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Alexander Nozik 2020-10-17 15:57:06 +03:00
commit e398e85416
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8
.gitignore vendored Normal file
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.idea/
*.iws
out/
.gradle
build/
!gradle-wrapper.jar

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build.gradle.kts Normal file
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import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
plugins {
kotlin("jvm") version "1.4.10"
application
}
group = "ru.mipt.npm"
version = "1.0-SNAPSHOT"
repositories {
jcenter()
mavenCentral()
}
dependencies {
implementation("kscience.plotlykt:plotlykt-server:0.2.0") {
exclude(module = "kotlinx-io")
}
implementation("org.apache.commons:commons-math3:3.6.1")
testImplementation(kotlin("test-junit5"))
testImplementation("org.junit.jupiter:junit-jupiter-api:5.6.0")
testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine:5.6.0")
}
tasks.test {
useJUnitPlatform()
}
tasks.withType<KotlinCompile>() {
kotlinOptions.jvmTarget = "11"
}
application {
mainClassName = "ru.mipt.npm.sim.epidemics.MainKt"
}

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gradle.properties Normal file
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kotlin.code.style=official

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gradle/wrapper/gradle-wrapper.jar vendored Normal file
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gradle/wrapper/gradle-wrapper.properties vendored Normal file
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distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-6.3-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists

183
gradlew vendored Normal file
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#!/usr/bin/env sh
#
# Copyright 2015 the original author or authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
##############################################################################
##
## Gradle start up script for UN*X
##
##############################################################################
# Attempt to set APP_HOME
# Resolve links: $0 may be a link
PRG="$0"
# Need this for relative symlinks.
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '/.*' > /dev/null; then
PRG="$link"
else
PRG=`dirname "$PRG"`"/$link"
fi
done
SAVED="`pwd`"
cd "`dirname \"$PRG\"`/" >/dev/null
APP_HOME="`pwd -P`"
cd "$SAVED" >/dev/null
APP_NAME="Gradle"
APP_BASE_NAME=`basename "$0"`
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
# Use the maximum available, or set MAX_FD != -1 to use that value.
MAX_FD="maximum"
warn () {
echo "$*"
}
die () {
echo
echo "$*"
echo
exit 1
}
# OS specific support (must be 'true' or 'false').
cygwin=false
msys=false
darwin=false
nonstop=false
case "`uname`" in
CYGWIN* )
cygwin=true
;;
Darwin* )
darwin=true
;;
MINGW* )
msys=true
;;
NONSTOP* )
nonstop=true
;;
esac
CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
# Determine the Java command to use to start the JVM.
if [ -n "$JAVA_HOME" ] ; then
if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
# IBM's JDK on AIX uses strange locations for the executables
JAVACMD="$JAVA_HOME/jre/sh/java"
else
JAVACMD="$JAVA_HOME/bin/java"
fi
if [ ! -x "$JAVACMD" ] ; then
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
else
JAVACMD="java"
which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
# Increase the maximum file descriptors if we can.
if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
MAX_FD_LIMIT=`ulimit -H -n`
if [ $? -eq 0 ] ; then
if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
MAX_FD="$MAX_FD_LIMIT"
fi
ulimit -n $MAX_FD
if [ $? -ne 0 ] ; then
warn "Could not set maximum file descriptor limit: $MAX_FD"
fi
else
warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
fi
fi
# For Darwin, add options to specify how the application appears in the dock
if $darwin; then
GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
fi
# For Cygwin or MSYS, switch paths to Windows format before running java
if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
APP_HOME=`cygpath --path --mixed "$APP_HOME"`
CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
JAVACMD=`cygpath --unix "$JAVACMD"`
# We build the pattern for arguments to be converted via cygpath
ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
SEP=""
for dir in $ROOTDIRSRAW ; do
ROOTDIRS="$ROOTDIRS$SEP$dir"
SEP="|"
done
OURCYGPATTERN="(^($ROOTDIRS))"
# Add a user-defined pattern to the cygpath arguments
if [ "$GRADLE_CYGPATTERN" != "" ] ; then
OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
fi
# Now convert the arguments - kludge to limit ourselves to /bin/sh
i=0
for arg in "$@" ; do
CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
else
eval `echo args$i`="\"$arg\""
fi
i=`expr $i + 1`
done
case $i in
0) set -- ;;
1) set -- "$args0" ;;
2) set -- "$args0" "$args1" ;;
3) set -- "$args0" "$args1" "$args2" ;;
4) set -- "$args0" "$args1" "$args2" "$args3" ;;
5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
esac
fi
# Escape application args
save () {
for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
echo " "
}
APP_ARGS=`save "$@"`
# Collect all arguments for the java command, following the shell quoting and substitution rules
eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
exec "$JAVACMD" "$@"

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@rem
@rem Copyright 2015 the original author or authors.
@rem
@rem Licensed under the Apache License, Version 2.0 (the "License");
@rem you may not use this file except in compliance with the License.
@rem You may obtain a copy of the License at
@rem
@rem https://www.apache.org/licenses/LICENSE-2.0
@rem
@rem Unless required by applicable law or agreed to in writing, software
@rem distributed under the License is distributed on an "AS IS" BASIS,
@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@rem See the License for the specific language governing permissions and
@rem limitations under the License.
@rem
@if "%DEBUG%" == "" @echo off
@rem ##########################################################################
@rem
@rem Gradle startup script for Windows
@rem
@rem ##########################################################################
@rem Set local scope for the variables with windows NT shell
if "%OS%"=="Windows_NT" setlocal
set DIRNAME=%~dp0
if "%DIRNAME%" == "" set DIRNAME=.
set APP_BASE_NAME=%~n0
set APP_HOME=%DIRNAME%
@rem Resolve any "." and ".." in APP_HOME to make it shorter.
for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
@rem Find java.exe
if defined JAVA_HOME goto findJavaFromJavaHome
set JAVA_EXE=java.exe
%JAVA_EXE% -version >NUL 2>&1
if "%ERRORLEVEL%" == "0" goto init
echo.
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
echo.
echo Please set the JAVA_HOME variable in your environment to match the
echo location of your Java installation.
goto fail
:findJavaFromJavaHome
set JAVA_HOME=%JAVA_HOME:"=%
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
if exist "%JAVA_EXE%" goto init
echo.
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
echo.
echo Please set the JAVA_HOME variable in your environment to match the
echo location of your Java installation.
goto fail
:init
@rem Get command-line arguments, handling Windows variants
if not "%OS%" == "Windows_NT" goto win9xME_args
:win9xME_args
@rem Slurp the command line arguments.
set CMD_LINE_ARGS=
set _SKIP=2
:win9xME_args_slurp
if "x%~1" == "x" goto execute
set CMD_LINE_ARGS=%*
:execute
@rem Setup the command line
set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
@rem Execute Gradle
"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
:end
@rem End local scope for the variables with windows NT shell
if "%ERRORLEVEL%"=="0" goto mainEnd
:fail
rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
rem the _cmd.exe /c_ return code!
if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
exit /b 1
:mainEnd
if "%OS%"=="Windows_NT" endlocal
:omega

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rootProject.name = "epidemics-sim"

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src/main/kotlin/ru/mipt/npm/sim/epidemics/Behavior.kt Normal file
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package ru.mipt.npm.sim.epidemics
import org.apache.commons.math3.random.RandomGenerator
interface Behavior {
/**
* Generate daily contact for given [subject]
*/
fun generateDailyContacts(generator: RandomGenerator, subject: Subject, date: Int): List<Int>
}
object DefaultBehavior : Behavior {
@OptIn(ExperimentalStdlibApi::class)
override fun generateDailyContacts(
generator: RandomGenerator,
subject: Subject,
date: Int
): List<Int> = buildList {
subject.closeContacts.forEach { contact ->
if (generator.nextDouble() < 0.5) {
add(contact)
}
}
subject.otherContacts.forEach { contact ->
if (generator.nextDouble() < 0.1) {
add(contact)
}
}
}
}

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src/main/kotlin/ru/mipt/npm/sim/epidemics/DefaultEpidemicsModel.kt Normal file
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package ru.mipt.npm.sim.epidemics
import org.apache.commons.math3.random.JDKRandomGenerator
import org.apache.commons.math3.random.RandomGenerator
typealias Population = Map<Int, SubjectState>
interface EpidemicsModel {
fun generatePopulation(generator: RandomGenerator, size: Int = 1000): Population
fun propagateSubjectState(generator: RandomGenerator, subjectState: SubjectState, date: Int): SubjectState
fun propagate(generator: RandomGenerator, population: Population, date: Int): Population
}
//TODO add model parametrization
object DefaultEpidemicsModel : EpidemicsModel {
override fun generatePopulation(generator: RandomGenerator, size: Int): Population {
//TODO add custom distributions
return generatePopulation(generator, size, 3, 10)
}
@OptIn(ExperimentalStdlibApi::class)
fun generatePopulation(
generator: RandomGenerator,
size: Int,
closeContactsNum: Int,
otherContactsNum: Int
): Population {
return (0 until size).associateWith { subjectId ->
val closeContacts = buildList<Int> {
repeat(closeContactsNum) {
val id = generator.nextInt(size)
if (id != subjectId) {
add(id)
}
}
}
val otherContacts = buildList<Int> {
repeat(otherContactsNum) {
val id = generator.nextInt(size)
if (id != subjectId) {
add(id)
}
}
}
val subject = Subject(subjectId, closeContacts, otherContacts)
return@associateWith SubjectState(subject)
}
}
override fun propagateSubjectState(generator: RandomGenerator, subjectState: SubjectState, date: Int): SubjectState {
when (subjectState.state) {
InfectionState.SUSCEPTIBLE, InfectionState.RECOVERED -> {
//do nothing
}
InfectionState.EXPOSED -> {
//TODO add custom distributions
if (date - subjectState.exposedDate!! >= 3) {
subjectState.infect(date)
}
}
InfectionState.INFECTIOUS -> {
if (generator.nextDouble() < 0.1) {
subjectState.recover(date)
}
}
}
return subjectState
}
val behavior = DefaultBehavior
override fun propagate(generator: RandomGenerator, population: Population, date: Int): Population {
//TODO check population health and change behavior
population.values.forEach {
propagateSubjectState(generator, it, date)
}
population.forEach { (_, subj) ->
val contacts: List<Int> = behavior.generateDailyContacts(generator, subj.subject, date)
contacts.forEach { contactId ->
val otherContact = population[contactId]
?: error("Undefined subject with id $contactId")
if (subj.state == InfectionState.INFECTIOUS && generator.nextDouble() < 0.25) {
otherContact.expose(date)
}
if (otherContact.state == InfectionState.INFECTIOUS && generator.nextDouble() < 0.25) {
subj.expose(date)
}
}
}
return population
}
}

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src/main/kotlin/ru/mipt/npm/sim/epidemics/Subject.kt Normal file
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package ru.mipt.npm.sim.epidemics
enum class InfectionState {
SUSCEPTIBLE,
EXPOSED,
INFECTIOUS,
RECOVERED
}
class Subject(
val id: Int,
val closeContacts: List<Int>,
val otherContacts: List<Int>
)
class SubjectState(
val subject: Subject
) {
var state: InfectionState = InfectionState.SUSCEPTIBLE
private set
var exposedDate: Int? = null
private set
var infectedDate: Int? = null
private set
var recoveryDate: Int? = null
private set
fun expose(date: Int) {
if (state == InfectionState.SUSCEPTIBLE) {
state = InfectionState.EXPOSED
exposedDate = date
}
}
fun infect(date: Int) {
if (state != InfectionState.EXPOSED) error("Expected 'EXPOSED' state")
state = InfectionState.INFECTIOUS
infectedDate = date
}
fun recover(date: Int) {
if (state != InfectionState.INFECTIOUS) error("Expected 'EXPOSED' state")
state = InfectionState.RECOVERED
recoveryDate = date
}
}

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src/main/kotlin/ru/mipt/npm/sim/epidemics/main.kt Normal file
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package ru.mipt.npm.sim.epidemics
import org.apache.commons.math3.random.JDKRandomGenerator
fun main() {
val generator = JDKRandomGenerator()
val population = DefaultEpidemicsModel.generatePopulation(generator)
var date = 0
val patientZero = generator.nextInt(population.size)
population[patientZero]?.expose(0)
while (
!population.values.all {
it.state == InfectionState.RECOVERED || it.state == InfectionState.SUSCEPTIBLE
}
) {
date++
DefaultEpidemicsModel.propagate(generator, population, date)
}
println("Epidemics ended at $date")
println(population.count { it.value.state == InfectionState.RECOVERED })
population.show()
}

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src/main/kotlin/ru/mipt/npm/sim/epidemics/visualization.kt Normal file
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package ru.mipt.npm.sim.epidemics
import kscience.plotly.*
data class PopulationState(val infected: Int, val recovered: Int)
@OptIn(ExperimentalStdlibApi::class)
fun Population.collectData(): Map<Int, PopulationState>{
val maxRecoveryDate = values.map{ it.recoveryDate ?: 0 }.max() ?: 1
return (0..maxRecoveryDate).associateWith {date->
val infected = values.count {
(it.exposedDate ?: Int.MAX_VALUE) <= date && it.recoveryDate?:Int.MAX_VALUE > date
}
val recovered = values.count { (it.recoveryDate ?: Int.MAX_VALUE) <= date }
PopulationState(infected,recovered)
}
}
fun Population.show(): Plot {
val data = collectData()
val plot = Plotly.plot {
trace {
name = "infected"
x.set(data.keys.toIntArray())
y.set(data.values.map { it.infected })
}
trace{
name = "recovered"
x.set(data.keys.toIntArray())
y.set(data.values.map { it.recovered })
}
}
plot.makeFile()
return plot
}