/*************************************************************************
which_unimolecular:
In: the reaction we're testing
Out: int containing which unimolecular reaction occurs (one must occur)
*************************************************************************/
int which_unimolecular(struct rxn *rx, struct abstract_molecule *a,
struct rng_state *rng) {
if (rx->n_pathways == 1) {
return 0;
}
int max = rx->n_pathways - 1;
double match = rng_dbl(rng);
if (!rx->rates) {
match = match * rx->cum_probs[max];
return binary_search_double(rx->cum_probs, match, max, 1);
}
/* Cooperativity case: Check neighboring molecules */
else {
double cum_probs[rx->n_pathways];
for (int m = 0; m < rx->n_pathways; ++m) {
if (!rx->rates[m])
cum_probs[m] = rx->cum_probs[m];
else if (m == 0)
cum_probs[m] = macro_lookup_rate(rx->rates[m], a, rx->pb_factor);
else
cum_probs[m] = cum_probs[m - 1] +
macro_lookup_rate(rx->rates[m], a, rx->pb_factor);
}
match = match * cum_probs[max];
return binary_search_double(cum_probs, match, max, 1);
}
}
/*************************************************************************
test_bimolecular
In: the reaction we're testing
a scaling coefficient depending on how many timesteps we've
moved at once (1.0 means one timestep) and/or missing interaction area
local probability factor (positive only for the reaction between two
surface molecules, otherwise equal to zero)
reaction partners
Out: RX_NO_RX if no reaction occurs
int containing which reaction pathway to take if one does occur
Note: If this reaction does not return RX_NO_RX, then we update
counters appropriately assuming that the reaction does take place.
*************************************************************************/
int test_bimolecular(struct rxn *rx, double scaling, double local_prob_factor,
struct abstract_molecule *a1, struct abstract_molecule *a2,
struct rng_state *rng) {
if (a1 != NULL && a2 != NULL) {
assert(periodic_boxes_are_identical(a1->periodic_box, a2->periodic_box));
}
/* rescale probabilities for the case of the reaction
between two surface molecules */
double min_noreaction_p = rx->min_noreaction_p;
if (local_prob_factor > 0) {
min_noreaction_p = rx->min_noreaction_p * local_prob_factor;
}
/* Check if we missed any reactions
Instead of scaling rx->cum_probs array we scale random probability */
double p = 0.0; /* random number probability */
if (min_noreaction_p < scaling) /* Definitely CAN scale enough */
{
/* Instead of scaling rx->cum_probs array we scale random probability */
p = rng_dbl(rng) * scaling;
if (p >= min_noreaction_p)
return RX_NO_RX;
} else /* May or may not scale enough. check varying pathways. */
{
double max_p = rx->cum_probs[rx->n_pathways - 1];
if (local_prob_factor > 0)
max_p *= local_prob_factor;
if (max_p >= scaling) /* we cannot scale enough. add missed rxns */
{
/* How may reactions will we miss? */
if (scaling == 0.0)
rx->n_skipped += GIGANTIC;
else
rx->n_skipped += (max_p / scaling) - 1.0;
/* Keep the proportions of outbound pathways the same. */
p = rng_dbl(rng) * max_p;
} else /* we can scale enough */
{
/* Instead of scaling rx->cum_probs array we scale random probability */
p = rng_dbl(rng) * scaling;
if (p >= max_p)
return RX_NO_RX;
}
}
/* If we have only fixed pathways... */
int M = rx->n_pathways - 1;
if (local_prob_factor > 0)
return binary_search_double(rx->cum_probs, p, M, local_prob_factor);
else
return binary_search_double(rx->cum_probs, p, M, 1);
}
/**
* @brief binary_search
* Effettua una ricerca binaria di n sull'array ordinato v.
* Restituisce -1 se n non è presente nell'array.
* @param n: numero da cercare
* @param first: indice del primo elemento dell'array
* @param last: indice dell'ultimo elemento dell'array
* @param v: array su cui effettuare la ricerca
* @return l'indice di n nell'array.
* se n non è presente, restituisce -1.
*/
int binary_search_double(double n, int first, int last, QVector<double> & v) {
int mid;
if (first <= last){
mid = (first + last) / 2;
if (v[mid] < n) return (binary_search_double (n, mid+1, last, v) );
if (v[mid] == n) return mid;
if (v[mid] > n) return (binary_search_double (n, first, mid-1, v) );
}
return -1;
}
/*************************************************************************
test_intersect
In: the reaction we're testing
a probability multiplier depending on how many timesteps we've
moved at once (1.0 means one timestep)
Out: RX_NO_RX if no reaction occurs (assume reflection)
int containing which reaction occurs if one does occur
Note: If not RX_NO_RX, and not the trasparency shortcut, then we
update counters assuming the reaction will take place.
*************************************************************************/
int test_intersect(struct rxn *rx, double scaling, struct rng_state *rng) {
double p;
if (rx->n_pathways <= RX_SPECIAL)
return rx->n_pathways;
if (rx->cum_probs[rx->n_pathways - 1] > scaling) {
if (scaling <= 0.0)
rx->n_skipped += GIGANTIC;
else
rx->n_skipped += rx->cum_probs[rx->n_pathways - 1] / scaling - 1.0;
p = rng_dbl(rng) * rx->cum_probs[rx->n_pathways - 1];
} else {
p = rng_dbl(rng) * scaling;
if (p > rx->cum_probs[rx->n_pathways - 1])
return RX_NO_RX;
}
int M = rx->n_pathways - 1;
if (p > rx->cum_probs[M])
return RX_NO_RX;
int max = rx->n_pathways - 1;
double match = rng_dbl(rng);
match = match * rx->cum_probs[max];
return binary_search_double(rx->cum_probs, match, max, 1);
}
/*************************************************************************
test_many_unimol:
In: an array of reactions we're testing
the number of elements in the array of reactions
abstract molecule that undergoes reaction
Out: NULL if no reaction occurs (safety check, do not expect to happen),
reaction object otherwise (one must always occur)
*************************************************************************/
struct rxn *test_many_unimol(struct rxn **rx, int n,
struct abstract_molecule *a,
struct rng_state *rng) {
if (n == 0) {
return NULL;
}
if (n == 1) {
return rx[0];
}
double rxp[n]; /* array of cumulative rxn probabilities */
rxp[0] = rx[0]->max_fixed_p;
int i; /* index in the array of reactions - return value */
for (i = 1; i < n; i++) {
rxp[i] = rxp[i - 1] + rx[i]->max_fixed_p;
}
double p = rng_dbl(rng) * rxp[n - 1];
/* Pick the reaction that happens */
i = binary_search_double(rxp, p, n - 1, 1);
return rx[i];
}
/*************************************************************************
test_many_intersect:
In: an array of reactions we're testing
a probability multiplier depending on how many timesteps we've
moved at once (1.0 means one timestep)
the number of elements in the array of reactions
placeholder for the chosen pathway in the reaction (return value)
Out: RX_NO_RX if no reaction occurs (assume reflection)
index in the reaction array if reaction does occur
Note: If not RX_NO_RX, and not the trasparency shortcut, then we
update counters assuming the reaction will take place.
*************************************************************************/
int test_many_intersect(struct rxn **rx, double scaling, int n,
int *chosen_pathway, struct rng_state *rng) {
if (n == 1)
return test_intersect(rx[0], scaling, rng);
// array of cumulative rxn probabilities
double rxp[n];
rxp[0] = rx[0]->max_fixed_p / scaling;
int i; /* index in the array of reactions - return value */
for (i = 1; i < n; i++) {
rxp[i] = rxp[i - 1] + rx[i]->max_fixed_p / scaling;
}
double p;
if (rxp[n - 1] > 1.0) {
double f = rxp[n - 1] - 1.0; /* Number of failed reactions */
for (i = 0; i < n; i++) /* Distribute failures */
{
rx[i]->n_skipped +=
f * (rx[i]->cum_probs[rx[i]->n_pathways - 1]) / rxp[n - 1];
}
p = rng_dbl(rng) * rxp[n - 1];
} else {
p = rng_dbl(rng);
if (p > rxp[n - 1])
return RX_NO_RX;
}
/* Pick the reaction that happens */
i = binary_search_double(rxp, p, n - 1, 1);
struct rxn *my_rx = rx[i];
if (i > 0)
p = (p - rxp[i - 1]);
p = p * scaling;
/* Now pick the pathway within that reaction */
*chosen_pathway =
binary_search_double(my_rx->cum_probs, p, my_rx->n_pathways - 1, 1);
return i;
}
/*************************************************************************
which_unimolecular:
In: the reaction we're testing
Out: int containing which unimolecular reaction occurs (one must occur)
*************************************************************************/
int which_unimolecular(struct rxn *rx, struct abstract_molecule *a,
struct rng_state *rng) {
if (rx->n_pathways == 1) {
return 0;
}
int max = rx->n_pathways - 1;
double match = rng_dbl(rng);
match = match * rx->cum_probs[max];
return binary_search_double(rx->cum_probs, match, max, 1);
}
/*************************************************************************
test_many_unimol:
In: an array of reactions we're testing
the number of elements in the array of reactions
abstract molecule that undergoes reaction
Out: NULL if no reaction occurs (safety check, do not expect to happen),
reaction object otherwise (one must always occur)
*************************************************************************/
struct rxn *test_many_unimol(struct rxn **rx, int n,
struct abstract_molecule *a,
struct rng_state *rng) {
if (n == 0) {
return NULL;
}
if (n == 1) {
return rx[0];
}
double rxp[n]; /* array of cumulative rxn probabilities */
rxp[0] = rx[0]->max_fixed_p;
int path_idx;
if (rx[0]->rates) {
for (path_idx = rx[0]->n_pathways; --path_idx != 0;) {
if (!rx[0]->rates[path_idx]) {
break;
}
rxp[0] += macro_lookup_rate(rx[0]->rates[path_idx], a, rx[0]->pb_factor);
}
}
int i; /* index in the array of reactions - return value */
for (i = 1; i < n; i++) {
rxp[i] = rxp[i - 1] + rx[i]->max_fixed_p;
if (rx[i]->rates) {
for (path_idx = rx[i]->n_pathways; --path_idx != 0;) {
if (!rx[i]->rates[path_idx]) {
break;
}
rxp[i] +=
macro_lookup_rate(rx[i]->rates[path_idx], a, rx[i]->pb_factor);
}
}
}
double p = rng_dbl(rng) * rxp[n - 1];
/* Pick the reaction that happens */
i = binary_search_double(rxp, p, n - 1, 1);
return rx[i];
}
/*************************************************************************
test_many_reactions_all_neighbors:
In: an array of reactions we're testing
an array of scaling coefficients depending on how many timesteps
we've moved at once (1.0 means one timestep) and/or missing
interaction areas
an array of local probability factors for the corresponding reactions
the number of elements in the array of reactions
placeholder for the chosen pathway in the reaction (works as return
value)
Out: RX_NO_RX if no reaction occurs
index in the reaction array corresponding to which reaction occurs
if one does occur
Note: If this reaction does not return RX_NO_RX, then we update
counters appropriately assuming that the reaction does take place.
Note: this uses only one call to get a random double, so you can't
effectively sample events that happen less than 10^-9 of the
time (for 32 bit random number).
NOTE: This function should be used for now only for the reactions
between three surface molecules.
*************************************************************************/
int test_many_reactions_all_neighbors(struct rxn **rx, double *scaling,
double *local_prob_factor, int n,
int *chosen_pathway,
struct rng_state *rng) {
if (local_prob_factor == NULL)
mcell_internal_error("There is no local probability factor information in "
"the function 'test_many_reactions_all_neighbors().");
if (n == 1)
return test_bimolecular(rx[0], scaling[0], local_prob_factor[0], NULL, NULL,
rng);
double rxp[n]; /* array of cumulative rxn probabilities */
if (local_prob_factor[0] > 0) {
rxp[0] = (rx[0]->max_fixed_p) * local_prob_factor[0] / scaling[0];
} else {
rxp[0] = rx[0]->max_fixed_p / scaling[0];
}
// i: index in the array of reactions - return value
for (int i = 1; i < n; i++) {
if (local_prob_factor[i] > 0) {
rxp[i] =
rxp[i - 1] + (rx[i]->max_fixed_p) * local_prob_factor[i] / scaling[i];
} else {
rxp[i] = rxp[i - 1] + rx[i]->max_fixed_p / scaling[i];
}
}
double p;
if (rxp[n - 1] > 1.0) {
double f = rxp[n - 1] - 1.0; /* Number of failed reactions */
for (int i = 0; i < n; i++) /* Distribute failures */
{
if (local_prob_factor[i] > 0) {
rx[i]->n_skipped += f * ((rx[i]->cum_probs[rx[i]->n_pathways - 1]) *
local_prob_factor[i]) /
rxp[n - 1];
} else {
rx[i]->n_skipped +=
f * (rx[i]->cum_probs[rx[i]->n_pathways - 1]) / rxp[n - 1];
}
}
p = rng_dbl(rng) * rxp[n - 1];
} else {
p = rng_dbl(rng);
if (p > rxp[n - 1])
return RX_NO_RX;
}
/* Pick the reaction that happens */
int i = binary_search_double(rxp, p, n - 1, 1);
struct rxn *my_rx = rx[i];
double my_local_prob_factor = local_prob_factor[i];
if (i > 0)
p = (p - rxp[i - 1]);
p = p * scaling[i];
/* Now pick the pathway within that reaction */
int M = my_rx->n_pathways - 1;
if (my_local_prob_factor > 0) {
*chosen_pathway =
binary_search_double(my_rx->cum_probs, p, M, my_local_prob_factor);
} else {
*chosen_pathway = binary_search_double(my_rx->cum_probs, p, M, 1);
}
return i;
}
/*************************************************************************
test_many_bimolecular:
In: an array of reactions we're testing
scaling coefficients depending on how many timesteps we've moved
at once (1.0 means one timestep) and/or missing interaction areas
local probability factor for the corresponding reactions
the number of elements in the array of reactions
placeholder for the chosen pathway in the reaction (works as return
value)
a flag to indicate if
Out: RX_NO_RX if no reaction occurs
index in the reaction array corresponding to which reaction occurs
if one does occur
Note: If this reaction does not return RX_NO_RX, then we update
counters appropriately assuming that the reaction does take place.
Note: this uses only one call to get a random double, so you can't
effectively sample events that happen less than 10^-9 of the
time (for 32 bit random number).
NOTE: This function was merged with test_many_bimolecular_all_neighbors.
These two functions were almost identical, and the behavior of the
"all_neighbors" version is preserved with a flag that can be passed in.
For reactions between two surface molecules, set this flag to 1. For
such reactions (local_prob_factor > 0)
*************************************************************************/
int test_many_bimolecular(struct rxn **rx, double *scaling,
double local_prob_factor, int n, int *chosen_pathway,
struct abstract_molecule **complexes,
int *complex_limits, struct rng_state *rng,
int all_neighbors_flag) {
double rxp[2 * n]; /* array of cumulative rxn probabilities */
struct rxn *my_rx;
int i; /* index in the array of reactions - return value */
int m, M;
double p, f;
int has_coop_rate = 0;
int nmax;
if (all_neighbors_flag && local_prob_factor <= 0)
mcell_internal_error("Local probability factor = %g in the function "
"'test_many_bimolecular_all_neighbors().",
local_prob_factor);
if (n == 1) {
if (all_neighbors_flag)
return test_bimolecular(rx[0], scaling[0], local_prob_factor,
complexes[0], NULL, rng);
else
return test_bimolecular(rx[0], 0, scaling[0], complexes[0], NULL, rng);
}
/* Note: lots of division here, if we're CPU-bound,could invert the
definition of scaling_coefficients */
if (rx[0]->rates)
has_coop_rate = 1;
if (all_neighbors_flag && local_prob_factor > 0) {
rxp[0] = (rx[0]->max_fixed_p) * local_prob_factor / scaling[0];
} else {
rxp[0] = rx[0]->max_fixed_p / scaling[0];
}
for (i = 1; i < n; i++) {
if (all_neighbors_flag && local_prob_factor > 0) {
rxp[i] =
rxp[i - 1] + (rx[i]->max_fixed_p) * local_prob_factor / scaling[i];
} else {
rxp[i] = rxp[i - 1] + rx[i]->max_fixed_p / scaling[i];
}
if (rx[i]->rates)
has_coop_rate = 1;
}
if (has_coop_rate) {
for (; i < 2 * n; ++i) {
if (all_neighbors_flag && local_prob_factor > 0) {
rxp[i] = rxp[i - 1] +
(rx[i - n]->min_noreaction_p - rx[i - n]->max_fixed_p) *
local_prob_factor / scaling[i];
} else {
rxp[i] =
rxp[i - 1] +
(rx[i - n]->min_noreaction_p - rx[i - n]->max_fixed_p) / scaling[i];
}
}
}
nmax = i;
if (has_coop_rate) {
p = rng_dbl(rng);
/* Easy out - definitely no reaction */
if (p > rxp[nmax - 1])
return RX_NO_RX;
/* Might we have missed any? */
if (rxp[nmax - 1] > 1.0) {
double deficit = 0.0;
int cxNo = 0;
for (i = n; i < 2 * n; ++i) {
if (i - n >= complex_limits[cxNo])
++cxNo;
for (int n_path = 0; n_path < rx[i]->n_pathways; ++n_path) {
if (rx[i]->rates[n_path] == NULL)
continue;
deficit += macro_lookup_rate(rx[i]->rates[n_path], complexes[cxNo],
scaling[i - n] * rx[i]->pb_factor);
}
rxp[n] -= deficit;
}
/* Ok, did we REALLY miss any? */
if (rxp[nmax - 1] > 1.0) {
f = rxp[nmax - 1] - 1.0; /* Number of failed reactions */
for (i = 0; i < n; i++) /* Distribute failures */
{
if (all_neighbors_flag && local_prob_factor > 0) {
rx[i]->n_skipped += f * ((rx[i]->max_fixed_p) * local_prob_factor +
rxp[n + i] - rxp[n + i - 1]) /
rxp[n - 1];
} else {
rx[i]->n_skipped +=
f * (rx[i]->max_fixed_p + rxp[n + i] - rxp[n + i - 1]) /
rxp[n - 1];
}
}
p *= rxp[nmax - 1];
}
/* Was there any reaction? */
if (p > rxp[nmax - 1])
return RX_NO_RX;
/* Pick the reaction that happens. Note that the binary search is over
* 2*n items, not n. The first n are the fixed rate pathways of each of
* the n reactions, and the next n are the cooperative pathways. */
i = binary_search_double(rxp, p, nmax - 1, 1);
if (i > 0)
p = (p - rxp[i - 1]);
/* If it was a varying rate... */
if (i >= n) {
i -= n;
p = p * scaling[i];
cxNo = 0;
while (i >= complex_limits[cxNo])
++cxNo;
for (int n_path = 0; n_path < rx[i]->n_pathways; ++n_path) {
if (rx[i]->rates[n_path] == NULL)
continue;
double prob = macro_lookup_rate(rx[i]->rates[n_path], complexes[cxNo],
scaling[i] * rx[i]->pb_factor);
if (p > prob)
p -= prob;
else {
*chosen_pathway = n_path;
return i;
}
}
return RX_NO_RX;
}
/* else it was a fixed rate... */
else {
p = p * scaling[i];
/* Now pick the pathway within that reaction */
my_rx = rx[i];
M = my_rx->n_pathways - 1;
if (all_neighbors_flag && local_prob_factor > 0)
m = binary_search_double(my_rx->cum_probs, p, M, local_prob_factor);
else
m = binary_search_double(my_rx->cum_probs, p, M, 1);
*chosen_pathway = m;
return i;
}
}
/* We didn't miss any reactions and also don't need to consult the varying
* probabilities */
else if (p <= rxp[n - 1]) {
/* Pick the reaction that happens */
i = binary_search_double(rxp, p, n - 1, 1);
my_rx = rx[i];
if (i > 0)
p = (p - rxp[i - 1]);
p = p * scaling[i];
/* Now pick the pathway within that reaction */
M = my_rx->n_pathways - 1;
if (all_neighbors_flag && local_prob_factor > 0)
m = binary_search_double(my_rx->cum_probs, p, M, local_prob_factor);
else
m = binary_search_double(my_rx->cum_probs, p, M, 1);
*chosen_pathway = m;
return i;
}
/* The hard way. We're in the cooperativity region of probability space
* and will need to examine the varying probabilities. */
else {
p -= rxp[n - 1];
int cxNo = 0;
for (i = n; i < 2 * n; ++i) {
if (i - n >= complex_limits[cxNo])
++cxNo;
for (int n_path = 0; n_path < rx[i]->n_pathways; ++n_path) {
if (rx[i]->rates[n_path] == NULL)
continue;
double prob = macro_lookup_rate(rx[i]->rates[n_path], complexes[cxNo],
scaling[i - n] * rx[i]->pb_factor);
if (p > prob)
p -= prob;
else {
*chosen_pathway = n_path;
return i - n;
}
}
}
return RX_NO_RX;
}
mcell_internal_error("Should never reach this point in the code.");
return RX_NO_RX;
} else {
if (rxp[n - 1] > 1.0) {
f = rxp[n - 1] - 1.0; /* Number of failed reactions */
for (i = 0; i < n; i++) /* Distribute failures */
{
if (all_neighbors_flag && local_prob_factor > 0) {
rx[i]->n_skipped += f * ((rx[i]->cum_probs[rx[i]->n_pathways - 1]) *
local_prob_factor) /
rxp[n - 1];
} else {
rx[i]->n_skipped +=
f * (rx[i]->cum_probs[rx[i]->n_pathways - 1]) / rxp[n - 1];
}
}
p = rng_dbl(rng) * rxp[n - 1];
} else {
p = rng_dbl(rng);
if (p > rxp[n - 1])
return RX_NO_RX;
}
/* Pick the reaction that happens */
i = binary_search_double(rxp, p, n - 1, 1);
my_rx = rx[i];
if (i > 0)
p = (p - rxp[i - 1]);
p = p * scaling[i];
/* Now pick the pathway within that reaction */
M = my_rx->n_pathways - 1;
if (all_neighbors_flag && local_prob_factor > 0)
m = binary_search_double(my_rx->cum_probs, p, M, local_prob_factor);
else
m = binary_search_double(my_rx->cum_probs, p, M, 1);
*chosen_pathway = m;
return i;
}
}
/*************************************************************************
test_bimolecular
In: the reaction we're testing
a scaling coefficient depending on how many timesteps we've
moved at once (1.0 means one timestep) and/or missing interaction area
local probability factor (positive only for the reaction between two
surface molecules, otherwise equal to zero)
reaction partners
Out: RX_NO_RX if no reaction occurs
int containing which reaction pathway to take if one does occur
Note: If this reaction does not return RX_NO_RX, then we update
counters appropriately assuming that the reaction does take place.
*************************************************************************/
int test_bimolecular(struct rxn *rx, double scaling, double local_prob_factor,
struct abstract_molecule *a1, struct abstract_molecule *a2,
struct rng_state *rng) {
double p; /* random number probability */
struct abstract_molecule *subunit = NULL;
int have_varying = 0;
double varying_cum_probs[rx->n_pathways];
double min_noreaction_p, max_fixed_p;
/* rescale probabilities for the case of the reaction
between two surface molecules */
if (local_prob_factor > 0) {
min_noreaction_p = rx->min_noreaction_p * local_prob_factor;
max_fixed_p = rx->max_fixed_p * local_prob_factor;
} else {
min_noreaction_p = rx->min_noreaction_p;
max_fixed_p = rx->max_fixed_p;
}
/* Check if one of the molecules is a Macromol subunit */
if (rx->rates && a1 && a2) {
if (a1->flags & COMPLEX_MEMBER)
subunit = a1;
else if (a2->flags & COMPLEX_MEMBER)
subunit = a2;
}
/* Check if we missed any reactions */
if (min_noreaction_p < scaling) /* Definitely CAN scale enough */
{
/* Instead of scaling rx->cum_probs array we scale random probability */
p = rng_dbl(rng) * scaling;
if (p >= min_noreaction_p)
return RX_NO_RX;
} else /* May or may not scale enough. check varying pathways. */
{
double max_p;
/* Look up varying rxn rates, if needed */
if (subunit && (have_varying ||
get_varying_cum_probs(varying_cum_probs, rx, subunit))) {
max_p = varying_cum_probs[rx->n_pathways - 1];
if (local_prob_factor > 0)
max_p *= local_prob_factor;
have_varying = 1;
} else {
max_p = rx->cum_probs[rx->n_pathways - 1];
if (local_prob_factor > 0)
max_p *= local_prob_factor;
}
if (max_p >= scaling) /* we cannot scale enough. add missed rxns */
{
/* How may reactions will we miss? */
if (scaling == 0.0)
rx->n_skipped += GIGANTIC;
else
rx->n_skipped += (max_p / scaling) - 1.0;
/* Keep the proportions of outbound pathways the same. */
p = rng_dbl(rng) * max_p;
} else /* we can scale enough */
{
/* Instead of scaling rx->cum_probs array we scale random probability */
p = rng_dbl(rng) * scaling;
if (p >= max_p)
return RX_NO_RX;
}
}
int M;
/* If we have only fixed pathways... */
if (!subunit || p < max_fixed_p) {
novarying:
/* Perform binary search for reaction pathway */
M = rx->n_pathways - 1;
if (local_prob_factor > 0)
return binary_search_double(rx->cum_probs, p, M, local_prob_factor);
else
return binary_search_double(rx->cum_probs, p, M, 1);
} else {
/* Look up varying rxn rates, if needed */
if (subunit &&
(have_varying || get_varying_cum_probs(varying_cum_probs, rx, subunit)))
have_varying = 1;
else
goto novarying;
/* Check that we aren't in the non-reacting region of p-space */
if (local_prob_factor > 0) {
if (p > varying_cum_probs[rx->n_pathways - 1] * local_prob_factor)
return RX_NO_RX;
} else {
if (p > varying_cum_probs[rx->n_pathways - 1])
return RX_NO_RX;
}
/* Perform binary search for reaction pathway */
M = rx->n_pathways - 1;
if (local_prob_factor > 0)
return binary_search_double(varying_cum_probs, p, M, local_prob_factor);
else
return binary_search_double(varying_cum_probs, p, M, 1);
}
}
/*************************************************************************
test_many_bimolecular:
In: an array of reactions we're testing
scaling coefficients depending on how many timesteps we've moved
at once (1.0 means one timestep) and/or missing interaction areas
local probability factor for the corresponding reactions
the number of elements in the array of reactions
placeholder for the chosen pathway in the reaction (works as return
value)
a flag to indicate if
Out: RX_NO_RX if no reaction occurs
index in the reaction array corresponding to which reaction occurs
if one does occur
Note: If this reaction does not return RX_NO_RX, then we update
counters appropriately assuming that the reaction does take place.
Note: this uses only one call to get a random double, so you can't
effectively sample events that happen less than 10^-9 of the
time (for 32 bit random number).
NOTE: This function was merged with test_many_bimolecular_all_neighbors.
These two functions were almost identical, and the behavior of the
"all_neighbors" version is preserved with a flag that can be passed in.
For reactions between two surface molecules, set this flag to 1. For
such reactions local_prob_factor > 0.
*************************************************************************/
int test_many_bimolecular(struct rxn **rx, double *scaling,
double local_prob_factor, int n, int *chosen_pathway,
struct rng_state *rng,
int all_neighbors_flag) {
double rxp[2 * n]; /* array of cumulative rxn probabilities */
struct rxn *my_rx;
int i; /* index in the array of reactions - return value */
int m, M;
double p, f;
if (all_neighbors_flag && local_prob_factor <= 0)
mcell_internal_error("Local probability factor = %g in the function "
"'test_many_bimolecular_all_neighbors().",
local_prob_factor);
if (n == 1) {
if (all_neighbors_flag)
return test_bimolecular(rx[0], scaling[0], local_prob_factor, NULL, NULL, rng);
else
return test_bimolecular(rx[0], 0, scaling[0], NULL, NULL, rng);
}
/* Note: lots of division here, if we're CPU-bound,could invert the
definition of scaling_coefficients */
if (all_neighbors_flag && local_prob_factor > 0) {
rxp[0] = (rx[0]->max_fixed_p) * local_prob_factor / scaling[0];
} else {
rxp[0] = rx[0]->max_fixed_p / scaling[0];
}
for (i = 1; i < n; i++) {
if (all_neighbors_flag && local_prob_factor > 0) {
rxp[i] =
rxp[i - 1] + (rx[i]->max_fixed_p) * local_prob_factor / scaling[i];
} else {
rxp[i] = rxp[i - 1] + rx[i]->max_fixed_p / scaling[i];
}
}
if (rxp[n - 1] > 1.0) {
f = rxp[n - 1] - 1.0; /* Number of failed reactions */
for (i = 0; i < n; i++) /* Distribute failures */
{
if (all_neighbors_flag && local_prob_factor > 0) {
rx[i]->n_skipped += f * ((rx[i]->cum_probs[rx[i]->n_pathways - 1]) *
local_prob_factor) /
rxp[n - 1];
} else {
rx[i]->n_skipped +=
f * (rx[i]->cum_probs[rx[i]->n_pathways - 1]) / rxp[n - 1];
}
}
p = rng_dbl(rng) * rxp[n - 1];
} else {
p = rng_dbl(rng);
if (p > rxp[n - 1])
return RX_NO_RX;
}
/* Pick the reaction that happens */
i = binary_search_double(rxp, p, n - 1, 1);
my_rx = rx[i];
if (i > 0)
p = (p - rxp[i - 1]);
p = p * scaling[i];
/* Now pick the pathway within that reaction */
M = my_rx->n_pathways - 1;
if (all_neighbors_flag && local_prob_factor > 0)
m = binary_search_double(my_rx->cum_probs, p, M, local_prob_factor);
else
m = binary_search_double(my_rx->cum_probs, p, M, 1);
*chosen_pathway = m;
return i;
}
