Merge pull request #117 from ReactionMechanismGenerator/oneDMin

Calculating Lennard-Jones coefficients
ReactionMechanismGenerator · Apr 28, 2019 · c7b5474 · c7b5474
2 parents d40572b + 7db2a3c
commit c7b5474
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Showing 29 changed files with 2,035 additions and 307 deletions.
diff --git a/arc/arc_exceptions.py b/arc/arc_exceptions.py
@@ -27,6 +27,13 @@ class OutputError(Exception):
     pass
 
 
+class ParserError(Exception):
+    """
+    This exception is raised whenever an error occurs while parsing files
+    """
+    pass
+
+
 class ReactionError(Exception):
     """
     An exception class for exceptional behavior that occurs while working with reactions

diff --git a/arc/job/inputs.py b/arc/job/inputs.py
@@ -138,4 +138,34 @@
 
     'arkane_free_rotor':
         """FreeRotor(pivots={pivots}, top={top}, symmetry={symmetry})""",
+
+    'onedmin': """ 484040 10    ! Rand. no. seed, N_samples
+ geo.xyz      ! Name of geometry file; units are Angstroms
+ {bath}           ! Bath gas; allowed values are He, Ne, Ar, Kr, H2, N2, O2
+ 2 5          ! Rmin, Rmax; allowed center of mass range
+""",
+
+    'onedmin.molpro.x': """molpro -n 1 --nouse-logfile --no-xml-output -L /opt/molpro2012/molprop_2012_1_Linux_x86_64_i8/lib/ -d /scratch/$USER -o qc.out -s qc.in 
+""",
+
+    'onedmin.qc.mol': """***
+memory,500,m
+
+nosym
+noorient
+geometry
+GEOMETRY
+end
+
+basis,default=avdz,h=vdz
+{df-rhf}
+{df-rmp2}
+
+set,spin=SPIN
+
+molpro_energy=energy
+show[1,e25.15],molpro_energy
+
+---
+""",
 }
diff --git a/arc/job/job.py b/arc/job/job.py
diff --git a/arc/job/jobTest.py b/arc/job/jobTest.py
@@ -27,8 +27,8 @@ def setUpClass(cls):
         A method that is run before all unit tests in this class.
         """
         cls.maxDiff = None
-        cls.ess_settings = {'gaussian': ['server1','server2'], 'molpro': ['server2'],
-                            'qchem': ['server1'], 'ssh': False}
+        cls.ess_settings = {'gaussian': ['server1', 'server2'], 'molpro': ['server2'],
+                            'qchem': ['server1'], 'onedmin': ['server1'], 'ssh': False}
         cls.job1 = Job(project='project_test', ess_settings=cls.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'),
@@ -121,6 +121,22 @@ def test_automatic_ess_assignment(self):
         self.assertEqual(job0.memory, 15000)
         self.assertEqual(job0.max_job_time, 120)
 
+    def test_bath_gas(self):
+        """Test correctly assigning the bath_gas attribute"""
+        self.assertIsNone(self.job1.bath_gas)
+
+        job2 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc',
+                   xyz='C 0.0 0.0 0.0', job_type='onedmin', 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)
+        self.assertEqual(job2.bath_gas, 'N2')
+
+        job2 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc',
+                   xyz='C 0.0 0.0 0.0', job_type='onedmin', 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, bath_gas='Ar')
+        self.assertEqual(job2.bath_gas, 'Ar')
+
 
 ################################################################################
 

diff --git a/arc/job/ssh.py b/arc/job/ssh.py
@@ -1,6 +1,10 @@
 #!/usr/bin/env python
 # encoding: utf-8
 
+"""
+A module for SSHing into servers
+"""
+
 from __future__ import (absolute_import, division, print_function, unicode_literals)
 import logging
 import os
@@ -15,7 +19,7 @@
 ##################################################################
 
 
-class SSH_Client(object):
+class SSHClient(object):
     """
     This is a class for communicating with servers
     """
@@ -79,7 +83,7 @@ def upload_file(self, remote_file_path, local_file_path='', file_string=''):
         while not success and times_tried < max_times_to_try:
             times_tried += 1
             try:
-                write_file(sftp, ssh, remote_file_path, local_file_path, file_string)
+                write_file(sftp, remote_file_path, local_file_path, file_string)
             except IOError:
                 pass
             else:
@@ -195,7 +199,7 @@ def delete_job(self, job_id):
 
     def check_running_jobs_ids(self):
         """
-        Return a list of ``int`` representing job IDs of all jobs submited by the user on a server
+        Return a list of ``int`` representing job IDs of all jobs submitted by the user on a server
         """
         running_jobs_ids = list()
         cmd = check_status_command[servers[self.server]['cluster_soft']] + ' -u ' + servers[self.server]['un']
@@ -207,9 +211,11 @@ def check_running_jobs_ids(self):
         return running_jobs_ids
 
     def submit_job(self, remote_path):
+        """Submit a job"""
         job_status = ''
         job_id = 0
-        cmd = submit_command[servers[self.server]['cluster_soft']] + ' ' + submit_filename[servers[self.server]['cluster_soft']]
+        cmd = submit_command[servers[self.server]['cluster_soft']] + ' ' +\
+              submit_filename[servers[self.server]['cluster_soft']]
         stdout, stderr = self.send_command_to_server(cmd, remote_path)
         if len(stderr) > 0 or len(stdout) == 0:
             job_status = 'errored'
@@ -270,7 +276,8 @@ def get_last_modified_time(self, remote_file_path):
         return datetime.datetime.fromtimestamp(timestamp)
 
 
-def write_file(sftp, ssh, remote_file_path, local_file_path='', file_string=''):
+def write_file(sftp, remote_file_path, local_file_path='', file_string=''):
+    """Write content into a remote file (either write content or upload)"""
     with sftp.open(remote_file_path, "w") as f_remote:
         if file_string:
             f_remote.write(file_string)

diff --git a/arc/job/submit.py b/arc/job/submit.py
@@ -1,20 +1,24 @@
 #!/usr/bin/env python
 # encoding: utf-8
 
+"""
+Submit scripts
+sorted in a dictionary with server names as keys
+"""
 
 ##################################################################
 
 
 submit_scripts = {
-    'Slurm': {
-        # Gaussian09 on C3DDB
+    'c3ddb': {
+        # Gaussian09
         'gaussian': """#!/bin/bash -l
 #SBATCH -p defq
 #SBATCH -J {name}
 #SBATCH -N 1
 #SBATCH -n {cpus}
 #SBATCH --time={t_max}
-#SBATCH --mem-per-cpu 4500
+#SBATCH --mem-per-cpu {mem_cpu}
 
 module add c3ddb/gaussian/09.d01
 which g09
@@ -50,16 +54,22 @@
 rm -rf $WorkDir
 
 """,
-        # Gaussian16 on RMG
-        'gaussian16': """#!/bin/bash -l
-#SBATCH -p long
+
+        # Orca
+        'orca': """#!/bin/bash -l
+#SBATCH -p defq
 #SBATCH -J {name}
 #SBATCH -N 1
 #SBATCH -n {cpus}
 #SBATCH --time={t_max}
-#SBATCH --mem-per-cpu={mem_cpu}
+#SBATCH --mem-per-cpu {mem_cpu}
 
-which 16
+module add c3ddb/orca/4.0.0
+module add c3ddb/openmpi/2.0.2
+which orca
+
+export ORCA_DIR=/cm/shared/c3ddb/orca/4.0.0/
+export PATH=$PATH:$ORCA_DIR
 
 echo "============================================================"
 echo "Job ID : $SLURM_JOB_ID"
@@ -69,44 +79,34 @@
 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 .
+cp $SubmitDir/input.inp .
 
-g16 < input.gjf > input.log
-formchk  check.chk check.fchk
+${ORCA_DIR}/orca input.inp > input.log
 cp * $SubmitDir/
 
-rm -rf $GAUSS_SCRDIR
 rm -rf $WorkDir
 
 """,
+    },
 
-        # Orca on C3DDB:
-        'orca': """#!/bin/bash -l
-#SBATCH -p defq
+    'rmg': {
+        # Gaussian16
+        'gaussian16': """#!/bin/bash -l
+#SBATCH -p long
 #SBATCH -J {name}
 #SBATCH -N 1
 #SBATCH -n {cpus}
 #SBATCH --time={t_max}
-#SBATCH --mem-per-cpu 4500
-
-module add c3ddb/orca/4.0.0
-module add c3ddb/openmpi/2.0.2
-which orca
+#SBATCH --mem-per-cpu={mem_cpu}
 
-export ORCA_DIR=/cm/shared/c3ddb/orca/4.0.0/
-export PATH=$PATH:$ORCA_DIR
+which 16
 
 echo "============================================================"
 echo "Job ID : $SLURM_JOB_ID"
@@ -116,23 +116,29 @@
 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.inp .
+cp $SubmitDir/input.gjf .
 
-${ORCA_DIR}/orca input.inp > input.log
+g16 < input.gjf > input.log
+formchk  check.chk check.fchk
 cp * $SubmitDir/
 
+rm -rf $GAUSS_SCRDIR
 rm -rf $WorkDir
 
 """,
-
-        # Molpro 2015 on RMG
+        # Molpro 2015
         'molpro': """#!/bin/bash -l
 #SBATCH -p long
 #SBATCH -J {name}
@@ -161,9 +167,8 @@
 """,
     },
 
-
-    'OGE': {
-        # Gaussian16 on Pharos
+    'pharos': {
+        # Gaussian16
         'gaussian': """#!/bin/bash -l
 
 #$ -N {name}
@@ -189,7 +194,7 @@
 rm -r /scratch/{un}/{name}
 
 """,
-        # Gaussian03 on Pharos
+        # Gaussian03
         'gaussian03_pharos': """#!/bin/bash -l
 
 #$ -N {name}
@@ -215,7 +220,7 @@
 rm -r /scratch/{un}/{name}
 
 """,
-        # QChem 4.4 on Pharos:
+        # QChem 4.4
         'qchem': """#!/bin/bash -l
 
 #$ -N {name}
@@ -242,7 +247,7 @@
 rm -r /scratch/{un}/{name}
 
 """,
-        # Molpro 2012 on Pharos
+        # Molpro 2012
         'molpro': """#! /bin/bash -l
 
 #$ -N {name}
@@ -260,6 +265,26 @@
 mkdir -p /scratch/{un}/qlscratch
 
 molpro -d $sdir -n 6 input.in
+""",
+        # oneDMin
+        'onedmin': """#! /bin/bash -l
+
+#$ -N {name}
+#$ -l long{architecture}
+#$ -l h_rt={t_max}
+#$ -pe singlenode {cpus}
+#$ -l h=!node60.cluster
+#$ -cwd
+#$ -o out.txt
+#$ -e err.txt
+
+WorkDir=`pwd`
+cd
+sdir=/scratch/{un}
+mkdir -p /scratch/{un}/onedmin
+cd $WorkDir
+
+~/auto1dmin/exe/auto1dmin.x < input.in > output.out
 """,
     }
 }
diff --git a/arc/job/submitTest.py b/arc/job/submitTest.py
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+This module contains unit tests of the arc.job.submit module
+"""
+
+from __future__ import (absolute_import, division, print_function, unicode_literals)
+import unittest
+
+from arc.job.submit import submit_scripts
+
+################################################################################
+
+
+class TestSubmit(unittest.TestCase):
+    """
+    Contains unit tests for the submit module
+    """
+
+    def test_servers(self):
+        """Test server keys in submit_scripts"""
+        for server in submit_scripts.keys():
+            self.assertTrue(server in ['pharos', 'c3ddb', 'rmg'])
+
+
+################################################################################
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))