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Minor changes #133

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merged 3 commits into from
Jun 4, 2019
Merged

Minor changes #133

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36aae47
Updated isomorphic species check method name in rmgdb
Jun 3, 2019
8ee282b
Corrected local server check
xiaoruiDong Jun 4, 2019
55ad23a
Updated ESS check function name in iPython notebook
xiaoruiDong Jun 4, 2019
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2 changes: 2 additions & 0 deletions arc/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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8 changes: 4 additions & 4 deletions arc/rmgdb.py
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Expand Up @@ -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

Expand Down Expand Up @@ -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,
Expand All @@ -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,
Expand All @@ -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,
Expand Down
73 changes: 44 additions & 29 deletions ipython/ARC ESS diagnostics.ipynb
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Expand Up @@ -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)"
]
},
{
Expand All @@ -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": {
Expand All @@ -97,7 +112,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.15"
"version": "2.7.16"
}
},
"nbformat": 4,
Expand Down