minor changes

selimsami · Oct 7, 2024 · 9254867 · 9254867
1 parent f6490dc
commit 9254867
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Showing 4 changed files with 23 additions and 18 deletions.
diff --git a/qforce/molecule/dihedral_terms.py b/qforce/molecule/dihedral_terms.py
@@ -238,7 +238,7 @@ def get_dtype(topo, *args):
 
                 for atoms in atoms_comb:
                     d_type = get_dtype(topo, *atoms)
-                    phi = get_dihed(topo.coords[atoms])[0]
+                    # phi = get_dihed(topo.coords[atoms])[0]
                     # add_term('rigid', topo, atoms, phi, d_type)
                     add_term('rigid', topo, atoms, 2., np.pi, d_type+'_mult2')
 
@@ -247,13 +247,15 @@ def get_dtype(topo, *args):
                                  for r in topo.rings)]
 
                 for atoms in atoms_in_ring:
-                    phi = get_dihed(topo.coords[atoms])[0]
+                    # phi = get_dihed(topo.coords[atoms])[0]
                     d_type = get_dtype(topo, *atoms)
 
-                    if abs(phi) < 0.43625:  # check planarity < 25 degrees
-                        add_term('rigid', topo, atoms, phi, d_type)
-                    else:
-                        add_term('inversion', topo, atoms, phi, d_type)
+                    add_term('rigid', topo, atoms, 2., np.pi, d_type+'_mult2')
+
+                    # if abs(phi) < 0.43625:  # check planarity < 25 degrees
+                    #     add_term('rigid', topo, atoms, 2., np.pi, d_type+'_mult2')
+                    # else:
+                    #     add_term('inversion', topo, atoms, phi, d_type)
 
             else:
                 for atoms in atoms_comb:
@@ -296,17 +298,16 @@ def get_dtype(topo, *args):
                 #     continue
                 imp_type = f"ki_{topo.types[i]}"
                 if abs(phi) < 0.43625:  # check planarity < 25 degrees
-                    # add_term('improper', topo, atoms, phi, imp_type)
                     add_term('improper', topo,  [atoms[0], atoms[1], atoms[2], atoms[3]], phi, imp_type)
                     add_term('improper', topo, [atoms[0], atoms[1], atoms[3], atoms[2]], phi, imp_type)
                     add_term('improper', topo, [atoms[0], atoms[2], atoms[3], atoms[1]], phi, imp_type)
-                else:
-                    add_term('inversion', topo,  [atoms[0], atoms[1], atoms[2], atoms[3]], phi, imp_type)
-                    add_term('inversion', topo, [atoms[0], atoms[1], atoms[3], atoms[2]], phi, imp_type)
-                    add_term('inversion', topo, [atoms[0], atoms[2], atoms[1], atoms[3]], phi, imp_type)
-                    add_term('inversion', topo, [atoms[0], atoms[2], atoms[3], atoms[1]], phi, imp_type)
-                    add_term('inversion', topo, [atoms[0], atoms[3], atoms[1], atoms[2]], phi, imp_type)
-                    add_term('inversion', topo, [atoms[0], atoms[3], atoms[2], atoms[1]], phi, imp_type)
+                # else:
+                #     add_term('inversion', topo,  [atoms[0], atoms[1], atoms[2], atoms[3]], phi, imp_type)
+                #     add_term('inversion', topo, [atoms[0], atoms[1], atoms[3], atoms[2]], phi, imp_type)
+                #     add_term('inversion', topo, [atoms[0], atoms[2], atoms[1], atoms[3]], phi, imp_type)
+                #     add_term('inversion', topo, [atoms[0], atoms[2], atoms[3], atoms[1]], phi, imp_type)
+                #     add_term('inversion', topo, [atoms[0], atoms[3], atoms[1], atoms[2]], phi, imp_type)
+                #     add_term('inversion', topo, [atoms[0], atoms[3], atoms[2], atoms[1]], phi, imp_type)
 
         # add_term('pitorsion', topo, [1, 0, 3, 2, 4, 5], 0, 'test')
         # add_term('pitorsion', topo, [0, 2, 3, 1, 4, 5], 0, 'test')

diff --git a/qforce/pathkeeper.py b/qforce/pathkeeper.py
@@ -107,8 +107,8 @@ class Pathways:
 
     pathways = Pathlib({
         # folders
-        'preopt': '0_preopt',
-        'hessian': '1_hessian',
+        'preopt': 'crest',
+        'hessian': 'hessian',
         'addstruct': '5_additional',
         'hessian_charge': ['hessian', 'charge'],
         'hessian_energy': ['hessian', '${idx}_en_conformer'],

diff --git a/qforce/qm/crest.py b/qforce/qm/crest.py
@@ -15,7 +15,8 @@ def from_config(cls, config):
         return cls()
 
     def _commands(self, filename, basename, ncores):
-        return [f'bash {filename} > {filename}.shellout']
+        print(filename, basename)
+        return [f'bash {filename} > {basename}.out']
 
 
 class Crest(QMInterface):
@@ -169,7 +170,9 @@ def opt(self, file, job_name, settings, coords, atnums):
         base, filename = os.path.split(name)
         # Given that the xTB input has to be given in the command line.
         # We create the xTB command template here.
-        cmd = f'crest {job_name}_input.xyz {self.config.xtb_command} -T {settings.n_proc} '\
+        cmd = f'crest {job_name}_input.xyz --chrg {settings.charge} ' \
+              f'--uhf {settings.multiplicity - 1} ' \
+              f'{self.config.xtb_command} -T {settings.n_proc} -alpb water\n'
         # Write the hessian.inp which is the command line input
         file.write(cmd)
         # Write the coordinates, which is the standard xyz file.

diff --git a/qforce/qm/qm.py b/qforce/qm/qm.py
@@ -200,6 +200,7 @@ def get_hessian(self):
                 with open(calculation.inputfile, 'w') as file:
                     self.write_hessian(file, calculation.base, coords, atnums)
             hessians.append(calculation)
+            break
 
         folder = self.pathways.getdir("hessian")
         #