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: