Merge pull request #133 from ReactionMechanismGenerator/debug_isomorphic

Correct ESS check when running on a server
ReactionMechanismGenerator · Jun 4, 2019 · f893b48 · f893b48
2 parents c8e6dc2 + 55ad23a
commit f893b48
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Showing 3 changed files with 50 additions and 33 deletions.
diff --git a/arc/main.py b/arc/main.py
@@ -885,6 +885,8 @@ def determine_ess_settings(self, diagnostics=False):
         # look for ESS on remote servers ARC has access to
         logging.info('\n\nMapping servers...\n')
         for server in servers.keys():
+            if server == 'local':
+                continue
             if diagnostics:
                 logging.info('\nTrying {0}'.format(server))
             ssh = SSHClient(server)

diff --git a/arc/rmgdb.py b/arc/rmgdb.py
@@ -11,7 +11,7 @@
 
 from rmgpy import settings
 from rmgpy.data.rmg import RMGDatabase
-from rmgpy.reaction import isomorphic_species_lists
+from rmgpy.reaction import same_species_lists
 from rmgpy.data.kinetics.common import find_degenerate_reactions
 from rmgpy.exceptions import KineticsError
 
@@ -183,7 +183,7 @@ def loop_families(rmgdb, reaction):
         if len(reaction.products) == 1:
             for fam_rxn in family_reactions_by_r:
                 for product0 in reaction.products[0].molecule:
-                    if isomorphic_species_lists([product0], fam_rxn.products):
+                    if same_species_lists([product0], fam_rxn.products):
                         family_reactions_by_rnp.append(fam_rxn)
             degenerate_reactions = find_degenerate_reactions(rxn_list=family_reactions_by_rnp,
                                                              same_reactants=False,
@@ -192,7 +192,7 @@ def loop_families(rmgdb, reaction):
             for fam_rxn in family_reactions_by_r:
                 for product0 in reaction.products[0].molecule:
                     for product1 in reaction.products[1].molecule:
-                        if isomorphic_species_lists([product0, product1], fam_rxn.products):
+                        if same_species_lists([product0, product1], fam_rxn.products):
                             family_reactions_by_rnp.append(fam_rxn)
             degenerate_reactions = find_degenerate_reactions(rxn_list=family_reactions_by_rnp,
                                                              same_reactants=False,
@@ -202,7 +202,7 @@ def loop_families(rmgdb, reaction):
                 for product0 in reaction.products[0].molecule:
                     for product1 in reaction.products[1].molecule:
                         for product2 in reaction.products[2].molecule:
-                            if isomorphic_species_lists([product0, product1, product2], fam_rxn.products):
+                            if same_species_lists([product0, product1, product2], fam_rxn.products):
                                 family_reactions_by_rnp.append(fam_rxn)
             degenerate_reactions = find_degenerate_reactions(rxn_list=family_reactions_by_rnp,
                                                              same_reactants=False,

diff --git a/ipython/ARC ESS diagnostics.ipynb b/ipython/ARC ESS diagnostics.ipynb
@@ -16,61 +16,76 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "ARC execution initiated on Mon Dec 24 11:35:41 2018\n",
+      "ARC execution initiated on Tue Jun  4 10:43:03 2019\n",
       "\n",
       "###############################################################\n",
       "#                                                             #\n",
+      "#                 Automatic Rate Calculator                   #\n",
       "#                            ARC                              #\n",
       "#                                                             #\n",
-      "#   Version: 0.1                                              #\n",
+      "#   Version: 1.0.0                                            #\n",
       "#                                                             #\n",
       "###############################################################\n",
       "\n",
+      "The current git HEAD for ARC is:\n",
+      "    7e3cc3b3be02b926d33d3fd066ee9c1d60f12b2f\n",
+      "    Mon Jun 3 17:17:32 2019 -0400\n",
+      "\n",
       "Starting project Diagnostics\n",
+      "Using default level b3lyp/6-31+g(d,p) for refined conformer searches (after filtering via force fields)\n",
+      "Using default level b3lyp/6-31+g(d,p) for TS guesses comparison of different methods\n",
+      "Using default level wb97xd/6-311++g(d,p) for geometry optimizations\n",
+      "Using default level wb97xd/6-311++g(d,p) for frequency calculations\n",
+      "Using default level ccsd(t)-f12/cc-pvtz-f12 for single point calculations\n",
+      "Using default level wb97xd/6-311++g(d,p) for rotor scans\n",
+      "\n",
+      "Using the following ESS settings:\n",
+      "{'gaussian': ['pharos']}\n",
       "\n",
+      "Using ccsd(t)-f12/cc-pvtz-f12 as model chemistry for energy corrections in Arkane\n",
       "\n",
-      "Executing QM jobs remotely. Mapping servers...\n",
-      "Using Gaussian on pharos\n",
-      "Using QChem on pharos\n",
-      "Using Molpro on pharos\n",
       "\n",
       "\n",
-      "Using default level b97-d3/6-311+g(d,p) for refined conformer searches (after filtering via force fields)\n",
-      "Using default level wb97x-d3/6-311+g(d,p) for geometry optimizations\n",
-      "Using default level wb97x-d3/6-311+g(d,p) for frequency calculations\n",
-      "Using default level ccsd(t)-f12/cc-pvtz-f12 for single point calculations\n",
-      "Using ccsd(t)-f12/cc-pvtz-f12 as model chemistry for energy corrections in Arkane\n",
-      "Using default level b3lyp/6-311+g(d,p) for rotor scans\n",
+      " ***** Running ESS diagnostics: *****\n",
       "\n",
+      "Found the following ESS on the local machine:\n",
+      "[u'orca']\n",
       "\n",
       "\n",
-      " ***** Runnigng ESS diagnostics: *****\n",
-      "ARC is being excecuted on a PC (did not find \"SSH_CONNECTION\" in the os.environ dictionary\n",
       "\n",
       "\n",
-      "Executing QM jobs remotely. Mapping servers...\n",
+      "Mapping servers...\n",
+      "\n",
+      "\n",
       "Trying pharos\n",
-      "Found Gaussian on pharos: g03=[u'/opt/g03/g03\\n'], g09=[u'/usr/local/EStokTP/exe/g09\\n'], g16=[]\n",
-      "Found QChem on pharos\n",
-      "Found Molpro on pharos\n",
+      "  Found Gaussian on pharos: g03=[], g09=[], g16=[u'/opt/g16/g16\\n']\n",
+      "  Did NOT find QChem on pharos\n",
+      "  Did NOT find Orca on pharos\n",
+      "  Did NOT find Molpro on pharos\n",
+      "\n",
       "Trying rmg\n",
-      "Did NOT find Gaussian on rmg: g03=[], g09=[], g16=[]\n",
-      "Did NOT find QChem on rmg\n",
-      "Did NOT find Molpro on rmg\n",
-      "Using Gaussian on pharos\n",
-      "Using QChem on pharos\n",
-      "Using Molpro on pharos\n",
+      "  Found Gaussian on rmg: g03=[], g09=[], g16=[u'/opt/g16/g16\\n']\n",
+      "  Did NOT find QChem on rmg\n",
+      "  Found Orca on rmg\n",
+      "  Did NOT find Molpro on rmg\n",
+      "\n",
+      "\n",
+      "\n",
+      "Using Gaussian on ['pharos', 'rmg']\n",
+      "Using QChem on []\n",
+      "Using Orca on [u'local', 'rmg']\n",
+      "Using Molpro on []\n",
       "\n",
       "\n",
-      "ESS diagnostics completed\n"
+      "ESS diagnostics completed (elapsed time: 00:00:13)\n"
      ]
     }
    ],
    "source": [
     "import arc\n",
     "\n",
     "arc0 = arc.ARC(project='Diagnostics')\n",
-    "arc0.determine_remote(diagnostics=True)"
+    "arc0.determine_ess_settings(diagnostics=True)"
    ]
   },
   {
@@ -83,9 +98,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "rmg_env",
+   "display_name": "Python 2",
    "language": "python",
-   "name": "rmg_env"
+   "name": "python2"
   },
   "language_info": {
    "codemirror_mode": {
@@ -97,7 +112,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.15"
+   "version": "2.7.16"
   }
  },
  "nbformat": 4,