Merge pull request #405 from RagnarB83/NEW

CI now working with some basic tests: OpenMM, pyscf, xtb, geometric

ash/interfaces/interface_OpenMM.py

@@ -87,9 +87,10 @@ def __init__(self, printlevel=2, platform='CPU', numcores=1, topoforce=False, fo
             import openmm
             import openmm.app
             import openmm.unit
+            from packaging import version
             if self.printlevel > 0:
                 print("Imported OpenMM library version:", openmm.__version__)
-                if float(openmm.__version__) < 8.0:
+                if version.parse(openmm.__version__) < version.parse("8.1"):
                     print("Warning: OpenMM version < 8.1. OpenMM 8.1 or higher is recommended")
                     print("Some features may not work as intended in older versions")
         except ImportError:
@@ -344,7 +345,10 @@ def __init__(self, printlevel=2, platform='CPU', numcores=1, topoforce=False, fo
                 #OpenMM 8.1 allows us to do this easily by constructor, older versions requires hacky workarounds
                 # (see set_periodics_before_system_creation for those hacks)
                 #Note: https://github.com/openmm/openmm/issues/4078
-                if float(openmm.__version__) >= 8.1:
+                from packaging import version
+                #if float(openmm.__version__) >= 8.1:
+                if version.parse(openmm.__version__) >= version.parse("8.1"):
+
                     if PBCvectors is None:
                         temp_pbc_vecs=None
                     else:
@@ -856,6 +860,7 @@ def __init__(self, printlevel=2, platform='CPU', numcores=1, topoforce=False, fo
     #Function that handles periodicity in forcefield objects (for Amber, CHARMM). TODO: Test GROMACS and XML
     def set_periodics_before_system_creation(self,PBCvectors,periodic_cell_dimensions,CHARMMfiles,Amberfiles,use_parmed):
         import openmm
+        from packaging import version
         if use_parmed is True:
             import parmed
         print("Inspecting periodicity input before system creation")
@@ -882,7 +887,8 @@ def set_periodics_before_system_creation(self,PBCvectors,periodic_cell_dimension
                 print("Amber-prmtop getIfBox:", self.forcefield._prmtop.getIfBox())
                 self.forcefield._prmtop._raw_data['POINTERS'][27] = 1
                 print("Amber-prmtop getIfBox:", self.forcefield._prmtop.getIfBox())
-                if float(openmm.__version__) < 8.1:
+
+                if version.parse(openmm.__version__) < version.parse("8.1"):
                     print("Warning: Amber prmtop file detected and OpenMM version < 8.0")
                     print("Warning: Will assume cubic box and set PBC vectors in a hacky way")
                     self.forcefield._prmtop._raw_data["BOX_DIMENSIONS"] =np.array([0.0,0.0,0.0,0.0])
@@ -943,7 +949,7 @@ def set_periodics_before_system_creation(self,PBCvectors,periodic_cell_dimension
                 #Happens if no IFBOX defined in prmtop file but we still want periodicity
                 self.forcefield._prmtop._raw_data['POINTERS'][27] = 1
 
-                if float(openmm.__version__) < 8.1:
+                if version.parse(openmm.__version__) < version.parse("8.1"):
                     print("Warning: Amber prmtop file detected and OpenMM version < 8.1")
                     print("Warning: Will assume cubic box and set PBC vectors in a hacky way")
                     self.forcefield._prmtop._raw_data["BOX_DIMENSIONS"] =np.array([0.0,0.0,0.0,0.0])
@@ -2209,6 +2215,7 @@ def clean_up_constraints_list(fragment=None, constraints=None):
 def OpenMM_Opt(fragment=None, theory=None, maxiter=1000, tolerance=1, enforcePeriodicBox=True,
                traj_frequency=100, use_reporter=True):
     import openmm
+    from packaging import version
     module_init_time = time.time()
     print_line_with_mainheader("OpenMM Optimization")
 
@@ -2226,7 +2233,8 @@ def OpenMM_Opt(fragment=None, theory=None, maxiter=1000, tolerance=1, enforcePer
     print("Number of atoms:", fragment.numatoms)
     print("Max iterations:", maxiter)
     print(f"Tolerance: {tolerance} kj/mol/nm:")
-    if float(openmm.__version__) >= 8.1:
+    #if float(openmm.__version__) >= 8.1:
+    if version.parse(openmm.__version__) >= version.parse("8.1"):
         print("Will write to trajectory every {} iterations".format(traj_frequency))
 
     print("OpenMM autoconstraints:", openmmobject.autoconstraints)
@@ -2269,7 +2277,8 @@ def OpenMM_Opt(fragment=None, theory=None, maxiter=1000, tolerance=1, enforcePer
     #New in OpenMM 8.1: reporters for minimizer
     #StateDataReporter
     #############################################
-    if float(openmm.__version__ ) >= 8.1 and use_reporter is True:
+    #if float(openmm.__version__ ) >= 8.1 and use_reporter is True:
+    if version.parse(openmm.__version__) >= version.parse("8.1") and use_reporter is True:
         class Reporter(openmm.openmm.MinimizationReporter):
             def report(self, iteration,x,grad,args):
                 try:
@@ -2356,7 +2365,9 @@ def get_state(self):
     print("")
     #####################################
     print("Starting minimization.")
-    if float(openmm.__version__) >= 8.1 and use_reporter is True:
+    #if float(openmm.__version__) >= 8.1 and use_reporter is True:
+    if version.parse(openmm.__version__) >= version.parse("8.1") and use_reporter is True:
+
         print("OpenMM versions >= 8.1. Will use a reporter to output progress")
         print("OpenMM_Opt trajectory will be written to: OpenMMOpt_traj.xyz")
         #Removing possible old traj file

ash/interfaces/interface_pyscf.py

@@ -2159,7 +2159,7 @@ def prepare_run(self, current_coords=None, current_MM_coords=None, MMcharges=Non
 
 
         #Setting number of electrons for system (used by load_chkfile etc)
-        self.num_electrons  = int(ash.modules.module_coords.nucchargelist(elems) - charge)
+        self.num_electrons  = int(ash.modules.module_coords.nucchargelist(qm_elems) - charge)
         print("Number of electrons:", self.num_electrons)
         print()
 
@@ -2226,7 +2226,7 @@ def prepare_run(self, current_coords=None, current_MM_coords=None, MMcharges=Non
         #FROZEN ORBITALS in CC
         ##############################
         if self.CC or self.MP2:
-            self.set_frozen_core_settings(elems)
+            self.set_frozen_core_settings(qm_elems)
 
         ##############################
         #EMBEDDING OPTIONS
@@ -2407,7 +2407,7 @@ def actualrun(self, current_coords=None, current_MM_coords=None, MMcharges=None,
                 #NOTE: this is not entirely correct since occupied orbitals are natural orbitals rather than frozen HF orbitals as in the original method
                 #Not sure how much it matters
                 if self.FNO is True:
-                    mo_coefficients = self.setup_FNO(elems=elems)
+                    mo_coefficients = self.setup_FNO(elems=qm_elems)
                 #Calling CC run function
                 self. CC_energy,self.ccobject = self.run_CC(self.mf,frozen_orbital_indices=self.frozen_orbital_indices, CCmethod=self.CCmethod, 
                             CC_direct=self.CC_direct, mo_coefficients=mo_coefficients)
@@ -2420,7 +2420,7 @@ def actualrun(self, current_coords=None, current_MM_coords=None, MMcharges=None,
             #####################
             if self.CAS is True:
                 print("CAS run is on!")
-                self.run_CAS(elems=elems)
+                self.run_CAS(elems=qm_elems)
         else:
             if self.printlevel >1:
                 print("No post-SCF job.")