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Small world network implementation. WIP commit prior to FLAMEGPU_INIT…
…_FUNC refactor
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| rng_seed,param_id,duration,n_total,n_seed_infection,population_0_9,population_10_19,population_20_29,population_30_39,population_40_49,population_50_59,population_60_69,population_70_79,population_80,household_size_1,household_size_2,household_size_3,household_size_4,household_size_5,household_size_6,p_interaction_susceptible_to_exposed,mean_time_to_infected,sd_time_to_infected,mean_time_to_recovered,sd_time_to_recovered,mean_time_to_susceptible,sd_time_to_susceptible,relative_susceptibility_0_9,relative_susceptibility_10_19,relative_susceptibility_20_29,relative_susceptibility_30_39,relative_susceptibility_40_49,relative_susceptibility_50_59,relative_susceptibility_60_69,relative_susceptibility_70_79,relative_susceptibility_80,child_network_adults,elderly_network_adults,relative_transmission_household,relative_transmission_occupation,relative_transmission_random,daily_fraction_work,mean_random_interactions_0_19,sd_random_interactions_0_19,mean_random_interactions_20_69,sd_random_interactions_20_69,mean_random_interactions_70plus,sd_random_interactions_70plus | ||
| 12,0,60,32,4,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,0.001,2,2,4,4,3,3 | ||
| 12,1,365,32,4,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,0.001,2,2,4,4,3,3 | ||
| 12,2,365,1024,8,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,0.001,2,2,4,4,3,3 | ||
| 12,3,365,4096,8,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,0.001,2,2,4,4,3,3 | ||
| 12,4,365,4096,8,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,0.001,2,2,4,4,3,3 | ||
| 12,5,365,65536,8,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,0.001,2,2,4,4,3,3 | ||
| rng_seed,param_id,duration,n_total,n_seed_infection,population_0_9,population_10_19,population_20_29,population_30_39,population_40_49,population_50_59,population_60_69,population_70_79,population_80,household_size_1,household_size_2,household_size_3,household_size_4,household_size_5,household_size_6,p_interaction_susceptible_to_exposed,mean_time_to_infected,sd_time_to_infected,mean_time_to_recovered,sd_time_to_recovered,mean_time_to_susceptible,sd_time_to_susceptible,relative_susceptibility_0_9,relative_susceptibility_10_19,relative_susceptibility_20_29,relative_susceptibility_30_39,relative_susceptibility_40_49,relative_susceptibility_50_59,relative_susceptibility_60_69,relative_susceptibility_70_79,relative_susceptibility_80,child_network_adults,elderly_network_adults,relative_transmission_household,relative_transmission_occupation,relative_transmission_random,mean_work_interactions_child,mean_work_interactions_adult,mean_work_interactions_elderly,daily_fraction_work,work_network_rewire,mean_random_interactions_0_19,sd_random_interactions_0_19,mean_random_interactions_20_69,sd_random_interactions_20_69,mean_random_interactions_70plus,sd_random_interactions_70plus | ||
| 12,0,60,32,4,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,10,7,3,0.5,0.1,2,2,4,4,3,3 | ||
| 12,1,365,32,4,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,10,7,3,0.5,0.1,2,2,4,4,3,3 | ||
| 12,2,365,1024,8,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,10,7,3,0.5,0.1,2,2,4,4,3,3 | ||
| 12,3,365,4096,8,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,10,7,3,0.5,0.1,2,2,4,4,3,3 | ||
| 12,4,365,4096,8,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,10,7,3,0.5,0.1,2,2,4,4,3,3 | ||
| 12,5,365,65536,8,331,370,374,371,361,415,377,270,142,442,492,208,165,51,27,0.10,3.5,2.0,7.0,2.0,28,10.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.2,0.2,2.0,0.5,0.5,10,7,3,0.5,0.1,2,2,4,4,3,3 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,122 @@ | ||
| #include "exateppabm/network.h" | ||
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| #include <exception> | ||
| #include <iostream> | ||
| #include <string> | ||
| #include <utility> | ||
| #include <vector> | ||
| #include <unordered_set> | ||
| #include <random> | ||
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| #include "flamegpu/flamegpu.h" | ||
| #include "fmt/core.h" | ||
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| namespace exateppabm { | ||
| namespace network { | ||
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| UndirectedNetwork generateFullyConnectedUndirectedNetwork(std::vector<flamegpu::id_t> nodes) { | ||
| UndirectedNetwork network = {}; | ||
| network.nodes = nodes; | ||
| if (nodes.size() <= 1) { | ||
| return network; | ||
| } | ||
| std::uint32_t N = static_cast<std::int32_t>(nodes.size()); | ||
| std::uint32_t E = (N * (N - 1)) / 2; | ||
| network.edges.reserve(E); | ||
| // Generate edges in ascending order for the undirected graph. | ||
| for (std::uint32_t i = 0; i < N; ++i) { | ||
| for (std::uint32_t j = i + 1; j < N; ++j) { | ||
| network.edges.push_back({i, j}); | ||
| } | ||
| } | ||
| return network; | ||
| } | ||
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| // @todo - should the initial lattice be randomised rather than sequential? | ||
| // @todo - should the graph be directed or undirected? Data structure is directed, so do pairs need rewiring together? | ||
| UndirectedNetwork generateSmallWorldUndirectedNetwork(std::vector<flamegpu::id_t> nodes, std::uint32_t K, double p_rewire, std::mt19937_64 rng) { | ||
| // fmt::print("@todo - check if small world network should be directed or undirected\n"); | ||
| UndirectedNetwork network = {}; | ||
| network.nodes = nodes; | ||
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| // Return early with an empty network if 0 or 1 nodes, so no room for non-self edges | ||
| if (network.nodes.size() <= 1) { | ||
| return network; | ||
| } | ||
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| // If K is 0 (or 1), no edges so do nothing | ||
| if (K <= 1) { | ||
| // throw std::runtime_error("@todo values - small world network K (" + std::to_string(K) + ") must be > 1"); | ||
| return network; | ||
| } else if (K == network.nodes.size()) { | ||
| // If K == Node count, the graph is fully connected, so return a fully connected graph | ||
| return generateFullyConnectedUndirectedNetwork(nodes); | ||
| } else if (K >= network.nodes.size()) { | ||
| // Raise an exception if K is too large | ||
| throw std::runtime_error(std::string("@todo values - small world network K(") + std::to_string(K) + ") must be less than |N| (" + std::to_string(network.nodes.size()) + ")"); | ||
| } | ||
| // If K is odd, use K-1 | ||
| if (K % 2 == 1) { | ||
| K = K - 1; | ||
| } | ||
|
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| // p_rewire must be between 0 and 1. | ||
| if (p_rewire < 0 || p_rewire > 1) { | ||
| throw std::runtime_error("generateSmallWorldNetwork p must be in [0, 1]. @todo include value"); | ||
| } | ||
|
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| // Initialise the edges as a lattice network, going K edges in each direction. | ||
| // Use signed integers to make modulo possible | ||
| std::int32_t N = static_cast<std::int32_t>(nodes.size()); | ||
| std::int32_t E = (N * K) / 2; | ||
| network.edges.reserve(E); | ||
| for (std::int32_t i = 0; i < N; ++i) { | ||
| for (std::int32_t j = 1; j <= static_cast<std::int32_t>(K / 2); ++j) { | ||
| // only add the positive undirected edges | ||
| std::uint32_t s = static_cast<std::uint32_t>(i); | ||
| std::uint32_t d = static_cast<std::uint32_t>((i + j) % N); | ||
| // Ensure that the edge source node is lower than the destination, to simplify avoiding duplicate edges | ||
| if (s > d) { | ||
| std::swap(s, d); | ||
| } | ||
| network.edges.push_back({s, d}); | ||
| // network.edges.push_back({static_cast<std::uint32_t>(i), static_cast<std::uint32_t>((i + j) % N)}); | ||
| // network.edges.push_back({static_cast<std::uint32_t>(i), static_cast<std::uint32_t>((i - j + N) % N)}); | ||
| } | ||
| } | ||
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| // If the network is fully connected (enough edges for each node to be connected to every other node), rewiring is not needed, so adjust the probability to prevent infinite loops. | ||
| std::int32_t MAX_E = (N * (N - 1)) / 2; | ||
| if (E >= MAX_E) { | ||
| p_rewire = 0.0; | ||
| } | ||
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| // If p_rewire is 0, no need to loop over the edges | ||
| if (p_rewire >= 0.0) { | ||
| // Get a uniform dist [0, 1) | ||
| std::uniform_real_distribution<double> p_dist(0.0, 1.0); | ||
| // Get a uniform integer distribution from [0, N) for generating new edge indices | ||
| std::uniform_int_distribution<std::uint32_t> dest_dist(0, N-1); | ||
| // Randomly rewire edges | ||
| for (auto& edge : network.edges) { | ||
| if (p_dist(rng) < p_rewire) { | ||
| std::uint32_t newDest = dest_dist(rng); | ||
| // Repeat the generation until the edge is not a self-edge, nor duplicate | ||
| // Not using do while so the search for the edge is ok. | ||
| // @note - this will be a challenge to parallelise efficiently without atomics (i.e. stable matching) | ||
| // @note - this will be expensive for large networks, an edge matrix would be cheaper (at the cost of N*N memory) | ||
| // @todo - need to avoid directed edge duplicates. | ||
| while (newDest == edge.source || std::find(network.edges.begin(), network.edges.end(), UndirectedNetwork::Edge{edge.source, newDest}) != network.edges.end()) { | ||
| newDest = dest_dist(rng); | ||
| } | ||
| edge.dest = newDest; | ||
| } | ||
| } | ||
| } | ||
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| return network; | ||
| } | ||
|
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| } // namespace network | ||
| } // namespace exateppabm |
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