Disable scaled positions

carmm/analyse/counterpoise_onepot.py

@@ -57,6 +57,11 @@ def counterpoise_calc(complex_struc, a_id, b_id, fhi_calc=None, a_name=None, b_n
     # Empty sites does not work with forces. Remove compute_forces.
     if 'compute_forces' in fhi_calc.parameters:
         fhi_calc.parameters.pop('compute_forces')
+    if 'sc_accuracy_forces' in fhi_calc.parameters:
+        if verbose:
+            print('Stop calculation as there is a convergence criterion regarding force.', '\n',
+                  'Empty sites does not work with forces. Remove and check how it affects your results.')
+        raise KeyError('Found sc_accuracy_forces in parameters! FHI-aims can not calculate forces on empty sites.')
     # Create an empty list to store energies for postprocessing.
     energies = []
     for index in range(4):
@@ -72,10 +77,9 @@ def counterpoise_calc(complex_struc, a_id, b_id, fhi_calc=None, a_name=None, b_n
             energies.append(energy_i)
         else:
             fhi_calc.template.outputname = species_list[index] + '.out'
-            properties = fhi_calc.implemented_properties
-            parameters = fhi_calc.parameters
-            parameters['ghosts'] = ghosts_lists_cp[index]
-            fhi_calc.template.update_parameters(properties, parameters)
+            fhi_calc.parameters['ghosts'] = ghosts_lists_cp[index]
+            # Scaled positions does not work with empty sites.
+            fhi_calc.parameters['scaled'] = False
             structures_cp[index].calc = fhi_calc
             if dry_run:
                 structures_cp[index].calc.template.write_input(fhi_calc.profile, fhi_calc.directory,
@@ -192,14 +196,17 @@ def calculate_energy_ghost_compatible(calc, atoms=None, properties=['energy'],
 
     """
     from ase.calculators.calculator import Calculator
-    import subprocess
+    import subprocess, os
     Calculator.calculate(calc, atoms, properties, system_changes)
-    calc.write_input(calc.atoms, properties, system_changes, ghosts=ghosts)
+    # Write inputfiles. Scaled positions does not work with empty sites.
+    calc.write_input(calc.atoms, properties, system_changes, ghosts=ghosts, scaled=False)
     command = calc.command
 
     if dry_run:  # Only for CI tests
         command = ''  # Used to be 'ls'
-    converged = calc.read_convergence()
+    converged = False
+    if os.path.exists(calc.directory+'/'+calc.outfilename):
+        converged = calc.read_convergence()
     if (not converged) or dry_run:
         subprocess.check_call(command, shell=True, cwd=calc.directory)
 

examples/analyse_counterpoise.py

@@ -14,6 +14,7 @@ def test_analyse_counterpoise():
     from carmm.analyse.counterpoise_onepot import counterpoise_calc
     from carmm.run.aims_calculator import get_aims_calculator
     from carmm.run.aims_path import set_aims_command
+    from unittest import TestCase
 
     # This is an example script for using counterpoise_calc for counterpoise (CP) correction. Please note the species
     # files in data/CO_BSSE are fake ones and default species settings are also deleted from aims.out.
@@ -39,6 +40,12 @@ def test_analyse_counterpoise():
                                  verbose=True, dry_run=True)
     cp_symbol = counterpoise_calc(CO, a_id=['C'], b_id=['O'], fhi_calc=toy_calc, dry_run=True)
 
+    # Test to make sure sc_accuracy_forces is not set, as FHI-aims can't calculate forces with empty sites
+    toy_calc.parameters['sc_accuracy_forces'] = 0.0001
+    forces_check = TestCase()
+    with forces_check.assertRaises(KeyError):
+        counterpoise_calc(CO, a_id=['C'], b_id=['O'], fhi_calc=toy_calc, dry_run=True, verbose=True)
+
     # CP correction = A_only + B_only - A_plus_ghost - B_plus_ghost
     # This value should be added to the energy change of interest, such as adsorption energy.