Updated libs, README.md

README.md

@@ -61,9 +61,31 @@ For the language server to work properly, all MCNP inputs are required to:
 
 MCNP is insensitive to these requirements, but they are necessary for validation.
 
+## Known Issues
+
+There are some syntaxes that can be used in MCNP, but are treated as invalid by the  
+Language Server. 
+- Deprecated formats are not necessarily supported. The Language Server was designed  
+for the current MCNP6.2 syntax. 
+- Having a line continuation character `&` at the end of the last line on a multi-line card. 
+- Exponent notations that do not use the `E`. 
+- The multiplier operator `xM` is not accepted on every card.
+    - It will work on cards where it is commonly used like `IMP`.
+- Using excess parentheses on `FM` cards. Only use the required amount. Examples:
+    - Error: `fm4  ((-1 5 -1))`
+    - Good: `fm4  (-1 5 -1)`
+- Ordering of mixed numeric and symbolic particle types on `SI`. Symbols must come  
+before number. Examples:
+    - Error: `SI14 L 1 2 H` 
+    - Error: `SI14 L 1 H 2`
+    - Good: `SI14 L H 1 2`  
+- A blank line with 5+ spaces followed by an indented line. To avoid this error, simply:
+    - Remove all spaces on the lines between deck sections.
+    - Or avoid indenting the first card of a section.
+
 ## Tips for Troubleshooting
 
-- The easiest way to cause a large number of errors is with a broken reference.
+- The easiest way to cause numerous errors is with a broken reference.
     - For example, expect errors on your Cell cards until all Surfaces and Materials  
   have been defined.
     - Note that VS Code will track references between files in your working directory.  
@@ -76,7 +98,7 @@ MCNP is insensitive to these requirements, but they are necessary for validation
     - `READ` is supported only as a data card.
 - Try inputting all optional parameters for a card.
     - The language server might be expecting the full card specification.
-- Double check the syntax described in the MCNP6.2 manual.
+- Double-check the syntax described in the MCNP6.2 manual.
 
 # Run and Plot Options
 These features need to be configured through the `Extension Settings` menu.  

mcnp-server/bin/mcnp-server

@@ -1,7 +1,7 @@
-#!/usr/bin/env sh
+#!/bin/sh
 
 #
-# Copyright 2015 the original author or authors.
+# Copyright © 2015-2021 the original authors.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -17,78 +17,113 @@
 #
 
 ##############################################################################
-##
-##  gov.lanl.mcnp.ide start up script for UN*X
-##
+#
+#   gov.lanl.mcnp.ide start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh gov.lanl.mcnp.ide
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GOV_LANL_MCNP_IDE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
 ##############################################################################
 
 # 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
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
 done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/.." >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
+
+APP_HOME=$( cd "${APP_HOME:-./}.." && pwd -P ) || exit
 
 APP_NAME="gov.lanl.mcnp.ide"
-APP_BASE_NAME=`basename "$0"`
+APP_BASE_NAME=${0##*/}
 
 # Add default JVM options here. You can also use JAVA_OPTS and GOV_LANL_MCNP_IDE_OPTS to pass JVM options to this script.
 DEFAULT_JVM_OPTS=""
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
 
 warn () {
     echo "$*"
-}
+} >&2
 
 die () {
     echo
     echo "$*"
     echo
     exit 1
-}
+} >&2
 
 # 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
-    ;;
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
 esac
 
-CLASSPATH=$APP_HOME/lib/gov.lanl.mcnp.ide-1.0.0-SNAPSHOT.jar:$APP_HOME/lib/gov.lanl.mcnp-1.0.0-SNAPSHOT.jar:$APP_HOME/lib/org.eclipse.xtext.xbase.ide-2.20.0.jar:$APP_HOME/lib/org.eclipse.xtext.ide-2.20.0.jar:$APP_HOME/lib/org.eclipse.xtext.xbase-2.20.0.jar:$APP_HOME/lib/org.eclipse.xtext.common.types-2.20.0.jar:$APP_HOME/lib/org.eclipse.xtext-2.20.0.jar:$APP_HOME/lib/org.eclipse.xtext.util-2.20.0.jar:$APP_HOME/lib/org.eclipse.lsp4j-0.8.1.jar:$APP_HOME/lib/org.eclipse.lsp4j.generator-0.8.1.jar:$APP_HOME/lib/org.eclipse.xtend.lib-2.20.0.jar:$APP_HOME/lib/org.eclipse.xtend.lib.macro-2.20.0.jar:$APP_HOME/lib/org.eclipse.xtext.xbase.lib-2.20.0.jar:$APP_HOME/lib/guava-27.1-jre.jar:$APP_HOME/lib/jsr305-3.0.2.jar:$APP_HOME/lib/error_prone_annotations-2.2.0.jar:$APP_HOME/lib/guice-3.0.jar:$APP_HOME/lib/classgraph-4.8.35.jar:$APP_HOME/lib/reload4j-1.2.19.jar:$APP_HOME/lib/antlr-runtime-3.2.jar:$APP_HOME/lib/asm-commons-7.2.jar:$APP_HOME/lib/asm-analysis-7.2.jar:$APP_HOME/lib/asm-tree-7.2.jar:$APP_HOME/lib/asm-7.2.jar:$APP_HOME/lib/org.eclipse.emf.common-2.12.0.jar:$APP_HOME/lib/org.eclipse.emf.ecore-2.12.0.jar:$APP_HOME/lib/org.eclipse.emf.ecore.change-2.11.0.jar:$APP_HOME/lib/org.eclipse.emf.ecore.xmi-2.12.0.jar:$APP_HOME/lib/org.eclipse.lsp4j.jsonrpc-0.8.1.jar:$APP_HOME/lib/org.eclipse.equinox.common-3.10.500.jar:$APP_HOME/lib/org.eclipse.osgi-3.15.0.jar:$APP_HOME/lib/javax.inject-1.jar:$APP_HOME/lib/aopalliance-1.0.jar:$APP_HOME/lib/gson-2.8.2.jar:$APP_HOME/lib/failureaccess-1.0.1.jar:$APP_HOME/lib/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar:$APP_HOME/lib/checker-qual-2.5.2.jar:$APP_HOME/lib/j2objc-annotations-1.1.jar:$APP_HOME/lib/animal-sniffer-annotations-1.17.jar
+CLASSPATH=$APP_HOME/lib/gov.lanl.mcnp.ide-1.0.0-SNAPSHOT.jar:$APP_HOME/lib/gov.lanl.mcnp-1.0.0-SNAPSHOT.jar:$APP_HOME/lib/org.eclipse.xtext.xbase.ide-2.27.0.jar:$APP_HOME/lib/org.eclipse.xtext.ide-2.27.0.jar:$APP_HOME/lib/org.eclipse.xtext.xbase-2.27.0.jar:$APP_HOME/lib/org.eclipse.xtext.common.types-2.27.0.jar:$APP_HOME/lib/org.eclipse.xtext-2.27.0.jar:$APP_HOME/lib/org.eclipse.xtext.util-2.27.0.jar:$APP_HOME/lib/guice-5.0.1.jar:$APP_HOME/lib/aopalliance-1.0.jar:$APP_HOME/lib/org.eclipse.lsp4j-0.14.0.jar:$APP_HOME/lib/org.eclipse.lsp4j.generator-0.14.0.jar:$APP_HOME/lib/org.eclipse.xtend.lib-2.27.0.jar:$APP_HOME/lib/org.eclipse.xtend.lib.macro-2.27.0.jar:$APP_HOME/lib/org.eclipse.xtext.xbase.lib-2.27.0.jar:$APP_HOME/lib/guava-30.1-jre.jar:$APP_HOME/lib/jsr305-3.0.2.jar:$APP_HOME/lib/error_prone_annotations-2.3.4.jar:$APP_HOME/lib/classgraph-4.8.138.jar:$APP_HOME/lib/reload4j-1.2.19.jar:$APP_HOME/lib/antlr-runtime-3.2.jar:$APP_HOME/lib/org.eclipse.emf.ecore.change-2.14.0.jar:$APP_HOME/lib/org.eclipse.emf.ecore.xmi-2.16.0.jar:$APP_HOME/lib/org.eclipse.emf.ecore-2.20.0.jar:$APP_HOME/lib/org.eclipse.emf.common-2.17.0.jar:$APP_HOME/lib/org.eclipse.lsp4j.jsonrpc-0.14.0.jar:$APP_HOME/lib/org.eclipse.equinox.common-3.13.0.jar:$APP_HOME/lib/org.eclipse.osgi-3.16.0.jar:$APP_HOME/lib/asm-9.3.jar:$APP_HOME/lib/javax.inject-1.jar:$APP_HOME/lib/gson-2.8.9.jar:$APP_HOME/lib/failureaccess-1.0.1.jar:$APP_HOME/lib/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar:$APP_HOME/lib/checker-qual-3.5.0.jar:$APP_HOME/lib/j2objc-annotations-1.3.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="$JAVA_HOME/jre/sh/java"
+        JAVACMD=$JAVA_HOME/jre/sh/java
     else
-        JAVACMD="$JAVA_HOME/bin/java"
+        JAVACMD=$JAVA_HOME/bin/java
     fi
     if [ ! -x "$JAVACMD" ] ; then
         die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -97,92 +132,102 @@ Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
     fi
 else
-    JAVACMD="java"
+    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: $MAX_FD_LIMIT"
-    fi
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
 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
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GOV_LANL_MCNP_IDE_OPTS environment variables.
 
 # 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
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
     # 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\""
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
         fi
-        i=$((i+1))
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
     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;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GOV_LANL_MCNP_IDE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
 
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GOV_LANL_MCNP_IDE_OPTS -classpath "\"$CLASSPATH\"" org.eclipse.xtext.ide.server.ServerLauncher "$APP_ARGS"
+set -- \
+        -classpath "$CLASSPATH" \
+        org.eclipse.xtext.ide.server.ServerLauncher \
+        "$@"
 
-# 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 "$0")"
-fi
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GOV_LANL_MCNP_IDE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
 
 exec "$JAVACMD" "$@"