Merge branch 'upstream' into fork

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.h

@@ -34,8 +34,8 @@
 
 #include "ReferencePlatform.h"
 #include "openmm/RpmdKernels.h"
-#include "SimTKUtilities/RealVec.h"
-#include "SimTKReference/fftpack.h"
+#include "RealVec.h"
+#include "fftpack.h"
 
 namespace OpenMM {
 

plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp

@@ -42,7 +42,7 @@
 #include "openmm/System.h"
 #include "openmm/RPMDIntegrator.h"
 #include "openmm/VirtualSite.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

tests/TestParser.cpp

@@ -175,6 +175,7 @@ int main() {
         verifyEvaluation("5*2", 10.0);
         verifyEvaluation("2*3+4*5", 26.0);
         verifyEvaluation("2^-3", 0.125);
+        verifyEvaluation("1e+2", 100.0);
         verifyEvaluation("-x", 2.0, 3.0, -2.0);
         verifyEvaluation("y^-x", 3.0, 2.0, 0.125);
         verifyEvaluation("1/-x", 3.0, 2.0, -1.0/3.0);

wrappers/python/simtk/openmm/app/data/hydrogens.xml

@@ -16,7 +16,7 @@
   <H name="HOP3" parent="OP3"/>
  </Residue>
  <Residue name="ACE">
-  <H name="H" parent="C"/>
+  <H name="H" parent="C" terminal="C"/>
   <H name="H1" parent="CH3"/>
   <H name="H2" parent="CH3"/>
   <H name="H3" parent="CH3"/>
@@ -313,7 +313,7 @@
   <H name="H1" parent="C"/>
   <H name="H2" parent="C"/>
   <H name="H3" parent="C"/>
-  <H name="HN2" parent="N"/>
+  <H name="HN2" parent="N" terminal="N"/>
  </Residue>
  <Residue name="ORN">
   <H name="H" parent="N"/>

wrappers/python/simtk/openmm/app/forcefield.py

@@ -1046,6 +1046,13 @@ class GBSAOBCGenerator:
             force.setSolventDielectric(float(args['solventDielectric']))
         sys.addForce(force)
 
+    def postprocessSystem(self, sys, data, args):
+        # Disable the reaction field approximation, since it produces bad results when combined with GB.
+        
+        for force in sys.getForces():
+            if isinstance(force, mm.NonbondedForce):
+                force.setReactionFieldDielectric(1.0)
+
 parsers["GBSAOBCForce"] = GBSAOBCGenerator.parseElement
 
 

wrappers/python/simtk/openmm/app/gromacstopfile.py

@@ -448,6 +448,7 @@ class GromacsTopFile(object):
             gb.setSoluteDielectric(soluteDielectric)
             gb.setSolventDielectric(solventDielectric)
             sys.addForce(gb)
+            nb.setReactionFieldDielectric(1.0)
         elif implicitSolvent is not None:
             raise ValueError('Illegal value for implicitSolvent')
         bonds = None

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -824,6 +824,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
             gb.setCutoffDistance(nonbondedCutoff)
         else:
             raise Exception("Illegal nonbonded method for use with GBSA")
+        force.setReactionFieldDielectric(1.0)
 
     # TODO: Add GBVI terms?
 

wrappers/python/src/swig_doxygen/OpenMM.i

@@ -64,6 +64,14 @@ using namespace OpenMM;
 
 %include OpenMM_headers.i
 
+%pythoncode %{
+  # when we import * from the python module, we only want to import the
+  # actual classes, and not the swigregistration methods, which have already
+  # been called, and are now unneeded by the user code, and only pollute the
+  # namespace
+  __all__ = [k for k in locals().keys() if not k.endswith('_swigregister')]
+%}
+
 /*
 %extend OpenMM::XmlSerializer {
     %template(XmlSerializer_serialize_AndersenThermostat) XmlSerializer::serialize<AndersenThermostat>;

wrappers/python/src/swig_doxygen/swig_lib/python/pythoncode.i

@@ -5,6 +5,7 @@ try:
 except:
     pass
 
+import sys
 import math
 RMIN_PER_SIGMA=math.pow(2, 1/6.0)
 RVDW_PER_SIGMA=math.pow(2, 1/6.0)/2.0
@@ -273,14 +274,15 @@ def stripUnits(args):
     """
     newArgList=[]
     for arg in args:
-        if unit.is_quantity(arg):
+        if 'numpy' in sys.modules and isinstance(arg, numpy.ndarray):
+           arg = arg.tolist()
+        elif unit.is_quantity(arg):
             # JDC: Ugly workaround for OpenMM using 'bar' for fundamental pressure unit.
             if arg.unit.is_compatible(unit.bar):
                 arg = arg / unit.bar
             else:
                 arg=arg.value_in_unit_system(unit.md_unit_system)                
             # JDC: End workaround.
-            #arg=arg.value_in_unit_system(unit.md_unit_system)
         elif isinstance(arg, dict):
             newKeys = stripUnits(arg.keys())
             newValues = stripUnits(arg.values())