Changes to tmpdir behaviour; tweaks to the tutorial docs

docs/tutorials/tutorial_2.rst

@@ -192,8 +192,8 @@ Having transformed into a supercell, the calculation of the screening parameters
 The code is doing this because of what we provided for the ``orbital_groups`` in the input file:
 
 .. literalinclude:: ../../tutorials/tutorial_2/si.json
-  :lines: 10-12
-  :lineno-start: 10
+  :lines: 9-11
+  :lineno-start: 9
   :emphasize-lines: 2
 
 which tells the code to use the same parameter for orbitals belonging to the same group. In this instance we are calculating a single screening parameter for all four filled orbitals, and a single screening parameter for the empty orbitals.

koopmans/workflows/_folding.py

@@ -30,56 +30,58 @@ def _run(self):
         self.print('Folding to supercell', style='subheading')
 
         if self.parameters.init_orbitals in ['mlwfs', 'projwfs']:
-            # Loop over the various subblocks that we have wannierized separately
-            for block in self.projections:
-                # Create the calculator
-                calc_w2k = self.new_calculator('wann2kcp', spin_component=block.spin, wan_mode='wannier2kcp',
-                                               directory=block.directory)
-                calc_w2k.prefix = 'w2kcp'
-
-                # Checking that gamma_trick is consistent with gamma_only
-                if calc_w2k.parameters.gamma_trick and not self.kpoints.gamma_only:
-                    calc_w2k.parameters.gamma_trick = False
-                elif not calc_w2k.parameters.gamma_trick and self.kpoints.gamma_only:
-                    calc_w2k.parameters.gamma_trick = True
+            with utils.chdir('wannier'):
+                # Loop over the various subblocks that we have wannierized separately
+                for block in self.projections:
+                    # Create the calculator
+                    calc_w2k = self.new_calculator('wann2kcp', spin_component=block.spin, wan_mode='wannier2kcp',
+                                                   directory=block.directory)
+                    calc_w2k.prefix = 'w2kcp'
+
+                    # Checking that gamma_trick is consistent with gamma_only
+                    if calc_w2k.parameters.gamma_trick and not self.kpoints.gamma_only:
+                        calc_w2k.parameters.gamma_trick = False
+                    elif not calc_w2k.parameters.gamma_trick and self.kpoints.gamma_only:
+                        calc_w2k.parameters.gamma_trick = True
+                    else:
+                        pass
+
+                    # Run the calculator
+                    self.run_calculator(calc_w2k)
+
+                if self.parameters.spin_polarized:
+                    spins = ['up', 'down']
                 else:
-                    pass
-
-                # Run the calculator
-                self.run_calculator(calc_w2k)
-
-            if self.parameters.spin_polarized:
-                spins = ['up', 'down']
-            else:
-                spins = [None, None]
-
-            # Merging evcw files
-            for occ in [True, False]:
-                for spin, evc_index in zip(spins, [1, 2]):
-                    subset = self.projections.get_subset(occ=occ, spin=spin)
-
-                    if len(subset) > 1:
-                        output_directory = Path(subset[0].merge_directory)
-                        output_directory.mkdir(exist_ok=True)
-                        if self.parameters.spin_polarized:
-                            evc_fname = f'evcw.dat'
-                        else:
-                            evc_fname = f'evcw{evc_index}.dat'
-                        command = ' '.join([f'{calculators.bin_directory}/merge_evc.x -nr {np.prod(self.kpoints.grid)}']
-                                           + [f'-i {b.directory}/{evc_fname}' for b in subset]
-                                           + [f'-o {output_directory}/{evc_fname}'])
-                        if occ:
-                            label = 'occupied'
-                        else:
-                            label = 'empty'
-                        label += f' spin {evc_index}'
-                        if self.parameters.from_scratch or not (output_directory / evc_fname).exists():
-                            self.parameters.from_scratch = True
-                            self.print(f'Merging the {label} band blocks... ', end='')
-                            utils.system_call(command)
-                            self.print('done')
-                        else:
-                            self.print(f'Not merging the {label} band blocks as this is already complete')
+                    spins = [None, None]
+
+                # Merging evcw files
+                for occ in [True, False]:
+                    for spin, evc_index in zip(spins, [1, 2]):
+                        subset = self.projections.get_subset(occ=occ, spin=spin)
+
+                        if len(subset) > 1:
+                            output_directory = Path(subset[0].merge_directory)
+                            output_directory.mkdir(exist_ok=True)
+                            if self.parameters.spin_polarized:
+                                evc_fname = f'evcw.dat'
+                            else:
+                                evc_fname = f'evcw{evc_index}.dat'
+                            command = ' '.join([f'{calculators.bin_directory}/merge_evc.x -nr '
+                                               f'{np.prod(self.kpoints.grid)}']
+                                               + [f'-i {b.directory}/{evc_fname}' for b in subset]
+                                               + [f'-o {output_directory}/{evc_fname}'])
+                            if occ:
+                                label = 'occupied'
+                            else:
+                                label = 'empty'
+                            label += f' spin {evc_index}'
+                            if self.parameters.from_scratch or not (output_directory / evc_fname).exists():
+                                self.parameters.from_scratch = True
+                                self.print(f'Merging the {label} band blocks... ', end='')
+                                utils.system_call(command)
+                                self.print('done')
+                            else:
+                                self.print(f'Not merging the {label} band blocks as this is already complete')
 
         else:
             # Create the calculator

koopmans/workflows/_koopmans_dscf.py

@@ -333,7 +333,7 @@ def perform_initialization(self) -> None:
             fold_workflow = workflows.FoldToSupercellWorkflow.fromparent(self)
 
             # Do this in the same directory as the wannierization
-            fold_workflow.run(subdirectory='init/wannier')
+            fold_workflow.run(subdirectory='init')
 
             # Convert self.atoms to the supercell
             self.primitive_to_supercell()

koopmans/workflows/_singlepoint.py

@@ -133,7 +133,8 @@ def _run(self) -> None:
                     if all(self.atoms.pbc) and self.calculator_parameters['ui'].do_smooth_interpolation:
                         if not Path('pkipz/postproc').is_dir():
                             utils.system_call('mkdir pkipz/postproc')
-                        utils.system_call(f'rsync -a ki/postproc/wannier pkipz/postproc/')
+                        for dir in ['wannier', 'TMP', 'pdos']:
+                            utils.system_call(f'rsync -a ki/postproc/{dir} pkipz/postproc/')
 
                     # KIPZ
                     utils.system_call('rsync -a ki/final/ kipz/init/')
@@ -143,7 +144,8 @@ def _run(self) -> None:
                         utils.system_call('rsync -a ki/init/wannier kipz/init/')
                     if all(self.atoms.pbc) and self.calculator_parameters['ui'].do_smooth_interpolation:
                         # Copy over the smooth PBE calculation from KI for KIPZ to use
-                        utils.system_call('rsync -a ki/postproc/wannier kipz/postproc/')
+                        for dir in ['wannier', 'TMP', 'pdos']:
+                            utils.system_call(f'rsync -a ki/postproc/{dir} kipz/postproc/')
 
         else:
             # self.functional != all and self.method != 'dfpt'

koopmans/workflows/_wannierize.py

@@ -293,10 +293,6 @@ def new_calculator(self, calc_type, *args, **kwargs) -> CalcExtType:
             if self._force_nspin2 and not self.parameters.spin_polarized:
                 calc.parameters.spin_component = 'up'
 
-        # Use a unified tmp directory
-        if 'outdir' in calc.parameters.valid:
-            calc.parameters.outdir = Path('wannier/TMP').resolve()
-
         return calc
 
     def merge_wannier_files(self, block: List[projections.ProjectionBlock], prefix: str = 'wann'):

koopmans/workflows/_workflow.py

@@ -340,6 +340,8 @@ def run(self, subdirectory: Optional[Union[str, Path]] = None, from_scratch: Opt
         self.print_preamble()
 
         if not self.parent:
+            if self.parameters.from_scratch:
+                self._remove_tmpdirs()
             self._run_sanity_checks()
 
         if self.parent:
@@ -1287,17 +1289,24 @@ def plot_bandstructure(self,
         # Close the figure
         plt.close()
 
+    def _remove_tmpdirs(self):
+        '''
+        Removes tmpdirs
+        '''
+
+        all_outdirs = [calc.parameters.get('outdir', None) for calc in self.calculations]
+        outdirs = set([o.resolve() for o in all_outdirs if o is not None and o.resolve().exists()])
+        for outdir in outdirs:
+            shutil.rmtree(outdir)
+
     def _teardown(self):
         '''
         Performs final tasks before the workflow completes
         '''
 
         # Removing tmpdirs
         if not self.parameters.keep_tmpdirs:
-            all_outdirs = [calc.parameters.get('outdir', None) for calc in self.calculations]
-            outdirs = set([o.resolve() for o in all_outdirs if o is not None and o.resolve().exists()])
-            for outdir in outdirs:
-                shutil.rmtree(outdir)
+            self._remove_tmpdirs()
 
 
 def get_version(module):

tests/benchmarks/test_convergence_h2o0-ecutwfc_20d0-cell_size_1d0-dft_nspin1.json

@@ -9,8 +9,8 @@
   "nbnd": 5,
   "ecutrho": 80.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_20d0-cell_size_1d0-dft_nspin2.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 80.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_20d0-cell_size_1d0-dft_nspin2_dummy.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 80.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_20d0-cell_size_1d1-dft_nspin1.json

@@ -9,8 +9,8 @@
   "nbnd": 5,
   "ecutrho": 80.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_20d0-cell_size_1d1-dft_nspin2.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 80.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_20d0-cell_size_1d1-dft_nspin2_dummy.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 80.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_20d0-cell_size_1d2-dft_nspin1.json

@@ -9,8 +9,8 @@
   "nbnd": 5,
   "ecutrho": 80.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_20d0-cell_size_1d2-dft_nspin2.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 80.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_20d0-cell_size_1d2-dft_nspin2_dummy.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 80.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_30d0-cell_size_1d0-dft_nspin1.json

@@ -9,8 +9,8 @@
   "nbnd": 5,
   "ecutrho": 120.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_30d0-cell_size_1d0-dft_nspin2.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 120.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_30d0-cell_size_1d0-dft_nspin2_dummy.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 120.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_30d0-cell_size_1d1-dft_nspin1.json

@@ -9,8 +9,8 @@
   "nbnd": 5,
   "ecutrho": 120.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_30d0-cell_size_1d1-dft_nspin2.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 120.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_30d0-cell_size_1d1-dft_nspin2_dummy.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 120.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_30d0-cell_size_1d2-dft_nspin1.json

@@ -9,8 +9,8 @@
   "nbnd": 5,
   "ecutrho": 120.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_30d0-cell_size_1d2-dft_nspin2.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 120.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"

tests/benchmarks/test_convergence_h2o0-ecutwfc_30d0-cell_size_1d2-dft_nspin2_dummy.json

@@ -11,8 +11,8 @@
   "nbnd": 5,
   "ecutrho": 120.0,
   "pseudopotentials": {
-   "H": "H_ONCV_PBE-1.2.upf",
-   "O": "O_ONCV_PBE-1.2.upf"
+   "O": "O_ONCV_PBE-1.2.upf",
+   "H": "H_ONCV_PBE-1.2.upf"
   },
   "pseudo_dir": {
    "__path__": "../../../../../pseudos/sg15_v1.2/pbe"