Merge pull request #458 from ReactionMechanismGenerator/gromacs

Deprecate Gromacs support

arc/common.py

@@ -170,7 +170,7 @@ def check_ess_settings(ess_settings: Optional[dict] = None) -> dict:
                                 f'strings. Got: {server_list} which is a {type(server_list)}')
     # run checks:
     for ess, server_list in settings_dict.items():
-        if ess.lower() not in ['gaussian', 'qchem', 'molpro', 'orca', 'terachem', 'onedmin', 'gromacs']:
+        if ess.lower() not in ['gaussian', 'qchem', 'molpro', 'orca', 'terachem', 'onedmin']:
             raise SettingsError(f'Recognized ESS software are Gaussian, QChem, Molpro, Orca, TeraChem or OneDMin. '
                                 f'Got: {ess}')
         for server in server_list:

arc/job/job.py

@@ -87,7 +87,6 @@ class Job(object):
                                             determine it). Defaults to None. Important, e.g., if a Species is a bi-rad
                                             singlet, in which case the job should be unrestricted with
                                             multiplicity = 1.
-        conformers (str, optional): A path to the YAML file conformer coordinates for a Gromacs MD job.
         radius (float, optional): The species radius in Angstrom.
         directed_scans (list): Entries are lists of four-atom dihedral scan indices to constrain during a directed scan.
         directed_dihedrals (list): The dihedral angles of a directed scan job corresponding to ``directed_scans``.
@@ -111,7 +110,6 @@ class Job(object):
         radius (float): The species radius in Angstrom.
         n_atoms (int): The number of atoms in self.xyz.
         conformer (int): Conformer number if optimizing conformers.
-        conformers (str): A path to the YAML file conformer coordinates for a Gromacs MD job.
         is_ts (bool): Whether this species represents a transition structure.
         level (Level): The level of theory to use.
         job_type (str): The job's type.
@@ -214,7 +212,6 @@ def __init__(self,
                  scan_res: Optional[int] = None,
                  checkfile: Optional[str] = None,
                  number_of_radicals: Optional[int] = None,
-                 conformers: Optional[str] = None,
                  radius: Optional[float] = None,
                  directed_scan_type: Optional[str] = None,
                  directed_scans: Optional[list] = None,
@@ -254,7 +251,6 @@ def __init__(self,
         self.directed_dihedrals = [float(d) for d in directed_dihedrals] if directed_dihedrals is not None \
             else directed_scans  # it's a string in the restart dict
         self.conformer = conformer
-        self.conformers = conformers
         self.is_ts = is_ts
         self.ess_trsh_methods = ess_trsh_methods or list()
         self.args = {'keyword': {'general': args}} if isinstance(args, str) else args or dict()
@@ -289,13 +285,11 @@ def __init__(self,
 
         # allowed job types:
         job_types = ['conformer', 'opt', 'freq', 'optfreq', 'sp', 'composite', 'bde', 'scan', 'directed_scan',
-                     'gsm', 'irc', 'ts_guess', 'orbitals', 'onedmin', 'ff_param_fit', 'gromacs']
+                     'gsm', 'irc', 'ts_guess', 'orbitals', 'onedmin']
         if self.job_type not in job_types:
             raise ValueError(f'Job type {self.job_type} not understood. Must be one of the following:\n{job_types}')
-        if self.xyz is None and not self.job_type == 'gromacs':
+        if self.xyz is None:
             raise InputError(f'{self.job_type} Job of species {self.species_name} got None for xyz')
-        if self.job_type == 'gromacs' and self.conformers is None:
-            raise InputError(f'{self.job_type} Job of species {self.species_name} got None for conformers')
         if self.job_type == 'directed_scan' and (self.directed_dihedrals is None or self.directed_scans is None
                                                  or self.directed_scan_type is None):
             raise InputError(f'Must have the directed_dihedrals, directed_scans, and directed_scan_type attributes '
@@ -412,8 +406,6 @@ def as_dict(self) -> dict:
             job_dict['rotor_index'] = self.rotor_index
         if self.checkfile is not None:
             job_dict['checkfile'] = self.checkfile
-        if self.conformers is not None:
-            job_dict['conformers'] = self.conformers
         if self.radius is not None:
             job_dict['radius'] = self.radius
         if self.irc_direction is not None:
@@ -806,24 +798,6 @@ def write_input_file(self):
                                  'PRINT_ORBITALS  TRUE\n   GUI           2',
                              key1='block')
 
-        elif self.job_type == 'ff_param_fit' and self.software == 'gaussian':
-            job_type_1, job_type_2 = 'opt', 'freq'
-            self.input += """
-
---Link1--
-%chk=check.chk
-%mem={memory}mb
-%NProcShared={cpus}
-
-# HF/6-31G(d) SCF=Tight Pop=MK IOp(6/33=2,6/41=10,6/42=17) scf(maxcyc=500) guess=read geom=check Maxdisk=2GB
-
-name
-
-{charge} {multiplicity}
-
-
-"""
-
         elif self.job_type == 'freq':
             if self.software == 'gaussian':
                 job_type_2 = 'freq iop(7/33=1) scf=(tight, direct) integral=(grid=ultrafine, Acc2E=12)'
@@ -1526,10 +1500,9 @@ def set_cpu_and_mem(self):
         elif self.software.lower() in ['orca']:
             # Orca's memory is per cpu core and in MB
             self.input_file_memory = math.ceil(self.total_job_memory_gb * 1024 / self.cpu_cores)
-        elif self.software.lower() in ['qchem', 'gromacs']:
+        elif self.software.lower() in ['qchem']:
             # QChem manages its memory automatically, for now ARC will not intervene
             # see http://www.q-chem.com/qchem-website/manual/qchem44_manual/CCparallel.html
-            # Also not managing memory for Gromacs
             self.input_file_memory = math.ceil(self.total_job_memory_gb)
 
     def set_file_paths(self):
@@ -1580,31 +1553,6 @@ def set_file_paths(self):
             self.additional_files_to_upload.append({'name': 'qc.mol', 'source': 'input_files', 'make_x': False,
                                                     'local': 'onedmin.qc.mol',
                                                     'remote': os.path.join(self.remote_path, 'qc.mol')})
-        if self.job_type == 'gromacs':
-            self.additional_files_to_upload.append({'name': 'gaussian.out', 'source': 'path', 'make_x': False,
-                                                    'local': os.path.join(self.project_directory, 'calcs', 'Species',
-                                                                          self.species_name, 'ff_param_fit',
-                                                                          'gaussian.out'),
-                                                    'remote': os.path.join(self.remote_path, 'gaussian.out')})
-            self.additional_files_to_upload.append({'name': 'coords.yml', 'source': 'path', 'make_x': False,
-                                                    'local': self.conformers,
-                                                    'remote': os.path.join(self.remote_path, 'coords.yml')})
-            self.additional_files_to_upload.append({'name': 'acpype.py', 'source': 'path', 'make_x': False,
-                                                    'local': os.path.join(ARC_PATH, 'arc', 'scripts', 'conformers',
-                                                                          'acpype.py'),
-                                                    'remote': os.path.join(self.remote_path, 'acpype.py')})
-            self.additional_files_to_upload.append({'name': 'mdconf.py', 'source': 'path', 'make_x': False,
-                                                    'local': os.path.join(ARC_PATH, 'arc', 'scripts', 'conformers',
-                                                                          'mdconf.py'),
-                                                    'remote': os.path.join(self.remote_path, 'mdconf.py')})
-            self.additional_files_to_upload.append({'name': 'M00.tleap', 'source': 'path', 'make_x': False,
-                                                    'local': os.path.join(ARC_PATH, 'arc', 'scripts', 'conformers',
-                                                                          'M00.tleap'),
-                                                    'remote': os.path.join(self.remote_path, 'M00.tleap')})
-            self.additional_files_to_upload.append({'name': 'mdp.mdp', 'source': 'path', 'make_x': False,
-                                                    'local': os.path.join(ARC_PATH, 'arc', 'scripts', 'conformers',
-                                                                          'mdp.mdp'),
-                                                    'remote': os.path.join(self.remote_path, 'mdp.mdp')})
             if self.software == 'terachem':
                 self.additional_files_to_upload.append({'name': 'geo', 'source': 'path', 'make_x': False,
                                                         'local': os.path.join(self.local_path, 'coord.xyz'),

arc/job/jobTest.py

@@ -317,45 +317,6 @@ def test_set_file_paths(self):
         self.assertIn('qc.mol', self.job1.additional_files_to_upload[2]['remote'])
         self.assertEqual(self.job1.additional_files_to_upload[2]['local'], 'onedmin.qc.mol')
 
-        self.job1.job_type = 'gromacs'
-        self.job1.set_file_paths()
-        self.assertEqual(len(self.job1.additional_files_to_upload), 6)
-
-        self.assertEqual(self.job1.additional_files_to_upload[0]['source'], 'path')
-        self.assertEqual(self.job1.additional_files_to_upload[0]['name'], 'gaussian.out')
-        self.assertFalse(self.job1.additional_files_to_upload[0]['make_x'])
-        self.assertIn('gaussian.out', self.job1.additional_files_to_upload[0]['remote'])
-        self.assertIn('gaussian.out', self.job1.additional_files_to_upload[0]['local'])
-
-        self.assertEqual(self.job1.additional_files_to_upload[1]['source'], 'path')
-        self.assertEqual(self.job1.additional_files_to_upload[1]['name'], 'coords.yml')
-        self.assertFalse(self.job1.additional_files_to_upload[1]['make_x'])
-        self.assertIn('coords.yml', self.job1.additional_files_to_upload[1]['remote'])
-
-        self.assertEqual(self.job1.additional_files_to_upload[2]['source'], 'path')
-        self.assertEqual(self.job1.additional_files_to_upload[2]['name'], 'acpype.py')
-        self.assertFalse(self.job1.additional_files_to_upload[2]['make_x'])
-        self.assertIn('acpype.py', self.job1.additional_files_to_upload[2]['remote'])
-        self.assertIn('acpype.py', self.job1.additional_files_to_upload[2]['local'])
-
-        self.assertEqual(self.job1.additional_files_to_upload[3]['source'], 'path')
-        self.assertEqual(self.job1.additional_files_to_upload[3]['name'], 'mdconf.py')
-        self.assertFalse(self.job1.additional_files_to_upload[3]['make_x'])
-        self.assertIn('mdconf.py', self.job1.additional_files_to_upload[3]['remote'])
-        self.assertIn('mdconf.py', self.job1.additional_files_to_upload[3]['local'])
-
-        self.assertEqual(self.job1.additional_files_to_upload[4]['source'], 'path')
-        self.assertEqual(self.job1.additional_files_to_upload[4]['name'], 'M00.tleap')
-        self.assertFalse(self.job1.additional_files_to_upload[4]['make_x'])
-        self.assertIn('M00.tleap', self.job1.additional_files_to_upload[4]['remote'])
-        self.assertIn('M00.tleap', self.job1.additional_files_to_upload[4]['local'])
-
-        self.assertEqual(self.job1.additional_files_to_upload[5]['source'], 'path')
-        self.assertEqual(self.job1.additional_files_to_upload[5]['name'], 'mdp.mdp')
-        self.assertFalse(self.job1.additional_files_to_upload[5]['make_x'])
-        self.assertIn('mdp.mdp', self.job1.additional_files_to_upload[5]['remote'])
-        self.assertIn('mdp.mdp', self.job1.additional_files_to_upload[5]['local'])
-
     def test_format_max_job_time(self):
         """Test that the maximum job time can be formatted properly, including days, minutes, and seconds"""
         test_job = Job.__new__(Job)

arc/level.py

@@ -465,13 +465,6 @@ def deduce_software(self,
                                  f'levels_ess is:\n{levels_ess}')
             self.software = 'onedmin'
 
-        # Gromacs
-        if job_type == 'gromacs':
-            if 'gromacs' not in supported_ess:
-                raise ValueError(f'Could not find the Gromacs software to run the MD job {self.method}.\n'
-                                 f'levels_ess is:\n{levels_ess}')
-            self.software = 'gromacs'
-
         # QChem
         if job_type == 'orbitals':
             # currently we only have a script to print orbitals on QChem,
@@ -488,7 +481,7 @@ def deduce_software(self,
             self.software = 'orca'
 
         # Gaussian
-        if self.method_type == 'composite' or job_type == 'composite' or job_type == 'ff_param_fit' or job_type == 'irc' \
+        if self.method_type == 'composite' or job_type == 'composite' or job_type == 'irc' \
                 or any([sum(['iop' in value.lower() for value in subdict.values()]) for subdict in self.args.values()]):
             if 'gaussian' not in supported_ess:
                 raise ValueError(f'Could not find Gaussian to run the {self.method}.\n'

arc/plotter.py

@@ -868,8 +868,13 @@ def save_conformers_file(project_directory: str,
 
 # *** Torsions ***
 
-def plot_torsion_angles(torsion_angles, torsions_sampling_points=None, wells_dict=None, e_conformers=None,
-                        de_threshold=5.0, plot_path=None):
+def plot_torsion_angles(torsion_angles,
+                        torsions_sampling_points=None,
+                        wells_dict=None,
+                        e_conformers=None,
+                        de_threshold=5.0,
+                        plot_path=None,
+                        ):
     """
     Plot the torsion angles of the generated conformers.
 
@@ -904,7 +909,8 @@ def plot_torsion_angles(torsion_angles, torsions_sampling_points=None, wells_dic
                      np.zeros_like(np.arange(len(sampling_points[tuple(torsion)]))), 'ro', alpha=0.35, ms=7)
         axs.frameon = False
         axs.set_ylabel(str(torsion), labelpad=10)
-        axs.set_yticklabels(['' for _ in range(len(torsions))])
+        axs.set_yticks(axs.get_yticks().tolist())
+        axs.set_yticklabels(['' for _ in range(len(axs.get_yticks().tolist()))])
         axs.tick_params(axis='y',  # changes apply to the x-axis
                         which='both',  # both major and minor ticks are affected
                         left=False,  # ticks along the bottom edge are off
@@ -956,7 +962,8 @@ def plot_torsion_angles(torsion_angles, torsions_sampling_points=None, wells_dic
             axs[i].set_ylabel(str(torsion), labelpad=10)
             # axs[i].yaxis.label.set_rotation(0)
             if e_conformers is None:
-                axs[i].set_yticklabels(['' for _ in range(len(torsions))])
+                axs[i].set_yticks(axs[i].get_yticks().tolist())
+                axs[i].set_yticklabels(['' for _ in range(len(axs[i].get_yticks().tolist()))])
                 axs[i].tick_params(axis='y',  # changes apply to the x-axis
                                    which='both',  # both major and minor ticks are affected
                                    left=False,  # ticks along the bottom edge are off