j=0; j<data->nsens; j++ ) {
highest[j] = 0;
lowest[j] = 0;
for ( i=0; i<om->neq; i++ ) {
if ( data->sensitivity[i][j] > highest[j] )
highest[j] = data->sensitivity[i][j];
if ( data->sensitivity[i][j] < lowest[j] )
lowest[j] = data->sensitivity[i][j];
}
}
for ( i=0; i<om->neq; i++ ) {
for ( j=0; j<data->nsens; j++ ) {
if ( (data->sensitivity[i][j] > threshold*highest[j]) ||
(data->sensitivity[i][j] < threshold*lowest[j]) ) {
fprintf(f ,"%s->%s [label=\"%g\" ",
om->names[om->index_sens[j]],
om->names[i],
data->sensitivity[i][j]);
if ( data->sensitivity[i][j] < 0 ) {
fprintf(f ,"arrowhead=tee color=red];\n");
}
else {
fprintf(f ,"];\n");
}
}
}
}
for ( i=0; i<om->neq; i++ ) {
fprintf(f ,"%s [label=\"%s\"];", om->names[i],
om->names[i]);
}
for ( i=0; i<data->nsens; i++ ) {
fprintf(f ,"%s [label=\"%s\"];", om->names[om->index_sens[i]],
om->names[om->index_sens[i]]);
}
fprintf(f, "}\n");
return 1;
}
static int printXMGReactionTimeCourse ( cvodeData_t *data )
{
int i, j, k, n;
double maxY, minY, result;
Model_t *m;
Reaction_t *r;
KineticLaw_t *kl;
ASTNode_t **kls;
odeModel_t *om = data->model;
cvodeResults_t *results = data->results;
maxY = 0.0;
minY = 0.0;
fprintf(stderr,
"Printing time development of reaction fluxes to XMGrace!\n");
if ( om->m == NULL ) {
fprintf(stderr, "Error: No reaction model availabe\n");
return 1;
}
else m = om->m;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr, "Error: Couldn't open XMGrace\n");
return 1;
}
GracePrintf("yaxis label \"%s\"", "flux [substance/time]");
if ( Model_isSetName(m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(m),
"reaction flux time courses");
else if ( Model_isSetId(m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(m),
"reaction flux time courses");
else
GracePrintf("subtitle \"model has no name, %s/id\"",
"reaction flux time courses");
/* print legend */
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
if ( Reaction_isSetName(r) )
GracePrintf("g0.s%d legend \"%s: %s \"\n", i+1,
Reaction_getId(r), Reaction_getName(r));
else
GracePrintf("g0.s%d legend \"%s \"\n", i+1, Reaction_getId(r));
}
GracePrintf("legend 1.155, 0.85");
GracePrintf("legend font 8");
GracePrintf("legend char size 0.6");
if(!(kls = (ASTNode_t **)calloc(Model_getNumReactions(m),
sizeof(ASTNode_t *))))
fprintf(stderr, "failed!\n");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
kl = Reaction_getKineticLaw(r);
kls[i] = copyAST(KineticLaw_getMath(kl));
AST_replaceNameByParameters(kls[i], KineticLaw_getListOfParameters(kl));
AST_replaceConstants(m, kls[i]);
}
/* evaluate flux for each time point and print to XMGrace */
for ( i=0; i<=results->nout; i++ ) {
n = 1;
/* set time and variable values to values at time[k] */
data->currenttime = results->time[i];
for ( j=0; j<data->model->neq; j++ )
data->value[j] = results->value[j][i];
/* evaluate kinetic law expressions */
for ( j=0; j<Model_getNumReactions(m); j++ ) {
result = evaluateAST(kls[j], data);
if ( result > maxY ) {
maxY = result;
GracePrintf("world ymax %g", 1.25*maxY);
}
if ( result < minY ) {
minY = result;
GracePrintf("world ymin %g", 1.25*minY);
}
GracePrintf("g0.s%d point %g, %g",
n, results->time[i], result);
n++;
}
}
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
closeXMGrace(data, "flux");
/* free temporary ASTNodes */
for ( i=0; i<Model_getNumReactions(m); i++ )
ASTNode_free(kls[i]);
free(kls);
return 0;
}
void printPhase(cvodeData_t *data)
{
#if !USE_GRACE
fprintf(stderr,
"odeSolver has been compiled without XMGRACE functionality.\n");
fprintf(stderr,
"Phase diagrams can only be printed to XMGrace at the moment.\n");
#else
int i,j;
double maxY;
double minY;
double maxX;
char *x;
double xvalue;
char *y;
double yvalue;
cvodeResults_t *results;
maxY = 1.0;
maxX = 1.0;
minY = 0.0;
if ( data==NULL || data->results==NULL ) {
Warn(stderr,
"No data available to print! Please integrate model first!\n");
return;
}
results = data->results;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr,
"Error: Couldn't open XMGrace\n");
return;
}
GracePrintf("world xmax %g", 1.25*maxX);
GracePrintf("world ymax %g", 1.25*maxY);
GracePrintf("xaxis tick major %g", (1.25*maxX)/12.5);
/* GracePrintf("xaxis tick minor %d", (int) data->currenttime/100); */
GracePrintf("yaxis tick major %g", (1.25*maxY)/12.5 );
if ( Model_isSetName(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(data->model->m),
"phase diagram");
else if ( Model_isSetId(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(data->model->m),
"phase diagram");
else
GracePrintf("subtitle \"model has no name, %s/id\"", "phase diagram");
GracePrintf("xaxis label \"species 1\"");
GracePrintf("yaxis label \"species 2\"");
printf("Please enter the IDs and NOT the NAMES of species!\n");
printf("In interactive mode press 'c' to see ID/NAME pairs.\n\n");
printf("Please enter the ID of the species for the x axis: ");
x = get_line(stdin);
x = util_trim(x);
GracePrintf("xaxis label \"%s\"", x);
GracePrintf("redraw");
printf("Please enter the ID of the species for the y axis: ");
y = get_line(stdin);
y = util_trim(y);
GracePrintf("yaxis label \"%s\"", y);
GracePrintf("redraw");
/* check if species exist */
xvalue = 1;
yvalue = 1;
for ( j=0; j<data->model->neq; j++ ) {
if ( !strcmp(x, data->model->names[j]) ) {
xvalue = 0;
GracePrintf("xaxis label \"%s\"", data->model->names[j]);
}
if ( !strcmp(y, data->model->names[j]) ) {
yvalue = 0;
GracePrintf("yaxis label \"%s\"", data->model->names[j]);
}
}
if ( xvalue || yvalue ) {
fprintf(stderr, "One of the entered species does not exist.\n");
GraceClose();
fprintf(stderr, "XMGrace subprocess closed. Please try again");
free(x);
free(y);
return;
}
fprintf(stderr, "Printing phase diagram to XMGrace!\n");
for ( i=0; i<=results->nout; ++i ) {
for ( j=0; j<data->model->neq; j++ ){
if ( !strcmp(x, data->model->names[j]) ) {
xvalue = results->value[j][i];
}
if ( !strcmp(y, data->model->names[j]) ) {
yvalue = results->value[j][i];
}
}
GracePrintf("g0.s1 point %g, %g", xvalue, yvalue);
if ( yvalue > maxY ) {
maxY = 1.25*yvalue;
GracePrintf("world ymax %g", maxY);
GracePrintf("yaxis tick major %g", maxY/10);
}
if ( xvalue > maxX ) {
maxX = 1.25*xvalue;
GracePrintf("world xmax %g", maxX);
GracePrintf("xaxis tick major %g", maxX/10);
}
/*
redrawing on each 10th step gives an impression,
how fast the two values change within the phase
diagram.
*/
if ( i%10 == 0 ) {
GracePrintf("redraw");
}
}
GracePrintf("redraw");
closeXMGrace(data, "phase");
free(x);
free(y);
#endif
return;
}
static int printXMGOdeTimeCourse(cvodeData_t *data)
{
int i, j, n;
double maxY;
double minY;
double result;
cvodeResults_t *results;
maxY = 0.01;
minY = 0.0;
fprintf(stderr,
"Printing time development of the ODEs (rates) to XMGrace!\n");
results = data->results;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr,
"Error: Couldn't open XMGrace\n");
return 1;
}
GracePrintf("yaxis label \"%s\"", "ODE values");
if ( Model_isSetName(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(data->model->m),
"ODEs time course");
else if ( Model_isSetId(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(data->model->m),
"ODEs time course");
else
GracePrintf("subtitle \"model has no name/id, %s\"",
"ODEs time course");
/* print legend */
if ( printXMGLegend(data, data->model->neq) > 0 ){
fprintf(stderr,
"Warning: Couldn't print legend\n");
return 1;
}
/* evaluate ODE at each time point and print to XMGrace */
for ( i=0; i<=results->nout; ++i ) {
n = 1;
data->currenttime = results->time[i];
for ( j=0; j<data->model->neq; j++ ) {
data->value[j] = results->value[j][i];
}
for ( j=0; j<data->model->neq; j++ ) {
result = evaluateAST(data->model->ode[j],data);
if ( result > maxY ) {
maxY = result;
GracePrintf("world ymax %g", 1.25*maxY);
}
if ( result < minY ) {
minY = result;
GracePrintf("world ymin %g", 1.25*minY);
}
GracePrintf("g0.s%d point %g, %g",
n, results->time[i], result);
n++;
}
/*
if ( i%10 == 0 ) {
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
}
*/
}
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
closeXMGrace(data, "rates");
return 0;
}
static int printXMGJacobianTimeCourse ( cvodeData_t *data )
{
int i, j, k, n;
double maxY;
double minY;
double result;
cvodeResults_t *results;
maxY = 0.0;
minY = 0.0;
fprintf(stderr,
"Printing time development of the jacobian matrix to XMGrace!\n");
results = data->results;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr,
"Error: Couldn't open XMGrace\n");
return 1;
}
GracePrintf("yaxis label \"%s\"", "jacobian matrix value");
if ( Model_isSetName(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(data->model->m),
"jacobian matrix time course");
else if ( Model_isSetId(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(data->model->m),
"jacobian matrix time course");
else
GracePrintf("subtitle \"model has no name, %s/id\"",
"jacobian matrix time course");
/* print legend */
n = 1;
for ( i=0; i<data->model->neq; i++ ) {
for ( j=0; j<data->model->neq; j++ ) {
GracePrintf("g0.s%d legend \"%s / %s\"\n",
n, data->model->names[i], data->model->names[j]);
n++;
}
}
GracePrintf("legend 1.155, 0.85");
GracePrintf("legend font 8");
GracePrintf("legend char size 0.6");
/* evaluate jacobian matrix for each time point and print to XMGrace */
for ( k = 0; k<=results->nout; k++ ) {
n = 1;
data->currenttime = results->time[i];
for ( i=0; i<data->model->neq; i++ ) {
/* set specie values to values at time[k] */
data->value[i] = results->value[i][k];
for ( j=0; j<data->model->neq; j++ ) {
result = evaluateAST(data->model->jacob[i][j], data);
if ( result > maxY ) {
maxY = result;
GracePrintf("world ymax %g", 1.25*maxY);
}
if ( result < minY ) {
minY = result;
GracePrintf("world ymin %g", 1.25*minY);
}
GracePrintf("g0.s%d point %g, %g",
n, results->time[k], result);
n++;
}
}
/*
if ( k%10 == 0 ) {
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
}
*/
}
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
closeXMGrace(data, "jac");
return 0;
}