Smirnoff Interaction energy

src/interaction.py

@@ -179,7 +179,7 @@ def get(self, mvals, AGrad=False, AHess=False):
 
         def callM(mvals_, dielectric=False):
             logger.info("\r")
-            pvals = self.FF.make(mvals_)
+            self.FF.make(mvals_)
             return self.engine.interaction_energy(self.select1, self.select2)
 
         logger.info("Executing\r")
@@ -193,7 +193,7 @@ def callM(mvals_, dielectric=False):
             np.savetxt('M.txt',emm)
             np.savetxt('Q.txt',self.eqm)
             import pickle
-            pickle.dump((self.name, self.label, self.prefactor, self.eqm, emm), open("qm_vs_mm.p",'w'))
+            pickle.dump((self.name, self.label, self.prefactor, self.eqm, emm), open("qm_vs_mm.p",'wb'))
             # select the qm and mm data that has >0 weight to plot
             qm_data, mm_data = [], []
             for i in range(len(self.eqm)):
@@ -206,8 +206,8 @@ def callM(mvals_, dielectric=False):
         if AGrad or AHess:
             for p in self.pgrad:
                 dV[p,:], _ = f12d3p(fdwrap(callM, mvals, p), h = self.h, f0 = emm)
-            # Create the force field one last time.
-            pvals  = self.FF.make(mvals)
+            # # Create the force field one last time.
+            # pvals  = self.FF.make(mvals)
 
         Answer['X'] = np.dot(self.prefactor*D/self.divisor,D/self.divisor)
         for p in self.pgrad:
@@ -218,15 +218,16 @@ def callM(mvals_, dielectric=False):
         if not in_fd():
             self.emm = emm
             self.objective = Answer['X']
+            self.FF.make(mvals)
 
         ## QYD: try to clean up OpenMM engine.simulation objects to free up GPU memory
-        try:
-            if self.engine.name == 'openmm':
-                if hasattr(self.engine, 'simulation'): del self.engine.simulation
-                if hasattr(self.engine, 'A'): del self.engine.A
-                if hasattr(self.engine, 'B'): del self.engine.B
-        except:
-            pass
+        # try:
+        #     if self.engine.name == 'openmm':
+        #         if hasattr(self.engine, 'simulation'): del self.engine.simulation
+        #         if hasattr(self.engine, 'A'): del self.engine.A
+        #         if hasattr(self.engine, 'B'): del self.engine.B
+        # except:
+        #     pass
 
         return Answer
 

src/objective.py

@@ -37,7 +37,7 @@
     logger.warning("OpenMM module import failed; check OpenMM package\n")
 
 try:
-    from forcebalance.smirnoffio import AbInitio_SMIRNOFF, Liquid_SMIRNOFF, Vibration_SMIRNOFF, Hessian_SMIRNOFF, OptGeoTarget_SMIRNOFF, TorsionProfileTarget_SMIRNOFF, smirnoff_analyze_parameter_coverage
+    from forcebalance.smirnoffio import AbInitio_SMIRNOFF, Liquid_SMIRNOFF, Vibration_SMIRNOFF, Hessian_SMIRNOFF, OptGeoTarget_SMIRNOFF, TorsionProfileTarget_SMIRNOFF, smirnoff_analyze_parameter_coverage, Interaction_SMIRNOFF
 except:
     logger.warning(traceback.format_exc())
     logger.warning("SMIRNOFF module import failed; check SMIRNOFF package\n")
@@ -112,6 +112,7 @@
     'INTERACTION_GMX':Interaction_GMX,
     'INTERACTION_TINKER':Interaction_TINKER,
     'INTERACTION_OPENMM':Interaction_OpenMM,
+    'INTERACTION_SMIRNOFF': Interaction_SMIRNOFF,
     'BINDINGENERGY_TINKER':BindingEnergy_TINKER,
     'BINDINGENERGY_GMX':BindingEnergy_GMX,
     'BINDINGENERGY_OPENMM':BindingEnergy_OpenMM,

src/openmmio.py

@@ -8,6 +8,8 @@
 from builtins import zip
 from builtins import range
 import os
+
+import openmm
 from forcebalance import BaseReader
 from forcebalance.abinitio import AbInitio
 from forcebalance.binding import BindingEnergy

src/smirnoffio.py

@@ -795,16 +795,25 @@ def submit_jobs(self, mvals, AGrad=False, AHess=False):
 #         ## Initialize base class.
 #         super(BindingEnergy_OpenMM,self).__init__(options,tgt_opts,forcefield)
 
-# class Interaction_SMIRNOFF(Interaction):
-#     """ Interaction matching using OpenMM. """
-#     def __init__(self,options,tgt_opts,forcefield):
-#         ## Default file names for coordinates and key file.
-#         self.set_option(tgt_opts,'coords',default="all.pdb")
-#         self.set_option(tgt_opts,'openmm_precision','precision',default="double", forceprint=True)
-#         self.set_option(tgt_opts,'openmm_platform','platname',default="Reference", forceprint=True)
-#         self.engine_ = OpenMM
-#         ## Initialize base class.
-#         super(Interaction_OpenMM,self).__init__(options,tgt_opts,forcefield)
+class Interaction_SMIRNOFF(Interaction):
+    """ Interaction matching using OpenMM. """
+    def __init__(self,options,tgt_opts,forcefield):
+        ## Default file names for coordinates and key file.
+        # file for the whole topology
+        self.set_option(tgt_opts, 'pdb', default="top.pdb")
+        # cords of the system along some scan coordinate
+        self.set_option(tgt_opts,'coords',default="scan.xyz")
+        # a list of the separate mol2 files
+        self.set_option(tgt_opts, 'mol2', forceprint=True)
+        self.set_option(tgt_opts,'openmm_precision','precision',default="double", forceprint=True)
+        self.set_option(tgt_opts,'openmm_platform','platname',default="Reference", forceprint=True)
+        self.engine_ = SMIRNOFF
+        ## Initialize base class.
+        super(Interaction_SMIRNOFF,self).__init__(options,tgt_opts,forcefield)
+
+    def submit_jobs(self, mvals, AGrad=False, AHess=False):
+        # we update the self.pgrads here so it's not overwritten in rtarget.py
+        smirnoff_update_pgrads(self)
 
 # class Moments_SMIRNOFF(Moments):
 #     """ Multipole moment matching using OpenMM. """