Merge remote-tracking branch 'origin/master' into qc

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

@@ -263,7 +263,7 @@ class Modeller(object):
          - positiveIon (string='Na+') the type of positive ion to add.  Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
          - negativeIon (string='Cl-') the type of negative ion to add.  Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. Be aware
            that not all force fields support all ion types.
-         - ionicString (concentration=0*molar) the total concentration of ions (both positive and negative) to add.  This
+         - ionicStrength (concentration=0*molar) the total concentration of ions (both positive and negative) to add.  This
            does not include ions that are added to neutralize the system.
         """
         # Pick a unit cell size.
@@ -952,14 +952,14 @@ class Modeller(object):
                                     # This is a virtual site.  Compute its position by the correct rule.
 
                                     if site.type == 'average2':
-                                        position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]]
+                                        position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]]
                                     elif site.type == 'average3':
-                                        position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]] + site.weights[2]*templateAtomPositions[index+site.atoms[2]]
+                                        position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]] + site.weights[2]*templateAtomPositions[site.atoms[2]]
                                     elif site.type == 'outOfPlane':
-                                        v1 = templateAtomPositions[index+site.atoms[1]] - templateAtomPositions[index+site.atoms[0]]
-                                        v2 = templateAtomPositions[index+site.atoms[2]] - templateAtomPositions[index+site.atoms[0]]
+                                        v1 = templateAtomPositions[site.atoms[1]] - templateAtomPositions[site.atoms[0]]
+                                        v2 = templateAtomPositions[site.atoms[2]] - templateAtomPositions[site.atoms[0]]
                                         cross = Vec3(v1[1]*v2[2]-v1[2]*v2[1], v1[2]*v2[0]-v1[0]*v2[2], v1[0]*v2[1]-v1[1]*v2[0])
-                                        position = templateAtomPositions[index+site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross
+                                        position = templateAtomPositions[site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross
                             if position is None and atom.type in drudeTypeMap:
                                 # This is a Drude particle.  Put it on top of its parent atom.
 

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -272,7 +272,7 @@ UNITS = {
 ("AmoebaPiTorsionForce",                  "getPiTorsionParameters")                        :  ( None, (None, None, None, None, None,  None, 'unit.kilojoule_per_mole')),
 
 ("AmoebaStretchBendForce",                "getNumStretchBends")                            :  ( None, ()),
-("AmoebaStretchBendForce",                "getStretchBendParameters")                      :  ( None, (None, None, None, 'unit.nanometer', 'unit.nanometer', 'unit.radian', 'unit.kilojoule_per_mole/unit.nanometer')),
+("AmoebaStretchBendForce",                "getStretchBendParameters")                      :  ( None, (None, None, None, 'unit.nanometer', 'unit.nanometer', 'unit.radian', 'unit.kilojoule_per_mole/unit.nanometer/unit.degree')),
 
 ("AmoebaTorsionTorsionForce",             "getNumTorsionTorsions")                         :  ( None, ()),
 ("AmoebaTorsionTorsionForce",             "getNumTorsionTorsionGrids")                     :  ( None, ()),

wrappers/python/tests/TestAmberInpcrdFile.py

+import unittest
+from validateConstraints import *
+from simtk.openmm.app import *
+from simtk.openmm import *
+from simtk.unit import *
+import simtk.openmm.app.element as elem
+
+def compareByElement(array1, array2, cmp):
+    for x, y in zip(array1, array2):
+        cmp(x, y)
+
+class TestAmberInpcrdFile(unittest.TestCase):
+    """Test the Amber inpcrd file parser"""
+ 
+    def test_CrdVelBox(self):
+        """ Test parsing ASCII restarts with crds, vels, and box """
+        cmp = self.assertAlmostEqual
+        inpcrd = AmberInpcrdFile('systems/crds_vels_box.rst7')
+        self.assertEqual(len(inpcrd.positions), 2101)
+        compareByElement(inpcrd.positions[-1].value_in_unit(angstroms),
+                         [3.5958082, 8.4176792, -8.2954064], cmp)
+        compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picoseconds),
+                         [0.3091332*20.455, 0.7355925*20.455, -0.1206961*20.455], cmp)
+        compareByElement(inpcrd.boxVectors[0].value_in_unit(angstroms),
+                         [30.2642725, 0.0, 0.0], cmp)
+
+    def test_NetCDF(self):
+        """ Test NetCDF restart file parsing """
+        cmp = self.assertAlmostEqual
+        try:
+            from scipy.io import netcdf
+        except ImportError:
+            print('Not testing NetCDF file parser... scipy cannot be found')
+        else:
+            inpcrd = AmberInpcrdFile('systems/amber.ncrst')
+            self.assertEqual(len(inpcrd.positions), 2101)
+            compareByElement(inpcrd.positions[0].value_in_unit(angstroms),
+                             [6.82122492718229, 6.6276250662042, -8.51668999892245],
+                             cmp)
+            compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picosecond),
+                             [0.349702202733541*20.455, 0.391525333168534*20.455,
+                              0.417941679767662*20.455], cmp)
+            self.assertAlmostEqual(inpcrd.boxVectors[0][0].value_in_unit(angstroms),
+                                   30.2642725, places=6)
+
+    def test_CrdBox(self):
+        """ Test parsing ASCII restarts with only crds and box """
+        inpcrd = AmberInpcrdFile('systems/crds_box.rst7')
+        self.assertEqual(len(inpcrd.positions), 18660)
+        self.assertTrue(inpcrd.velocities is None)
+        self.assertTrue(inpcrd.boxVectors is not None)
+
+    def test_CrdVel(self):
+        inpcrd = AmberInpcrdFile('systems/crds_vels.rst7')
+        self.assertTrue(inpcrd.boxVectors is None)
+        self.assertTrue(inpcrd.velocities is not None)
+
+    def test_CrdOnly(self):
+        inpcrd = AmberInpcrdFile('systems/crdsonly.rst7')
+        self.assertTrue(inpcrd.boxVectors is None)
+        self.assertTrue(inpcrd.velocities is None)
+
+if __name__ == '__main__':
+    unittest.main()

wrappers/python/tests/systems/crds_vels.rst7

+ACE                                                                             
+   28  0.1100000E+05
+   6.9962325   7.1345361  -3.9713983   7.4756482   6.1688310  -3.8111566
+   8.5024408   6.3930528  -3.5221598   7.4708173   5.7449547  -4.8153505
+   6.8002949   5.4664470  -2.6846071   7.1210336   4.3039353  -2.4099316
+   5.8138412   6.2015113  -2.0369948   5.6437332   7.0956281  -2.4748521
+   4.9765730   5.7180343  -0.9552686   5.5952335   5.0377318  -0.3699927
+   4.5105579   6.8291112   0.0795226   5.4196673   7.2692444   0.4892821
+   3.8405864   7.5537576  -0.3832260   3.7600399   6.2095975   1.2450279
+   3.0614461   7.0866468   2.0205499   3.9472641   4.9020081   1.4914431
+   3.4219922   4.6877864   2.2659097   3.7335795   4.9588789  -1.4954454
+   2.9265073   5.7168640  -2.1242842   4.4787994   4.4294475   0.8466484
+   2.5980237   6.7854333   2.8054767   3.2160253   7.9534080   1.6378901
+   3.5172878   3.6766505  -1.2008776   4.1472250   3.2061006  -0.5669477
+   2.4677851   2.8846866  -1.7794578   2.8829398   2.5139385  -2.7166333
+   2.3438054   2.0729996  -1.0625940   1.5440133   3.4553999  -1.8744943
+   0.3799223   0.0175576   1.1999574   0.3523292  -0.2043193   0.0353460
+   1.1942188  -1.4410315  -1.7982354  -0.5852708  -0.9087781   0.3223661
+   0.1459748   0.0526223   0.2682160  -0.0465667  -0.1870169   0.1459932
+  -0.2892203   0.0015456  -0.0112940   0.1854616  -0.2737819  -0.7785389
+  -0.2392158   0.1749611  -0.1239180  -0.3400171   0.0531231  -0.1587713
+  -0.4704835  -0.1493877  -0.2567553  -0.6101138  -0.0392770  -0.0635170
+   0.5715057   0.1942655  -1.2772686  -0.1237689  -0.3449472   0.2714899
+  -0.0185239  -0.0150607   0.0391274  -0.1280282  -0.0046097  -0.1994271
+  -0.3155035   0.3668607  -0.2215361   0.1294219  -0.1747917  -0.0917708
+   0.0742998   0.1509489  -0.2851266   0.4923665  -1.0386246   1.0229978
+  -0.8227836   1.0624132   0.0013427  -0.0778814  -0.1859122  -0.3774084
+   0.2098003   0.1213628  -0.2466628  -0.1936209  -0.2478820  -0.1148687
+   0.0315637   0.2866246  -0.0746640  -0.5854400  -0.8935872   0.0990994
+   0.6063127  -0.1110186  -0.4168450  -0.8390447  -1.1240213  -0.3891693

wrappers/python/tests/systems/crdsonly.rst7

+ACE 
+   28
+   1.8662825   1.2455949   0.6672110   1.9626006   2.1938026   0.1396779
+   1.2497428   2.9104392   0.5454310   1.7619492   2.0427757  -0.9201889
+   3.3659937   2.7323333   0.3106630   4.1907627   2.1039510   0.9734519
+   3.6273756   3.8949435  -0.2849918   2.8777368   4.3392797  -0.7950028
+   4.9163808   4.5976032  -0.2534247   5.4756521   4.2709258   0.6250439
+   5.7163632   4.2049342  -1.5101182   5.8371260   3.1200826  -1.5317512
+   5.1471196   4.4947601  -2.3959905   7.1055802   4.8539661  -1.5508595
+   7.9498622   4.6375603  -0.4939507   7.4316586   5.6201081  -2.6386852
+   8.3150784   5.9901727  -2.5863945   4.7269796   6.1275619  -0.1377803
+   3.7336230   6.6808666  -0.6238468   6.7262793   5.6692474  -3.2868494
+   8.7967113   5.0771061  -0.5933179   7.5650193   4.0788360   0.1842201
+   5.6831501   6.8163892   0.4999151   6.4763527   6.2959896   0.8529456
+   5.6745238   8.2651257   0.7063732   4.7905547   8.5573927   1.2769756
+   6.5663801   8.5705282   1.2568739   5.6602885   8.7808127  -0.2560452

wrappers/python/tests/systems/water-box-216.prmtop

@@ -1054,7 +1054,7 @@ BLA BLA BLA BLA BLA BLA BLA BLA
        3       3       3       3       3       3
 %FLAG BOX_DIMENSIONS                                                            
 %FORMAT(5E16.8)                                                                 
-  5.15661795E+03  1.87743490E+01  1.87743490E+01  1.87743490E+01
+  9.00000000E+01  1.87743490E+01  1.87743490E+01  1.87743490E+01
 %FLAG RADIUS_SET                                                                
 %FORMAT(1a80)                                                                   
 modified Bondi radii (mbondi)