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Commit bceea302 authored by Peter Eastman's avatar Peter Eastman
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Merge remote-tracking branch 'origin/master' into qc

parents 2e6397b7 a1b2641c
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Showing with 11556 additions and 8 deletions
wrappers/python/simtk/openmm/app/modeller.py
View file @ bceea302
...@@ -263,7 +263,7 @@ class Modeller(object): ...@@ -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+' - 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 - 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. 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. does not include ions that are added to neutralize the system.
""" """
# Pick a unit cell size. # Pick a unit cell size.
...@@ -952,14 +952,14 @@ class Modeller(object): ...@@ -952,14 +952,14 @@ class Modeller(object):
# This is a virtual site. Compute its position by the correct rule. # This is a virtual site. Compute its position by the correct rule.
if site.type == 'average2': 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': 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': elif site.type == 'outOfPlane':
v1 = templateAtomPositions[index+site.atoms[1]] - templateAtomPositions[index+site.atoms[0]] v1 = templateAtomPositions[site.atoms[1]] - templateAtomPositions[site.atoms[0]]
v2 = templateAtomPositions[index+site.atoms[2]] - templateAtomPositions[index+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]) 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: if position is None and atom.type in drudeTypeMap:
# This is a Drude particle. Put it on top of its parent atom. # This is a Drude particle. Put it on top of its parent atom.
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ bceea302
...@@ -272,7 +272,7 @@ UNITS = { ...@@ -272,7 +272,7 @@ UNITS = {
("AmoebaPiTorsionForce", "getPiTorsionParameters") : ( None, (None, None, None, None, None, None, 'unit.kilojoule_per_mole')), ("AmoebaPiTorsionForce", "getPiTorsionParameters") : ( None, (None, None, None, None, None, None, 'unit.kilojoule_per_mole')),
("AmoebaStretchBendForce", "getNumStretchBends") : ( None, ()), ("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", "getNumTorsionTorsions") : ( None, ()),
("AmoebaTorsionTorsionForce", "getNumTorsionTorsionGrids") : ( None, ()), ("AmoebaTorsionTorsionForce", "getNumTorsionTorsionGrids") : ( None, ()),
......
wrappers/python/tests/TestAmberInpcrdFile.py 0 → 100644
View file @ bceea302
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_box.rst7 0 → 100644
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wrappers/python/tests/systems/crds_vels.rst7 0 → 100644
View file @ bceea302
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/crds_vels_box.rst7 0 → 100644
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This diff is collapsed.
wrappers/python/tests/systems/crdsonly.rst7 0 → 100644
View file @ bceea302
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
View file @ bceea302
...@@ -1054,7 +1054,7 @@ BLA BLA BLA BLA BLA BLA BLA BLA ...@@ -1054,7 +1054,7 @@ BLA BLA BLA BLA BLA BLA BLA BLA
3 3 3 3 3 3 3 3 3 3 3 3
%FLAG BOX_DIMENSIONS %FLAG BOX_DIMENSIONS
%FORMAT(5E16.8) %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 %FLAG RADIUS_SET
%FORMAT(1a80) %FORMAT(1a80)
modified Bondi radii (mbondi) modified Bondi radii (mbondi)
......
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