Neo branch

ash/__init__.py

@@ -121,6 +121,7 @@
 from .interfaces.interface_Grimme_corrections import DFTD4Theory, calc_DFTD4, calc_gcp, gcpTheory
 from .interfaces.interface_torch import TorchTheory
 from .interfaces.interface_mace import MACETheory
+from .interfaces.interface_fairchem import FairchemTheory
 from .interfaces.interface_packmol import packmol_solvate
 
 # MM: external and internal
@@ -171,6 +172,7 @@
 
 # Geometry optimization
 from .functions.functions_optimization import SimpleOpt, BernyOpt
+from .interfaces.interface_dlfind import DLFIND_optimizer
 
 # geomeTRIC interface
 from .interfaces.interface_geometric_new import geomeTRICOptimizer,GeomeTRICOptimizerClass

ash/functions/functions_elstructure.py

@@ -2037,7 +2037,7 @@ def make_molden_file(fragment, AO_basis, MO_coeffs, MO_energies=None, MO_occs=No
     #Basis set
     ###########
     #TODO. Check
-    shell_to_angmom = {"s":0,"p":1,"d":2,"f":3}
+    shell_to_angmom = {"s":0,"p":1,"d":2,"f":3,"g":4}
     gtostring="""[GTO]
 """
     #Looping over each atom in AO_basis object

ash/interfaces/interface_ASE.py

@@ -151,6 +151,7 @@ def get_forces(self, atomsobj):
             print_time_rel(timeA, modulename="get_forces : new")
             return self.forces
 
+
     #Option 2: Dummy ASE class where we create the attributes and methods we want
     #Too complicated
 

ash/interfaces/interface_GPAW.py

@@ -25,7 +25,7 @@ def __init__(self, printsetting=False, printlevel=2, numcores=1, label="gpaw", f
 
         self.theorynamelabel="GPAW"
         self.theorytype="QM"
-        self.analytic_hessian=True
+        self.analytic_hessian=False
         self.printlevel=printlevel
         self.label=label
         self.numcores=numcores

ash/interfaces/interface_MRCC.py

@@ -456,7 +456,7 @@ def convert_MRCC_Molden_file(mrccoutputfile=None, moldenfile=None, mrccdensityfi
     if os.path.isfile("mrccnew.molden") is False:
         print("Error: Multiwfn failed to create new Molden file. Exiting.")
         ashexit()
-    print("Created new Molden file: ")
+    print("Created new Molden file: mrccnew.molden")
     print("This file contains the natural orbitals of the correlated density from MRCC")
 
 

ash/interfaces/interface_ORCA.py

@@ -771,10 +771,9 @@ def run(self, current_coords=None, charge=None, mult=None, current_MM_coords=Non
         if Hessian is True:
             print("Reading Hessian from file:", self.filename+".hess")
             self.hessian = Hessgrab(self.filename+".hess")
-
             self.ir_intensities = grab_IR_intensities(self.filename+'.hess')
 
-        if Grad == True:
+        if Grad is True:
             grad =ORCAgradientgrab(engradfile)
             self.grad = self.grad + grad
             if self.printlevel >= 3:
@@ -1261,11 +1260,11 @@ def tddftintens_grab(file):
     with open(file) as f:
         for line in f:
             if tddftgrab==True:
-                if len(line.split()) == 8:
-                        intensities.append(float(line.split()[3]))
+                if '->' in line:
+                        intensities.append(float(line.split()[-5]))
                 if len(line.split()) == 0:
                     tddftgrab=False
-            if 'State   Energy    Wavelength  fosc         T2        TX        TY        TZ' in line:
+            if 'fosc(D2)' in line:
                 tddftgrab=True
     return intensities
 
@@ -1299,7 +1298,6 @@ def grab_IR_intensities(filename):
     intensities=[]
     with open(filename) as f:
         for line in f:
-            print(line)
             if grab:
                 if len(line.split()) == 6:
                     intens = float(line.split()[2])

ash/interfaces/interface_OpenMM.py

@@ -3882,17 +3882,16 @@ def set_sim_reporters(self,simulation,restart=False):
                 openmm.app.PDBReporter(self.trajfilename+'.pdb', self.traj_frequency,
                                                          enforcePeriodicBox=self.enforcePeriodicBox))
         elif self.trajectory_file_option == 'DCD':
-            # NOTE: Disabling for now
-            # with open('initial_MDfrag_step1.pdb', 'w') as f: openmm.app.pdbfile.PDBFile
-            # .writeModel(openmmobject.topology, self.simulation.context.getState(getPositions=True,
-            # enforcePeriodicBox=enforcePeriodicBox).getPositions(), f)
-            # print("Wrote PDB")
-
             #Note: using append keyword here if restarting
-            print('DCDReporter added')
+            # Check first if file exists for restart (OpenMM errors otherwise)
+            if restart is True and os.path.isfile(f"{self.trajfilename}.dcd") is False:
+                print("Warning: restart option was active but trajectory file not existing. Will create new file")
+                restart=False
+
             simulation.reporters.append(
                 openmm.app.DCDReporter(self.trajfilename+'.dcd', self.traj_frequency, append=restart,
                                                          enforcePeriodicBox=self.enforcePeriodicBox))
+            print('DCDReporter added')
         elif self.trajectory_file_option == 'NetCDFReporter':
             print("NetCDFReporter traj format selected. This requires mdtraj. Importing.")
             mdtraj = MDtraj_import()