Merge branch 'master' into checkpoint-reporter

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

@@ -39,6 +39,7 @@ from simtk.openmm.app.topology import Residue
 from simtk.openmm.vec3 import Vec3
 from simtk.openmm import System, Context, NonbondedForce, CustomNonbondedForce, HarmonicBondForce, HarmonicAngleForce, VerletIntegrator, LocalEnergyMinimizer
 from simtk.unit import nanometer, molar, elementary_charge, amu, gram, liter, degree, sqrt, acos, is_quantity, dot, norm
+import simtk.unit as unit
 import element as elem
 import os
 import random
@@ -843,7 +844,9 @@ class Modeller(object):
                     if atom.element is not None:
                         newIndex[i] = index
                         index += 1
-                        newTemplate.atoms.append(ForceField._TemplateAtomData(atom.name, atom.type, atom.element))
+                        newAtom = ForceField._TemplateAtomData(atom.name, atom.type, atom.element)
+                        newAtom.externalBonds = atom.externalBonds
+                        newTemplate.atoms.append(newAtom)
                 for b1, b2 in template.bonds:
                     if b1 in newIndex and b2 in newIndex:
                         newTemplate.bonds.append((newIndex[b1], newIndex[b2]))
@@ -968,7 +971,7 @@ class Modeller(object):
                                 # and hope that energy minimization will fix it.
 
                                 knownPositions = [x for x in templateAtomPositions if x is not None]
-                                position = sum(knownPositions)/len(knownPositions)
+                                position = unit.sum(knownPositions)/len(knownPositions)
                             newPositions.append(position*nanometer)
         for bond in self.topology.bonds():
             if bond[0] in newAtoms and bond[1] in newAtoms:

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

@@ -201,9 +201,12 @@ class StateDataReporter(object):
         if self._density:
             values.append((self._totalMass/volume).value_in_unit(unit.gram/unit.item/unit.milliliter))
         if self._speed:
-            elapsedDays = (clockTime-self._initialClockTime)/86400
+            elapsedDays = (clockTime-self._initialClockTime)/86400.0
             elapsedNs = (state.getTime()-self._initialSimulationTime).value_in_unit(unit.nanosecond)
+            if elapsedDays > 0.0:
                 values.append('%.3g' % (elapsedNs/elapsedDays))
+            else:
+                values.append('--')
         if self._remainingTime:
             elapsedSeconds = clockTime-self._initialClockTime
             elapsedSteps = simulation.currentStep-self._initialSteps

wrappers/python/src/swig_doxygen/OpenMM.i

@@ -13,10 +13,10 @@ See https://simtk.org/home/pyopenmm for details"
 
 %module (docstring=DOCSTRING) openmm
 
-%include "typemaps.i"
 %include "factory.i"
 %include "std_string.i"
 %include "std_iostream.i"
+%include "typemaps.i"
 
 %include "std_map.i"
 %include "std_pair.i"

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

@@ -156,3 +156,36 @@
   $3 = &tempC;
 }
 
+%typemap(out) std::string OpenMM::Context::createCheckpoint{
+    // createCheckpoint returns a bytes object
+    $result = PyBytes_FromStringAndSize($1.c_str(), $1.length());
+}
+
+
+%typemap(in) std::string {
+    // if we have a C++ method that takes in a std::string, we're most happy to accept
+    // a python bytes object. But if the user passes in a unicode object we'll try
+    // to recover by encoding it to UTF-8 bytes
+    PyObject* temp = NULL;
+    char* c_str = NULL;
+    Py_ssize_t len = 0;
+
+    if (PyUnicode_Check($input)) {
+        temp = PyUnicode_AsUTF8String($input);
+        if (temp == NULL) {
+            SWIG_exception_fail(SWIG_TypeError, "'utf-8' codec can't decode byte");
+        }
+        PyBytes_AsStringAndSize(temp, &c_str, &len);
+        Py_XDECREF(temp);
+    } else if (PyBytes_Check($input)) {
+        PyBytes_AsStringAndSize($input, &c_str, &len);
+    } else {
+         SWIG_exception_fail(SWIG_TypeError, "argument must be str or bytes");
+    }
+
+    if (c_str == NULL) {
+        SWIG_exception_fail(SWIG_TypeError, "argument must be str or bytes");
+    }
+
+    $1 = std::string(c_str, len);
+}
\ No newline at end of file

wrappers/python/tests/TestBytes.py

+import unittest
+import simtk.openmm as mm
+
+
+class TestBytes(unittest.TestCase):
+    def test_createCheckpoint(self):
+        system = mm.System()
+        system.addParticle(1.0)
+        refPositions = [(0,0,0)]
+
+        context = mm.Context(system, mm.VerletIntegrator(0))
+        context.setPositions(refPositions)
+        chk = context.createCheckpoint()
+        # check that the return value of createCheckpoint is of type bytes (non-unicode)
+        assert isinstance(chk, bytes)
+
+        # set the positions to something random then reload the checkpoint, and
+        # make sure that the positions get restored correctly
+        context.setPositions([(12345, 12345, 123451)])
+        context.loadCheckpoint(chk)
+        newPositions = context.getState(getPositions=True).getPositions()._value
+
+        assert newPositions == refPositions
+
+        # try encoding the checkpoint in utf-8. OpenMM should be able to handle this too
+        context.setPositions([(12345, 12345, 123451)])
+        context.loadCheckpoint(chk.decode('utf-8'))
+        newPositions = context.getState(getPositions=True).getPositions()._value
+
+        assert newPositions == refPositions
+
+
+if __name__ == '__main__':
+    unittest.main()
+
+