Migrate to git. Update versions

.gitignore

@@ -0,0 +1,5 @@
+/.gradle/
+/.idea/
+/build/
+/output/
+!gradle-wrapper.jar

.hgignore

@@ -1,13 +0,0 @@
-
-\.orig$
-\.orig\..*$
-\.chg\..*$
-\.rej$
-\.conflict\~$
-.gradle/
-output/
-.ipynb_checkpoints/
-notebooks/images/
-build/
-.idea/*
-!gradle-wrapper.jar

build.gradle

@@ -1,15 +1,14 @@
 plugins {
-    id "org.jetbrains.kotlin.jvm" version "1.3.10"
-    id "java"
+    id "org.jetbrains.kotlin.jvm" version "1.4.10"
     id "application"
 }
 
-group = 'inr.numass'
-version = 'dev'
+group = 'ru.inr.mass'
+version = '1.0.0'
 
 description = "Numass trapping simulation"
 
-mainClassName = "inr.numass.trapping.TrappingKt"
+mainClassName = "ru.inr.mass.trapping.TrappingKt"
 
 repositories {
     mavenCentral()

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.7-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.5-bin.zip

gradlew

@@ -1,5 +1,21 @@
 #!/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
@@ -28,7 +44,7 @@ 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=""
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
@@ -66,6 +82,7 @@ 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
@@ -109,10 +126,11 @@ if $darwin; then
     GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
 fi
 
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$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
@@ -138,19 +156,19 @@ if $cygwin ; then
         else
             eval `echo args$i`="\"$arg\""
         fi
-        i=$((i+1))
+        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" ;;
+        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
 
@@ -159,14 +177,9 @@ save () {
     for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
     echo " "
 }
-APP_ARGS=$(save "$@")
+APP_ARGS=`save "$@"`
 
 # 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"
 
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
-  cd "$(dirname "$0")"
-fi
-
 exec "$JAVACMD" "$@"

gradlew.bat

@@ -1,3 +1,19 @@
+@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
@@ -13,15 +29,18 @@ 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=
+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
+if "%ERRORLEVEL%" == "0" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -35,7 +54,7 @@ goto fail
 set JAVA_HOME=%JAVA_HOME:"=%
 set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
-if exist "%JAVA_EXE%" goto init
+if exist "%JAVA_EXE%" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -45,28 +64,14 @@ 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%
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
 
 :end
 @rem End local scope for the variables with windows NT shell

src/main/kotlin/ru/inr/mass/trapping/FunctionCache.kt

@@ -1,23 +1,23 @@
-package inr.numass.trapping
+package ru.inr.mass.trapping
 
 import java.util.*
 
-class FunctionCache(val xPrecision: Double, val function: (Double) -> Double) {
+class FunctionCache(private val xPrecision: Double, val function: (Double) -> Double) {
     private val values = TreeMap<Double, Double>()
 
     operator fun invoke(x: Double): Double {
         val floor: MutableMap.MutableEntry<Double, Double>? = values.floorEntry(x)
         val ceil: MutableMap.MutableEntry<Double, Double>? = values.ceilingEntry(x)
-        if (floor == null || ceil == null || ceil.key - floor.key <= xPrecision) {
+        return if (floor == null || ceil == null || ceil.key - floor.key <= xPrecision) {
             val newValue = function(x)
             values[x] = newValue
-            return newValue
+            newValue
         } else {
             val x0 = floor.key
             val x1 = ceil.key
             val y0 = floor.value
             val y1 = ceil.value
-            return y0 + (x - x0) * (y1 - y0) / (x1 - x0)
+            y0 + (x - x0) * (y1 - y0) / (x1 - x0)
         }
     }
 }

src/main/kotlin/ru/inr/mass/trapping/MultiCounter.kt

@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.trapping
+package ru.inr.mass.trapping
 
 import java.io.PrintStream
 import java.lang.Integer.valueOf
-import java.util.HashMap
+import java.util.*
 
 /**
  * TODO есть объект MultiDimensionalCounter, исползовать его?

src/main/kotlin/ru/inr/mass/trapping/RandomGeneratorBridge.kt

@@ -1,9 +1,9 @@
-package inr.numass.trapping
+package ru.inr.mass.trapping
 
 import org.apache.commons.math3.random.RandomGenerator
 import org.apache.commons.rng.UniformRandomProvider
 
-class RandomGeneratorBridge(val provider: UniformRandomProvider) : RandomGenerator {
+class RandomGeneratorBridge(private val provider: UniformRandomProvider) : RandomGenerator {
     override fun nextBoolean(): Boolean = provider.nextBoolean()
 
     override fun nextFloat(): Float = provider.nextFloat()

src/main/kotlin/ru/inr/mass/trapping/Scatter.kt

@@ -1,4 +1,4 @@
-package inr.numass.trapping
+package ru.inr.mass.trapping
 
 import org.apache.commons.math3.random.RandomGenerator
 import org.apache.commons.math3.util.FastMath.*
@@ -845,7 +845,7 @@ object Scatter {
         val lnt: Double
         if (E < 16.0) {
             sigma = 1e-40
-        } else if (E >= 16.0 && E <= 250.0) {
+        } else if (E in 16.0..250.0) {
             t = E / B
             u = U / B
             r = R / B
@@ -951,11 +951,10 @@ object Scatter {
     private fun sigmadiss15(E: Double): Double {
         var lnsigma: Double = 0.0
         val lnE: Double = log(E)
-        var lnEn: Double
         val Emin: Double = 16.5
         var n: Int
         //  E is in eV
-        lnEn = 1.0
+        var lnEn: Double = 1.0
         val sigma = if (E < Emin) {
             0.0
         } else {

src/main/kotlin/ru/inr/mass/trapping/SimulationManager.kt

@@ -1,4 +1,4 @@
-package inr.numass.trapping
+package ru.inr.mass.trapping
 
 import org.apache.commons.math3.analysis.interpolation.LinearInterpolator
 import org.apache.commons.math3.random.JDKRandomGenerator

src/main/kotlin/ru/inr/mass/trapping/Simulator.kt

@@ -2,7 +2,7 @@
  * To change this template, choose Tools | Templates
  * and open the template in the editor.
  */
-package inr.numass.trapping
+package ru.inr.mass.trapping
 
 import org.apache.commons.math3.distribution.ExponentialDistribution
 import org.apache.commons.math3.geometry.euclidean.threed.Rotation
@@ -11,6 +11,8 @@ import org.apache.commons.math3.random.RandomGenerator
 import org.apache.commons.math3.util.FastMath.*
 import org.apache.commons.math3.util.Pair
 import org.apache.commons.math3.util.Precision
+import ru.inr.mass.trapping.Scatter.counter
+import ru.inr.mass.trapping.Scatter.debug
 
 /**
  * @author Darksnake

src/main/kotlin/ru/inr/mass/trapping/Trapping.kt

@@ -1,10 +1,10 @@
-package inr.numass.trapping
+package ru.inr.mass.trapping
 
 import java.time.Duration
 import java.time.Instant
 
 
-fun main(args: Array<String>) {
+fun main() {
     //val z = doubleArrayOf(-1.736, -1.27, -0.754, -0.238, 0.278, 0.794, 1.31, 1.776)
     //val b = doubleArrayOf(3.70754, 0.62786, 0.60474, 0.60325, 0.60333, 0.60503, 0.6285, 3.70478)
     //        System.out.println("Press any key to start...");