Add RPMD features

src/data/npt.py

@@ -312,7 +312,7 @@ def main():
     # Number of threads, multiple timestep integrator, anisotropic box etc.
     threads = TgtOptions.get('md_threads', 1)
     mts = TgtOptions.get('mts_integrator', 0)
-    rpmd_beads = TgtOptions.get('rpmd_beads', 0)
+    rpmd_beads = TgtOptions.get('rpmd_beads', [])
     force_cuda = TgtOptions.get('force_cuda', 0)
     nbarostat = TgtOptions.get('n_mcbarostat', 25)
     anisotropic = TgtOptions.get('anisotropic_box', 0)
@@ -367,7 +367,7 @@ def main():
         EngOpts["gas"]["gmx_top"] = os.path.splitext(gas_fnm)[0] + ".top"
         EngOpts["gas"]["gmx_mdp"] = os.path.splitext(gas_fnm)[0] + ".mdp"
         if force_cuda: logger.warn("force_cuda option has no effect on Gromacs engine.")
-        if rpmd_beads > 0: raise RuntimeError("Gromacs cannot handle RPMD.")
+        if len(rpmd_beads) > 0: raise RuntimeError("Gromacs cannot handle RPMD.")
         if mts: logger.warn("Gromacs not configured for multiple timestep integrator.")
         if anisotropic: logger.warn("Gromacs not configured for anisotropic box scaling.")
     elif engname == "tinker":
@@ -376,7 +376,7 @@ def main():
         EngOpts["liquid"]["tinker_key"] = os.path.splitext(liquid_fnm)[0] + ".key"
         EngOpts["gas"]["tinker_key"] = os.path.splitext(gas_fnm)[0] + ".key"
         if force_cuda: logger.warn("force_cuda option has no effect on Tinker engine.")
-        if rpmd_beads > 0: raise RuntimeError("TINKER cannot handle RPMD.")
+        if len(rpmd_beads) > 0: raise RuntimeError("TINKER cannot handle RPMD.")
         if mts: logger.warn("Tinker not configured for multiple timestep integrator.")
     EngOpts["liquid"].update(GenOpts)
     EngOpts["gas"].update(GenOpts)
@@ -420,7 +420,7 @@ def main():
     Volumes = prop_return['Volumes']
     Dips = prop_return['Dips']
     EDA = prop_return['Ecomps']
-
+    #getone = prop_return['One'] 
     # Create a bunch of physical constants.
     # Energies are in kJ/mol
     # Lengths are in nanometers.
@@ -492,6 +492,10 @@ def main():
     #  Condensed phase properties and derivatives. #
     #==============================================#
 
+    #----
+    # Just get one
+    #----
+
     #----
     # Density
     #----

src/forcefield.py

@@ -223,7 +223,7 @@ def __init__(self, options, verbose=True):
         ## AMOEBA mutual dipole convergence tolerance.
         self.set_option(options, 'amoeba_eps')
         ## Switch for rigid water molecules
-        self.set_option(options, 'rigid_water')
+        self.set_option(options, 'rigid_water', forceprint=True)
         ## Bypass the transformation and use physical parameters directly
         self.set_option(options, 'use_pvals')
 
@@ -1115,7 +1115,8 @@ def build_qtrans2(tq, qid, qmap):
     def list_map(self):
         """ Create the plist, which is like a reversed version of the parameter map.  More convenient for printing. """
         if len(self.map) == 0:
-            warn_press_key('The parameter map has no elements (Okay if we are not actually tuning any parameters.)')
+            #warn_press_key('The parameter map has no elements (Okay if we are not actually tuning any parameters.)')
+            logger.warning('The parameter map has no elements (Okay if we are not actually tuning any parameters.)\n')
         else:
             self.plist = [[] for j in range(max([self.map[i] for i in self.map])+1)]
             for i in self.map: