int main(int, char *[]){
// sanity check on test matrix - should be symetrical
check_symmetry(test_multiplication_result);
bool rval = true;
TEST_EACH_VALUE_PAIR
std::cout << (rval ? "success!" : "failure") << std::endl;
return ! rval ;
}
/*------------------------------------------------------------*/
PUBLIC void read_parameter_file(const char fname[]){
char *line, ident[256];
enum parset type;
int r;
if (!(fp=fopen(fname,"r"))) {
fprintf(stderr,
"\nread_parameter_file:\n"
"\t\tcan't open file %s\n"
"\t\tusing default parameters instead.\n", fname);
return;
}
if (!(line = get_line(fp))) {
fprintf(stderr," File %s is inproper.\n", fname);
fclose(fp);
return;
}
if (strncmp(line,"## RNAfold parameter file v2.0",30)!=0) {
fprintf(stderr,
"Missing header line in file.\n"
"May be this file has not v2.0 format.\n"
"Use INTERRUPT-key to stop.\n");
}
free(line);
while((line=get_line(fp))) {
r = sscanf(line, "# %255s", ident);
if (r==1) {
type = gettype(ident);
switch (type){
case QUIT: break;
case S: rd_2dim(&(stack37[0][0]), NBPAIRS+1, NBPAIRS+1, 1, 1);
break;
case S_H: rd_2dim(&(stackdH[0][0]), NBPAIRS+1, NBPAIRS+1, 1, 1);
break;
case HP: rd_1dim(&(hairpin37[0]), 31, 0);
break;
case HP_H: rd_1dim(&(hairpindH[0]), 31, 0);
break;
case B: rd_1dim(&(bulge37[0]), 31, 0);
break;
case B_H: rd_1dim(&(bulgedH[0]), 31, 0);
break;
case IL: rd_1dim(&(internal_loop37[0]), 31, 0);
break;
case IL_H: rd_1dim(&(internal_loopdH[0]), 31, 0);
break;
case MME: rd_3dim(&(mismatchExt37[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MME_H: rd_3dim(&(mismatchExtdH[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMH: rd_3dim(&(mismatchH37[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMH_H: rd_3dim(&(mismatchHdH[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMI: rd_3dim(&(mismatchI37[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMI_H: rd_3dim(&(mismatchIdH[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMI1N: rd_3dim(&(mismatch1nI37[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMI1N_H: rd_3dim(&(mismatch1nIdH[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMI23: rd_3dim(&(mismatch23I37[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMI23_H: rd_3dim(&(mismatch23IdH[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMM: rd_3dim(&(mismatchM37[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case MMM_H: rd_3dim(&(mismatchMdH[0][0][0]),
NBPAIRS+1, 5, 5,
1, 0, 0);
break;
case INT11: rd_4dim(&(int11_37[0][0][0][0]),
NBPAIRS+1, NBPAIRS+1, 5, 5,
1, 1, 0, 0);
break;
case INT11_H: rd_4dim(&(int11_dH[0][0][0][0]),
NBPAIRS+1, NBPAIRS+1, 5, 5,
1, 1, 0, 0);
break;
case INT21: rd_5dim(&(int21_37[0][0][0][0][0]),
NBPAIRS+1, NBPAIRS+1, 5, 5, 5,
1, 1, 0, 0, 0);
break;
case INT21_H: rd_5dim(&(int21_dH[0][0][0][0][0]),
NBPAIRS+1, NBPAIRS+1, 5, 5, 5,
1, 1, 0, 0, 0);
break;
case INT22: rd_6dim_slice(&(int22_37[0][0][0][0][0][0]),
NBPAIRS+1, NBPAIRS+1, 5, 5, 5, 5,
1, 1, 1, 1, 1, 1,
1, 1, 0, 0, 0, 0);
update_nst(int22_37);
break;
case INT22_H: rd_6dim_slice(&(int22_dH[0][0][0][0][0][0]),
NBPAIRS+1, NBPAIRS+1, 5, 5, 5, 5,
1, 1, 1, 1, 1, 1,
1, 1, 0, 0, 0, 0);
update_nst(int22_dH);
break;
case D5: rd_2dim(&(dangle5_37[0][0]), NBPAIRS+1, 5, 1, 0);
break;
case D5_H: rd_2dim(&(dangle5_dH[0][0]), NBPAIRS+1, 5, 1, 0);
break;
case D3: rd_2dim(&(dangle3_37[0][0]), NBPAIRS+1, 5, 1, 0);
break;
case D3_H: rd_2dim(&(dangle3_dH[0][0]), NBPAIRS+1, 5, 1, 0);
break;
case ML: {
int values[6];
rd_1dim(&values[0], 6, 0);
ML_BASE37 = values[0];
ML_BASEdH = values[1];
ML_closing37 = values[2];
ML_closingdH = values[3];
ML_intern37 = values[4];
ML_interndH = values[5];
}
break;
case NIN: {
int values[3];
rd_1dim(&values[0], 3, 0);
ninio37 = values[0];
niniodH = values[1];
MAX_NINIO = values[2];
}
break;
case MISC: {
int values[4];
rd_1dim(&values[0], 4, 0);
DuplexInit37 = values[0];
DuplexInitdH = values[1];
TerminalAU37 = values[2];
TerminalAUdH = values[3];
}
break;
case TL: rd_Tetraloop37();
break;
case TRI: rd_Triloop37();
break;
case HEX: rd_Hexaloop37();
break;
default: /* do nothing but complain */
fprintf(stderr,"read_epars: Unknown field identifier in `%s'\n", line);
}
} /* else ignore line */
free(line);
}
fclose(fp);
check_symmetry();
return;
}
int m2sim_runge_kutta_substep(m2sim *m2, double dt, double rkparam)
{
int err = 0;
err += m2sim_calculate_gradient(m2);
check_symmetry(m2, "A");
err += m2sim_calculate_flux(m2); /* FAILURES: bad eigenvalues */
check_symmetry(m2, "B");
err += m2sim_synchronize_guard(m2); /* so that Godunov fluxes are communicated */
check_symmetry(m2, "C");
err += m2sim_calculate_emf(m2);
check_symmetry(m2, "D");
err += m2sim_exchange_flux(m2, dt);
check_symmetry(m2, "E");
err += m2sim_add_source_terms(m2, dt);
check_symmetry(m2, "F");
err += m2sim_average_runge_kutta(m2, rkparam);
check_symmetry(m2, "G");
err += m2sim_enforce_boundary_condition(m2);
check_symmetry(m2, "H");
err += m2sim_magnetic_flux_to_cell_center(m2);
check_symmetry(m2, "I");
err += m2sim_from_conserved_all(m2);
check_symmetry(m2, "J");
err += m2sim_synchronize_guard(m2);
check_symmetry(m2, "K");
return err;
}
/*------------------------------------------------------------*/
PUBLIC void read_parameter_file(const char fname[])
{
char *line, ident[32];
enum parset type;
int r, changed=0;
if (!(fp=fopen(fname,"r"))) {
fprintf(stderr,
"\nread_parameter_file:\n"
"\t\tcan't open file %s\n"
"\t\tusing default parameters instead.\n", fname);
return;
}
if (!(line = get_line(fp))) {
fprintf(stderr," File %s is inproper.\n", fname);
fclose(fp);
return;
}
if (strncmp(line,"## RNAfold parameter file",25)!=0) {
fprintf(stderr,
"Missing header line in file.\n"
"May be this file has incorrect format.\n"
"Use INTERRUPT-key to stop.\n");
}
free(line);
while((line=get_line(fp))) {
r = sscanf(line, "# %31s", ident);
if (r==1) {
type = gettype(ident);
switch (type)
{
case QUIT: break;
case SH: rd_stacks(enthalpies); changed |= SH; break;
case S: rd_stacks(stack37); changed |= S; break;
case HP: rd_loop(hairpin37); changed |= HP; break;
case B: rd_loop(bulge37); changed |= B; break;
case IL: rd_loop(internal_loop37); changed |= IL; break;
case MMH: rd_mismatch(mismatchH37); changed |= MMH; break;
case MMI: rd_mismatch(mismatchI37); changed |= MMI; break;
case MMM: rd_mismatch(mismatchM37); changed |= MMM; break;
case MM_H: rd_mismatch(mism_H); changed |= MM_H; break;
case INT11: rd_int11(int11_37); changed |= INT11; break;
case INT11_H:rd_int11(int11_H); changed |= INT11_H; break;
case INT21: rd_int21(int21_37); changed |= INT21; break;
case INT21_H:rd_int21(int21_H); changed |= INT21_H; break;
case INT22: rd_int22(int22_37); changed |= INT22; break;
case INT22_H:rd_int22(int22_H); changed |= INT22_H; break;
case DE5: rd_dangle(dangle5_37); changed |= DE5; break;
case DE5_H: rd_dangle(dangle5_H); changed |= DE5_H; break;
case DE3: rd_dangle(dangle3_37); changed |= DE3; break;
case DE3_H: rd_dangle(dangle3_H); changed |= DE3_H; break;
case ML: rd_MLparams(); changed |= ML; break;
case NIN: rd_ninio(); changed |= NIN; break;
case TL: rd_Tetra_loop(); changed |= TL; break;
case TRI: rd_Tri_loop(); changed |= TRI; break;
case MISC: rd_misc(); changed |= MISC; break;
default: /* maybe it's a temperature */
r=sscanf(ident, "%f", &rtemp);
if (r!=1) fprintf(stderr," Unknown field identifier in `%s'\n", line);
}
} /* else ignore line */
free(line);
}
fclose(fp);
check_symmetry();
return;
}
