From 36aae478ef5d2e34a787f700a2e3a6a971646576 Mon Sep 17 00:00:00 2001 From: Xiaorui Dong Date: Mon, 3 Jun 2019 16:59:29 -0400 Subject: [PATCH 1/3] Updated isomorphic species check method name in rmgdb --- arc/rmgdb.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/arc/rmgdb.py b/arc/rmgdb.py index 6cefd6a0bb..d986047127 100644 --- 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, From 8ee282b0ec4dd20abb8b52a826b515a318a0c704 Mon Sep 17 00:00:00 2001 From: Xiaorui Dong Date: Tue, 4 Jun 2019 11:57:53 -0400 Subject: [PATCH 2/3] Corrected local server check --- arc/main.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/arc/main.py b/arc/main.py index 3ead27b462..a65199c2d1 100644 --- 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) From 55ad23a7247dd767eb986f4d43530122284796c5 Mon Sep 17 00:00:00 2001 From: Xiaorui Dong Date: Tue, 4 Jun 2019 11:59:08 -0400 Subject: [PATCH 3/3] Updated ESS check function name in iPython notebook --- ipython/ARC ESS diagnostics.ipynb | 73 +++++++++++++++++++------------ 1 file changed, 44 insertions(+), 29 deletions(-) diff --git a/ipython/ARC ESS diagnostics.ipynb b/ipython/ARC ESS diagnostics.ipynb index e635c665bb..d5d493405d 100644 --- a/ipython/ARC ESS diagnostics.ipynb +++ b/ipython/ARC ESS diagnostics.ipynb @@ -16,53 +16,68 @@ "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" ] } ], @@ -70,7 +85,7 @@ "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,