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make sure to use atomics in main update loop
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@atmyers
atmyers committed Jan 25, 2024
1 parent afffd94 commit 43dbcce
Showing 1 changed file with 42 additions and 36 deletions.
78 changes: 42 additions & 36 deletions src/AgentContainer.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1227,36 +1227,38 @@ void AgentContainer::interactAgentsHomeWork ( MultiFab& /*mask_behavior*/ /*!< M
amrex::Real social_scale = 1.0; // TODO this should vary based on cell
amrex::Real work_scale = 1.0; // TODO this should vary based on cell

auto prob = prob_ptr[j];

/* Determine what connections these individuals have */
if ((nborhood_ptr[i] == nborhood_ptr[j]) && (family_ptr[i] == family_ptr[j]) && (!DAYTIME)) {
if (age_group_ptr[i] <= 1) { /* Transmitter i is a child */
if (school_ptr[i] < 0) { // not attending school, use _SC contacts
prob_ptr[j] *= 1.0 - infect * lparm->xmit_child_SC[age_group_ptr[j]];
prob *= 1.0 - infect * lparm->xmit_child_SC[age_group_ptr[j]];
} else {
prob_ptr[j] *= 1.0 - infect * lparm->xmit_child[age_group_ptr[j]];
prob *= 1.0 - infect * lparm->xmit_child[age_group_ptr[j]];
}
}
else {
if (school_ptr[i] < 0) { // not attending school, use _SC contacts
prob_ptr[j] *= 1.0 - infect * lparm->xmit_adult_SC[age_group_ptr[j]];
prob *= 1.0 - infect * lparm->xmit_adult_SC[age_group_ptr[j]];
} else {
prob_ptr[j] *= 1.0 - infect * lparm->xmit_adult[age_group_ptr[j]];
prob *= 1.0 - infect * lparm->xmit_adult[age_group_ptr[j]];
}
}
}
/* check for common neighborhood cluster: */
else if ((nborhood_ptr[i] == nborhood_ptr[j]) && (!withdrawn_ptr[i]) && (!withdrawn_ptr[j]) && (!DAYTIME)) {
if (age_group_ptr[i] <= 1) { /* Transmitter i is a child */
if (school_ptr[i] < 0) // not attending school, use _SC contacts
prob_ptr[j] *= 1.0 - infect * lparm->xmit_nc_child_SC[age_group_ptr[j]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_nc_child_SC[age_group_ptr[j]] * social_scale;
else
prob_ptr[j] *= 1.0 - infect * lparm->xmit_nc_child[age_group_ptr[j]] * social_scale;
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_ptr[j] *= 1.0 - infect * lparm->xmit_nc_adult_SC[age_group_ptr[j]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_nc_adult_SC[age_group_ptr[j]] * social_scale;
else
prob_ptr[j] *= 1.0 - infect * lparm->xmit_nc_adult[age_group_ptr[j]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_nc_adult[age_group_ptr[j]] * social_scale;
}
}

Expand All @@ -1265,31 +1267,31 @@ void AgentContainer::interactAgentsHomeWork ( MultiFab& /*mask_behavior*/ /*!< M

/* Should always be in the same community = same cell */
if (school_ptr[i] < 0) // not attending school, use _SC contacts
prob_ptr[j] *= 1.0 - infect * lparm->xmit_comm_SC[age_group_ptr[j]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_comm_SC[age_group_ptr[j]] * social_scale;
else
prob_ptr[j] *= 1.0 - infect * lparm->xmit_comm[age_group_ptr[j]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_comm[age_group_ptr[j]] * social_scale;

/* Workgroup transmission */
if (DAYTIME && workgroup_ptr[i] && (work_i_ptr[i] >= 0)) { // transmitter i at work
if ((work_i_ptr[j] >= 0) && (workgroup_ptr[i] == workgroup_ptr[j])) { // coworker
prob_ptr[j] *= 1.0 - infect * lparm->xmit_work * work_scale;
prob *= 1.0 - infect * lparm->xmit_work * work_scale;
}
}

// /* Neighborhood? */
if (nborhood_ptr[i] == nborhood_ptr[j]) {
if (school_ptr[i] < 0) // not attending school, use _SC contacts
prob_ptr[j] *= 1.0 - infect * lparm->xmit_hood_SC[age_group_ptr[j]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_hood_SC[age_group_ptr[j]] * social_scale;
else
prob_ptr[j] *= 1.0 - infect * lparm->xmit_hood[age_group_ptr[j]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_hood[age_group_ptr[j]] * social_scale;

if ((school_ptr[i] == school_ptr[j]) && DAYTIME) {
if (school_ptr[i] > 5) {
/* Playgroup */
prob_ptr[j] *= 1.0 - infect * lparm->xmit_school[6] * social_scale;
prob *= 1.0 - infect * lparm->xmit_school[6] * social_scale;
} else if (school_ptr[i] == 5) {
/* Day care */
prob_ptr[j] *= 1.0 - infect * lparm->xmit_school[5] * social_scale;
prob *= 1.0 - infect * lparm->xmit_school[5] * social_scale;
}
}
} /* same neighborhood */
Expand All @@ -1299,15 +1301,16 @@ void AgentContainer::interactAgentsHomeWork ( MultiFab& /*mask_behavior*/ /*!< M
(school_ptr[i] > 0) && (school_ptr[i] < 5)) {
if (age_group_ptr[i] <= 1) { /* Transmitter i is a child */
if (age_group_ptr[j] <= 1) { /* Receiver j is a child */
prob_ptr[j] *= 1.0 - infect * lparm->xmit_school[school_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_school[school_ptr[i]] * social_scale;
} else { // Child student -> adult teacher/staff transmission
prob_ptr[j] *= 1.0 - infect * lparm->xmit_sch_c2a[school_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_sch_c2a[school_ptr[i]] * social_scale;
}
} else if (age_group_ptr[j] <= 1) { // Adult teacher/staff -> child student
prob_ptr[j] *= 1.0 - infect * lparm->xmit_sch_a2c[school_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_sch_a2c[school_ptr[i]] * social_scale;
}
}
} /* within society */
Gpu::Atomic::Multiply(&prob_ptr[j], prob);
} else if (status_ptr[j] == Status::infected && status_ptr[i] != Status::infected) {
if (counter_ptr[j] < lparm->incubation_length) { continue; }
// j can infect i
Expand All @@ -1319,19 +1322,21 @@ void AgentContainer::interactAgentsHomeWork ( MultiFab& /*mask_behavior*/ /*!< M
amrex::Real social_scale = 1.0; // TODO this should vary based on cell
amrex::Real work_scale = 1.0; // TODO this should vary based on cell

auto prob = prob_ptr[i];

/* Determine what connections these individuals have */
if ((nborhood_ptr[i] == nborhood_ptr[j]) && (family_ptr[i] == family_ptr[j]) && (! DAYTIME)) {
if (age_group_ptr[j] <= 1) { /* Transmitter j is a child */
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob_ptr[i] *= 1.0 - infect * lparm->xmit_child_SC[age_group_ptr[i]];
prob *= 1.0 - infect * lparm->xmit_child_SC[age_group_ptr[i]];
} else {
prob_ptr[i] *= 1.0 - infect * lparm->xmit_child[age_group_ptr[i]];
prob *= 1.0 - infect * lparm->xmit_child[age_group_ptr[i]];
}
} else {
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob_ptr[i] *= 1.0 - infect * lparm->xmit_adult_SC[age_group_ptr[i]];
prob *= 1.0 - infect * lparm->xmit_adult_SC[age_group_ptr[i]];
} else {
prob_ptr[i] *= 1.0 - infect * lparm->xmit_adult[age_group_ptr[i]];
prob *= 1.0 - infect * lparm->xmit_adult[age_group_ptr[i]];
}
}
}
Expand All @@ -1340,15 +1345,15 @@ void AgentContainer::interactAgentsHomeWork ( MultiFab& /*mask_behavior*/ /*!< M
else if ((nborhood_ptr[i] == nborhood_ptr[j]) && (!withdrawn_ptr[i]) && (!withdrawn_ptr[j]) && (!DAYTIME)) {
if (age_group_ptr[j] <= 1) { /* Transmitter i is a child */
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob_ptr[i] *= 1.0 - infect * lparm->xmit_nc_child_SC[age_group_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_nc_child_SC[age_group_ptr[i]] * social_scale;
} else {
prob_ptr[i] *= 1.0 - infect * lparm->xmit_nc_child[age_group_ptr[i]] * social_scale;
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_ptr[i] *= 1.0 - infect * lparm->xmit_nc_adult_SC[age_group_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_nc_adult_SC[age_group_ptr[i]] * social_scale;
} else {
prob_ptr[i] *= 1.0 - infect * lparm->xmit_nc_adult[age_group_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_nc_adult[age_group_ptr[i]] * social_scale;
}
}
}
Expand All @@ -1359,33 +1364,33 @@ void AgentContainer::interactAgentsHomeWork ( MultiFab& /*mask_behavior*/ /*!< M
// 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_ptr[i] *= 1.0 - infect * lparm->xmit_comm_SC[age_group_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_comm_SC[age_group_ptr[i]] * social_scale;
} else {
prob_ptr[i] *= 1.0 - infect * lparm->xmit_comm[age_group_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_comm[age_group_ptr[i]] * social_scale;
}

/* Workgroup transmission */
if (DAYTIME && workgroup_ptr[j] && (work_i_ptr[j] >= 0)) { // transmitter j at work
if ((work_i_ptr[i] >= 0) && (workgroup_ptr[i] == workgroup_ptr[j])) { // coworker
prob_ptr[i] *= 1.0 - infect * lparm->xmit_work * work_scale;
prob *= 1.0 - infect * lparm->xmit_work * work_scale;
}
}

/* Neighborhood? */
if (nborhood_ptr[i] == nborhood_ptr[j]) {
if (school_ptr[j] < 0) { // not attending school, use _SC contacts
prob_ptr[i] *= 1.0 - infect * lparm->xmit_hood_SC[age_group_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_hood_SC[age_group_ptr[i]] * social_scale;
} else {
prob_ptr[i] *= 1.0 - infect * lparm->xmit_hood[age_group_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_hood[age_group_ptr[i]] * social_scale;
}

if ((school_ptr[i] == school_ptr[j]) && DAYTIME) {
if (school_ptr[i] > 5) {
/* Playgroup */
prob_ptr[i] *= 1.0 - infect * lparm->xmit_school[6] * social_scale;
prob *= 1.0 - infect * lparm->xmit_school[6] * social_scale;
} else if (school_ptr[i] == 5) {
/* Day care */
prob_ptr[i] *= 1.0 - infect * lparm->xmit_school[5] * social_scale;
prob *= 1.0 - infect * lparm->xmit_school[5] * social_scale;
}
}
} /* same neighborhood */
Expand All @@ -1395,15 +1400,16 @@ void AgentContainer::interactAgentsHomeWork ( MultiFab& /*mask_behavior*/ /*!< M
(school_ptr[i] > 0) && (school_ptr[i] < 5)) {
if (age_group_ptr[i] <= 1) { /* Receiver i is a child */
if (age_group_ptr[j] <= 1) { /* Transmitter j is a child */
prob_ptr[i] *= 1.0 - infect * lparm->xmit_school[school_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_school[school_ptr[i]] * social_scale;
} else { // Adult teacher/staff -> child student transmission
prob_ptr[i] *= 1.0 - infect * lparm->xmit_sch_a2c[school_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_sch_a2c[school_ptr[i]] * social_scale;
}
} else if (age_group_ptr[j] <= 1) { // Child student -> adult teacher/staff
prob_ptr[i] *= 1.0 - infect * lparm->xmit_sch_c2a[school_ptr[i]] * social_scale;
prob *= 1.0 - infect * lparm->xmit_sch_c2a[school_ptr[i]] * social_scale;
}
}
} /* within society */
Gpu::Atomic::Multiply(&prob_ptr[i], prob);
}
}
});
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