Merge pull request #56 from ReactionMechanismGenerator/ts

Added reactions to ARC

.gitignore

@@ -31,3 +31,6 @@ scratch/
 
 # csv database
 *.csv
+
+# iPython files
+*.ipynb_*

.travis.yml

@@ -19,11 +19,22 @@ before_install:
 cache: pip
 install:
   - cd ARC
-  - pip install -r requirements.txt
-  - conda install -y -c rmg rmg
-  - conda install -y -c rdkit rdkit
+  - conda env create -q -f environment.yml
+  - source activate arc_env
+  - cd ..
+  - git clone https://github.com/ReactionMechanismGenerator/RMG-Py
+  - cd RMG-Py
+  - export PYTHONPATH=$PYTHONPATH:$(pwd)
+  - make
+  - cd ..
+  - git clone https://github.com/ReactionMechanismGenerator/RMG-database
+  - git clone https://github.com/alongd/AutoTST
+  - cd AutoTST
+  - export PYTHONPATH=$PYTHONPATH:$(pwd)
+  - cd ..
   - conda install -y -c conda-forge codecov
   - conda list
+  - cd ARC
 
 script:
   - make test

arc/exceptions.py

@@ -7,61 +7,60 @@
 
 class InputError(Exception):
     """
-    An exception raised when parsing an input file for any module.
-    Pass a string describing the error.
+    An exception raised when parsing an input file for any module
     """
     pass
 
 class OutputError(Exception):
     """
-    This exception is raised whenever an error occurs while saving output
-    information. Pass a string describing the circumstances of the exceptional
-    behavior.
+    This exception is raised whenever an error occurs while saving output information
     """
     pass
 
 class SettingsError(Exception):
     """
-    An exception raised when dealing with settings.
+    An exception raised when dealing with settings
     """
     pass
 
 class SpeciesError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with
-    chemical species. Pass a string describing the circumstances that caused the
-    exceptional behavior.
+    An exception class for exceptional behavior that occurs while working with chemical species
+    """
+    pass
+
+class TSError(Exception):
+    """
+    An exception class for exceptional behavior that occurs while working with transition states
+    """
+    pass
+
+class ReactionError(Exception):
+    """
+    An exception class for exceptional behavior that occurs while working with reactions
     """
     pass
 
 class RotorError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with
-    chemical species. Pass a string describing the circumstances that caused the
-    exceptional behavior.
+    An exception class for exceptional behavior that occurs while working with rotors
     """
     pass
 
 class SchedulerError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with
-    chemical species. Pass a string describing the circumstances that caused the
-    exceptional behavior.
+    An exception class for exceptional behavior that occurs while working with the scheduler
     """
     pass
 
 class JobError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with
-    chemical species. Pass a string describing the circumstances that caused the
-    exceptional behavior.
+    An exception class for exceptional behavior that occurs while working with jobs
     """
     pass
 
 class ServerError(Exception):
     """
-    An exception class for exceptional behavior that occurs while working with
-    chemical species. Pass a string describing the circumstances that caused the
-    exceptional behavior.
+    An exception class for exceptional behavior that occurs while working with servers
     """
     pass

arc/job/inputs.py

@@ -22,21 +22,21 @@
                 'scf=(tight,direct) int=finegrid irc=(rcfc,forward,maxpoints=100,stepsize=10) geom=check' for irc f
                 'scf=(tight,direct) int=finegrid irc=(rcfc,reverse,maxpoints=100,stepsize=10) geom=check' for irc r
     scan: '\nD 3 1 5 8 S 36 10.000000' (with the line break)
-    restricted: '' or 'u' or restricted / unrestricted
+    restricted: '' or 'u' for restricted / unrestricted
 
 qchem:
     job_type_1: 'opt', 'ts', 'sp'
     job_type_2: 'freq'.
-    fine: '\n   GEOM_OPT_TOL_GRADIENT 15\n   GEOM_OPT_TOL_DISPLACEMENT 60\n   GEOM_OPT_TOL_ENERGY 5'
-    restricted: 'false' or 'true' or restricted / unrestricted
+    fine: '\n   GEOM_OPT_TOL_GRADIENT 15\n   GEOM_OPT_TOL_DISPLACEMENT 60\n   GEOM_OPT_TOL_ENERGY 5\n   XC_GRID SG-3'
+    restricted: 'false' or 'true' for restricted / unrestricted
 """
 
 input_files = {
     'gaussian': """%chk=check.chk
 %mem={memory}mb
 %nproc=8
 
-# {job_type_1} {restricted}{method}{slash}{basis} {job_type_2} {fine} {trsh}
+#P {job_type_1} {restricted}{method}{slash}{basis} {job_type_2} {fine} {trsh}
 
 name
 

arc/job/job.py

@@ -92,10 +92,10 @@ def __init__(self, project, settings, species_name, xyz, job_type, level_of_theo
         self.ess_trsh_methods = ess_trsh_methods if ess_trsh_methods is not None else list()
         self.trsh = trsh
         self.initial_trsh = initial_trsh if initial_trsh is not None else dict()
-        job_types = ['conformer', 'opt', 'freq', 'optfreq', 'sp', 'composite', 'scan', 'gsm', 'irc']
+        job_types = ['conformer', 'opt', 'freq', 'optfreq', 'sp', 'composite', 'scan', 'gsm', 'irc', 'ts_guess']
         # the 'conformer' job type is identical to 'opt', but we differentiate them to be identifiable in Scheduler
         if job_type not in job_types:
-            raise ValueError("Job type {0} not understood. Must be on of the following: {1}".format(
+            raise ValueError("Job type {0} not understood. Must be one of the following:\n{1}".format(
                 job_type, job_types))
         self.job_type = job_type
         if self.job_num < 0:
@@ -134,6 +134,11 @@ def __init__(self, project, settings, species_name, xyz, job_type, level_of_theo
                         self.software = 'qchem'
                     elif self.settings['molpro']:
                         self.software = 'molpro'
+                elif 'wb97xd' in self.method:
+                    if not self.settings['gaussian']:
+                        raise JobError('Could not find the Gaussian software to run {0}/{1}'.format(
+                            self.method, self.basis_set))
+                    self.software = 'gaussian'
                 elif 'b97' in self.method or 'm06-2x' in self.method or 'def2' in self.basis_set:
                     if not self.settings['qchem']:
                         raise JobError('Could not find the QChem software to run {0}/{1}'.format(
@@ -318,7 +323,6 @@ def write_input_file(self):
         Write a software-specific job-specific input file.
         Saves the file locally and also uploads it to the server.
         """
-
         if self.initial_trsh and not self.trsh:
             # use the default trshs defined by the user in the initial_trsh dictionary
             if self.software in self.initial_trsh:
@@ -383,6 +387,11 @@ def write_input_file(self):
                     job_type_1 = 'opt'
                 if self.fine:
                     fine = '\n   GEOM_OPT_TOL_GRADIENT 15\n   GEOM_OPT_TOL_DISPLACEMENT 60\n   GEOM_OPT_TOL_ENERGY 5'
+                    if 'b' in self.level_of_theory:
+                        # Try to capture DFT levels (containing the letter 'b'?), and det a fine DFT grid
+                        # See 4.4.5.2 Standard Quadrature Grids, S in
+                        # http://www.q-chem.com/qchem-website/manual/qchem50_manual/sect-DFT.html
+                        fine += '\n   XC_GRID 3'
             elif self.software == 'molpro':
                 if self.is_ts:
                     job_type_1 = "\noptg,root=2,method=qsd,readhess,savexyz='geometry.xyz'"
@@ -484,7 +493,7 @@ def write_input_file(self):
             if self.software != 'molpro':
                 raise JobError('Can only run MRCI on Molpro, not {0}'.format(self.software))
             if self.occ > 16:
-                raise JobError('Will not excecute an MRCI calculation with more than 16 occupied orbitals.'
+                raise JobError('Will not execute an MRCI calculation with more than 16 occupied orbitals.'
                                'Selective occ, closed, core, frozen keyword still not implemented.')
             else:
                 try:
@@ -639,11 +648,6 @@ def _check_job_ess_status(self):
                 for line in lines[::-1]:
                     if 'Thank you very much for using Q-Chem' in line:
                         done = True
-                    elif 'opt' in self.job_type or 'conformer' in self.job_type or 'ts' in self.job_type:
-                            if 'MAXIMUM OPTIMIZATION CYCLES REACHED' in line:
-                                return 'errored: unconverged, max opt cycles reached'
-                            elif 'OPTIMIZATION CONVERGED' in line and done:  # `done` should already be assigned
-                                return 'done'
                     elif 'SCF failed' in line:
                         return 'errored: {0}'.format(line)
                     elif 'error' in line and 'DIIS' not in line:
@@ -653,6 +657,11 @@ def _check_job_ess_status(self):
                     elif 'Invalid charge/multiplicity combination' in line:
                         raise SpeciesError('The multiplicity and charge combination for species {0} are wrong.'.format(
                             self.species_name))
+                    if 'opt' in self.job_type or 'conformer' in self.job_type or 'ts' in self.job_type:
+                        if 'MAXIMUM OPTIMIZATION CYCLES REACHED' in line:
+                            return 'errored: unconverged, max opt cycles reached'
+                        elif 'OPTIMIZATION CONVERGED' in line and done:  # `done` should already be assigned
+                            return 'done'
                 if done:
                     return 'done'
                 else:
@@ -661,7 +670,6 @@ def _check_job_ess_status(self):
                     else:
                         return 'errored: Unknown reason'
             elif self.software == 'molpro':
-                prev_line = ''
                 for line in lines[::-1]:
                     if 'molpro calculation terminated' in line.lower()\
                             or 'variable memory released' in line.lower():
@@ -677,7 +685,6 @@ def _check_job_ess_status(self):
                         #        the request was for real words`
                         # add_mem = (float(line.split()[-2]) - float(prev_line.split()[0])) / 1e6
                         return 'errored: additional memory (mW) required: {0}'.format(float(line.split()[-2]) / 1e6)
-                    prev_line = line
                 for line in lines[::-1]:
                     if 'the problem occurs' in line:
                         return 'errored: ' + line

arc/job/jobTest.py

@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+This module contains unit tests of the arc.job.job module
+"""
+
+from __future__ import (absolute_import, division, print_function, unicode_literals)
+import unittest
+import os
+
+from arc.job.job import Job
+from arc.settings import arc_path
+
+################################################################################
+
+
+class TestJob(unittest.TestCase):
+    """
+    Contains unit tests for the Job class
+    """
+
+    @classmethod
+    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,
+                       project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
+
+    def test_as_dict(self):
+        """Test Job.as_dict()"""
+        job_dict = self.job1.as_dict()
+        dt = job_dict['date_time']
+        expected_dict = {u'date_time': dt,
+                         u'ess_trsh_methods': [],
+                         u'fine': True,
+                         u'job_id': 0,
+                         u'job_name': u'opt_a100',
+                         u'job_num': 100,
+                         u'job_server_name': u'a100',
+                         u'job_status': [u'initializing', u'initializing'],
+                         u'job_type': u'opt',
+                         u'level_of_theory': u'b3lyp/6-31+g(d)',
+                         u'memory': 1500,
+                         u'occ': None,
+                         u'pivots': [],
+                         u'project_directory': os.path.join(arc_path, 'Projects', 'project_test'),
+                         u'run_time': u'',
+                         u'scan': u'',
+                         u'server': None,
+                         u'shift': u'',
+                         u'trsh': u'',
+                         u'xyz': u'C 0.0 0.0 0.0'}
+        self.assertEqual(job_dict, expected_dict)
+
+
+################################################################################
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))