RMG-database v2.3.0 release

meta.yaml → .conda/meta.yaml

@@ -4,7 +4,7 @@ package:
   version: {{ environ.get('GIT_DESCRIBE_TAG', '') }}
 
 source:
-  path: .
+  path: ../
 
 build:
   number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}

.travis.yml

@@ -23,6 +23,9 @@ before_install:
   # Update conda
   - conda update --yes conda
   - conda info -a
+  # Set git info
+  - git config --global user.name "Travis Deploy"
+  - git config --global user.email "[email protected]"
 
 jobs:
   include:
@@ -50,7 +53,7 @@ jobs:
         - conda config --add channels rmg
         - conda config --set anaconda_upload yes
       script:
-        - conda build --token $CONDA_TOKEN --user rmg RMG-database
+        - conda build --token $CONDA_TOKEN --user rmg RMG-database/.conda
     - os: osx
       install:
         # Setup conda build
@@ -59,4 +62,4 @@ jobs:
         - conda config --add channels rmg
         - conda config --set anaconda_upload yes
       script:
-        - conda build --token $CONDA_TOKEN --user rmg RMG-database
+        - conda build --token $CONDA_TOKEN --user rmg RMG-database/.conda

deploy.sh

@@ -2,55 +2,30 @@
 
 set -e # exit with nonzero exit code if anything fails
 
-openssl aes-256-cbc -K $encrypted_02f40ca58e32_key -iv $encrypted_02f40ca58e32_iv -in deploy_key.enc -out deploy_key -d
-
 echo 'Travis Build Dir: '$TRAVIS_BUILD_DIR
 
-if $TRAVIS_PULL_REQUEST
-  then
-    DEPLOY_BRANCH=$TRAVIS_PULL_REQUEST
+if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
+  DEPLOY_BRANCH=$TRAVIS_PULL_REQUEST
 else
   DEPLOY_BRANCH=$TRAVIS_BRANCH
 fi
 
 # Deploy built site to this branch
-echo Deploy branch: $DEPLOY_BRANCH
+echo "DEPLOY_BRANCH: $DEPLOY_BRANCH"
 
-# SSH URL of the RMG/RMG-tests repo that is pushed to:
-REPO=git@github.com:ReactionMechanismGenerator/RMG-tests.git
+# URL for the official RMG-tests repository
+REPO=https://${GH_TOKEN}@github.com/ReactionMechanismGenerator/RMG-tests.git
 
 if [ -n "$TRAVIS_BUILD_ID" ]; then
 
-  #
-  # Set the following environment variables in the travis configuration (.travis.yml)
-  #
-  #   DEPLOY_BRANCH    - The only branch that Travis should deploy from
-  #   GIT_NAME         - The Git user name
-  #   GIT_EMAIL        - The Git user email
-  #
-  GIT_NAME="Travis Deploy"
-  GIT_EMAIL="[email protected]"
-  echo DEPLOY_BRANCH: $DEPLOY_BRANCH
-  echo GIT_NAME: $GIT_NAME
-  echo GIT_EMAIL: $GIT_EMAIL
   if [ "$TRAVIS_BRANCH" != "$DEPLOY_BRANCH" ]; then
     echo "Travis should only deploy from the DEPLOY_BRANCH ($DEPLOY_BRANCH) branch"
     exit 0
-  else
-    if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
-      echo "Travis should not deploy from pull requests"
-      exit 0
-    else
-
-      # use the decrypted deploy SSH key as
-      # the credentials to push to the RMG-tests repo:
-      chmod 600 deploy_key
-      eval `ssh-agent -s`
-      ssh-add deploy_key
-      git config --global user.name "$GIT_NAME"
-      git config --global user.email "$GIT_EMAIL"
-    fi
+  elif [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
+    echo "Travis should not deploy from pull requests"
+    exit 0
   fi
+
 fi
 
 # create a temporary folder:
@@ -76,4 +51,4 @@ git checkout $RMGTESTSBRANCH
 git commit --allow-empty -m rmgdb-$REV
 
 # push to the branch to the RMG/RMG-tests repo:
-git push -f $REPO $RMGTESTSBRANCH > /dev/null
+git push -f $REPO $RMGTESTSBRANCH > /dev/null

input/forbiddenStructures.py

@@ -316,18 +316,19 @@
 
 entry(
     label = "N2SO",
-    species =
+    group =
 """
-1 O u0 p2 c0 {2,D}
-2 S u0 p1 c0 {1,D} {3,D}
-3 N u0 p0 c+1 {2,D} {4,D}
-4 N u0 p2 c-1 {3,D}
+1 O u0 {2,[S,D]}
+2 S u0 {1,[S,D]} {3,[S,D]}
+3 N u0 {2,[S,D]} {4,[S,D]}
+4 N u0 {3,[S,D]}
 """,
     shortDesc = u"""""",
     longDesc =
 u"""
-The N2--SO complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable NN--SO bond length),
+The N2--SO complex isn't sable (i.e., NNSO's geometry cannot be optimized with a reasonable NN--SO bond length),
 yet it is predicted by RMG, e.g, by R_Addition_Multiple_Bond of [S][O] to N#N.
+N2SO2 is forbidden as well in this group for the same reason.
 """,
 )
 

input/kinetics/families/1+2_Cycloaddition/groups.py

@@ -10,8 +10,8 @@
 template(reactants=["multiplebond", "elec_def"], products=["cycle"], ownReverse=False)
 
 reverse = "Three_Ring_Cleavage"
-
 reversible = True
+
 recipe(actions=[
     ['CHANGE_BOND', '*1', -1, '*2'],
     ['FORM_BOND', '*1', 1, '*3'],
@@ -70,11 +70,11 @@
     label = "me_carbene",
     group = 
 """
-1 *3 C  u0 p1 {2,S} {3,S}
-2    Cs u0 {1,S} {4,S} {5,S} {6,S}
+1    Cs u0 {2,S} {3,S} {4,S} {5,S}
+2 *3 C  u0 p1 {1,S} {6,S}
 3    H  u0 {1,S}
-4    H  u0 {2,S}
-5    H  u0 {2,S}
+4    H  u0 {1,S}
+5    H  u0 {1,S}
 6    H  u0 {2,S}
 """,
     kinetics = None,
@@ -102,15 +102,15 @@
     label = "dime_carbene",
     group = 
 """
-1 *3 C  u0 p1 {2,S} {3,S}
-2    Cs u0 {1,S} {4,S} {5,S} {6,S}
-3    Cs u0 {1,S} {7,S} {8,S} {9,S}
-4    H  u0 {2,S}
-5    H  u0 {2,S}
-6    H  u0 {2,S}
-7    H  u0 {3,S}
-8    H  u0 {3,S}
-9    H  u0 {3,S}
+1    Cs u0 {3,S} {4,S} {5,S} {6,S}
+2    Cs u0 {3,S} {7,S} {8,S} {9,S}
+3 *3 C  u0 p1 {1,S} {2,S}
+4    H  u0 {1,S}
+5    H  u0 {1,S}
+6    H  u0 {1,S}
+7    H  u0 {2,S}
+8    H  u0 {2,S}
+9    H  u0 {2,S}
 """,
     kinetics = None,
 )