Skip to content

Commit

Permalink
for each interaction type, implemented a binary (one-on-one) interact…
Browse files Browse the repository at this point in the history 
…ion kernel between an infectious and a susceptible agent; calling that in the main interaction function
  • Loading branch information
@debog
debog committed Feb 9, 2024
1 parent 42bdd56 commit c46e6f8
Show file tree
Hide file tree
Showing 4 changed files with 238 additions and 263 deletions.
105 changes: 54 additions & 51 deletions src/InteractionLocHome.H
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,49 @@
#include <AMReX_Particles.H>

#include "Locations.H"
#include "DiseaseParm.H"
#include "AgentDefinitions.H"

using namespace amrex;

/*! \brief One-on-one interaction between an infectious agent and a susceptible agent.
*
* This function defines the one-on-one interaction between an infectious agent and a
* susceptible agent at home. */
AMREX_GPU_DEVICE AMREX_FORCE_INLINE
static void binaryInteractionHome ( const int a_i, /*!< Index of infectious agent */
const int a_j, /*!< Index of susceptible agent */
const DiseaseParm* const a_lparm, /*!< disease paramters */
const int* const a_age_group_ptr, /*!< age group */
const int* const a_family_ptr, /*!< family */
const int* const a_nborhood_ptr, /*!< neighborhood */
const int* const a_school_ptr, /*!< school */
ParticleReal* const a_prob_ptr /*!< infection probability */)
{
Real infect = a_lparm->infect;
infect *= a_lparm->vac_eff;
//infect *= i_mask;
//infect *= j_mask;
auto prob = a_prob_ptr[a_j];
if ( (a_nborhood_ptr[a_i] == a_nborhood_ptr[a_j])
&& (a_family_ptr[a_i] == a_family_ptr[a_j]) ) {
if (a_age_group_ptr[a_i] <= 1) { /* Transmitter i is a child */
if (a_school_ptr[a_i] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * a_lparm->xmit_child_SC[a_age_group_ptr[a_j]];
} else {
prob *= 1.0 - infect * a_lparm->xmit_child[a_age_group_ptr[a_j]];
}
} else {
if (a_school_ptr[a_i] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * a_lparm->xmit_adult_SC[a_age_group_ptr[a_j]];
} else {
prob *= 1.0 - infect * a_lparm->xmit_adult[a_age_group_ptr[a_j]];
}
}
}
Gpu::Atomic::Multiply(&a_prob_ptr[a_j], prob);
}

/*! \brief Class describing agent interactions at home */
template <typename ACType /*!< agent container type */, typename AType /*!< agent type */>
class InteractionLocHome : public InteractionLocation<ACType,AType>
Expand Down Expand Up @@ -153,61 +192,25 @@ void InteractionLocHome<ACType,AType>::interactAgents(ACType& a_agents, /*!<
if ( isInfectious( i, status_ptr,counter_ptr,lparm->incubation_length )
&& isSusceptible( j, status_ptr ) ) {

// i can infect j
Real infect = lparm->infect;
infect *= lparm->vac_eff;
//infect *= i_mask;
//infect *= j_mask;

auto prob = prob_ptr[j];
if ( (nborhood_ptr[i] == nborhood_ptr[j])
&& (family_ptr[i] == family_ptr[j]) ) {
if (age_group_ptr[i] <= 1) { /* Transmitter i is a child */
if (school_ptr[i] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_child_SC[age_group_ptr[j]];
} else {
prob *= 1.0 - infect * lparm->xmit_child[age_group_ptr[j]];
}
}
else {
if (school_ptr[i] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_adult_SC[age_group_ptr[j]];
} else {
prob *= 1.0 - infect * lparm->xmit_adult[age_group_ptr[j]];
}
}
}
Gpu::Atomic::Multiply(&prob_ptr[j], prob);
binaryInteractionHome( i, j,
lparm,
age_group_ptr,
family_ptr,
nborhood_ptr,
school_ptr,
prob_ptr );

} else if ( isInfectious( j, status_ptr,counter_ptr,lparm->incubation_length )
&& isSusceptible( i, status_ptr ) ) {

// j can infect i
Real infect = lparm->infect;
infect *= lparm->vac_eff;
//infect *= i_mask;
//infect *= j_mask;

auto prob = prob_ptr[i];
/* Determine what connections these individuals have */
if ( (nborhood_ptr[i] == nborhood_ptr[j])
&& (family_ptr[i] == family_ptr[j]) ) {
if (age_group_ptr[j] <= 1) { /* Transmitter j is a child */
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_child_SC[age_group_ptr[i]];
} else {
prob *= 1.0 - infect * lparm->xmit_child[age_group_ptr[i]];
}
} else {
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_adult_SC[age_group_ptr[i]];
} else {
prob *= 1.0 - infect * lparm->xmit_adult[age_group_ptr[i]];
}
}
}

Gpu::Atomic::Multiply(&prob_ptr[i], prob);
binaryInteractionHome( j, i,
lparm,
age_group_ptr,
family_ptr,
nborhood_ptr,
school_ptr,
prob_ptr );

}
}
});
Expand Down
175 changes: 79 additions & 96 deletions src/InteractionLocNborhood.H
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,64 @@

using namespace amrex;

/*! \brief One-on-one interaction between an infectious agent and a susceptible agent.
*
* This function defines the one-on-one interaction between an infectious agent and a
* susceptible agent in a neighborhood. */
AMREX_GPU_DEVICE AMREX_FORCE_INLINE
static void binaryInteractionNborhood ( const int a_i, /*!< Index of infectious agent */
const int a_j, /*!< Index of susceptible agent */
const DiseaseParm* const a_lparm, /*!< disease paramters */
const Real a_social_scale, /*!< Social scale */
const int* const a_age_group_ptr, /*!< age group */
const int* const a_family_ptr, /*!< family */
const int* const a_nborhood_ptr, /*!< neighborhood */
const int* const a_school_ptr, /*!< school */
ParticleReal* const a_prob_ptr /*!< infection probability */)
{
Real infect = a_lparm->infect;
infect *= a_lparm->vac_eff;
//infect *= i_mask;
//infect *= j_mask;
auto prob = a_prob_ptr[a_j];

/* check for common neighborhood cluster: */
if ( (a_nborhood_ptr[a_i] == a_nborhood_ptr[a_j])
&& ((a_family_ptr[a_i] / 4) == (a_family_ptr[a_j] / 4)) ) {
if (a_age_group_ptr[a_i] <= 1) { /* Transmitter i is a child */
if (a_school_ptr[a_i] < 0) // not attending school, use _SC contacts
prob *= 1.0 - infect * a_lparm->xmit_nc_child_SC[a_age_group_ptr[a_j]] * a_social_scale;
else
prob *= 1.0 - infect * a_lparm->xmit_nc_child[a_age_group_ptr[a_j]] * a_social_scale;
}
else {
if (a_school_ptr[a_i] < 0) // not attending school, use _SC contacts
prob *= 1.0 - infect * a_lparm->xmit_nc_adult_SC[a_age_group_ptr[a_j]] * a_social_scale;
else
prob *= 1.0 - infect * a_lparm->xmit_nc_adult[a_age_group_ptr[a_j]] * a_social_scale;
}
}

// school < 0 means a child normally attends school, but not today
/* Should always be in the same community = same cell */
if (a_school_ptr[a_i] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * a_lparm->xmit_comm_SC[a_age_group_ptr[a_j]] * a_social_scale;
} else {
prob *= 1.0 - infect * a_lparm->xmit_comm[a_age_group_ptr[a_j]] * a_social_scale;
}
// /* Neighborhood? */
if (a_nborhood_ptr[a_i] == a_nborhood_ptr[a_j]) {
if (a_school_ptr[a_i] < 0) {
// not attending school, use _SC contacts
prob *= 1.0 - infect * a_lparm->xmit_hood_SC[a_age_group_ptr[a_j]] * a_social_scale;
} else {
prob *= 1.0 - infect * a_lparm->xmit_hood[a_age_group_ptr[a_j]] * a_social_scale;
}
}

Gpu::Atomic::Multiply(&a_prob_ptr[a_j], prob);
}

/*! \brief Class describing agent interactions at neighborhood */
template <typename ACType /*!< agent container type */, typename AType /*!< agent type */>
class InteractionLocNborhood : public InteractionLocation<ACType,AType>
Expand Down Expand Up @@ -136,6 +194,9 @@ void InteractionLocNborhood<ACType,AType>::interactAgents(ACType& a_agents, /
|| notSusceptible( i, status_ptr ) ) {
return;
}
if (withdrawn_ptr[i]) {
return;
}

//Real i_mask = mask_arr(home_i_ptr[i], home_j_ptr[i], 0);
for (unsigned int jj = cell_start; jj < cell_stop; ++jj) {
Expand All @@ -147,112 +208,34 @@ void InteractionLocNborhood<ACType,AType>::interactAgents(ACType& a_agents, /
|| notSusceptible( j, status_ptr ) ) {
continue;
}
if (withdrawn_ptr[j]) {
continue;
}

if ( isInfectious( i, status_ptr,counter_ptr,lparm->incubation_length )
&& isSusceptible( j, status_ptr ) ) {

// i can infect j
Real infect = lparm->infect;
infect *= lparm->vac_eff;
//infect *= i_mask;
//infect *= j_mask;

Real social_scale = 1.0; // TODO this should vary based on cell
auto prob = prob_ptr[j];

/* check for common neighborhood cluster: */
if ( (nborhood_ptr[i] == nborhood_ptr[j])
&& (!withdrawn_ptr[i]) && (!withdrawn_ptr[j])
&& ((family_ptr[i] / 4) == (family_ptr[j] / 4)) ) {
if (age_group_ptr[i] <= 1) { /* Transmitter i is a child */
if (school_ptr[i] < 0) // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_nc_child_SC[age_group_ptr[j]] * social_scale;
else
prob *= 1.0 - infect * lparm->xmit_nc_child[age_group_ptr[j]] * social_scale;
}
else {
if (school_ptr[i] < 0) // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_nc_adult_SC[age_group_ptr[j]] * social_scale;
else
prob *= 1.0 - infect * lparm->xmit_nc_adult[age_group_ptr[j]] * social_scale;
}
}

// /* Home isolation or household quarantine? */
if ( (!withdrawn_ptr[i]) && (!withdrawn_ptr[j]) ) {
// school < 0 means a child normally attends school, but not today
/* Should always be in the same community = same cell */
if (school_ptr[i] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_comm_SC[age_group_ptr[j]] * social_scale;
} else {
prob *= 1.0 - infect * lparm->xmit_comm[age_group_ptr[j]] * social_scale;
}
// /* Neighborhood? */
if (nborhood_ptr[i] == nborhood_ptr[j]) {
if (school_ptr[i] < 0) {
// not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_hood_SC[age_group_ptr[j]] * social_scale;
} else {
prob *= 1.0 - infect * lparm->xmit_hood[age_group_ptr[j]] * social_scale;
}
}
}

Gpu::Atomic::Multiply(&prob_ptr[j], prob);
binaryInteractionNborhood( i, j,
lparm, social_scale,
age_group_ptr,
family_ptr,
nborhood_ptr,
school_ptr,
prob_ptr );

} else if ( isInfectious( j, status_ptr,counter_ptr,lparm->incubation_length )
&& isSusceptible( i, status_ptr ) ) {

// j can infect i
Real infect = lparm->infect;
infect *= lparm->vac_eff;
//infect *= i_mask;
//infect *= j_mask;

Real social_scale = 1.0; // TODO this should vary based on cell
auto prob = prob_ptr[i];

/* check for common neighborhood cluster: */
if ( (nborhood_ptr[i] == nborhood_ptr[j])
&& (!withdrawn_ptr[i])
&& (!withdrawn_ptr[j])
&& ((family_ptr[i] / 4) == (family_ptr[j] / 4)) ) {
if (age_group_ptr[j] <= 1) { /* Transmitter i is a child */
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_nc_child_SC[age_group_ptr[i]] * social_scale;
} else {
prob *= 1.0 - infect * lparm->xmit_nc_child[age_group_ptr[i]] * social_scale;
}
} else {
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_nc_adult_SC[age_group_ptr[i]] * social_scale;
} else {
prob *= 1.0 - infect * lparm->xmit_nc_adult[age_group_ptr[i]] * social_scale;
}
}
}

/* Home isolation or household quarantine? */
// TODO - be careful about withdrawn versus at home...
if ( (!withdrawn_ptr[i]) && (!withdrawn_ptr[j]) ) {
// school < 0 means a child normally attends school, but not today
/* Should always be in the same community = same cell */
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_comm_SC[age_group_ptr[i]] * social_scale;
} else {
prob *= 1.0 - infect * lparm->xmit_comm[age_group_ptr[i]] * social_scale;
}
/* Neighborhood? */
if (nborhood_ptr[i] == nborhood_ptr[j]) {
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob *= 1.0 - infect * lparm->xmit_hood_SC[age_group_ptr[i]] * social_scale;
} else {
prob *= 1.0 - infect * lparm->xmit_hood[age_group_ptr[i]] * social_scale;
}
}
}

Gpu::Atomic::Multiply(&prob_ptr[i], prob);
binaryInteractionNborhood( j, i,
lparm, social_scale,
age_group_ptr,
family_ptr,
nborhood_ptr,
school_ptr,
prob_ptr );

}
}
});
Expand Down
Loading

0 comments on commit c46e6f8

Please sign in to comment.