Merge pull request #109 from ReactionMechanismGenerator/misc

Miscellaneous changes

.gitignore

@@ -15,12 +15,12 @@
 # PyCharm project files
 .idea/*
 
-# settings file
-arc/settings.py
-
 # Projects
 Projects/
 
+# Examples
+examples/
+
 # Unit test files
 .coverage
 testing/*

ARC.py

@@ -63,10 +63,7 @@ def main():
         verbose = logging.DEBUG
     elif args.quiet:
         verbose = logging.WARNING
-    try:
-        input_dict['verbose']
-    except KeyError:
-        input_dict['verbose'] = verbose
+    input_dict['verbose'] = input_dict['verbose'] if 'verbose' in input_dict else verbose
     arc_object = ARC(input_dict=input_dict, project_directory=project_directory)
     arc_object.execute()
 

arc/arc_exceptions.py

@@ -13,71 +13,71 @@ class InputError(Exception):
     pass
 
 
-class OutputError(Exception):
+class JobError(Exception):
     """
-    This exception is raised whenever an error occurs while saving output information
+    An exception class for exceptional behavior that occurs while working with jobs
     """
     pass
 
 
-class SettingsError(Exception):
+class OutputError(Exception):
     """
-    An exception raised when dealing with settings
+    This exception is raised whenever an error occurs while saving output information
     """
     pass
 
 
-class SpeciesError(Exception):
+class ReactionError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with chemical species
+    An exception class for exceptional behavior that occurs while working with reactions
     """
     pass
 
 
-class TSError(Exception):
+class RotorError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with transition states
+    An exception class for exceptional behavior that occurs while working with rotors
     """
     pass
 
 
-class ReactionError(Exception):
+class SanitizationError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with reactions
+    Exception class to handle errors during SMILES perception.
     """
     pass
 
 
-class RotorError(Exception):
+class SchedulerError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with rotors
+    An exception class for exceptional behavior that occurs while working with the scheduler
     """
     pass
 
 
-class SchedulerError(Exception):
+class ServerError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with the scheduler
+    An exception class for exceptional behavior that occurs while working with servers
     """
     pass
 
 
-class JobError(Exception):
+class SettingsError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with jobs
+    An exception raised when dealing with settings
     """
     pass
 
 
-class ServerError(Exception):
+class SpeciesError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with servers
+    An exception class for exceptional behavior that occurs while working with chemical species
     """
     pass
 
 
-class SanitizationError(Exception):
+class TSError(Exception):
     """
-    Exception class to handle errors during SMILES perception.
+    An exception class for exceptional behavior that occurs while working with transition states
     """
     pass

arc/job/inputs.py

@@ -36,7 +36,7 @@
 input_files = {
     'gaussian': """%chk=check.chk
 %mem={memory}mb
-%nproc=8
+%nproc={cpus}
 
 #P {job_type_1} {restricted}{method}{slash}{basis} {job_type_2} {fine} {trsh} iop(2/9=2000)
 
@@ -113,7 +113,7 @@
 
 """,
 
-    'arkane_species': """#!/usr/bin/env python
+    'arkane_input_species': """#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 linear = {linear}{bonds}

arc/job/jobTest.py

@@ -27,9 +27,9 @@ def setUpClass(cls):
         A method that is run before all unit tests in this class.
         """
         cls.maxDiff = None
-        settings = {'gaussian': 'server1', 'molpro': 'server2', 'qchem': 'server1', 'ssh': False}
-        cls.job1 = Job(project='project_test', settings=settings, species_name='tst_spc', xyz='C 0.0 0.0 0.0',
-                       job_type='opt', level_of_theory='b3lyp/6-31+g(d)', multiplicity=1,
+        ess_settings = {'gaussian': ['server1','server2'], 'molpro': ['server2'], 'qchem': ['server1'], 'ssh': False}
+        cls.job1 = Job(project='project_test', ess_settings=ess_settings, species_name='tst_spc', xyz='C 0.0 0.0 0.0',
+                       job_type='opt', level_of_theory='b3lyp/6-31+g(d)', multiplicity=1, testing=True,
                        project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
         cls.job1.initial_time = datetime.datetime(2019, 3, 15, 19, 53, 7, 0)
         cls.job1.final_time = datetime.datetime(2019, 3, 15, 19, 53, 8, 0)

arc/job/ssh.py

@@ -112,7 +112,11 @@ def _download_file(self, remote_file_path, local_file_path):
         Download a file from `remote_file_path` to `local_file_path`.
         """
         sftp, ssh = self.connect()
-        sftp.get(remotepath=remote_file_path, localpath=local_file_path)
+        try:
+            sftp.get(remotepath=remote_file_path, localpath=local_file_path)
+        except IOError:
+            logging.warning('Got an IOError when trying to download file {0} from {1}'.format(remote_file_path,
+                                                                                              self.server))
         sftp.close()
         ssh.close()
 
@@ -257,7 +261,10 @@ def try_connecting(self):
     def get_last_modified_time(self, remote_file_path):
         """returns the last modified time of `remote_file` in a datetime format"""
         sftp, ssh = self.connect()
-        timestamp = sftp.stat(remote_file_path).st_mtime
+        try:
+            timestamp = sftp.stat(remote_file_path).st_mtime
+        except IOError:
+            return None
         sftp.close()
         ssh.close()
         return datetime.datetime.fromtimestamp(timestamp)

arc/job/submit.py

@@ -12,7 +12,7 @@
 #SBATCH -p defq
 #SBATCH -J {name}
 #SBATCH -N 1
-#SBATCH -n 8
+#SBATCH -n {cpus}
 #SBATCH --time={t_max}
 #SBATCH --mem-per-cpu 4500
 
@@ -48,14 +48,55 @@
 rm -rf $GAUSS_SCRDIR
 rm -rf $WorkDir
 
+""",
+        # Gaussian16 on RMG
+        'gaussian16': """#!/bin/bash -l
+#SBATCH -p long
+#SBATCH -J {name}
+#SBATCH -N 1
+#SBATCH -n {cpus}
+#SBATCH --time={t_max}
+#SBATCH --mem-per-cpu={mem_cpu}
+
+which 16
+
+echo "============================================================"
+echo "Job ID : $SLURM_JOB_ID"
+echo "Job Name : $SLURM_JOB_NAME"
+echo "Starting on : $(date)"
+echo "Running on node : $SLURMD_NODENAME"
+echo "Current directory : $(pwd)"
+echo "============================================================"
+
+WorkDir=/scratch/users/{un}/$SLURM_JOB_NAME-$SLURM_JOB_ID
+SubmitDir=`pwd`
+
+GAUSS_SCRDIR=/scratch/users/{un}/g16/$SLURM_JOB_NAME-$SLURM_JOB_ID
+export GAUSS_SCRDIR
+
+mkdir -p $GAUSS_SCRDIR
+mkdir -p $WorkDir
+
+cd $WorkDir
+. $g16root/g16/bsd/g16.profile
+
+cp $SubmitDir/input.gjf .
+
+g16 < input.gjf > input.log
+formchk  check.chk check.fchk
+cp * $SubmitDir/
+
+rm -rf $GAUSS_SCRDIR
+rm -rf $WorkDir
+
 """,
 
         # Orca on C3DDB:
         'orca': """#!/bin/bash -l
 #SBATCH -p defq
 #SBATCH -J {name}
 #SBATCH -N 1
-#SBATCH -n 8
+#SBATCH -n {cpus}
 #SBATCH --time={t_max}
 #SBATCH --mem-per-cpu 4500
 
@@ -95,7 +136,7 @@
 #SBATCH -p long
 #SBATCH -J {name}
 #SBATCH -N 1
-#SBATCH -n 8
+#SBATCH -n {cpus}
 #SBATCH --time={t_max}
 #SBATCH --mem-per-cpu={mem_cpu}
 
@@ -112,7 +153,7 @@
 sdir=/scratch/{un}/$SLURM_JOB_NAME-$SLURM_JOB_ID
 mkdir -p $sdir
 
-molpro -n 8 -d $sdir input.in
+molpro -n {cpus} -d $sdir input.in
 
 rm -rf $sdir
 
@@ -125,10 +166,9 @@
         'gaussian': """#!/bin/bash -l
 
 #$ -N {name}
-#$ -l long
-#$ -l harpertown
+#$ -l long{architecture}
 #$ -l h_rt={t_max}
-#$ -pe singlenode 6
+#$ -pe singlenode {cpus}
 #$ -l h=!node60.cluster
 #$ -cwd
 #$ -o out.txt
@@ -152,10 +192,9 @@
         'gaussian03_pharos': """#!/bin/bash -l
 
 #$ -N {name}
-#$ -l long
-#$ -l harpertown
+#$ -l long{architecture}
 #$ -l h_rt={t_max}
-#$ -pe singlenode 6
+#$ -pe singlenode {cpus}
 #$ -l h=!node60.cluster
 #$ -cwd
 #$ -o out.txt
@@ -179,10 +218,9 @@
         'qchem': """#!/bin/bash -l
 
 #$ -N {name}
-#$ -l long
-#$ -l harpertown
+#$ -l long{architecture}
 #$ -l h_rt={t_max}
-#$ -pe singlenode 6
+#$ -pe singlenode {cpus}
 #$ -l h=!node60.cluster
 #$ -cwd
 #$ -o out.txt
@@ -207,10 +245,9 @@
         'molpro': """#! /bin/bash -l
 
 #$ -N {name}
-#$ -l long
-#$ -l harpertown
+#$ -l long{architecture}
 #$ -l h_rt={t_max}
-#$ -pe singlenode 6
+#$ -pe singlenode {cpus}
 #$ -l h=!node60.cluster
 #$ -cwd
 #$ -o out.txt